rapids/config.yaml

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########################################################################################################################
# GLOBAL CONFIGURATION #
########################################################################################################################
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# See https://www.rapids.science/latest/setup/configuration/#participant-files
PIDS: ['p031', 'p032', 'p033', 'p034', 'p035', 'p036', 'p037', 'p038', 'p039', 'p040', 'p042', 'p043', 'p044', 'p045', 'p046', 'p049', 'p050', 'p052', 'p053', 'p054', 'p055', 'p057', 'p058', 'p059', 'p060', 'p061', 'p062', 'p064', 'p067', 'p068', 'p069', 'p070', 'p071', 'p072', 'p073', 'p074', 'p075', 'p076', 'p077', 'p078', 'p079', 'p080', 'p081', 'p082', 'p083', 'p084', 'p085', 'p086', 'p088', 'p089', 'p090', 'p091', 'p092', 'p093', 'p106', 'p107']
# See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files
CREATE_PARTICIPANT_FILES:
USERNAMES_CSV: "data/external/main_study_usernames.csv"
CSV_FILE_PATH: "data/external/main_study_participants.csv" # see docs for required format
PHONE_SECTION:
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ADD: True
IGNORED_DEVICE_IDS: []
FITBIT_SECTION:
ADD: False
IGNORED_DEVICE_IDS: []
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EMPATICA_SECTION:
ADD: True
IGNORED_DEVICE_IDS: []
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# See https://www.rapids.science/latest/setup/configuration/#time-segments
TIME_SEGMENTS: &time_segments
Squashed commit of the following: commit 8a6b52a97c95dcd8b70b980b4f46421b1a847905 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:35:49 2022 +0000 Switch to 30_before ERS with corresponding targets. commit 244a05373014b14bc4c75db8ceb68a04dc5328df Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:19:43 2022 +0000 Change output files settings to nonstandardized. commit be0324fd01d70c58a9eefd84ccb23d06a42ab57c Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 28 12:44:25 2022 +0000 Fix some bugs and set categorical columns as categories dtypes. commit 99c2fab8f9ab9cf2ed40a952019f994299b78c05 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 16 09:50:18 2022 +0000 Fix a bug in the making of the individual model (when there is no target in the participants columns). commit 286de93bfd55710d77c2e4bab899e73381f9a4a3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 11:21:51 2022 +0000 Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic. commit ab803ee49c2898d2dd4d49de64f763f549c077e3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 10:14:07 2022 +0000 Add additional appraisal targets. commit 621f11b2d98cb3e17d86c3be902ebd40f94d3079 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 09:53:31 2022 +0000 Fix a bug related to wrong user input (duplicated events). commit bd41f42a5da7e28b9de190a53b5f2195fad0920d Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:07:36 2022 +0000 Rename target_ to segmenting_ method. commit a543ce372f1fd6cdd402be8ebdbe54610e449ce2 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:04:16 2022 +0000 Add comments for event_related_script understanding. commit 74b454b07bf69bdcd0517a940c5296e5f77c492e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 11 09:15:12 2022 +0000 Apply changes to string answers to make them language-generic. commit 6ebe83e47ea4da0066f4cd9dedbdb726cef5d06c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 12:42:52 2022 +0000 Improve the ERS extract method with a couple of validations. commit 00350ef8ca2ef43aed71f76609917021ce920f31 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:32:58 2022 +0000 Change config for stressfulness event target method. commit e4985c91214ac6ecd43501d52b67816d26d4fdef Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:29:11 2022 +0000 Override stressfulness event target with extracted values from csv. commit a668b6e8dad4dd393802ed4d5e948d6d42d60a01 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 09:37:27 2022 +0000 Extract ERS and stress event targets to csv files (completed). commit 9199b53ded1c5d858882d9826aa15e5e2102ab08 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 9 15:11:51 2022 +0000 Get, join and start processing required ERS stress event data. commit f3c6a66da9a7ce92d4296436927f48b3d1a467b8 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 15:53:43 2022 +0000 Begin with stress events in the ERS script. commit 0b3e9226b3c683e87ef758756f0d83350642a716 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 14:44:24 2022 +0000 Make small corrections in ERS file. commit 2d83f7ddecbc3880e8d901fc2aae25621a280f75 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 11:32:05 2022 +0000 Begin the ERS logic for 90-minutes events. commit 1da72a7cbe3178ef911ddb263ea30e5da79407ad Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 09:45:37 2022 +0000 Rename targets method in config. commit 9f441afc16ff9b75e131eb47d41edb570b51190c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 15:09:04 2022 +0000 Begin ERS logic for 90-minutes events. commit c1c9f4d05ac8bdf03f4759623165f8e795eaa5a9 Merge: 62f46ea3 7ab0280d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:58 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 62f46ea3763ba47af2a7c62d6b0b453cfd549929 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:53 2022 +0000 Prepare method-based logic for ERS generating. commit 7ab0280d7ed23022a4d2de0caa7bba3a43dff9d4 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 08:58:08 2022 +0000 Correctly rename stressful event target variable. commit eefa9f3f4d4c95374dd31907787ed767c636fe37 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 14:49:54 2022 +0000 Add new target: stressfulness_event. commit 5e8174dd41f5a4c2aa35c74fb4bd9b19a918d1c4 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:52:45 2022 +0000 Add new target: stressfulness_period. commit 35c1a762e7179c7b11f8f1154c1a4f4133402324 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:51:18 2022 +0000 Improve filtering by esm_session and device_id. commit 02264b21fd43212dd4636d300321e254da392149 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 09:30:12 2022 +0000 Add logic for target selection in ERS processing. commit 0ce8723bdb72bafa40924ff4fd3a2328e81808eb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 2 14:01:21 2022 +0000 Extend imputation logic within the cleaning script. commit 30b38bfc028b6e3261701feb915f9e3820a77c75 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 28 09:00:13 2022 +0000 Fix the generating procedure of ERS file for participants with multiple devices. commit cd137af15a9f03724593595a152f34a24323088f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:20:15 2022 +0000 Config for 30 minute EMA segments. commit 3c0585a566ede91dd97e2ba0a6617a4f42e72617 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:12:56 2022 +0000 Remove obsolete comments. commit 6b487fcf7b64a722e9c5486764155764332ba73c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:11:42 2022 +0000 Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script. commit 5d17c92e54427cc70a7f747be398ad59af98c5bf Merge: a31fdd14 0d143e6a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:20 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit a31fdd1479193a67b6a6985cc42fdc66ac7be1a4 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:08 2022 +0000 Start to test empatica_data_yield precieved error. commit 936324d234b6636366b1a569793452a4cca54847 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:17:27 2022 +0000 Switch config for 30 minutes event related segments. commit da0a4596f814a40997efe782239cb296e89fe606 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:16:25 2022 +0000 Add additional ESM processing logic for ERS csv extraction. commit d4d74818e69eab2755f988391978400096902b5d Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:14:32 2022 +0000 Fix a bug - missing time_segment column when df is empty commit 14ff59914b4b3071ff7a40bf9daaba558ff66746 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:59:46 2022 +0000 Fix to correct dtypes. commit 6ab0ac5329d0be06bbe8357203422c7d981c325a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:57:26 2022 +0000 Optimize memory consumption with dtype definition while reading csv file. commit 0d143e6aadaf9b67b2fbfd6cdf8c218d5720f157 Merge: 8acac501 b92a3aa3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:28:27 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 8acac501251105332d1d3d4863e88744b9528844 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:26:43 2022 +0000 Add safenet when features dataframe is empty. commit b92a3aa37a1968b7129cdb2b7ebaf9beda981428 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:25:22 2022 +0000 Remove unwanted output or other error producing code. commit bfd637eb9c40872b954b608aef420b24393d3e6f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 08:53:44 2022 +0000 Improve strings formatting in straw_events file. commit 0d81ad5756c54f03b2b200b801672b9eb39f27d5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 19 13:35:04 2022 +0000 Debug assignment of segments to rows commit cea451d344e3b0bcc110c77f2845a9077bbe5d75 Merge: e88bbd54 cf38d9f1 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:06 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit e88bbd548fcd2bb1f9057b27b572afa5a6d028a5 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:00 2022 +0000 Add new daily segment and filter by segment in the cleaning script. commit cf38d9f175c5bcc9d0f8c70f49e59d2b56d8ada7 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 17 15:07:33 2022 +0000 Implement ERS generating logic. commit f3ca56cdbf22d7eed38f920889c4b19f49da7760 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 14 14:46:28 2022 +0000 Start with ERS logic integration within Snakemake. commit 797aa98f4fe2faf411c5130d27c51c5c606e5c0e Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:50 2022 +0000 Config for ERS testing. commit 9baff159cd1a61019410838efefa4b59a6c4981c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:23 2022 +0000 Changes needed for testing and starting of the Event-Related Segments. commit 0f21273508654133a51d1e20e485c3de33dc2779 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:32:51 2022 +0000 Bugs fix commit 55517eb737463e21c6f6ad18f4711d38bd02fec5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:23:11 2022 +0000 Necessary commit before proceeding. commit de15a52dba43325c171584464995fa4311403e7e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:36:23 2022 +0000 Bug fix commit 1ad25bb5727d30affd2ee063386f2f5ca52e0d63 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:26:17 2022 +0000 Few modifications of some imputation values in cleaning script and feature extraction. commit 9884b383cf6e1b339738deea8cc54a6d264e5c87 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 10 16:45:38 2022 +0000 Testing new data with AutoML. commit 2dc89c083c99d43da5e1eb9cbc1c07d39901f27d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 7 08:52:12 2022 +0000 Small changes in cleaning overall commit 001d40072973797f159b94b48ac3add10138f58e Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 14:28:12 2022 +0000 Clean features and create input files based on all possible targets. commit 1e38d9bf1e4d1caa10ff8c5245a59a9b20d4d7f9 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 13:27:38 2022 +0000 Standardization and correlation visualization in overall cleaning script. commit a34412a18dbd75aafa9f3bba9303ab6a962cec03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 14:16:55 2022 +0000 E4 data yield corrections. Changes in overal cs - standardization. commit 437459648f16f71acec6794a07404bfeb781f907 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 13:35:05 2022 +0000 Errors fix: individual script - treat participants missing data. commit 53f6cc60d5d8262a3bbb3cad82e2ebf49cb9e2a5 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 13:06:39 2022 +0000 Config and cleaning script necessary changes ... commit bbeabeee6ff7e3f8cc429470404c2c4b246b6a22 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 12:53:31 2022 +0000 Last changes before processing on the server. commit 44531c6d94705757110df6d087f3762699d7211a Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 30 10:04:07 2022 +0000 Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds. commit 7ac7cd5a3714521fc9a36a8371554a921df132fe Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 14:33:21 2022 +0000 Preparation of the overall cleaning script. commit 68fd69dadab8c7e14095469d5ed1d9921b4c0ce7 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:55:25 2022 +0000 Cleaning script for individuals: corrections and comments. commit a4f0d056a047aaf3458b043eba5e98df76da039a Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:44:27 2022 +0000 Fillna for app foreground and activity recognition commit 6286e7a44c7e2e99116b83fc3c06ce4398d022e5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:47:08 2022 +0000 firstuseafter column removed from contextual imputation commit 9b3447febd075f4dc5ede6a4071f72821835e7a2 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:40:05 2022 +0000 Contextual imputation correction commit d6adda30cf95e6d9660e6001225dee461bbe3704 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:37:51 2022 +0000 Contextual imputation on time(first/last) features. commit 8af4ef11dc711dffd86c71c99b15e9451aa94ecd Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 10:02:47 2022 +0000 Contextual imputation by feature type. commit 536b9494cdfbc6b31d41a74126ac6af1d8fe62e0 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 14:12:08 2022 +0000 Cleaning script corrections commit f0b87c9dd02d31223c2b69c2586221ffe202e21f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 09:54:15 2022 +0000 Debugging of the empatica data yield integration. commit 7fcdb873fe910f7243fb71ffe56abfdd9ebb81e3 Merge: 5c7bb0f4 bd53dc16 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:50:29 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 5c7bb0f4c14ab4413ed3682268bb7e65ac56fc83 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:48:32 2022 +0000 Config changes commit bd53dc1684b2b6fadf5653e2a9cc00c953410149 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 26 15:54:00 2022 +0000 Empatica data yield usage in the cleaning script. commit d9a574c550f8beb1cf5662e164ffa66048106dc9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 23 13:24:50 2022 +0000 Changes in the cleaning script and preparation of empatica data yield method. commit 19aa8707c0b61790d9d4c1834944c1711d8777aa Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 22 13:45:51 2022 +0000 Redefined cleaning steps after revision commit 247d758cb7eaa93ed9c7df2b0711325ffa27d985 Merge: 90ee99e4 7493aaa6 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:18:01 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 90ee99e4b99eeb32650df06d60e43c0ee1e66a87 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:16:00 2022 +0000 Remove TODO comments commit 7493aaa64368f81adbf478b43411063f56a9a87e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 12:57:55 2022 +0000 Small changes in cleaning scrtipt and missing vals testing. commit eaf4340afd7db8a43174a4789cfb9ba5a831dac4 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 08:03:48 2022 +0000 Small imputation and cleaning corrections. commit a96ea508c628d8c8c736126b65772c06c7cf4ddc Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:34:02 2022 +0000 Fill NaN of Empatica's SD second order feature (must be tested). commit 52e11cdcab51ec8ef97d379304e9297dd233773f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:54 2022 +0000 Configurations for new standardization path. commit 92aff93e65f765ca531bf414c2bdb2e6d7ca1240 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:16 2022 +0000 Remove standardization script. commit 18b63127deefb7cee0061ed741af179a4d6fdb01 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 06:16:26 2022 +0000 Removed all standardizaton rules and configurations. commit 62982866cd9f3f45a335d26b67c3fdf3035c6d1e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 13:24:21 2022 +0000 Phone wifi visible inspection (WIP) commit 0ce6da5444b7d0e3a30c8f6ca73422dc88d928b2 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 11:30:08 2022 +0000 kNN imputation relocation and execution only on specific columns. commit e3b78c8a85084b4cd873350df5bc2b75009fae83 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 10:58:57 2022 +0000 Impute selected phone features with 0. Wifi visible, screen, and light. commit 7d85f75d218ef9b3af5ae077343a58e62bb5fa2c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 09:03:30 2022 +0000 Changes in phone features NaN values script. commit 385e21409d1d3978588fea56cc26a8d241e3af35 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 14:16:58 2022 +0000 Changes in NaN values testing script. commit 18002f59e1c0e161f68b2a4cc217e62a6a86e467 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 10:48:59 2022 +0000 Doryab bluetooth and locations features fill in NaN values. commit 3cf7ca41aac7772c89ac90ad0a26e938d39f3f34 Merge: d27a4a71 d5ab5a03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 15:38:32 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit d5ab5a0394cdd395088723ff80d78f2257f8e37c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 14:13:03 2022 +0000 Writing testing scripts to determine the point of manual imputation. commit dfbb758902bebdbe86b42753b0252b96ec6e791f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 13:54:06 2022 +0000 Changes in AutoML params and environment.yml commit 4ec371ed96102d4b1f3b85557cb5fc3c388c1cef Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 09:51:03 2022 +0000 Testing auto-sklearn commit d27a4a71c81a50f4d30e5eb5bd9b664610da268a Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 12 13:44:17 2022 +0000 Reorganisation and reordering of the cleaning script. commit 15d792089d3b37dd381b1cb02b11f1106920d304 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:33:36 2022 +0000 Changes in cleaning script: - target extracted from config to remove rows where target is nan - prepared sns.heatmap for further missing values analysis - necessary changes in config and participant p01 - picture of heatmap which shows the values state after cleaning commit cb351e0ff6f6325e86fb2867116a44505a44eae1 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:06:57 2022 +0000 Unnecessary line (rows with no target value will be removed in cleaning script). commit 86299d346b5c3d706190db0dc14555309d17629f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 09:57:21 2022 +0000 Impute phone and sms NAs with 0 commit 3f7ec80c18b1237c49dfdd9a6736cdf518e0b7fb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Aug 31 10:18:50 2022 +0000 Preparation a) phone_calls 0 imputation b) remove rows with NaN target
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TYPE: EVENT # FREQUENCY, PERIODIC, EVENT
FILE: "data/external/straw_events.csv"
INCLUDE_PAST_PERIODIC_SEGMENTS: TRUE # Only relevant if TYPE=PERIODIC, see docs
Squashed commit of the following: commit 8a6b52a97c95dcd8b70b980b4f46421b1a847905 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:35:49 2022 +0000 Switch to 30_before ERS with corresponding targets. commit 244a05373014b14bc4c75db8ceb68a04dc5328df Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:19:43 2022 +0000 Change output files settings to nonstandardized. commit be0324fd01d70c58a9eefd84ccb23d06a42ab57c Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 28 12:44:25 2022 +0000 Fix some bugs and set categorical columns as categories dtypes. commit 99c2fab8f9ab9cf2ed40a952019f994299b78c05 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 16 09:50:18 2022 +0000 Fix a bug in the making of the individual model (when there is no target in the participants columns). commit 286de93bfd55710d77c2e4bab899e73381f9a4a3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 11:21:51 2022 +0000 Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic. commit ab803ee49c2898d2dd4d49de64f763f549c077e3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 10:14:07 2022 +0000 Add additional appraisal targets. commit 621f11b2d98cb3e17d86c3be902ebd40f94d3079 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 09:53:31 2022 +0000 Fix a bug related to wrong user input (duplicated events). commit bd41f42a5da7e28b9de190a53b5f2195fad0920d Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:07:36 2022 +0000 Rename target_ to segmenting_ method. commit a543ce372f1fd6cdd402be8ebdbe54610e449ce2 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:04:16 2022 +0000 Add comments for event_related_script understanding. commit 74b454b07bf69bdcd0517a940c5296e5f77c492e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 11 09:15:12 2022 +0000 Apply changes to string answers to make them language-generic. commit 6ebe83e47ea4da0066f4cd9dedbdb726cef5d06c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 12:42:52 2022 +0000 Improve the ERS extract method with a couple of validations. commit 00350ef8ca2ef43aed71f76609917021ce920f31 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:32:58 2022 +0000 Change config for stressfulness event target method. commit e4985c91214ac6ecd43501d52b67816d26d4fdef Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:29:11 2022 +0000 Override stressfulness event target with extracted values from csv. commit a668b6e8dad4dd393802ed4d5e948d6d42d60a01 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 09:37:27 2022 +0000 Extract ERS and stress event targets to csv files (completed). commit 9199b53ded1c5d858882d9826aa15e5e2102ab08 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 9 15:11:51 2022 +0000 Get, join and start processing required ERS stress event data. commit f3c6a66da9a7ce92d4296436927f48b3d1a467b8 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 15:53:43 2022 +0000 Begin with stress events in the ERS script. commit 0b3e9226b3c683e87ef758756f0d83350642a716 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 14:44:24 2022 +0000 Make small corrections in ERS file. commit 2d83f7ddecbc3880e8d901fc2aae25621a280f75 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 11:32:05 2022 +0000 Begin the ERS logic for 90-minutes events. commit 1da72a7cbe3178ef911ddb263ea30e5da79407ad Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 09:45:37 2022 +0000 Rename targets method in config. commit 9f441afc16ff9b75e131eb47d41edb570b51190c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 15:09:04 2022 +0000 Begin ERS logic for 90-minutes events. commit c1c9f4d05ac8bdf03f4759623165f8e795eaa5a9 Merge: 62f46ea3 7ab0280d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:58 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 62f46ea3763ba47af2a7c62d6b0b453cfd549929 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:53 2022 +0000 Prepare method-based logic for ERS generating. commit 7ab0280d7ed23022a4d2de0caa7bba3a43dff9d4 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 08:58:08 2022 +0000 Correctly rename stressful event target variable. commit eefa9f3f4d4c95374dd31907787ed767c636fe37 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 14:49:54 2022 +0000 Add new target: stressfulness_event. commit 5e8174dd41f5a4c2aa35c74fb4bd9b19a918d1c4 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:52:45 2022 +0000 Add new target: stressfulness_period. commit 35c1a762e7179c7b11f8f1154c1a4f4133402324 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:51:18 2022 +0000 Improve filtering by esm_session and device_id. commit 02264b21fd43212dd4636d300321e254da392149 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 09:30:12 2022 +0000 Add logic for target selection in ERS processing. commit 0ce8723bdb72bafa40924ff4fd3a2328e81808eb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 2 14:01:21 2022 +0000 Extend imputation logic within the cleaning script. commit 30b38bfc028b6e3261701feb915f9e3820a77c75 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 28 09:00:13 2022 +0000 Fix the generating procedure of ERS file for participants with multiple devices. commit cd137af15a9f03724593595a152f34a24323088f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:20:15 2022 +0000 Config for 30 minute EMA segments. commit 3c0585a566ede91dd97e2ba0a6617a4f42e72617 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:12:56 2022 +0000 Remove obsolete comments. commit 6b487fcf7b64a722e9c5486764155764332ba73c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:11:42 2022 +0000 Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script. commit 5d17c92e54427cc70a7f747be398ad59af98c5bf Merge: a31fdd14 0d143e6a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:20 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit a31fdd1479193a67b6a6985cc42fdc66ac7be1a4 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:08 2022 +0000 Start to test empatica_data_yield precieved error. commit 936324d234b6636366b1a569793452a4cca54847 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:17:27 2022 +0000 Switch config for 30 minutes event related segments. commit da0a4596f814a40997efe782239cb296e89fe606 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:16:25 2022 +0000 Add additional ESM processing logic for ERS csv extraction. commit d4d74818e69eab2755f988391978400096902b5d Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:14:32 2022 +0000 Fix a bug - missing time_segment column when df is empty commit 14ff59914b4b3071ff7a40bf9daaba558ff66746 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:59:46 2022 +0000 Fix to correct dtypes. commit 6ab0ac5329d0be06bbe8357203422c7d981c325a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:57:26 2022 +0000 Optimize memory consumption with dtype definition while reading csv file. commit 0d143e6aadaf9b67b2fbfd6cdf8c218d5720f157 Merge: 8acac501 b92a3aa3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:28:27 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 8acac501251105332d1d3d4863e88744b9528844 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:26:43 2022 +0000 Add safenet when features dataframe is empty. commit b92a3aa37a1968b7129cdb2b7ebaf9beda981428 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:25:22 2022 +0000 Remove unwanted output or other error producing code. commit bfd637eb9c40872b954b608aef420b24393d3e6f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 08:53:44 2022 +0000 Improve strings formatting in straw_events file. commit 0d81ad5756c54f03b2b200b801672b9eb39f27d5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 19 13:35:04 2022 +0000 Debug assignment of segments to rows commit cea451d344e3b0bcc110c77f2845a9077bbe5d75 Merge: e88bbd54 cf38d9f1 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:06 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit e88bbd548fcd2bb1f9057b27b572afa5a6d028a5 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:00 2022 +0000 Add new daily segment and filter by segment in the cleaning script. commit cf38d9f175c5bcc9d0f8c70f49e59d2b56d8ada7 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 17 15:07:33 2022 +0000 Implement ERS generating logic. commit f3ca56cdbf22d7eed38f920889c4b19f49da7760 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 14 14:46:28 2022 +0000 Start with ERS logic integration within Snakemake. commit 797aa98f4fe2faf411c5130d27c51c5c606e5c0e Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:50 2022 +0000 Config for ERS testing. commit 9baff159cd1a61019410838efefa4b59a6c4981c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:23 2022 +0000 Changes needed for testing and starting of the Event-Related Segments. commit 0f21273508654133a51d1e20e485c3de33dc2779 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:32:51 2022 +0000 Bugs fix commit 55517eb737463e21c6f6ad18f4711d38bd02fec5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:23:11 2022 +0000 Necessary commit before proceeding. commit de15a52dba43325c171584464995fa4311403e7e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:36:23 2022 +0000 Bug fix commit 1ad25bb5727d30affd2ee063386f2f5ca52e0d63 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:26:17 2022 +0000 Few modifications of some imputation values in cleaning script and feature extraction. commit 9884b383cf6e1b339738deea8cc54a6d264e5c87 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 10 16:45:38 2022 +0000 Testing new data with AutoML. commit 2dc89c083c99d43da5e1eb9cbc1c07d39901f27d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 7 08:52:12 2022 +0000 Small changes in cleaning overall commit 001d40072973797f159b94b48ac3add10138f58e Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 14:28:12 2022 +0000 Clean features and create input files based on all possible targets. commit 1e38d9bf1e4d1caa10ff8c5245a59a9b20d4d7f9 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 13:27:38 2022 +0000 Standardization and correlation visualization in overall cleaning script. commit a34412a18dbd75aafa9f3bba9303ab6a962cec03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 14:16:55 2022 +0000 E4 data yield corrections. Changes in overal cs - standardization. commit 437459648f16f71acec6794a07404bfeb781f907 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 13:35:05 2022 +0000 Errors fix: individual script - treat participants missing data. commit 53f6cc60d5d8262a3bbb3cad82e2ebf49cb9e2a5 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 13:06:39 2022 +0000 Config and cleaning script necessary changes ... commit bbeabeee6ff7e3f8cc429470404c2c4b246b6a22 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 12:53:31 2022 +0000 Last changes before processing on the server. commit 44531c6d94705757110df6d087f3762699d7211a Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 30 10:04:07 2022 +0000 Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds. commit 7ac7cd5a3714521fc9a36a8371554a921df132fe Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 14:33:21 2022 +0000 Preparation of the overall cleaning script. commit 68fd69dadab8c7e14095469d5ed1d9921b4c0ce7 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:55:25 2022 +0000 Cleaning script for individuals: corrections and comments. commit a4f0d056a047aaf3458b043eba5e98df76da039a Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:44:27 2022 +0000 Fillna for app foreground and activity recognition commit 6286e7a44c7e2e99116b83fc3c06ce4398d022e5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:47:08 2022 +0000 firstuseafter column removed from contextual imputation commit 9b3447febd075f4dc5ede6a4071f72821835e7a2 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:40:05 2022 +0000 Contextual imputation correction commit d6adda30cf95e6d9660e6001225dee461bbe3704 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:37:51 2022 +0000 Contextual imputation on time(first/last) features. commit 8af4ef11dc711dffd86c71c99b15e9451aa94ecd Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 10:02:47 2022 +0000 Contextual imputation by feature type. commit 536b9494cdfbc6b31d41a74126ac6af1d8fe62e0 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 14:12:08 2022 +0000 Cleaning script corrections commit f0b87c9dd02d31223c2b69c2586221ffe202e21f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 09:54:15 2022 +0000 Debugging of the empatica data yield integration. commit 7fcdb873fe910f7243fb71ffe56abfdd9ebb81e3 Merge: 5c7bb0f4 bd53dc16 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:50:29 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 5c7bb0f4c14ab4413ed3682268bb7e65ac56fc83 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:48:32 2022 +0000 Config changes commit bd53dc1684b2b6fadf5653e2a9cc00c953410149 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 26 15:54:00 2022 +0000 Empatica data yield usage in the cleaning script. commit d9a574c550f8beb1cf5662e164ffa66048106dc9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 23 13:24:50 2022 +0000 Changes in the cleaning script and preparation of empatica data yield method. commit 19aa8707c0b61790d9d4c1834944c1711d8777aa Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 22 13:45:51 2022 +0000 Redefined cleaning steps after revision commit 247d758cb7eaa93ed9c7df2b0711325ffa27d985 Merge: 90ee99e4 7493aaa6 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:18:01 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 90ee99e4b99eeb32650df06d60e43c0ee1e66a87 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:16:00 2022 +0000 Remove TODO comments commit 7493aaa64368f81adbf478b43411063f56a9a87e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 12:57:55 2022 +0000 Small changes in cleaning scrtipt and missing vals testing. commit eaf4340afd7db8a43174a4789cfb9ba5a831dac4 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 08:03:48 2022 +0000 Small imputation and cleaning corrections. commit a96ea508c628d8c8c736126b65772c06c7cf4ddc Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:34:02 2022 +0000 Fill NaN of Empatica's SD second order feature (must be tested). commit 52e11cdcab51ec8ef97d379304e9297dd233773f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:54 2022 +0000 Configurations for new standardization path. commit 92aff93e65f765ca531bf414c2bdb2e6d7ca1240 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:16 2022 +0000 Remove standardization script. commit 18b63127deefb7cee0061ed741af179a4d6fdb01 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 06:16:26 2022 +0000 Removed all standardizaton rules and configurations. commit 62982866cd9f3f45a335d26b67c3fdf3035c6d1e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 13:24:21 2022 +0000 Phone wifi visible inspection (WIP) commit 0ce6da5444b7d0e3a30c8f6ca73422dc88d928b2 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 11:30:08 2022 +0000 kNN imputation relocation and execution only on specific columns. commit e3b78c8a85084b4cd873350df5bc2b75009fae83 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 10:58:57 2022 +0000 Impute selected phone features with 0. Wifi visible, screen, and light. commit 7d85f75d218ef9b3af5ae077343a58e62bb5fa2c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 09:03:30 2022 +0000 Changes in phone features NaN values script. commit 385e21409d1d3978588fea56cc26a8d241e3af35 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 14:16:58 2022 +0000 Changes in NaN values testing script. commit 18002f59e1c0e161f68b2a4cc217e62a6a86e467 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 10:48:59 2022 +0000 Doryab bluetooth and locations features fill in NaN values. commit 3cf7ca41aac7772c89ac90ad0a26e938d39f3f34 Merge: d27a4a71 d5ab5a03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 15:38:32 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit d5ab5a0394cdd395088723ff80d78f2257f8e37c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 14:13:03 2022 +0000 Writing testing scripts to determine the point of manual imputation. commit dfbb758902bebdbe86b42753b0252b96ec6e791f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 13:54:06 2022 +0000 Changes in AutoML params and environment.yml commit 4ec371ed96102d4b1f3b85557cb5fc3c388c1cef Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 09:51:03 2022 +0000 Testing auto-sklearn commit d27a4a71c81a50f4d30e5eb5bd9b664610da268a Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 12 13:44:17 2022 +0000 Reorganisation and reordering of the cleaning script. commit 15d792089d3b37dd381b1cb02b11f1106920d304 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:33:36 2022 +0000 Changes in cleaning script: - target extracted from config to remove rows where target is nan - prepared sns.heatmap for further missing values analysis - necessary changes in config and participant p01 - picture of heatmap which shows the values state after cleaning commit cb351e0ff6f6325e86fb2867116a44505a44eae1 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:06:57 2022 +0000 Unnecessary line (rows with no target value will be removed in cleaning script). commit 86299d346b5c3d706190db0dc14555309d17629f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 09:57:21 2022 +0000 Impute phone and sms NAs with 0 commit 3f7ec80c18b1237c49dfdd9a6736cdf518e0b7fb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Aug 31 10:18:50 2022 +0000 Preparation a) phone_calls 0 imputation b) remove rows with NaN target
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TAILORED_EVENTS: # Only relevant if TYPE=EVENT
COMPUTE: True
SEGMENTING_METHOD: "stress_event" # 30_before, 90_before, stress_event
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INTERVAL_OF_INTEREST: 10 # duration of event of interest [minutes]
IOI_ERROR_TOLERANCE: 5 # interval of interest erorr tolerance (before and after IOI) [minutes]
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# See https://www.rapids.science/latest/setup/configuration/#timezone-of-your-study
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TIMEZONE:
TYPE: MULTIPLE
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SINGLE:
TZCODE: Europe/Ljubljana
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MULTIPLE:
TZ_FILE: data/external/timezone.csv
TZCODES_FILE: data/external/multiple_timezones.csv
IF_MISSING_TZCODE: USE_DEFAULT
DEFAULT_TZCODE: Europe/Ljubljana
FITBIT:
ALLOW_MULTIPLE_TZ_PER_DEVICE: False
INFER_FROM_SMARTPHONE_TZ: False
########################################################################################################################
# PHONE #
########################################################################################################################
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# See https://www.rapids.science/latest/setup/configuration/#data-stream-configuration
PHONE_DATA_STREAMS:
USE: aware_postgresql
# AVAILABLE:
aware_mysql:
DATABASE_GROUP: MY_GROUP
aware_postgresql:
DATABASE_GROUP: PSQL_STRAW
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aware_csv:
FOLDER: data/external/aware_csv
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aware_influxdb:
DATABASE_GROUP: MY_GROUP
# Sensors ------
# https://www.rapids.science/latest/features/phone-accelerometer/
PHONE_ACCELEROMETER:
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CONTAINER: accelerometer
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PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
SRC_SCRIPT: src/features/phone_accelerometer/rapids/main.py
PANDA:
COMPUTE: False
VALID_SENSED_MINUTES: False
FEATURES:
exertional_activity_episode: ["sumduration", "maxduration", "minduration", "avgduration", "medianduration", "stdduration"]
nonexertional_activity_episode: ["sumduration", "maxduration", "minduration", "avgduration", "medianduration", "stdduration"]
SRC_SCRIPT: src/features/phone_accelerometer/panda/main.py
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# See https://www.rapids.science/latest/features/phone-activity-recognition/
PHONE_ACTIVITY_RECOGNITION:
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CONTAINER:
ANDROID: google_ar
IOS: plugin_ios_activity_recognition
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EPISODE_THRESHOLD_BETWEEN_ROWS: 5 # minutes. Max time difference for two consecutive rows to be considered within the same AR episode.
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PROVIDERS:
RAPIDS:
COMPUTE: True
FEATURES: ["count", "mostcommonactivity", "countuniqueactivities", "durationstationary", "durationmobile", "durationvehicle"]
ACTIVITY_CLASSES:
STATIONARY: ["still", "tilting"]
MOBILE: ["on_foot", "walking", "running", "on_bicycle"]
VEHICLE: ["in_vehicle"]
SRC_SCRIPT: src/features/phone_activity_recognition/rapids/main.py
# See https://www.rapids.science/latest/features/phone-applications-crashes/
PHONE_APPLICATIONS_CRASHES:
CONTAINER: applications_crashes
APPLICATION_CATEGORIES:
CATALOGUE_SOURCE: FILE # FILE (genres are read from CATALOGUE_FILE) or GOOGLE (genres are scrapped from the Play Store)
CATALOGUE_FILE: "data/external/stachl_application_genre_catalogue.csv"
UPDATE_CATALOGUE_FILE: False # if CATALOGUE_SOURCE is equal to FILE, whether or not to update CATALOGUE_FILE, if CATALOGUE_SOURCE is equal to GOOGLE all scraped genres will be saved to CATALOGUE_FILE
SCRAPE_MISSING_CATEGORIES: False # whether or not to scrape missing genres, only effective if CATALOGUE_SOURCE is equal to FILE. If CATALOGUE_SOURCE is equal to GOOGLE, all genres are scraped anyway
PROVIDERS: # None implemented yet but this sensor can be used in PHONE_DATA_YIELD
# See https://www.rapids.science/latest/features/phone-applications-foreground/
PHONE_APPLICATIONS_FOREGROUND:
CONTAINER: applications
APPLICATION_CATEGORIES:
CATALOGUE_SOURCE: FILE # FILE (genres are read from CATALOGUE_FILE) or GOOGLE (genres are scrapped from the Play Store)
CATALOGUE_FILE: "data/external/stachl_application_genre_catalogue.csv"
PACKAGE_NAMES_HASHED: True
UPDATE_CATALOGUE_FILE: False # if CATALOGUE_SOURCE is equal to FILE, whether or not to update CATALOGUE_FILE, if CATALOGUE_SOURCE is equal to GOOGLE all scraped genres will be saved to CATALOGUE_FILE
SCRAPE_MISSING_CATEGORIES: False # whether or not to scrape missing genres, only effective if CATALOGUE_SOURCE is equal to FILE. If CATALOGUE_SOURCE is equal to GOOGLE, all genres are scraped anyway
PROVIDERS:
RAPIDS:
COMPUTE: True
INCLUDE_EPISODE_FEATURES: True
SINGLE_CATEGORIES: ["all", "email"]
MULTIPLE_CATEGORIES:
social: ["socialnetworks", "socialmediatools"]
entertainment: ["entertainment", "gamingknowledge", "gamingcasual", "gamingadventure", "gamingstrategy", "gamingtoolscommunity", "gamingroleplaying", "gamingaction", "gaminglogic", "gamingsports", "gamingsimulation"]
CUSTOM_CATEGORIES:
social_media: ["com.google.android.youtube", "com.snapchat.android", "com.instagram.android", "com.zhiliaoapp.musically", "com.facebook.katana"]
dating: ["com.tinder", "com.relance.happycouple", "com.kiwi.joyride"]
SINGLE_APPS: ["top1global", "com.facebook.moments", "com.google.android.youtube", "com.twitter.android"] # There's no entropy for single apps
EXCLUDED_CATEGORIES: []
EXCLUDED_APPS: ["com.fitbit.FitbitMobile", "com.aware.plugin.upmc.cancer"] # TODO list system apps?
FEATURES:
APP_EVENTS: ["countevent", "timeoffirstuse", "timeoflastuse", "frequencyentropy"]
APP_EPISODES: ["countepisode", "minduration", "maxduration", "meanduration", "sumduration"]
IGNORE_EPISODES_SHORTER_THAN: 0 # in minutes, set to 0 to disable
IGNORE_EPISODES_LONGER_THAN: 300 # in minutes, set to 0 to disable
SRC_SCRIPT: src/features/phone_applications_foreground/rapids/main.py
2021-01-13 23:08:19 +01:00
# See https://www.rapids.science/latest/features/phone-applications-notifications/
PHONE_APPLICATIONS_NOTIFICATIONS:
CONTAINER: notifications
APPLICATION_CATEGORIES:
CATALOGUE_SOURCE: FILE # FILE (genres are read from CATALOGUE_FILE) or GOOGLE (genres are scrapped from the Play Store)
CATALOGUE_FILE: "data/external/stachl_application_genre_catalogue.csv"
UPDATE_CATALOGUE_FILE: False # if CATALOGUE_SOURCE is equal to FILE, whether or not to update CATALOGUE_FILE, if CATALOGUE_SOURCE is equal to GOOGLE all scraped genres will be saved to CATALOGUE_FILE
SCRAPE_MISSING_CATEGORIES: False # whether or not to scrape missing genres, only effective if CATALOGUE_SOURCE is equal to FILE. If CATALOGUE_SOURCE is equal to GOOGLE, all genres are scraped anyway
2021-01-13 23:08:19 +01:00
PROVIDERS: # None implemented yet but this sensor can be used in PHONE_DATA_YIELD
# See https://www.rapids.science/latest/features/phone-battery/
PHONE_BATTERY:
2021-03-13 00:14:49 +01:00
CONTAINER: battery
EPISODE_THRESHOLD_BETWEEN_ROWS: 30 # minutes. Max time difference for two consecutive rows to be considered within the same battery episode.
PROVIDERS:
RAPIDS:
COMPUTE: True
FEATURES: ["countdischarge", "sumdurationdischarge", "countcharge", "sumdurationcharge", "avgconsumptionrate", "maxconsumptionrate"]
SRC_SCRIPT: src/features/phone_battery/rapids/main.py
# See https://www.rapids.science/latest/features/phone-bluetooth/
PHONE_BLUETOOTH:
2021-03-13 00:14:49 +01:00
CONTAINER: bluetooth
PROVIDERS:
RAPIDS:
Squashed commit of the following: commit 8a6b52a97c95dcd8b70b980b4f46421b1a847905 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:35:49 2022 +0000 Switch to 30_before ERS with corresponding targets. commit 244a05373014b14bc4c75db8ceb68a04dc5328df Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:19:43 2022 +0000 Change output files settings to nonstandardized. commit be0324fd01d70c58a9eefd84ccb23d06a42ab57c Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 28 12:44:25 2022 +0000 Fix some bugs and set categorical columns as categories dtypes. commit 99c2fab8f9ab9cf2ed40a952019f994299b78c05 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 16 09:50:18 2022 +0000 Fix a bug in the making of the individual model (when there is no target in the participants columns). commit 286de93bfd55710d77c2e4bab899e73381f9a4a3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 11:21:51 2022 +0000 Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic. commit ab803ee49c2898d2dd4d49de64f763f549c077e3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 10:14:07 2022 +0000 Add additional appraisal targets. commit 621f11b2d98cb3e17d86c3be902ebd40f94d3079 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 09:53:31 2022 +0000 Fix a bug related to wrong user input (duplicated events). commit bd41f42a5da7e28b9de190a53b5f2195fad0920d Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:07:36 2022 +0000 Rename target_ to segmenting_ method. commit a543ce372f1fd6cdd402be8ebdbe54610e449ce2 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:04:16 2022 +0000 Add comments for event_related_script understanding. commit 74b454b07bf69bdcd0517a940c5296e5f77c492e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 11 09:15:12 2022 +0000 Apply changes to string answers to make them language-generic. commit 6ebe83e47ea4da0066f4cd9dedbdb726cef5d06c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 12:42:52 2022 +0000 Improve the ERS extract method with a couple of validations. commit 00350ef8ca2ef43aed71f76609917021ce920f31 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:32:58 2022 +0000 Change config for stressfulness event target method. commit e4985c91214ac6ecd43501d52b67816d26d4fdef Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:29:11 2022 +0000 Override stressfulness event target with extracted values from csv. commit a668b6e8dad4dd393802ed4d5e948d6d42d60a01 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 09:37:27 2022 +0000 Extract ERS and stress event targets to csv files (completed). commit 9199b53ded1c5d858882d9826aa15e5e2102ab08 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 9 15:11:51 2022 +0000 Get, join and start processing required ERS stress event data. commit f3c6a66da9a7ce92d4296436927f48b3d1a467b8 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 15:53:43 2022 +0000 Begin with stress events in the ERS script. commit 0b3e9226b3c683e87ef758756f0d83350642a716 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 14:44:24 2022 +0000 Make small corrections in ERS file. commit 2d83f7ddecbc3880e8d901fc2aae25621a280f75 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 11:32:05 2022 +0000 Begin the ERS logic for 90-minutes events. commit 1da72a7cbe3178ef911ddb263ea30e5da79407ad Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 09:45:37 2022 +0000 Rename targets method in config. commit 9f441afc16ff9b75e131eb47d41edb570b51190c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 15:09:04 2022 +0000 Begin ERS logic for 90-minutes events. commit c1c9f4d05ac8bdf03f4759623165f8e795eaa5a9 Merge: 62f46ea3 7ab0280d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:58 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 62f46ea3763ba47af2a7c62d6b0b453cfd549929 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:53 2022 +0000 Prepare method-based logic for ERS generating. commit 7ab0280d7ed23022a4d2de0caa7bba3a43dff9d4 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 08:58:08 2022 +0000 Correctly rename stressful event target variable. commit eefa9f3f4d4c95374dd31907787ed767c636fe37 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 14:49:54 2022 +0000 Add new target: stressfulness_event. commit 5e8174dd41f5a4c2aa35c74fb4bd9b19a918d1c4 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:52:45 2022 +0000 Add new target: stressfulness_period. commit 35c1a762e7179c7b11f8f1154c1a4f4133402324 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:51:18 2022 +0000 Improve filtering by esm_session and device_id. commit 02264b21fd43212dd4636d300321e254da392149 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 09:30:12 2022 +0000 Add logic for target selection in ERS processing. commit 0ce8723bdb72bafa40924ff4fd3a2328e81808eb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 2 14:01:21 2022 +0000 Extend imputation logic within the cleaning script. commit 30b38bfc028b6e3261701feb915f9e3820a77c75 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 28 09:00:13 2022 +0000 Fix the generating procedure of ERS file for participants with multiple devices. commit cd137af15a9f03724593595a152f34a24323088f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:20:15 2022 +0000 Config for 30 minute EMA segments. commit 3c0585a566ede91dd97e2ba0a6617a4f42e72617 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:12:56 2022 +0000 Remove obsolete comments. commit 6b487fcf7b64a722e9c5486764155764332ba73c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:11:42 2022 +0000 Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script. commit 5d17c92e54427cc70a7f747be398ad59af98c5bf Merge: a31fdd14 0d143e6a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:20 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit a31fdd1479193a67b6a6985cc42fdc66ac7be1a4 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:08 2022 +0000 Start to test empatica_data_yield precieved error. commit 936324d234b6636366b1a569793452a4cca54847 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:17:27 2022 +0000 Switch config for 30 minutes event related segments. commit da0a4596f814a40997efe782239cb296e89fe606 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:16:25 2022 +0000 Add additional ESM processing logic for ERS csv extraction. commit d4d74818e69eab2755f988391978400096902b5d Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:14:32 2022 +0000 Fix a bug - missing time_segment column when df is empty commit 14ff59914b4b3071ff7a40bf9daaba558ff66746 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:59:46 2022 +0000 Fix to correct dtypes. commit 6ab0ac5329d0be06bbe8357203422c7d981c325a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:57:26 2022 +0000 Optimize memory consumption with dtype definition while reading csv file. commit 0d143e6aadaf9b67b2fbfd6cdf8c218d5720f157 Merge: 8acac501 b92a3aa3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:28:27 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 8acac501251105332d1d3d4863e88744b9528844 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:26:43 2022 +0000 Add safenet when features dataframe is empty. commit b92a3aa37a1968b7129cdb2b7ebaf9beda981428 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:25:22 2022 +0000 Remove unwanted output or other error producing code. commit bfd637eb9c40872b954b608aef420b24393d3e6f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 08:53:44 2022 +0000 Improve strings formatting in straw_events file. commit 0d81ad5756c54f03b2b200b801672b9eb39f27d5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 19 13:35:04 2022 +0000 Debug assignment of segments to rows commit cea451d344e3b0bcc110c77f2845a9077bbe5d75 Merge: e88bbd54 cf38d9f1 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:06 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit e88bbd548fcd2bb1f9057b27b572afa5a6d028a5 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:00 2022 +0000 Add new daily segment and filter by segment in the cleaning script. commit cf38d9f175c5bcc9d0f8c70f49e59d2b56d8ada7 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 17 15:07:33 2022 +0000 Implement ERS generating logic. commit f3ca56cdbf22d7eed38f920889c4b19f49da7760 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 14 14:46:28 2022 +0000 Start with ERS logic integration within Snakemake. commit 797aa98f4fe2faf411c5130d27c51c5c606e5c0e Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:50 2022 +0000 Config for ERS testing. commit 9baff159cd1a61019410838efefa4b59a6c4981c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:23 2022 +0000 Changes needed for testing and starting of the Event-Related Segments. commit 0f21273508654133a51d1e20e485c3de33dc2779 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:32:51 2022 +0000 Bugs fix commit 55517eb737463e21c6f6ad18f4711d38bd02fec5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:23:11 2022 +0000 Necessary commit before proceeding. commit de15a52dba43325c171584464995fa4311403e7e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:36:23 2022 +0000 Bug fix commit 1ad25bb5727d30affd2ee063386f2f5ca52e0d63 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:26:17 2022 +0000 Few modifications of some imputation values in cleaning script and feature extraction. commit 9884b383cf6e1b339738deea8cc54a6d264e5c87 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 10 16:45:38 2022 +0000 Testing new data with AutoML. commit 2dc89c083c99d43da5e1eb9cbc1c07d39901f27d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 7 08:52:12 2022 +0000 Small changes in cleaning overall commit 001d40072973797f159b94b48ac3add10138f58e Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 14:28:12 2022 +0000 Clean features and create input files based on all possible targets. commit 1e38d9bf1e4d1caa10ff8c5245a59a9b20d4d7f9 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 13:27:38 2022 +0000 Standardization and correlation visualization in overall cleaning script. commit a34412a18dbd75aafa9f3bba9303ab6a962cec03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 14:16:55 2022 +0000 E4 data yield corrections. Changes in overal cs - standardization. commit 437459648f16f71acec6794a07404bfeb781f907 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 13:35:05 2022 +0000 Errors fix: individual script - treat participants missing data. commit 53f6cc60d5d8262a3bbb3cad82e2ebf49cb9e2a5 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 13:06:39 2022 +0000 Config and cleaning script necessary changes ... commit bbeabeee6ff7e3f8cc429470404c2c4b246b6a22 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 12:53:31 2022 +0000 Last changes before processing on the server. commit 44531c6d94705757110df6d087f3762699d7211a Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 30 10:04:07 2022 +0000 Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds. commit 7ac7cd5a3714521fc9a36a8371554a921df132fe Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 14:33:21 2022 +0000 Preparation of the overall cleaning script. commit 68fd69dadab8c7e14095469d5ed1d9921b4c0ce7 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:55:25 2022 +0000 Cleaning script for individuals: corrections and comments. commit a4f0d056a047aaf3458b043eba5e98df76da039a Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:44:27 2022 +0000 Fillna for app foreground and activity recognition commit 6286e7a44c7e2e99116b83fc3c06ce4398d022e5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:47:08 2022 +0000 firstuseafter column removed from contextual imputation commit 9b3447febd075f4dc5ede6a4071f72821835e7a2 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:40:05 2022 +0000 Contextual imputation correction commit d6adda30cf95e6d9660e6001225dee461bbe3704 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:37:51 2022 +0000 Contextual imputation on time(first/last) features. commit 8af4ef11dc711dffd86c71c99b15e9451aa94ecd Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 10:02:47 2022 +0000 Contextual imputation by feature type. commit 536b9494cdfbc6b31d41a74126ac6af1d8fe62e0 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 14:12:08 2022 +0000 Cleaning script corrections commit f0b87c9dd02d31223c2b69c2586221ffe202e21f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 09:54:15 2022 +0000 Debugging of the empatica data yield integration. commit 7fcdb873fe910f7243fb71ffe56abfdd9ebb81e3 Merge: 5c7bb0f4 bd53dc16 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:50:29 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 5c7bb0f4c14ab4413ed3682268bb7e65ac56fc83 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:48:32 2022 +0000 Config changes commit bd53dc1684b2b6fadf5653e2a9cc00c953410149 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 26 15:54:00 2022 +0000 Empatica data yield usage in the cleaning script. commit d9a574c550f8beb1cf5662e164ffa66048106dc9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 23 13:24:50 2022 +0000 Changes in the cleaning script and preparation of empatica data yield method. commit 19aa8707c0b61790d9d4c1834944c1711d8777aa Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 22 13:45:51 2022 +0000 Redefined cleaning steps after revision commit 247d758cb7eaa93ed9c7df2b0711325ffa27d985 Merge: 90ee99e4 7493aaa6 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:18:01 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 90ee99e4b99eeb32650df06d60e43c0ee1e66a87 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:16:00 2022 +0000 Remove TODO comments commit 7493aaa64368f81adbf478b43411063f56a9a87e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 12:57:55 2022 +0000 Small changes in cleaning scrtipt and missing vals testing. commit eaf4340afd7db8a43174a4789cfb9ba5a831dac4 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 08:03:48 2022 +0000 Small imputation and cleaning corrections. commit a96ea508c628d8c8c736126b65772c06c7cf4ddc Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:34:02 2022 +0000 Fill NaN of Empatica's SD second order feature (must be tested). commit 52e11cdcab51ec8ef97d379304e9297dd233773f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:54 2022 +0000 Configurations for new standardization path. commit 92aff93e65f765ca531bf414c2bdb2e6d7ca1240 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:16 2022 +0000 Remove standardization script. commit 18b63127deefb7cee0061ed741af179a4d6fdb01 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 06:16:26 2022 +0000 Removed all standardizaton rules and configurations. commit 62982866cd9f3f45a335d26b67c3fdf3035c6d1e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 13:24:21 2022 +0000 Phone wifi visible inspection (WIP) commit 0ce6da5444b7d0e3a30c8f6ca73422dc88d928b2 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 11:30:08 2022 +0000 kNN imputation relocation and execution only on specific columns. commit e3b78c8a85084b4cd873350df5bc2b75009fae83 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 10:58:57 2022 +0000 Impute selected phone features with 0. Wifi visible, screen, and light. commit 7d85f75d218ef9b3af5ae077343a58e62bb5fa2c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 09:03:30 2022 +0000 Changes in phone features NaN values script. commit 385e21409d1d3978588fea56cc26a8d241e3af35 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 14:16:58 2022 +0000 Changes in NaN values testing script. commit 18002f59e1c0e161f68b2a4cc217e62a6a86e467 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 10:48:59 2022 +0000 Doryab bluetooth and locations features fill in NaN values. commit 3cf7ca41aac7772c89ac90ad0a26e938d39f3f34 Merge: d27a4a71 d5ab5a03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 15:38:32 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit d5ab5a0394cdd395088723ff80d78f2257f8e37c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 14:13:03 2022 +0000 Writing testing scripts to determine the point of manual imputation. commit dfbb758902bebdbe86b42753b0252b96ec6e791f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 13:54:06 2022 +0000 Changes in AutoML params and environment.yml commit 4ec371ed96102d4b1f3b85557cb5fc3c388c1cef Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 09:51:03 2022 +0000 Testing auto-sklearn commit d27a4a71c81a50f4d30e5eb5bd9b664610da268a Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 12 13:44:17 2022 +0000 Reorganisation and reordering of the cleaning script. commit 15d792089d3b37dd381b1cb02b11f1106920d304 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:33:36 2022 +0000 Changes in cleaning script: - target extracted from config to remove rows where target is nan - prepared sns.heatmap for further missing values analysis - necessary changes in config and participant p01 - picture of heatmap which shows the values state after cleaning commit cb351e0ff6f6325e86fb2867116a44505a44eae1 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:06:57 2022 +0000 Unnecessary line (rows with no target value will be removed in cleaning script). commit 86299d346b5c3d706190db0dc14555309d17629f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 09:57:21 2022 +0000 Impute phone and sms NAs with 0 commit 3f7ec80c18b1237c49dfdd9a6736cdf518e0b7fb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Aug 31 10:18:50 2022 +0000 Preparation a) phone_calls 0 imputation b) remove rows with NaN target
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COMPUTE: False
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
SRC_SCRIPT: src/features/phone_bluetooth/rapids/main.R
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DORYAB:
COMPUTE: True
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FEATURES:
ALL:
DEVICES: ["countscans", "uniquedevices", "meanscans", "stdscans"]
SCANS_MOST_FREQUENT_DEVICE: ["withinsegments", "acrosssegments", "acrossdataset"]
SCANS_LEAST_FREQUENT_DEVICE: ["withinsegments", "acrosssegments", "acrossdataset"]
OWN:
DEVICES: ["countscans", "uniquedevices", "meanscans", "stdscans"]
SCANS_MOST_FREQUENT_DEVICE: ["withinsegments", "acrosssegments", "acrossdataset"]
SCANS_LEAST_FREQUENT_DEVICE: ["withinsegments", "acrosssegments", "acrossdataset"]
OTHERS:
DEVICES: ["countscans", "uniquedevices", "meanscans", "stdscans"]
SCANS_MOST_FREQUENT_DEVICE: ["withinsegments", "acrosssegments", "acrossdataset"]
SCANS_LEAST_FREQUENT_DEVICE: ["withinsegments", "acrosssegments", "acrossdataset"]
SRC_SCRIPT: src/features/phone_bluetooth/doryab/main.py
# See https://www.rapids.science/latest/features/phone-calls/
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PHONE_CALLS:
CONTAINER: call
PROVIDERS:
RAPIDS:
COMPUTE: True
FEATURES_TYPE: EPISODES # EVENTS or EPISODES
CALL_TYPES: [missed, incoming, outgoing]
FEATURES:
missed: [count, distinctcontacts, timefirstcall, timelastcall, countmostfrequentcontact]
incoming: [count, distinctcontacts, meanduration, sumduration, minduration, maxduration, stdduration, modeduration, entropyduration, timefirstcall, timelastcall, countmostfrequentcontact]
outgoing: [count, distinctcontacts, meanduration, sumduration, minduration, maxduration, stdduration, modeduration, entropyduration, timefirstcall, timelastcall, countmostfrequentcontact]
SRC_SCRIPT: src/features/phone_calls/rapids/main.R
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# See https://www.rapids.science/latest/features/phone-conversation/
PHONE_CONVERSATION: # TODO Adapt for speech
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CONTAINER:
ANDROID: plugin_studentlife_audio_android
IOS: plugin_studentlife_audio
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["minutessilence", "minutesnoise", "minutesvoice", "minutesunknown","sumconversationduration","avgconversationduration",
"sdconversationduration","minconversationduration","maxconversationduration","timefirstconversation","timelastconversation","noisesumenergy",
"noiseavgenergy","noisesdenergy","noiseminenergy","noisemaxenergy","voicesumenergy",
"voiceavgenergy","voicesdenergy","voiceminenergy","voicemaxenergy","silencesensedfraction","noisesensedfraction",
"voicesensedfraction","unknownsensedfraction","silenceexpectedfraction","noiseexpectedfraction","voiceexpectedfraction",
"unknownexpectedfraction","countconversation"]
RECORDING_MINUTES: 1
PAUSED_MINUTES : 3
SRC_SCRIPT: src/features/phone_conversation/rapids/main.py
# See https://www.rapids.science/latest/features/phone-data-yield/
PHONE_DATA_YIELD:
SENSORS: [#PHONE_ACCELEROMETER,
PHONE_ACTIVITY_RECOGNITION,
PHONE_APPLICATIONS_FOREGROUND,
PHONE_APPLICATIONS_NOTIFICATIONS,
PHONE_BATTERY,
PHONE_BLUETOOTH,
PHONE_CALLS,
PHONE_LIGHT,
PHONE_LOCATIONS,
PHONE_MESSAGES,
PHONE_SCREEN,
PHONE_WIFI_VISIBLE]
PROVIDERS:
RAPIDS:
COMPUTE: True
FEATURES: [ratiovalidyieldedminutes, ratiovalidyieldedhours]
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MINUTE_RATIO_THRESHOLD_FOR_VALID_YIELDED_HOURS: 0.5 # 0 to 1, minimum percentage of valid minutes in an hour to be considered valid.
SRC_SCRIPT: src/features/phone_data_yield/rapids/main.R
PHONE_ESM:
CONTAINER: esm
PROVIDERS:
STRAW:
COMPUTE: True
Squashed commit of the following: commit 8a6b52a97c95dcd8b70b980b4f46421b1a847905 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:35:49 2022 +0000 Switch to 30_before ERS with corresponding targets. commit 244a05373014b14bc4c75db8ceb68a04dc5328df Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:19:43 2022 +0000 Change output files settings to nonstandardized. commit be0324fd01d70c58a9eefd84ccb23d06a42ab57c Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 28 12:44:25 2022 +0000 Fix some bugs and set categorical columns as categories dtypes. commit 99c2fab8f9ab9cf2ed40a952019f994299b78c05 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 16 09:50:18 2022 +0000 Fix a bug in the making of the individual model (when there is no target in the participants columns). commit 286de93bfd55710d77c2e4bab899e73381f9a4a3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 11:21:51 2022 +0000 Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic. commit ab803ee49c2898d2dd4d49de64f763f549c077e3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 10:14:07 2022 +0000 Add additional appraisal targets. commit 621f11b2d98cb3e17d86c3be902ebd40f94d3079 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 09:53:31 2022 +0000 Fix a bug related to wrong user input (duplicated events). commit bd41f42a5da7e28b9de190a53b5f2195fad0920d Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:07:36 2022 +0000 Rename target_ to segmenting_ method. commit a543ce372f1fd6cdd402be8ebdbe54610e449ce2 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:04:16 2022 +0000 Add comments for event_related_script understanding. commit 74b454b07bf69bdcd0517a940c5296e5f77c492e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 11 09:15:12 2022 +0000 Apply changes to string answers to make them language-generic. commit 6ebe83e47ea4da0066f4cd9dedbdb726cef5d06c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 12:42:52 2022 +0000 Improve the ERS extract method with a couple of validations. commit 00350ef8ca2ef43aed71f76609917021ce920f31 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:32:58 2022 +0000 Change config for stressfulness event target method. commit e4985c91214ac6ecd43501d52b67816d26d4fdef Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:29:11 2022 +0000 Override stressfulness event target with extracted values from csv. commit a668b6e8dad4dd393802ed4d5e948d6d42d60a01 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 09:37:27 2022 +0000 Extract ERS and stress event targets to csv files (completed). commit 9199b53ded1c5d858882d9826aa15e5e2102ab08 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 9 15:11:51 2022 +0000 Get, join and start processing required ERS stress event data. commit f3c6a66da9a7ce92d4296436927f48b3d1a467b8 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 15:53:43 2022 +0000 Begin with stress events in the ERS script. commit 0b3e9226b3c683e87ef758756f0d83350642a716 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 14:44:24 2022 +0000 Make small corrections in ERS file. commit 2d83f7ddecbc3880e8d901fc2aae25621a280f75 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 11:32:05 2022 +0000 Begin the ERS logic for 90-minutes events. commit 1da72a7cbe3178ef911ddb263ea30e5da79407ad Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 09:45:37 2022 +0000 Rename targets method in config. commit 9f441afc16ff9b75e131eb47d41edb570b51190c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 15:09:04 2022 +0000 Begin ERS logic for 90-minutes events. commit c1c9f4d05ac8bdf03f4759623165f8e795eaa5a9 Merge: 62f46ea3 7ab0280d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:58 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 62f46ea3763ba47af2a7c62d6b0b453cfd549929 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:53 2022 +0000 Prepare method-based logic for ERS generating. commit 7ab0280d7ed23022a4d2de0caa7bba3a43dff9d4 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 08:58:08 2022 +0000 Correctly rename stressful event target variable. commit eefa9f3f4d4c95374dd31907787ed767c636fe37 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 14:49:54 2022 +0000 Add new target: stressfulness_event. commit 5e8174dd41f5a4c2aa35c74fb4bd9b19a918d1c4 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:52:45 2022 +0000 Add new target: stressfulness_period. commit 35c1a762e7179c7b11f8f1154c1a4f4133402324 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:51:18 2022 +0000 Improve filtering by esm_session and device_id. commit 02264b21fd43212dd4636d300321e254da392149 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 09:30:12 2022 +0000 Add logic for target selection in ERS processing. commit 0ce8723bdb72bafa40924ff4fd3a2328e81808eb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 2 14:01:21 2022 +0000 Extend imputation logic within the cleaning script. commit 30b38bfc028b6e3261701feb915f9e3820a77c75 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 28 09:00:13 2022 +0000 Fix the generating procedure of ERS file for participants with multiple devices. commit cd137af15a9f03724593595a152f34a24323088f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:20:15 2022 +0000 Config for 30 minute EMA segments. commit 3c0585a566ede91dd97e2ba0a6617a4f42e72617 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:12:56 2022 +0000 Remove obsolete comments. commit 6b487fcf7b64a722e9c5486764155764332ba73c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:11:42 2022 +0000 Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script. commit 5d17c92e54427cc70a7f747be398ad59af98c5bf Merge: a31fdd14 0d143e6a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:20 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit a31fdd1479193a67b6a6985cc42fdc66ac7be1a4 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:08 2022 +0000 Start to test empatica_data_yield precieved error. commit 936324d234b6636366b1a569793452a4cca54847 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:17:27 2022 +0000 Switch config for 30 minutes event related segments. commit da0a4596f814a40997efe782239cb296e89fe606 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:16:25 2022 +0000 Add additional ESM processing logic for ERS csv extraction. commit d4d74818e69eab2755f988391978400096902b5d Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:14:32 2022 +0000 Fix a bug - missing time_segment column when df is empty commit 14ff59914b4b3071ff7a40bf9daaba558ff66746 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:59:46 2022 +0000 Fix to correct dtypes. commit 6ab0ac5329d0be06bbe8357203422c7d981c325a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:57:26 2022 +0000 Optimize memory consumption with dtype definition while reading csv file. commit 0d143e6aadaf9b67b2fbfd6cdf8c218d5720f157 Merge: 8acac501 b92a3aa3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:28:27 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 8acac501251105332d1d3d4863e88744b9528844 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:26:43 2022 +0000 Add safenet when features dataframe is empty. commit b92a3aa37a1968b7129cdb2b7ebaf9beda981428 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:25:22 2022 +0000 Remove unwanted output or other error producing code. commit bfd637eb9c40872b954b608aef420b24393d3e6f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 08:53:44 2022 +0000 Improve strings formatting in straw_events file. commit 0d81ad5756c54f03b2b200b801672b9eb39f27d5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 19 13:35:04 2022 +0000 Debug assignment of segments to rows commit cea451d344e3b0bcc110c77f2845a9077bbe5d75 Merge: e88bbd54 cf38d9f1 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:06 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit e88bbd548fcd2bb1f9057b27b572afa5a6d028a5 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:00 2022 +0000 Add new daily segment and filter by segment in the cleaning script. commit cf38d9f175c5bcc9d0f8c70f49e59d2b56d8ada7 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 17 15:07:33 2022 +0000 Implement ERS generating logic. commit f3ca56cdbf22d7eed38f920889c4b19f49da7760 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 14 14:46:28 2022 +0000 Start with ERS logic integration within Snakemake. commit 797aa98f4fe2faf411c5130d27c51c5c606e5c0e Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:50 2022 +0000 Config for ERS testing. commit 9baff159cd1a61019410838efefa4b59a6c4981c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:23 2022 +0000 Changes needed for testing and starting of the Event-Related Segments. commit 0f21273508654133a51d1e20e485c3de33dc2779 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:32:51 2022 +0000 Bugs fix commit 55517eb737463e21c6f6ad18f4711d38bd02fec5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:23:11 2022 +0000 Necessary commit before proceeding. commit de15a52dba43325c171584464995fa4311403e7e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:36:23 2022 +0000 Bug fix commit 1ad25bb5727d30affd2ee063386f2f5ca52e0d63 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:26:17 2022 +0000 Few modifications of some imputation values in cleaning script and feature extraction. commit 9884b383cf6e1b339738deea8cc54a6d264e5c87 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 10 16:45:38 2022 +0000 Testing new data with AutoML. commit 2dc89c083c99d43da5e1eb9cbc1c07d39901f27d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 7 08:52:12 2022 +0000 Small changes in cleaning overall commit 001d40072973797f159b94b48ac3add10138f58e Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 14:28:12 2022 +0000 Clean features and create input files based on all possible targets. commit 1e38d9bf1e4d1caa10ff8c5245a59a9b20d4d7f9 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 13:27:38 2022 +0000 Standardization and correlation visualization in overall cleaning script. commit a34412a18dbd75aafa9f3bba9303ab6a962cec03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 14:16:55 2022 +0000 E4 data yield corrections. Changes in overal cs - standardization. commit 437459648f16f71acec6794a07404bfeb781f907 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 13:35:05 2022 +0000 Errors fix: individual script - treat participants missing data. commit 53f6cc60d5d8262a3bbb3cad82e2ebf49cb9e2a5 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 13:06:39 2022 +0000 Config and cleaning script necessary changes ... commit bbeabeee6ff7e3f8cc429470404c2c4b246b6a22 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 12:53:31 2022 +0000 Last changes before processing on the server. commit 44531c6d94705757110df6d087f3762699d7211a Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 30 10:04:07 2022 +0000 Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds. commit 7ac7cd5a3714521fc9a36a8371554a921df132fe Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 14:33:21 2022 +0000 Preparation of the overall cleaning script. commit 68fd69dadab8c7e14095469d5ed1d9921b4c0ce7 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:55:25 2022 +0000 Cleaning script for individuals: corrections and comments. commit a4f0d056a047aaf3458b043eba5e98df76da039a Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:44:27 2022 +0000 Fillna for app foreground and activity recognition commit 6286e7a44c7e2e99116b83fc3c06ce4398d022e5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:47:08 2022 +0000 firstuseafter column removed from contextual imputation commit 9b3447febd075f4dc5ede6a4071f72821835e7a2 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:40:05 2022 +0000 Contextual imputation correction commit d6adda30cf95e6d9660e6001225dee461bbe3704 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:37:51 2022 +0000 Contextual imputation on time(first/last) features. commit 8af4ef11dc711dffd86c71c99b15e9451aa94ecd Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 10:02:47 2022 +0000 Contextual imputation by feature type. commit 536b9494cdfbc6b31d41a74126ac6af1d8fe62e0 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 14:12:08 2022 +0000 Cleaning script corrections commit f0b87c9dd02d31223c2b69c2586221ffe202e21f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 09:54:15 2022 +0000 Debugging of the empatica data yield integration. commit 7fcdb873fe910f7243fb71ffe56abfdd9ebb81e3 Merge: 5c7bb0f4 bd53dc16 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:50:29 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 5c7bb0f4c14ab4413ed3682268bb7e65ac56fc83 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:48:32 2022 +0000 Config changes commit bd53dc1684b2b6fadf5653e2a9cc00c953410149 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 26 15:54:00 2022 +0000 Empatica data yield usage in the cleaning script. commit d9a574c550f8beb1cf5662e164ffa66048106dc9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 23 13:24:50 2022 +0000 Changes in the cleaning script and preparation of empatica data yield method. commit 19aa8707c0b61790d9d4c1834944c1711d8777aa Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 22 13:45:51 2022 +0000 Redefined cleaning steps after revision commit 247d758cb7eaa93ed9c7df2b0711325ffa27d985 Merge: 90ee99e4 7493aaa6 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:18:01 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 90ee99e4b99eeb32650df06d60e43c0ee1e66a87 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:16:00 2022 +0000 Remove TODO comments commit 7493aaa64368f81adbf478b43411063f56a9a87e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 12:57:55 2022 +0000 Small changes in cleaning scrtipt and missing vals testing. commit eaf4340afd7db8a43174a4789cfb9ba5a831dac4 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 08:03:48 2022 +0000 Small imputation and cleaning corrections. commit a96ea508c628d8c8c736126b65772c06c7cf4ddc Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:34:02 2022 +0000 Fill NaN of Empatica's SD second order feature (must be tested). commit 52e11cdcab51ec8ef97d379304e9297dd233773f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:54 2022 +0000 Configurations for new standardization path. commit 92aff93e65f765ca531bf414c2bdb2e6d7ca1240 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:16 2022 +0000 Remove standardization script. commit 18b63127deefb7cee0061ed741af179a4d6fdb01 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 06:16:26 2022 +0000 Removed all standardizaton rules and configurations. commit 62982866cd9f3f45a335d26b67c3fdf3035c6d1e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 13:24:21 2022 +0000 Phone wifi visible inspection (WIP) commit 0ce6da5444b7d0e3a30c8f6ca73422dc88d928b2 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 11:30:08 2022 +0000 kNN imputation relocation and execution only on specific columns. commit e3b78c8a85084b4cd873350df5bc2b75009fae83 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 10:58:57 2022 +0000 Impute selected phone features with 0. Wifi visible, screen, and light. commit 7d85f75d218ef9b3af5ae077343a58e62bb5fa2c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 09:03:30 2022 +0000 Changes in phone features NaN values script. commit 385e21409d1d3978588fea56cc26a8d241e3af35 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 14:16:58 2022 +0000 Changes in NaN values testing script. commit 18002f59e1c0e161f68b2a4cc217e62a6a86e467 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 10:48:59 2022 +0000 Doryab bluetooth and locations features fill in NaN values. commit 3cf7ca41aac7772c89ac90ad0a26e938d39f3f34 Merge: d27a4a71 d5ab5a03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 15:38:32 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit d5ab5a0394cdd395088723ff80d78f2257f8e37c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 14:13:03 2022 +0000 Writing testing scripts to determine the point of manual imputation. commit dfbb758902bebdbe86b42753b0252b96ec6e791f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 13:54:06 2022 +0000 Changes in AutoML params and environment.yml commit 4ec371ed96102d4b1f3b85557cb5fc3c388c1cef Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 09:51:03 2022 +0000 Testing auto-sklearn commit d27a4a71c81a50f4d30e5eb5bd9b664610da268a Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 12 13:44:17 2022 +0000 Reorganisation and reordering of the cleaning script. commit 15d792089d3b37dd381b1cb02b11f1106920d304 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:33:36 2022 +0000 Changes in cleaning script: - target extracted from config to remove rows where target is nan - prepared sns.heatmap for further missing values analysis - necessary changes in config and participant p01 - picture of heatmap which shows the values state after cleaning commit cb351e0ff6f6325e86fb2867116a44505a44eae1 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:06:57 2022 +0000 Unnecessary line (rows with no target value will be removed in cleaning script). commit 86299d346b5c3d706190db0dc14555309d17629f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 09:57:21 2022 +0000 Impute phone and sms NAs with 0 commit 3f7ec80c18b1237c49dfdd9a6736cdf518e0b7fb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Aug 31 10:18:50 2022 +0000 Preparation a) phone_calls 0 imputation b) remove rows with NaN target
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SCALES: ["PANAS_positive_affect", "PANAS_negative_affect", "JCQ_job_demand", "JCQ_job_control", "JCQ_supervisor_support", "JCQ_coworker_support",
"appraisal_stressfulness_period", "appraisal_stressfulness_event", "appraisal_threat", "appraisal_challenge"]
FEATURES: [mean]
SRC_SCRIPT: src/features/phone_esm/straw/main.py
# See https://www.rapids.science/latest/features/phone-keyboard/
PHONE_KEYBOARD:
CONTAINER: keyboard
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["sessioncount","averageinterkeydelay","averagesessionlength","changeintextlengthlessthanminusone","changeintextlengthequaltominusone","changeintextlengthequaltoone","changeintextlengthmorethanone","maxtextlength","lastmessagelength","totalkeyboardtouches"]
SRC_SCRIPT: src/features/phone_keyboard/rapids/main.py
# See https://www.rapids.science/latest/features/phone-light/
PHONE_LIGHT:
CONTAINER: light_sensor
PROVIDERS:
RAPIDS:
COMPUTE: True
FEATURES: ["count", "maxlux", "minlux", "avglux", "medianlux", "stdlux"]
SRC_SCRIPT: src/features/phone_light/rapids/main.py
# See https://www.rapids.science/latest/features/phone-locations/
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PHONE_LOCATIONS:
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CONTAINER: locations
LOCATIONS_TO_USE: ALL_RESAMPLED # ALL, GPS, ALL_RESAMPLED, OR FUSED_RESAMPLED
FUSED_RESAMPLED_CONSECUTIVE_THRESHOLD: 30 # minutes, only replicate location samples to the next sensed bin if the phone did not stop collecting data for more than this threshold
FUSED_RESAMPLED_TIME_SINCE_VALID_LOCATION: 720 # minutes, only replicate location samples to consecutive sensed bins if they were logged within this threshold after a valid location row
ACCURACY_LIMIT: 100 # meters, drops location coordinates with an accuracy equal or higher than this. This number means there's a 68% probability the true location is within this radius
PROVIDERS:
DORYAB:
COMPUTE: True
FEATURES: ["locationvariance","loglocationvariance","totaldistance","avgspeed","varspeed", "numberofsignificantplaces","numberlocationtransitions","radiusgyration","timeattop1location","timeattop2location","timeattop3location","movingtostaticratio","outlierstimepercent","maxlengthstayatclusters","minlengthstayatclusters","avglengthstayatclusters","stdlengthstayatclusters","locationentropy","normalizedlocationentropy","timeathome", "homelabel"]
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DBSCAN_EPS: 100 # meters
DBSCAN_MINSAMPLES: 5
THRESHOLD_STATIC : 1 # km/h
MAXIMUM_ROW_GAP: 300 # seconds
MINUTES_DATA_USED: False
CLUSTER_ON: PARTICIPANT_DATASET # PARTICIPANT_DATASET, TIME_SEGMENT, TIME_SEGMENT_INSTANCE
INFER_HOME_LOCATION_STRATEGY: DORYAB_STRATEGY # DORYAB_STRATEGY, SUN_LI_VEGA_STRATEGY
MINIMUM_DAYS_TO_DETECT_HOME_CHANGES: 3
CLUSTERING_ALGORITHM: DBSCAN # DBSCAN, OPTICS
RADIUS_FOR_HOME: 100
SRC_SCRIPT: src/features/phone_locations/doryab/main.py
BARNETT:
COMPUTE: True
FEATURES: ["hometime","disttravelled","rog","maxdiam","maxhomedist","siglocsvisited","avgflightlen","stdflightlen","avgflightdur","stdflightdur","probpause","siglocentropy","circdnrtn","wkenddayrtn"]
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IF_MULTIPLE_TIMEZONES: USE_MOST_COMMON
MINUTES_DATA_USED: False # Use this for quality control purposes, how many minutes of data (location coordinates gruped by minute) were used to compute features
SRC_SCRIPT: src/features/phone_locations/barnett/main.R
# See https://www.rapids.science/latest/features/phone-log/
PHONE_LOG:
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CONTAINER:
ANDROID: aware_log
IOS: ios_aware_log
PROVIDERS: # None implemented yet but this sensor can be used in PHONE_DATA_YIELD
# See https://www.rapids.science/latest/features/phone-messages/
PHONE_MESSAGES:
CONTAINER: sms
PROVIDERS:
RAPIDS:
COMPUTE: True
MESSAGES_TYPES : [received, sent]
FEATURES:
received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
sent: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
SRC_SCRIPT: src/features/phone_messages/rapids/main.R
# See https://www.rapids.science/latest/features/phone-screen/
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PHONE_SCREEN:
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CONTAINER: screen
PROVIDERS:
RAPIDS:
COMPUTE: True
REFERENCE_HOUR_FIRST_USE: 0
IGNORE_EPISODES_SHORTER_THAN: 0 # in minutes, set to 0 to disable
IGNORE_EPISODES_LONGER_THAN: 360 # in minutes, set to 0 to disable
FEATURES: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration", "firstuseafter"] # "episodepersensedminutes" needs to be added later
EPISODE_TYPES: ["unlock"]
SRC_SCRIPT: src/features/phone_screen/rapids/main.py
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# Custom added sensor
PHONE_SPEECH:
CONTAINER: speech
PROVIDERS:
STRAW:
COMPUTE: True
FEATURES: ["meanspeech", "stdspeech", "nlargest", "nsmallest", "medianspeech"]
SRC_SCRIPT: src/features/phone_speech/straw/main.py
# See https://www.rapids.science/latest/features/phone-wifi-connected/
PHONE_WIFI_CONNECTED:
CONTAINER: sensor_wifi
PROVIDERS:
RAPIDS:
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COMPUTE: False
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
SRC_SCRIPT: src/features/phone_wifi_connected/rapids/main.R
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# See https://www.rapids.science/latest/features/phone-wifi-visible/
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PHONE_WIFI_VISIBLE:
CONTAINER: wifi
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PROVIDERS:
RAPIDS:
COMPUTE: True
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FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
SRC_SCRIPT: src/features/phone_wifi_visible/rapids/main.R
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########################################################################################################################
# FITBIT #
########################################################################################################################
# See https://www.rapids.science/latest/setup/configuration/#data-stream-configuration
FITBIT_DATA_STREAMS:
USE: fitbitjson_mysql
# AVAILABLE:
fitbitjson_mysql:
DATABASE_GROUP: MY_GROUP
SLEEP_SUMMARY_LAST_NIGHT_END: 660 # a number ranged from 0 (midnight) to 1439 (23:59) which denotes number of minutes after midnight. By default, 660 (11:00).
fitbitparsed_mysql:
DATABASE_GROUP: MY_GROUP
SLEEP_SUMMARY_LAST_NIGHT_END: 660 # a number ranged from 0 (midnight) to 1439 (23:59) which denotes number of minutes after midnight. By default, 660 (11:00).
fitbitjson_csv:
FOLDER: data/external/fitbit_csv
SLEEP_SUMMARY_LAST_NIGHT_END: 660 # a number ranged from 0 (midnight) to 1439 (23:59) which denotes number of minutes after midnight. By default, 660 (11:00).
fitbitparsed_csv:
FOLDER: data/external/fitbit_csv
SLEEP_SUMMARY_LAST_NIGHT_END: 660 # a number ranged from 0 (midnight) to 1439 (23:59) which denotes number of minutes after midnight. By default, 660 (11:00).
# Sensors ------
# See https://www.rapids.science/latest/features/fitbit-calories-intraday/
FITBIT_CALORIES_INTRADAY:
CONTAINER: fitbit_data
PROVIDERS:
RAPIDS:
COMPUTE: False
EPISODE_TYPE: [sedentary, lightlyactive, fairlyactive, veryactive, mvpa, lowmet, highmet]
EPISODE_TIME_THRESHOLD: 5 # minutes
EPISODE_MET_THRESHOLD: 3
EPISODE_MVPA_CATEGORIES: [fairlyactive, veryactive]
EPISODE_REFERENCE_TIME: MIDNIGHT # or START_OF_THE_SEGMENT
FEATURES: [count, sumduration, avgduration, minduration, maxduration, stdduration, starttimefirst, endtimefirst, starttimelast, endtimelast, starttimelongest, endtimelongest, summet, avgmet, maxmet, minmet, stdmet, sumcalories, avgcalories, maxcalories, mincalories, stdcalories]
SRC_SCRIPT: src/features/fitbit_calories_intraday/rapids/main.R
# See https://www.rapids.science/latest/features/fitbit-data-yield/
FITBIT_DATA_YIELD:
SENSOR: FITBIT_HEARTRATE_INTRADAY
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: [ratiovalidyieldedminutes, ratiovalidyieldedhours]
MINUTE_RATIO_THRESHOLD_FOR_VALID_YIELDED_HOURS: 0.5 # 0 to 1, minimum percentage of valid minutes in an hour to be considered valid.
SRC_SCRIPT: src/features/fitbit_data_yield/rapids/main.R
# See https://www.rapids.science/latest/features/fitbit-heartrate-summary/
FITBIT_HEARTRATE_SUMMARY:
CONTAINER: heartrate_summary
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["maxrestinghr", "minrestinghr", "avgrestinghr", "medianrestinghr", "moderestinghr", "stdrestinghr", "diffmaxmoderestinghr", "diffminmoderestinghr", "entropyrestinghr"] # calories features' accuracy depend on the accuracy of the participants fitbit profile (e.g. height, weight) use these with care: ["sumcaloriesoutofrange", "maxcaloriesoutofrange", "mincaloriesoutofrange", "avgcaloriesoutofrange", "mediancaloriesoutofrange", "stdcaloriesoutofrange", "entropycaloriesoutofrange", "sumcaloriesfatburn", "maxcaloriesfatburn", "mincaloriesfatburn", "avgcaloriesfatburn", "mediancaloriesfatburn", "stdcaloriesfatburn", "entropycaloriesfatburn", "sumcaloriescardio", "maxcaloriescardio", "mincaloriescardio", "avgcaloriescardio", "mediancaloriescardio", "stdcaloriescardio", "entropycaloriescardio", "sumcaloriespeak", "maxcaloriespeak", "mincaloriespeak", "avgcaloriespeak", "mediancaloriespeak", "stdcaloriespeak", "entropycaloriespeak"]
SRC_SCRIPT: src/features/fitbit_heartrate_summary/rapids/main.py
# See https://www.rapids.science/latest/features/fitbit-heartrate-intraday/
FITBIT_HEARTRATE_INTRADAY:
CONTAINER: heartrate_intraday
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr", "minutesonoutofrangezone", "minutesonfatburnzone", "minutesoncardiozone", "minutesonpeakzone"]
SRC_SCRIPT: src/features/fitbit_heartrate_intraday/rapids/main.py
# See https://www.rapids.science/latest/features/fitbit-sleep-summary/
FITBIT_SLEEP_SUMMARY:
CONTAINER: sleep_summary
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["firstwaketime", "lastwaketime", "firstbedtime", "lastbedtime", "countepisode", "avgefficiency", "sumdurationafterwakeup", "sumdurationasleep", "sumdurationawake", "sumdurationtofallasleep", "sumdurationinbed", "avgdurationafterwakeup", "avgdurationasleep", "avgdurationawake", "avgdurationtofallasleep", "avgdurationinbed"]
SLEEP_TYPES: ["main", "nap", "all"]
SRC_SCRIPT: src/features/fitbit_sleep_summary/rapids/main.py
# See https://www.rapids.science/latest/features/fitbit-sleep-intraday/
FITBIT_SLEEP_INTRADAY:
CONTAINER: sleep_intraday
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES:
LEVELS_AND_TYPES: [countepisode, sumduration, maxduration, minduration, avgduration, medianduration, stdduration]
RATIOS_TYPE: [count, duration]
RATIOS_SCOPE: [ACROSS_LEVELS, ACROSS_TYPES, WITHIN_LEVELS, WITHIN_TYPES]
SLEEP_LEVELS:
INCLUDE_ALL_GROUPS: True
CLASSIC: [awake, restless, asleep]
STAGES: [wake, deep, light, rem]
UNIFIED: [awake, asleep]
SLEEP_TYPES: [main, nap, all]
SRC_SCRIPT: src/features/fitbit_sleep_intraday/rapids/main.py
PRICE:
COMPUTE: False
FEATURES: [avgduration, avgratioduration, avgstarttimeofepisodemain, avgendtimeofepisodemain, avgmidpointofepisodemain, stdstarttimeofepisodemain, stdendtimeofepisodemain, stdmidpointofepisodemain, socialjetlag, rmssdmeanstarttimeofepisodemain, rmssdmeanendtimeofepisodemain, rmssdmeanmidpointofepisodemain, rmssdmedianstarttimeofepisodemain, rmssdmedianendtimeofepisodemain, rmssdmedianmidpointofepisodemain]
SLEEP_LEVELS:
INCLUDE_ALL_GROUPS: True
CLASSIC: [awake, restless, asleep]
STAGES: [wake, deep, light, rem]
UNIFIED: [awake, asleep]
DAY_TYPES: [WEEKEND, WEEK, ALL]
LAST_NIGHT_END: 660 # number of minutes after midnight (11:00) 11*60
SRC_SCRIPT: src/features/fitbit_sleep_intraday/price/main.py
# See https://www.rapids.science/latest/features/fitbit-steps-summary/
FITBIT_STEPS_SUMMARY:
CONTAINER: steps_summary
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["maxsumsteps", "minsumsteps", "avgsumsteps", "mediansumsteps", "stdsumsteps"]
SRC_SCRIPT: src/features/fitbit_steps_summary/rapids/main.py
# See https://www.rapids.science/latest/features/fitbit-steps-intraday/
FITBIT_STEPS_INTRADAY:
CONTAINER: steps_intraday
EXCLUDE_SLEEP: # you can exclude step data that was logged during sleep periods
TIME_BASED:
EXCLUDE: False
START_TIME: "23:00"
END_TIME: "07:00"
FITBIT_BASED:
EXCLUDE: False
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES:
STEPS: ["sum", "max", "min", "avg", "std", "firststeptime", "laststeptime"]
SEDENTARY_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
ACTIVE_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
REFERENCE_HOUR: 0
THRESHOLD_ACTIVE_BOUT: 10 # steps
INCLUDE_ZERO_STEP_ROWS: False
SRC_SCRIPT: src/features/fitbit_steps_intraday/rapids/main.py
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########################################################################################################################
# EMPATICA #
########################################################################################################################
EMPATICA_DATA_STREAMS:
USE: empatica_zip
# AVAILABLE:
empatica_zip:
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FOLDER: data/external/empatica
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# Sensors ------
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# See https://www.rapids.science/latest/features/empatica-accelerometer/
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EMPATICA_ACCELEROMETER:
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CONTAINER: ACC
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PROVIDERS:
DBDP:
COMPUTE: False
FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
SRC_SCRIPT: src/features/empatica_accelerometer/dbdp/main.py
CR:
COMPUTE: True
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FEATURES: ["totalMagnitudeBand", "absoluteMeanBand", "varianceBand"] # Acc features
WINDOWS:
COMPUTE: True
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WINDOW_LENGTH: 15 # specify window length in seconds
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SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', 'count_windows']
SRC_SCRIPT: src/features/empatica_accelerometer/cr/main.py
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# See https://www.rapids.science/latest/features/empatica-heartrate/
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EMPATICA_HEARTRATE:
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CONTAINER: HR
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PROVIDERS:
DBDP:
COMPUTE: False
FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr"]
SRC_SCRIPT: src/features/empatica_heartrate/dbdp/main.py
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# See https://www.rapids.science/latest/features/empatica-temperature/
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EMPATICA_TEMPERATURE:
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CONTAINER: TEMP
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PROVIDERS:
DBDP:
COMPUTE: False
FEATURES: ["maxtemp", "mintemp", "avgtemp", "mediantemp", "modetemp", "stdtemp", "diffmaxmodetemp", "diffminmodetemp", "entropytemp"]
SRC_SCRIPT: src/features/empatica_temperature/dbdp/main.py
CR:
COMPUTE: True
FEATURES: ["maximum", "minimum", "meanAbsChange", "longestStrikeAboveMean", "longestStrikeBelowMean",
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"stdDev", "median", "meanChange", "sumSquared", "squareSumOfComponent", "sumOfSquareComponents"]
WINDOWS:
COMPUTE: True
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WINDOW_LENGTH: 300 # specify window length in seconds
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SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', 'count_windows']
SRC_SCRIPT: src/features/empatica_temperature/cr/main.py
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# See https://www.rapids.science/latest/features/empatica-electrodermal-activity/
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EMPATICA_ELECTRODERMAL_ACTIVITY:
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CONTAINER: EDA
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PROVIDERS:
DBDP:
COMPUTE: False
FEATURES: ["maxeda", "mineda", "avgeda", "medianeda", "modeeda", "stdeda", "diffmaxmodeeda", "diffminmodeeda", "entropyeda"]
SRC_SCRIPT: src/features/empatica_electrodermal_activity/dbdp/main.py
CR:
COMPUTE: True
FEATURES: ['mean', 'std', 'q25', 'q75', 'qd', 'deriv', 'power', 'numPeaks', 'ratePeaks', 'powerPeaks', 'sumPosDeriv', 'propPosDeriv', 'derivTonic',
'sigTonicDifference', 'freqFeats','maxPeakAmplitudeChangeBefore', 'maxPeakAmplitudeChangeAfter', 'avgPeakAmplitudeChangeBefore',
'avgPeakAmplitudeChangeAfter', 'avgPeakChangeRatio', 'maxPeakIncreaseTime', 'maxPeakDecreaseTime', 'maxPeakDuration', 'maxPeakChangeRatio',
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'avgPeakIncreaseTime', 'avgPeakDecreaseTime', 'avgPeakDuration', 'signalOverallChange', 'changeDuration', 'changeRate', 'significantIncrease',
'significantDecrease']
WINDOWS:
COMPUTE: True
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WINDOW_LENGTH: 60 # specify window length in seconds
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SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', count_windows, eda_num_peaks_non_zero]
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IMPUTE_NANS: True
SRC_SCRIPT: src/features/empatica_electrodermal_activity/cr/main.py
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# See https://www.rapids.science/latest/features/empatica-blood-volume-pulse/
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EMPATICA_BLOOD_VOLUME_PULSE:
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CONTAINER: BVP
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PROVIDERS:
DBDP:
COMPUTE: False
FEATURES: ["maxbvp", "minbvp", "avgbvp", "medianbvp", "modebvp", "stdbvp", "diffmaxmodebvp", "diffminmodebvp", "entropybvp"]
SRC_SCRIPT: src/features/empatica_blood_volume_pulse/dbdp/main.py
CR:
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COMPUTE: False
FEATURES: ['meanHr', 'ibi', 'sdnn', 'sdsd', 'rmssd', 'pnn20', 'pnn50', 'sd', 'sd2', 'sd1/sd2', 'numRR', # Time features
'VLF', 'LF', 'LFnorm', 'HF', 'HFnorm', 'LF/HF', 'fullIntegral'] # Freq features
WINDOWS:
COMPUTE: True
WINDOW_LENGTH: 300 # specify window length in seconds
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SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', 'count_windows', 'hrv_num_windows_non_nan']
SRC_SCRIPT: src/features/empatica_blood_volume_pulse/cr/main.py
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# See https://www.rapids.science/latest/features/empatica-inter-beat-interval/
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EMPATICA_INTER_BEAT_INTERVAL:
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CONTAINER: IBI
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PROVIDERS:
DBDP:
COMPUTE: False
FEATURES: ["maxibi", "minibi", "avgibi", "medianibi", "modeibi", "stdibi", "diffmaxmodeibi", "diffminmodeibi", "entropyibi"]
SRC_SCRIPT: src/features/empatica_inter_beat_interval/dbdp/main.py
CR:
COMPUTE: True
FEATURES: ['meanHr', 'ibi', 'sdnn', 'sdsd', 'rmssd', 'pnn20', 'pnn50', 'sd', 'sd2', 'sd1/sd2', 'numRR', # Time features
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'VLF', 'LF', 'LFnorm', 'HF', 'HFnorm', 'LF/HF', 'fullIntegral'] # Freq features
PATCH_WITH_BVP: True
WINDOWS:
COMPUTE: True
WINDOW_LENGTH: 300 # specify window length in seconds
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SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', 'count_windows', 'hrv_num_windows_non_nan']
SRC_SCRIPT: src/features/empatica_inter_beat_interval/cr/main.py
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# See https://www.rapids.science/latest/features/empatica-tags/
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EMPATICA_TAGS:
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CONTAINER: TAGS
PROVIDERS: # None implemented yet
########################################################################################################################
# PLOTS #
########################################################################################################################
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# Data quality ------
# See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#1-histograms-of-phone-data-yield
HISTOGRAM_PHONE_DATA_YIELD:
PLOT: False
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# See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#2-heatmaps-of-overall-data-yield
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HEATMAP_PHONE_DATA_YIELD_PER_PARTICIPANT_PER_TIME_SEGMENT:
PLOT: False
TIME: RELATIVE_TIME # ABSOLUTE_TIME or RELATIVE_TIME
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# See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#3-heatmap-of-recorded-phone-sensors
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HEATMAP_SENSORS_PER_MINUTE_PER_TIME_SEGMENT:
PLOT: False
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# See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#4-heatmap-of-sensor-row-count
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HEATMAP_SENSOR_ROW_COUNT_PER_TIME_SEGMENT:
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PLOT: False
SENSORS: []
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# Features ------
# See https://www.rapids.science/latest/visualizations/feature-visualizations/#1-heatmap-correlation-matrix
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HEATMAP_FEATURE_CORRELATION_MATRIX:
PLOT: False
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MIN_ROWS_RATIO: 0.5
CORR_THRESHOLD: 0.1
CORR_METHOD: "pearson" # choose from {"pearson", "kendall", "spearman"}
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########################################################################################################################
# Data Cleaning #
########################################################################################################################
ALL_CLEANING_INDIVIDUAL:
PROVIDERS:
RAPIDS:
Squashed commit of the following: commit 8a6b52a97c95dcd8b70b980b4f46421b1a847905 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:35:49 2022 +0000 Switch to 30_before ERS with corresponding targets. commit 244a05373014b14bc4c75db8ceb68a04dc5328df Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:19:43 2022 +0000 Change output files settings to nonstandardized. commit be0324fd01d70c58a9eefd84ccb23d06a42ab57c Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 28 12:44:25 2022 +0000 Fix some bugs and set categorical columns as categories dtypes. commit 99c2fab8f9ab9cf2ed40a952019f994299b78c05 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 16 09:50:18 2022 +0000 Fix a bug in the making of the individual model (when there is no target in the participants columns). commit 286de93bfd55710d77c2e4bab899e73381f9a4a3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 11:21:51 2022 +0000 Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic. commit ab803ee49c2898d2dd4d49de64f763f549c077e3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 10:14:07 2022 +0000 Add additional appraisal targets. commit 621f11b2d98cb3e17d86c3be902ebd40f94d3079 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 09:53:31 2022 +0000 Fix a bug related to wrong user input (duplicated events). commit bd41f42a5da7e28b9de190a53b5f2195fad0920d Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:07:36 2022 +0000 Rename target_ to segmenting_ method. commit a543ce372f1fd6cdd402be8ebdbe54610e449ce2 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:04:16 2022 +0000 Add comments for event_related_script understanding. commit 74b454b07bf69bdcd0517a940c5296e5f77c492e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 11 09:15:12 2022 +0000 Apply changes to string answers to make them language-generic. commit 6ebe83e47ea4da0066f4cd9dedbdb726cef5d06c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 12:42:52 2022 +0000 Improve the ERS extract method with a couple of validations. commit 00350ef8ca2ef43aed71f76609917021ce920f31 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:32:58 2022 +0000 Change config for stressfulness event target method. commit e4985c91214ac6ecd43501d52b67816d26d4fdef Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:29:11 2022 +0000 Override stressfulness event target with extracted values from csv. commit a668b6e8dad4dd393802ed4d5e948d6d42d60a01 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 09:37:27 2022 +0000 Extract ERS and stress event targets to csv files (completed). commit 9199b53ded1c5d858882d9826aa15e5e2102ab08 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 9 15:11:51 2022 +0000 Get, join and start processing required ERS stress event data. commit f3c6a66da9a7ce92d4296436927f48b3d1a467b8 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 15:53:43 2022 +0000 Begin with stress events in the ERS script. commit 0b3e9226b3c683e87ef758756f0d83350642a716 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 14:44:24 2022 +0000 Make small corrections in ERS file. commit 2d83f7ddecbc3880e8d901fc2aae25621a280f75 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 11:32:05 2022 +0000 Begin the ERS logic for 90-minutes events. commit 1da72a7cbe3178ef911ddb263ea30e5da79407ad Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 09:45:37 2022 +0000 Rename targets method in config. commit 9f441afc16ff9b75e131eb47d41edb570b51190c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 15:09:04 2022 +0000 Begin ERS logic for 90-minutes events. commit c1c9f4d05ac8bdf03f4759623165f8e795eaa5a9 Merge: 62f46ea3 7ab0280d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:58 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 62f46ea3763ba47af2a7c62d6b0b453cfd549929 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:53 2022 +0000 Prepare method-based logic for ERS generating. commit 7ab0280d7ed23022a4d2de0caa7bba3a43dff9d4 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 08:58:08 2022 +0000 Correctly rename stressful event target variable. commit eefa9f3f4d4c95374dd31907787ed767c636fe37 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 14:49:54 2022 +0000 Add new target: stressfulness_event. commit 5e8174dd41f5a4c2aa35c74fb4bd9b19a918d1c4 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:52:45 2022 +0000 Add new target: stressfulness_period. commit 35c1a762e7179c7b11f8f1154c1a4f4133402324 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:51:18 2022 +0000 Improve filtering by esm_session and device_id. commit 02264b21fd43212dd4636d300321e254da392149 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 09:30:12 2022 +0000 Add logic for target selection in ERS processing. commit 0ce8723bdb72bafa40924ff4fd3a2328e81808eb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 2 14:01:21 2022 +0000 Extend imputation logic within the cleaning script. commit 30b38bfc028b6e3261701feb915f9e3820a77c75 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 28 09:00:13 2022 +0000 Fix the generating procedure of ERS file for participants with multiple devices. commit cd137af15a9f03724593595a152f34a24323088f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:20:15 2022 +0000 Config for 30 minute EMA segments. commit 3c0585a566ede91dd97e2ba0a6617a4f42e72617 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:12:56 2022 +0000 Remove obsolete comments. commit 6b487fcf7b64a722e9c5486764155764332ba73c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:11:42 2022 +0000 Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script. commit 5d17c92e54427cc70a7f747be398ad59af98c5bf Merge: a31fdd14 0d143e6a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:20 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit a31fdd1479193a67b6a6985cc42fdc66ac7be1a4 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:08 2022 +0000 Start to test empatica_data_yield precieved error. commit 936324d234b6636366b1a569793452a4cca54847 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:17:27 2022 +0000 Switch config for 30 minutes event related segments. commit da0a4596f814a40997efe782239cb296e89fe606 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:16:25 2022 +0000 Add additional ESM processing logic for ERS csv extraction. commit d4d74818e69eab2755f988391978400096902b5d Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:14:32 2022 +0000 Fix a bug - missing time_segment column when df is empty commit 14ff59914b4b3071ff7a40bf9daaba558ff66746 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:59:46 2022 +0000 Fix to correct dtypes. commit 6ab0ac5329d0be06bbe8357203422c7d981c325a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:57:26 2022 +0000 Optimize memory consumption with dtype definition while reading csv file. commit 0d143e6aadaf9b67b2fbfd6cdf8c218d5720f157 Merge: 8acac501 b92a3aa3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:28:27 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 8acac501251105332d1d3d4863e88744b9528844 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:26:43 2022 +0000 Add safenet when features dataframe is empty. commit b92a3aa37a1968b7129cdb2b7ebaf9beda981428 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:25:22 2022 +0000 Remove unwanted output or other error producing code. commit bfd637eb9c40872b954b608aef420b24393d3e6f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 08:53:44 2022 +0000 Improve strings formatting in straw_events file. commit 0d81ad5756c54f03b2b200b801672b9eb39f27d5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 19 13:35:04 2022 +0000 Debug assignment of segments to rows commit cea451d344e3b0bcc110c77f2845a9077bbe5d75 Merge: e88bbd54 cf38d9f1 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:06 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit e88bbd548fcd2bb1f9057b27b572afa5a6d028a5 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:00 2022 +0000 Add new daily segment and filter by segment in the cleaning script. commit cf38d9f175c5bcc9d0f8c70f49e59d2b56d8ada7 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 17 15:07:33 2022 +0000 Implement ERS generating logic. commit f3ca56cdbf22d7eed38f920889c4b19f49da7760 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 14 14:46:28 2022 +0000 Start with ERS logic integration within Snakemake. commit 797aa98f4fe2faf411c5130d27c51c5c606e5c0e Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:50 2022 +0000 Config for ERS testing. commit 9baff159cd1a61019410838efefa4b59a6c4981c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:23 2022 +0000 Changes needed for testing and starting of the Event-Related Segments. commit 0f21273508654133a51d1e20e485c3de33dc2779 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:32:51 2022 +0000 Bugs fix commit 55517eb737463e21c6f6ad18f4711d38bd02fec5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:23:11 2022 +0000 Necessary commit before proceeding. commit de15a52dba43325c171584464995fa4311403e7e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:36:23 2022 +0000 Bug fix commit 1ad25bb5727d30affd2ee063386f2f5ca52e0d63 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:26:17 2022 +0000 Few modifications of some imputation values in cleaning script and feature extraction. commit 9884b383cf6e1b339738deea8cc54a6d264e5c87 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 10 16:45:38 2022 +0000 Testing new data with AutoML. commit 2dc89c083c99d43da5e1eb9cbc1c07d39901f27d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 7 08:52:12 2022 +0000 Small changes in cleaning overall commit 001d40072973797f159b94b48ac3add10138f58e Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 14:28:12 2022 +0000 Clean features and create input files based on all possible targets. commit 1e38d9bf1e4d1caa10ff8c5245a59a9b20d4d7f9 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 13:27:38 2022 +0000 Standardization and correlation visualization in overall cleaning script. commit a34412a18dbd75aafa9f3bba9303ab6a962cec03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 14:16:55 2022 +0000 E4 data yield corrections. Changes in overal cs - standardization. commit 437459648f16f71acec6794a07404bfeb781f907 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 13:35:05 2022 +0000 Errors fix: individual script - treat participants missing data. commit 53f6cc60d5d8262a3bbb3cad82e2ebf49cb9e2a5 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 13:06:39 2022 +0000 Config and cleaning script necessary changes ... commit bbeabeee6ff7e3f8cc429470404c2c4b246b6a22 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 12:53:31 2022 +0000 Last changes before processing on the server. commit 44531c6d94705757110df6d087f3762699d7211a Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 30 10:04:07 2022 +0000 Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds. commit 7ac7cd5a3714521fc9a36a8371554a921df132fe Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 14:33:21 2022 +0000 Preparation of the overall cleaning script. commit 68fd69dadab8c7e14095469d5ed1d9921b4c0ce7 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:55:25 2022 +0000 Cleaning script for individuals: corrections and comments. commit a4f0d056a047aaf3458b043eba5e98df76da039a Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:44:27 2022 +0000 Fillna for app foreground and activity recognition commit 6286e7a44c7e2e99116b83fc3c06ce4398d022e5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:47:08 2022 +0000 firstuseafter column removed from contextual imputation commit 9b3447febd075f4dc5ede6a4071f72821835e7a2 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:40:05 2022 +0000 Contextual imputation correction commit d6adda30cf95e6d9660e6001225dee461bbe3704 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:37:51 2022 +0000 Contextual imputation on time(first/last) features. commit 8af4ef11dc711dffd86c71c99b15e9451aa94ecd Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 10:02:47 2022 +0000 Contextual imputation by feature type. commit 536b9494cdfbc6b31d41a74126ac6af1d8fe62e0 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 14:12:08 2022 +0000 Cleaning script corrections commit f0b87c9dd02d31223c2b69c2586221ffe202e21f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 09:54:15 2022 +0000 Debugging of the empatica data yield integration. commit 7fcdb873fe910f7243fb71ffe56abfdd9ebb81e3 Merge: 5c7bb0f4 bd53dc16 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:50:29 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 5c7bb0f4c14ab4413ed3682268bb7e65ac56fc83 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:48:32 2022 +0000 Config changes commit bd53dc1684b2b6fadf5653e2a9cc00c953410149 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 26 15:54:00 2022 +0000 Empatica data yield usage in the cleaning script. commit d9a574c550f8beb1cf5662e164ffa66048106dc9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 23 13:24:50 2022 +0000 Changes in the cleaning script and preparation of empatica data yield method. commit 19aa8707c0b61790d9d4c1834944c1711d8777aa Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 22 13:45:51 2022 +0000 Redefined cleaning steps after revision commit 247d758cb7eaa93ed9c7df2b0711325ffa27d985 Merge: 90ee99e4 7493aaa6 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:18:01 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 90ee99e4b99eeb32650df06d60e43c0ee1e66a87 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:16:00 2022 +0000 Remove TODO comments commit 7493aaa64368f81adbf478b43411063f56a9a87e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 12:57:55 2022 +0000 Small changes in cleaning scrtipt and missing vals testing. commit eaf4340afd7db8a43174a4789cfb9ba5a831dac4 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 08:03:48 2022 +0000 Small imputation and cleaning corrections. commit a96ea508c628d8c8c736126b65772c06c7cf4ddc Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:34:02 2022 +0000 Fill NaN of Empatica's SD second order feature (must be tested). commit 52e11cdcab51ec8ef97d379304e9297dd233773f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:54 2022 +0000 Configurations for new standardization path. commit 92aff93e65f765ca531bf414c2bdb2e6d7ca1240 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:16 2022 +0000 Remove standardization script. commit 18b63127deefb7cee0061ed741af179a4d6fdb01 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 06:16:26 2022 +0000 Removed all standardizaton rules and configurations. commit 62982866cd9f3f45a335d26b67c3fdf3035c6d1e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 13:24:21 2022 +0000 Phone wifi visible inspection (WIP) commit 0ce6da5444b7d0e3a30c8f6ca73422dc88d928b2 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 11:30:08 2022 +0000 kNN imputation relocation and execution only on specific columns. commit e3b78c8a85084b4cd873350df5bc2b75009fae83 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 10:58:57 2022 +0000 Impute selected phone features with 0. Wifi visible, screen, and light. commit 7d85f75d218ef9b3af5ae077343a58e62bb5fa2c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 09:03:30 2022 +0000 Changes in phone features NaN values script. commit 385e21409d1d3978588fea56cc26a8d241e3af35 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 14:16:58 2022 +0000 Changes in NaN values testing script. commit 18002f59e1c0e161f68b2a4cc217e62a6a86e467 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 10:48:59 2022 +0000 Doryab bluetooth and locations features fill in NaN values. commit 3cf7ca41aac7772c89ac90ad0a26e938d39f3f34 Merge: d27a4a71 d5ab5a03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 15:38:32 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit d5ab5a0394cdd395088723ff80d78f2257f8e37c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 14:13:03 2022 +0000 Writing testing scripts to determine the point of manual imputation. commit dfbb758902bebdbe86b42753b0252b96ec6e791f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 13:54:06 2022 +0000 Changes in AutoML params and environment.yml commit 4ec371ed96102d4b1f3b85557cb5fc3c388c1cef Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 09:51:03 2022 +0000 Testing auto-sklearn commit d27a4a71c81a50f4d30e5eb5bd9b664610da268a Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 12 13:44:17 2022 +0000 Reorganisation and reordering of the cleaning script. commit 15d792089d3b37dd381b1cb02b11f1106920d304 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:33:36 2022 +0000 Changes in cleaning script: - target extracted from config to remove rows where target is nan - prepared sns.heatmap for further missing values analysis - necessary changes in config and participant p01 - picture of heatmap which shows the values state after cleaning commit cb351e0ff6f6325e86fb2867116a44505a44eae1 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:06:57 2022 +0000 Unnecessary line (rows with no target value will be removed in cleaning script). commit 86299d346b5c3d706190db0dc14555309d17629f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 09:57:21 2022 +0000 Impute phone and sms NAs with 0 commit 3f7ec80c18b1237c49dfdd9a6736cdf518e0b7fb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Aug 31 10:18:50 2022 +0000 Preparation a) phone_calls 0 imputation b) remove rows with NaN target
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COMPUTE: False
IMPUTE_SELECTED_EVENT_FEATURES:
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COMPUTE: False
MIN_DATA_YIELDED_MINUTES_TO_IMPUTE: 0.33
COLS_NAN_THRESHOLD: 1 # set to 1 to disable
COLS_VAR_THRESHOLD: True
ROWS_NAN_THRESHOLD: 1 # set to 1 to disable
DATA_YIELD_FEATURE: RATIO_VALID_YIELDED_HOURS # RATIO_VALID_YIELDED_HOURS or RATIO_VALID_YIELDED_MINUTES
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DATA_YIELD_RATIO_THRESHOLD: 0 # set to 0 to disable
DROP_HIGHLY_CORRELATED_FEATURES:
Squashed commit of the following: commit 43ecc243cb62bb31eed85cb477ca4131555c7fe7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 22 15:26:09 2022 +0000 Adding TODO comments commit 2df1ebf90c3a93812b112b8ed0ee4e23cd74533f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 21 13:59:23 2022 +0000 README update commit 5182c2b16dff3537aad42984b8ea5214743cdb32 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 21 11:03:01 2022 +0000 Few corrections for all_cleaning commit 3d9254c1b3bed6e95e631d4e0402548830a19534 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 21 10:28:05 2022 +0000 Adding the min overlap for corr threshold and preservation of esm cols. commit e27c49cc8fa4c51f9fe8e593a8d25e9a032ab393 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 21 09:02:00 2022 +0000 Commenting and cleaning. commit 31a47a5ee4569264e39d7c445525a6e64bb7700a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Jul 20 13:49:22 2022 +0000 Environment version change. commit 5b274ed8993f58e783bda6d82fce936764209c28 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 16:10:07 2022 +0000 Enabled cleaning for all participants + standardization files. commit 203fdb31e0f3c647ef8c8a60cb9531831b7ab924 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 14:14:51 2022 +0000 Features cleaning fixes after testing. Visualization script for phone features values. commit 176178d73b154c30b9eb9eb4a67514f00d6a924e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 09:05:14 2022 +0000 Revert "Necessary config changes." This reverts commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0. commit 26ea6512c9d512f95837e7b047fe510c1d196403 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 13:19:47 2022 +0000 Adding cleaning function condition and cleaning functionality. commit 575c29eef9c21e6f2d7832871e73bc0941643734 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:51:56 2022 +0000 Translation of the cleaning individual RAPIDS function from R to py. commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:02:18 2022 +0000 Necessary config changes. commit b5669f51612fbd8378848615d639677851ab032f Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 15:26:00 2022 +0000 Modified snakemake rule to dynamically choose script extention. commit 66636be1e8ae4828228b37c59b9df1faf3fc3d3d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 14:43:08 2022 +0000 Trying to modify the snakefile rule to execute scripts in two languages depended on the provider. commit 574778b00f3cbb368ef4bc74de15cf5070c65ea9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 09:49:41 2022 +0000 gitignore: adding required files so that RAPIDS can be run successfully. commit 71018ab178256970535e78961602ab8c7f0ebb14 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 08:34:19 2022 +0000 Standardization bug fixes commit 6253c470a624e6bfbb02e0c453b652452eb2dbbc Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 14 15:28:02 2022 +0000 Seperate rules for empatica vs. nonempatica standardization. Parameter in config that controls the creation of standardized merged files for individual and all participants.. commit 90f902778565e0896d3bae22ae8551be8b487e67 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 12 14:23:03 2022 +0000 Preparing for final csvs' standardization. commit d25dde3998786a9a582f5cda544ee104386778f9 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:47 2022 +0000 Revert "Changes in config to be reverted." This reverts commit bea7608e7095021fb7c53a9afa07074448fe4313. commit 6b23e70857e63deda98eb98d190af9090626c84b Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:26 2022 +0000 Enabled standardization for rest (previously active) phone features. Testing still needed. commit 8ec58a6f34ba3d42e5cc71d26e6d91837472ca5f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 09:07:55 2022 +0000 Enabled standardization for phone calls. All steps completed and tested. commit bea7608e7095021fb7c53a9afa07074448fe4313 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 07:47:51 2022 +0000 Changes in config to be reverted. commit 4e84ca0e51bf709bff56fd09437b95310ec6bedd Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:24 2022 +0000 Standardization for the rest of the features. commit cc581aa788e3d5c17131af8f3d5dd6b0c3b5aff7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:08 2022 +0000 README update again
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COMPUTE: True
MIN_OVERLAP_FOR_CORR_THRESHOLD: 0.5
CORR_THRESHOLD: 0.95
SRC_SCRIPT: src/features/all_cleaning_individual/rapids/main.R
Squashed commit of the following: commit 8a6b52a97c95dcd8b70b980b4f46421b1a847905 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:35:49 2022 +0000 Switch to 30_before ERS with corresponding targets. commit 244a05373014b14bc4c75db8ceb68a04dc5328df Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:19:43 2022 +0000 Change output files settings to nonstandardized. commit be0324fd01d70c58a9eefd84ccb23d06a42ab57c Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 28 12:44:25 2022 +0000 Fix some bugs and set categorical columns as categories dtypes. commit 99c2fab8f9ab9cf2ed40a952019f994299b78c05 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 16 09:50:18 2022 +0000 Fix a bug in the making of the individual model (when there is no target in the participants columns). commit 286de93bfd55710d77c2e4bab899e73381f9a4a3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 11:21:51 2022 +0000 Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic. commit ab803ee49c2898d2dd4d49de64f763f549c077e3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 10:14:07 2022 +0000 Add additional appraisal targets. commit 621f11b2d98cb3e17d86c3be902ebd40f94d3079 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 09:53:31 2022 +0000 Fix a bug related to wrong user input (duplicated events). commit bd41f42a5da7e28b9de190a53b5f2195fad0920d Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:07:36 2022 +0000 Rename target_ to segmenting_ method. commit a543ce372f1fd6cdd402be8ebdbe54610e449ce2 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:04:16 2022 +0000 Add comments for event_related_script understanding. commit 74b454b07bf69bdcd0517a940c5296e5f77c492e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 11 09:15:12 2022 +0000 Apply changes to string answers to make them language-generic. commit 6ebe83e47ea4da0066f4cd9dedbdb726cef5d06c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 12:42:52 2022 +0000 Improve the ERS extract method with a couple of validations. commit 00350ef8ca2ef43aed71f76609917021ce920f31 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:32:58 2022 +0000 Change config for stressfulness event target method. commit e4985c91214ac6ecd43501d52b67816d26d4fdef Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:29:11 2022 +0000 Override stressfulness event target with extracted values from csv. commit a668b6e8dad4dd393802ed4d5e948d6d42d60a01 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 09:37:27 2022 +0000 Extract ERS and stress event targets to csv files (completed). commit 9199b53ded1c5d858882d9826aa15e5e2102ab08 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 9 15:11:51 2022 +0000 Get, join and start processing required ERS stress event data. commit f3c6a66da9a7ce92d4296436927f48b3d1a467b8 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 15:53:43 2022 +0000 Begin with stress events in the ERS script. commit 0b3e9226b3c683e87ef758756f0d83350642a716 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 14:44:24 2022 +0000 Make small corrections in ERS file. commit 2d83f7ddecbc3880e8d901fc2aae25621a280f75 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 11:32:05 2022 +0000 Begin the ERS logic for 90-minutes events. commit 1da72a7cbe3178ef911ddb263ea30e5da79407ad Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 09:45:37 2022 +0000 Rename targets method in config. commit 9f441afc16ff9b75e131eb47d41edb570b51190c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 15:09:04 2022 +0000 Begin ERS logic for 90-minutes events. commit c1c9f4d05ac8bdf03f4759623165f8e795eaa5a9 Merge: 62f46ea3 7ab0280d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:58 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 62f46ea3763ba47af2a7c62d6b0b453cfd549929 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:53 2022 +0000 Prepare method-based logic for ERS generating. commit 7ab0280d7ed23022a4d2de0caa7bba3a43dff9d4 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 08:58:08 2022 +0000 Correctly rename stressful event target variable. commit eefa9f3f4d4c95374dd31907787ed767c636fe37 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 14:49:54 2022 +0000 Add new target: stressfulness_event. commit 5e8174dd41f5a4c2aa35c74fb4bd9b19a918d1c4 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:52:45 2022 +0000 Add new target: stressfulness_period. commit 35c1a762e7179c7b11f8f1154c1a4f4133402324 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:51:18 2022 +0000 Improve filtering by esm_session and device_id. commit 02264b21fd43212dd4636d300321e254da392149 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 09:30:12 2022 +0000 Add logic for target selection in ERS processing. commit 0ce8723bdb72bafa40924ff4fd3a2328e81808eb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 2 14:01:21 2022 +0000 Extend imputation logic within the cleaning script. commit 30b38bfc028b6e3261701feb915f9e3820a77c75 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 28 09:00:13 2022 +0000 Fix the generating procedure of ERS file for participants with multiple devices. commit cd137af15a9f03724593595a152f34a24323088f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:20:15 2022 +0000 Config for 30 minute EMA segments. commit 3c0585a566ede91dd97e2ba0a6617a4f42e72617 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:12:56 2022 +0000 Remove obsolete comments. commit 6b487fcf7b64a722e9c5486764155764332ba73c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:11:42 2022 +0000 Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script. commit 5d17c92e54427cc70a7f747be398ad59af98c5bf Merge: a31fdd14 0d143e6a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:20 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit a31fdd1479193a67b6a6985cc42fdc66ac7be1a4 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:08 2022 +0000 Start to test empatica_data_yield precieved error. commit 936324d234b6636366b1a569793452a4cca54847 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:17:27 2022 +0000 Switch config for 30 minutes event related segments. commit da0a4596f814a40997efe782239cb296e89fe606 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:16:25 2022 +0000 Add additional ESM processing logic for ERS csv extraction. commit d4d74818e69eab2755f988391978400096902b5d Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:14:32 2022 +0000 Fix a bug - missing time_segment column when df is empty commit 14ff59914b4b3071ff7a40bf9daaba558ff66746 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:59:46 2022 +0000 Fix to correct dtypes. commit 6ab0ac5329d0be06bbe8357203422c7d981c325a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:57:26 2022 +0000 Optimize memory consumption with dtype definition while reading csv file. commit 0d143e6aadaf9b67b2fbfd6cdf8c218d5720f157 Merge: 8acac501 b92a3aa3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:28:27 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 8acac501251105332d1d3d4863e88744b9528844 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:26:43 2022 +0000 Add safenet when features dataframe is empty. commit b92a3aa37a1968b7129cdb2b7ebaf9beda981428 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:25:22 2022 +0000 Remove unwanted output or other error producing code. commit bfd637eb9c40872b954b608aef420b24393d3e6f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 08:53:44 2022 +0000 Improve strings formatting in straw_events file. commit 0d81ad5756c54f03b2b200b801672b9eb39f27d5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 19 13:35:04 2022 +0000 Debug assignment of segments to rows commit cea451d344e3b0bcc110c77f2845a9077bbe5d75 Merge: e88bbd54 cf38d9f1 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:06 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit e88bbd548fcd2bb1f9057b27b572afa5a6d028a5 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:00 2022 +0000 Add new daily segment and filter by segment in the cleaning script. commit cf38d9f175c5bcc9d0f8c70f49e59d2b56d8ada7 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 17 15:07:33 2022 +0000 Implement ERS generating logic. commit f3ca56cdbf22d7eed38f920889c4b19f49da7760 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 14 14:46:28 2022 +0000 Start with ERS logic integration within Snakemake. commit 797aa98f4fe2faf411c5130d27c51c5c606e5c0e Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:50 2022 +0000 Config for ERS testing. commit 9baff159cd1a61019410838efefa4b59a6c4981c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:23 2022 +0000 Changes needed for testing and starting of the Event-Related Segments. commit 0f21273508654133a51d1e20e485c3de33dc2779 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:32:51 2022 +0000 Bugs fix commit 55517eb737463e21c6f6ad18f4711d38bd02fec5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:23:11 2022 +0000 Necessary commit before proceeding. commit de15a52dba43325c171584464995fa4311403e7e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:36:23 2022 +0000 Bug fix commit 1ad25bb5727d30affd2ee063386f2f5ca52e0d63 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:26:17 2022 +0000 Few modifications of some imputation values in cleaning script and feature extraction. commit 9884b383cf6e1b339738deea8cc54a6d264e5c87 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 10 16:45:38 2022 +0000 Testing new data with AutoML. commit 2dc89c083c99d43da5e1eb9cbc1c07d39901f27d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 7 08:52:12 2022 +0000 Small changes in cleaning overall commit 001d40072973797f159b94b48ac3add10138f58e Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 14:28:12 2022 +0000 Clean features and create input files based on all possible targets. commit 1e38d9bf1e4d1caa10ff8c5245a59a9b20d4d7f9 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 13:27:38 2022 +0000 Standardization and correlation visualization in overall cleaning script. commit a34412a18dbd75aafa9f3bba9303ab6a962cec03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 14:16:55 2022 +0000 E4 data yield corrections. Changes in overal cs - standardization. commit 437459648f16f71acec6794a07404bfeb781f907 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 13:35:05 2022 +0000 Errors fix: individual script - treat participants missing data. commit 53f6cc60d5d8262a3bbb3cad82e2ebf49cb9e2a5 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 13:06:39 2022 +0000 Config and cleaning script necessary changes ... commit bbeabeee6ff7e3f8cc429470404c2c4b246b6a22 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 12:53:31 2022 +0000 Last changes before processing on the server. commit 44531c6d94705757110df6d087f3762699d7211a Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 30 10:04:07 2022 +0000 Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds. commit 7ac7cd5a3714521fc9a36a8371554a921df132fe Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 14:33:21 2022 +0000 Preparation of the overall cleaning script. commit 68fd69dadab8c7e14095469d5ed1d9921b4c0ce7 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:55:25 2022 +0000 Cleaning script for individuals: corrections and comments. commit a4f0d056a047aaf3458b043eba5e98df76da039a Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:44:27 2022 +0000 Fillna for app foreground and activity recognition commit 6286e7a44c7e2e99116b83fc3c06ce4398d022e5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:47:08 2022 +0000 firstuseafter column removed from contextual imputation commit 9b3447febd075f4dc5ede6a4071f72821835e7a2 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:40:05 2022 +0000 Contextual imputation correction commit d6adda30cf95e6d9660e6001225dee461bbe3704 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:37:51 2022 +0000 Contextual imputation on time(first/last) features. commit 8af4ef11dc711dffd86c71c99b15e9451aa94ecd Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 10:02:47 2022 +0000 Contextual imputation by feature type. commit 536b9494cdfbc6b31d41a74126ac6af1d8fe62e0 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 14:12:08 2022 +0000 Cleaning script corrections commit f0b87c9dd02d31223c2b69c2586221ffe202e21f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 09:54:15 2022 +0000 Debugging of the empatica data yield integration. commit 7fcdb873fe910f7243fb71ffe56abfdd9ebb81e3 Merge: 5c7bb0f4 bd53dc16 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:50:29 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 5c7bb0f4c14ab4413ed3682268bb7e65ac56fc83 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:48:32 2022 +0000 Config changes commit bd53dc1684b2b6fadf5653e2a9cc00c953410149 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 26 15:54:00 2022 +0000 Empatica data yield usage in the cleaning script. commit d9a574c550f8beb1cf5662e164ffa66048106dc9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 23 13:24:50 2022 +0000 Changes in the cleaning script and preparation of empatica data yield method. commit 19aa8707c0b61790d9d4c1834944c1711d8777aa Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 22 13:45:51 2022 +0000 Redefined cleaning steps after revision commit 247d758cb7eaa93ed9c7df2b0711325ffa27d985 Merge: 90ee99e4 7493aaa6 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:18:01 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 90ee99e4b99eeb32650df06d60e43c0ee1e66a87 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:16:00 2022 +0000 Remove TODO comments commit 7493aaa64368f81adbf478b43411063f56a9a87e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 12:57:55 2022 +0000 Small changes in cleaning scrtipt and missing vals testing. commit eaf4340afd7db8a43174a4789cfb9ba5a831dac4 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 08:03:48 2022 +0000 Small imputation and cleaning corrections. commit a96ea508c628d8c8c736126b65772c06c7cf4ddc Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:34:02 2022 +0000 Fill NaN of Empatica's SD second order feature (must be tested). commit 52e11cdcab51ec8ef97d379304e9297dd233773f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:54 2022 +0000 Configurations for new standardization path. commit 92aff93e65f765ca531bf414c2bdb2e6d7ca1240 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:16 2022 +0000 Remove standardization script. commit 18b63127deefb7cee0061ed741af179a4d6fdb01 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 06:16:26 2022 +0000 Removed all standardizaton rules and configurations. commit 62982866cd9f3f45a335d26b67c3fdf3035c6d1e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 13:24:21 2022 +0000 Phone wifi visible inspection (WIP) commit 0ce6da5444b7d0e3a30c8f6ca73422dc88d928b2 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 11:30:08 2022 +0000 kNN imputation relocation and execution only on specific columns. commit e3b78c8a85084b4cd873350df5bc2b75009fae83 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 10:58:57 2022 +0000 Impute selected phone features with 0. Wifi visible, screen, and light. commit 7d85f75d218ef9b3af5ae077343a58e62bb5fa2c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 09:03:30 2022 +0000 Changes in phone features NaN values script. commit 385e21409d1d3978588fea56cc26a8d241e3af35 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 14:16:58 2022 +0000 Changes in NaN values testing script. commit 18002f59e1c0e161f68b2a4cc217e62a6a86e467 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 10:48:59 2022 +0000 Doryab bluetooth and locations features fill in NaN values. commit 3cf7ca41aac7772c89ac90ad0a26e938d39f3f34 Merge: d27a4a71 d5ab5a03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 15:38:32 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit d5ab5a0394cdd395088723ff80d78f2257f8e37c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 14:13:03 2022 +0000 Writing testing scripts to determine the point of manual imputation. commit dfbb758902bebdbe86b42753b0252b96ec6e791f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 13:54:06 2022 +0000 Changes in AutoML params and environment.yml commit 4ec371ed96102d4b1f3b85557cb5fc3c388c1cef Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 09:51:03 2022 +0000 Testing auto-sklearn commit d27a4a71c81a50f4d30e5eb5bd9b664610da268a Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 12 13:44:17 2022 +0000 Reorganisation and reordering of the cleaning script. commit 15d792089d3b37dd381b1cb02b11f1106920d304 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:33:36 2022 +0000 Changes in cleaning script: - target extracted from config to remove rows where target is nan - prepared sns.heatmap for further missing values analysis - necessary changes in config and participant p01 - picture of heatmap which shows the values state after cleaning commit cb351e0ff6f6325e86fb2867116a44505a44eae1 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:06:57 2022 +0000 Unnecessary line (rows with no target value will be removed in cleaning script). commit 86299d346b5c3d706190db0dc14555309d17629f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 09:57:21 2022 +0000 Impute phone and sms NAs with 0 commit 3f7ec80c18b1237c49dfdd9a6736cdf518e0b7fb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Aug 31 10:18:50 2022 +0000 Preparation a) phone_calls 0 imputation b) remove rows with NaN target
2022-12-08 17:04:39 +01:00
STRAW:
COMPUTE: True
Squashed commit of the following: commit 8a6b52a97c95dcd8b70b980b4f46421b1a847905 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:35:49 2022 +0000 Switch to 30_before ERS with corresponding targets. commit 244a05373014b14bc4c75db8ceb68a04dc5328df Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:19:43 2022 +0000 Change output files settings to nonstandardized. commit be0324fd01d70c58a9eefd84ccb23d06a42ab57c Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 28 12:44:25 2022 +0000 Fix some bugs and set categorical columns as categories dtypes. commit 99c2fab8f9ab9cf2ed40a952019f994299b78c05 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 16 09:50:18 2022 +0000 Fix a bug in the making of the individual model (when there is no target in the participants columns). commit 286de93bfd55710d77c2e4bab899e73381f9a4a3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 11:21:51 2022 +0000 Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic. commit ab803ee49c2898d2dd4d49de64f763f549c077e3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 10:14:07 2022 +0000 Add additional appraisal targets. commit 621f11b2d98cb3e17d86c3be902ebd40f94d3079 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 09:53:31 2022 +0000 Fix a bug related to wrong user input (duplicated events). commit bd41f42a5da7e28b9de190a53b5f2195fad0920d Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:07:36 2022 +0000 Rename target_ to segmenting_ method. commit a543ce372f1fd6cdd402be8ebdbe54610e449ce2 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:04:16 2022 +0000 Add comments for event_related_script understanding. commit 74b454b07bf69bdcd0517a940c5296e5f77c492e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 11 09:15:12 2022 +0000 Apply changes to string answers to make them language-generic. commit 6ebe83e47ea4da0066f4cd9dedbdb726cef5d06c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 12:42:52 2022 +0000 Improve the ERS extract method with a couple of validations. commit 00350ef8ca2ef43aed71f76609917021ce920f31 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:32:58 2022 +0000 Change config for stressfulness event target method. commit e4985c91214ac6ecd43501d52b67816d26d4fdef Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:29:11 2022 +0000 Override stressfulness event target with extracted values from csv. commit a668b6e8dad4dd393802ed4d5e948d6d42d60a01 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 09:37:27 2022 +0000 Extract ERS and stress event targets to csv files (completed). commit 9199b53ded1c5d858882d9826aa15e5e2102ab08 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 9 15:11:51 2022 +0000 Get, join and start processing required ERS stress event data. commit f3c6a66da9a7ce92d4296436927f48b3d1a467b8 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 15:53:43 2022 +0000 Begin with stress events in the ERS script. commit 0b3e9226b3c683e87ef758756f0d83350642a716 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 14:44:24 2022 +0000 Make small corrections in ERS file. commit 2d83f7ddecbc3880e8d901fc2aae25621a280f75 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 11:32:05 2022 +0000 Begin the ERS logic for 90-minutes events. commit 1da72a7cbe3178ef911ddb263ea30e5da79407ad Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 09:45:37 2022 +0000 Rename targets method in config. commit 9f441afc16ff9b75e131eb47d41edb570b51190c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 15:09:04 2022 +0000 Begin ERS logic for 90-minutes events. commit c1c9f4d05ac8bdf03f4759623165f8e795eaa5a9 Merge: 62f46ea3 7ab0280d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:58 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 62f46ea3763ba47af2a7c62d6b0b453cfd549929 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:53 2022 +0000 Prepare method-based logic for ERS generating. commit 7ab0280d7ed23022a4d2de0caa7bba3a43dff9d4 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 08:58:08 2022 +0000 Correctly rename stressful event target variable. commit eefa9f3f4d4c95374dd31907787ed767c636fe37 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 14:49:54 2022 +0000 Add new target: stressfulness_event. commit 5e8174dd41f5a4c2aa35c74fb4bd9b19a918d1c4 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:52:45 2022 +0000 Add new target: stressfulness_period. commit 35c1a762e7179c7b11f8f1154c1a4f4133402324 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:51:18 2022 +0000 Improve filtering by esm_session and device_id. commit 02264b21fd43212dd4636d300321e254da392149 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 09:30:12 2022 +0000 Add logic for target selection in ERS processing. commit 0ce8723bdb72bafa40924ff4fd3a2328e81808eb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 2 14:01:21 2022 +0000 Extend imputation logic within the cleaning script. commit 30b38bfc028b6e3261701feb915f9e3820a77c75 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 28 09:00:13 2022 +0000 Fix the generating procedure of ERS file for participants with multiple devices. commit cd137af15a9f03724593595a152f34a24323088f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:20:15 2022 +0000 Config for 30 minute EMA segments. commit 3c0585a566ede91dd97e2ba0a6617a4f42e72617 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:12:56 2022 +0000 Remove obsolete comments. commit 6b487fcf7b64a722e9c5486764155764332ba73c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:11:42 2022 +0000 Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script. commit 5d17c92e54427cc70a7f747be398ad59af98c5bf Merge: a31fdd14 0d143e6a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:20 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit a31fdd1479193a67b6a6985cc42fdc66ac7be1a4 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:08 2022 +0000 Start to test empatica_data_yield precieved error. commit 936324d234b6636366b1a569793452a4cca54847 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:17:27 2022 +0000 Switch config for 30 minutes event related segments. commit da0a4596f814a40997efe782239cb296e89fe606 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:16:25 2022 +0000 Add additional ESM processing logic for ERS csv extraction. commit d4d74818e69eab2755f988391978400096902b5d Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:14:32 2022 +0000 Fix a bug - missing time_segment column when df is empty commit 14ff59914b4b3071ff7a40bf9daaba558ff66746 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:59:46 2022 +0000 Fix to correct dtypes. commit 6ab0ac5329d0be06bbe8357203422c7d981c325a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:57:26 2022 +0000 Optimize memory consumption with dtype definition while reading csv file. commit 0d143e6aadaf9b67b2fbfd6cdf8c218d5720f157 Merge: 8acac501 b92a3aa3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:28:27 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 8acac501251105332d1d3d4863e88744b9528844 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:26:43 2022 +0000 Add safenet when features dataframe is empty. commit b92a3aa37a1968b7129cdb2b7ebaf9beda981428 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:25:22 2022 +0000 Remove unwanted output or other error producing code. commit bfd637eb9c40872b954b608aef420b24393d3e6f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 08:53:44 2022 +0000 Improve strings formatting in straw_events file. commit 0d81ad5756c54f03b2b200b801672b9eb39f27d5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 19 13:35:04 2022 +0000 Debug assignment of segments to rows commit cea451d344e3b0bcc110c77f2845a9077bbe5d75 Merge: e88bbd54 cf38d9f1 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:06 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit e88bbd548fcd2bb1f9057b27b572afa5a6d028a5 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:00 2022 +0000 Add new daily segment and filter by segment in the cleaning script. commit cf38d9f175c5bcc9d0f8c70f49e59d2b56d8ada7 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 17 15:07:33 2022 +0000 Implement ERS generating logic. commit f3ca56cdbf22d7eed38f920889c4b19f49da7760 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 14 14:46:28 2022 +0000 Start with ERS logic integration within Snakemake. commit 797aa98f4fe2faf411c5130d27c51c5c606e5c0e Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:50 2022 +0000 Config for ERS testing. commit 9baff159cd1a61019410838efefa4b59a6c4981c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:23 2022 +0000 Changes needed for testing and starting of the Event-Related Segments. commit 0f21273508654133a51d1e20e485c3de33dc2779 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:32:51 2022 +0000 Bugs fix commit 55517eb737463e21c6f6ad18f4711d38bd02fec5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:23:11 2022 +0000 Necessary commit before proceeding. commit de15a52dba43325c171584464995fa4311403e7e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:36:23 2022 +0000 Bug fix commit 1ad25bb5727d30affd2ee063386f2f5ca52e0d63 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:26:17 2022 +0000 Few modifications of some imputation values in cleaning script and feature extraction. commit 9884b383cf6e1b339738deea8cc54a6d264e5c87 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 10 16:45:38 2022 +0000 Testing new data with AutoML. commit 2dc89c083c99d43da5e1eb9cbc1c07d39901f27d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 7 08:52:12 2022 +0000 Small changes in cleaning overall commit 001d40072973797f159b94b48ac3add10138f58e Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 14:28:12 2022 +0000 Clean features and create input files based on all possible targets. commit 1e38d9bf1e4d1caa10ff8c5245a59a9b20d4d7f9 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 13:27:38 2022 +0000 Standardization and correlation visualization in overall cleaning script. commit a34412a18dbd75aafa9f3bba9303ab6a962cec03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 14:16:55 2022 +0000 E4 data yield corrections. Changes in overal cs - standardization. commit 437459648f16f71acec6794a07404bfeb781f907 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 13:35:05 2022 +0000 Errors fix: individual script - treat participants missing data. commit 53f6cc60d5d8262a3bbb3cad82e2ebf49cb9e2a5 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 13:06:39 2022 +0000 Config and cleaning script necessary changes ... commit bbeabeee6ff7e3f8cc429470404c2c4b246b6a22 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 12:53:31 2022 +0000 Last changes before processing on the server. commit 44531c6d94705757110df6d087f3762699d7211a Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 30 10:04:07 2022 +0000 Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds. commit 7ac7cd5a3714521fc9a36a8371554a921df132fe Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 14:33:21 2022 +0000 Preparation of the overall cleaning script. commit 68fd69dadab8c7e14095469d5ed1d9921b4c0ce7 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:55:25 2022 +0000 Cleaning script for individuals: corrections and comments. commit a4f0d056a047aaf3458b043eba5e98df76da039a Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:44:27 2022 +0000 Fillna for app foreground and activity recognition commit 6286e7a44c7e2e99116b83fc3c06ce4398d022e5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:47:08 2022 +0000 firstuseafter column removed from contextual imputation commit 9b3447febd075f4dc5ede6a4071f72821835e7a2 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:40:05 2022 +0000 Contextual imputation correction commit d6adda30cf95e6d9660e6001225dee461bbe3704 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:37:51 2022 +0000 Contextual imputation on time(first/last) features. commit 8af4ef11dc711dffd86c71c99b15e9451aa94ecd Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 10:02:47 2022 +0000 Contextual imputation by feature type. commit 536b9494cdfbc6b31d41a74126ac6af1d8fe62e0 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 14:12:08 2022 +0000 Cleaning script corrections commit f0b87c9dd02d31223c2b69c2586221ffe202e21f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 09:54:15 2022 +0000 Debugging of the empatica data yield integration. commit 7fcdb873fe910f7243fb71ffe56abfdd9ebb81e3 Merge: 5c7bb0f4 bd53dc16 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:50:29 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 5c7bb0f4c14ab4413ed3682268bb7e65ac56fc83 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:48:32 2022 +0000 Config changes commit bd53dc1684b2b6fadf5653e2a9cc00c953410149 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 26 15:54:00 2022 +0000 Empatica data yield usage in the cleaning script. commit d9a574c550f8beb1cf5662e164ffa66048106dc9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 23 13:24:50 2022 +0000 Changes in the cleaning script and preparation of empatica data yield method. commit 19aa8707c0b61790d9d4c1834944c1711d8777aa Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 22 13:45:51 2022 +0000 Redefined cleaning steps after revision commit 247d758cb7eaa93ed9c7df2b0711325ffa27d985 Merge: 90ee99e4 7493aaa6 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:18:01 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 90ee99e4b99eeb32650df06d60e43c0ee1e66a87 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:16:00 2022 +0000 Remove TODO comments commit 7493aaa64368f81adbf478b43411063f56a9a87e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 12:57:55 2022 +0000 Small changes in cleaning scrtipt and missing vals testing. commit eaf4340afd7db8a43174a4789cfb9ba5a831dac4 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 08:03:48 2022 +0000 Small imputation and cleaning corrections. commit a96ea508c628d8c8c736126b65772c06c7cf4ddc Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:34:02 2022 +0000 Fill NaN of Empatica's SD second order feature (must be tested). commit 52e11cdcab51ec8ef97d379304e9297dd233773f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:54 2022 +0000 Configurations for new standardization path. commit 92aff93e65f765ca531bf414c2bdb2e6d7ca1240 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:16 2022 +0000 Remove standardization script. commit 18b63127deefb7cee0061ed741af179a4d6fdb01 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 06:16:26 2022 +0000 Removed all standardizaton rules and configurations. commit 62982866cd9f3f45a335d26b67c3fdf3035c6d1e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 13:24:21 2022 +0000 Phone wifi visible inspection (WIP) commit 0ce6da5444b7d0e3a30c8f6ca73422dc88d928b2 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 11:30:08 2022 +0000 kNN imputation relocation and execution only on specific columns. commit e3b78c8a85084b4cd873350df5bc2b75009fae83 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 10:58:57 2022 +0000 Impute selected phone features with 0. Wifi visible, screen, and light. commit 7d85f75d218ef9b3af5ae077343a58e62bb5fa2c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 09:03:30 2022 +0000 Changes in phone features NaN values script. commit 385e21409d1d3978588fea56cc26a8d241e3af35 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 14:16:58 2022 +0000 Changes in NaN values testing script. commit 18002f59e1c0e161f68b2a4cc217e62a6a86e467 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 10:48:59 2022 +0000 Doryab bluetooth and locations features fill in NaN values. commit 3cf7ca41aac7772c89ac90ad0a26e938d39f3f34 Merge: d27a4a71 d5ab5a03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 15:38:32 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit d5ab5a0394cdd395088723ff80d78f2257f8e37c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 14:13:03 2022 +0000 Writing testing scripts to determine the point of manual imputation. commit dfbb758902bebdbe86b42753b0252b96ec6e791f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 13:54:06 2022 +0000 Changes in AutoML params and environment.yml commit 4ec371ed96102d4b1f3b85557cb5fc3c388c1cef Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 09:51:03 2022 +0000 Testing auto-sklearn commit d27a4a71c81a50f4d30e5eb5bd9b664610da268a Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 12 13:44:17 2022 +0000 Reorganisation and reordering of the cleaning script. commit 15d792089d3b37dd381b1cb02b11f1106920d304 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:33:36 2022 +0000 Changes in cleaning script: - target extracted from config to remove rows where target is nan - prepared sns.heatmap for further missing values analysis - necessary changes in config and participant p01 - picture of heatmap which shows the values state after cleaning commit cb351e0ff6f6325e86fb2867116a44505a44eae1 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:06:57 2022 +0000 Unnecessary line (rows with no target value will be removed in cleaning script). commit 86299d346b5c3d706190db0dc14555309d17629f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 09:57:21 2022 +0000 Impute phone and sms NAs with 0 commit 3f7ec80c18b1237c49dfdd9a6736cdf518e0b7fb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Aug 31 10:18:50 2022 +0000 Preparation a) phone_calls 0 imputation b) remove rows with NaN target
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PHONE_DATA_YIELD_FEATURE: RATIO_VALID_YIELDED_MINUTES # RATIO_VALID_YIELDED_HOURS or RATIO_VALID_YIELDED_MINUTES
PHONE_DATA_YIELD_RATIO_THRESHOLD: 0.5 # set to 0 to disable
EMPATICA_DATA_YIELD_RATIO_THRESHOLD: 0.5 # set to 0 to disable
ROWS_NAN_THRESHOLD: 0.33 # set to 1 to disable
COLS_NAN_THRESHOLD: 0.9 # set to 1 to remove only columns that contains all (100% of) NaN
Squashed commit of the following: commit 31a47a5ee4569264e39d7c445525a6e64bb7700a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Jul 20 13:49:22 2022 +0000 Environment version change. commit 5b274ed8993f58e783bda6d82fce936764209c28 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 16:10:07 2022 +0000 Enabled cleaning for all participants + standardization files. commit 203fdb31e0f3c647ef8c8a60cb9531831b7ab924 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 14:14:51 2022 +0000 Features cleaning fixes after testing. Visualization script for phone features values. commit 176178d73b154c30b9eb9eb4a67514f00d6a924e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 09:05:14 2022 +0000 Revert "Necessary config changes." This reverts commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0. commit 26ea6512c9d512f95837e7b047fe510c1d196403 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 13:19:47 2022 +0000 Adding cleaning function condition and cleaning functionality. commit 575c29eef9c21e6f2d7832871e73bc0941643734 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:51:56 2022 +0000 Translation of the cleaning individual RAPIDS function from R to py. commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:02:18 2022 +0000 Necessary config changes. commit b5669f51612fbd8378848615d639677851ab032f Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 15:26:00 2022 +0000 Modified snakemake rule to dynamically choose script extention. commit 66636be1e8ae4828228b37c59b9df1faf3fc3d3d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 14:43:08 2022 +0000 Trying to modify the snakefile rule to execute scripts in two languages depended on the provider. commit 574778b00f3cbb368ef4bc74de15cf5070c65ea9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 09:49:41 2022 +0000 gitignore: adding required files so that RAPIDS can be run successfully. commit 71018ab178256970535e78961602ab8c7f0ebb14 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 08:34:19 2022 +0000 Standardization bug fixes commit 6253c470a624e6bfbb02e0c453b652452eb2dbbc Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 14 15:28:02 2022 +0000 Seperate rules for empatica vs. nonempatica standardization. Parameter in config that controls the creation of standardized merged files for individual and all participants.. commit 90f902778565e0896d3bae22ae8551be8b487e67 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 12 14:23:03 2022 +0000 Preparing for final csvs' standardization. commit d25dde3998786a9a582f5cda544ee104386778f9 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:47 2022 +0000 Revert "Changes in config to be reverted." This reverts commit bea7608e7095021fb7c53a9afa07074448fe4313. commit 6b23e70857e63deda98eb98d190af9090626c84b Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:26 2022 +0000 Enabled standardization for rest (previously active) phone features. Testing still needed. commit 8ec58a6f34ba3d42e5cc71d26e6d91837472ca5f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 09:07:55 2022 +0000 Enabled standardization for phone calls. All steps completed and tested. commit bea7608e7095021fb7c53a9afa07074448fe4313 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 07:47:51 2022 +0000 Changes in config to be reverted. commit 4e84ca0e51bf709bff56fd09437b95310ec6bedd Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:24 2022 +0000 Standardization for the rest of the features. commit cc581aa788e3d5c17131af8f3d5dd6b0c3b5aff7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:08 2022 +0000 README update again
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COLS_VAR_THRESHOLD: True
DROP_HIGHLY_CORRELATED_FEATURES:
COMPUTE: True
MIN_OVERLAP_FOR_CORR_THRESHOLD: 0.5
CORR_THRESHOLD: 0.95
Squashed commit of the following: commit 8a6b52a97c95dcd8b70b980b4f46421b1a847905 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:35:49 2022 +0000 Switch to 30_before ERS with corresponding targets. commit 244a05373014b14bc4c75db8ceb68a04dc5328df Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:19:43 2022 +0000 Change output files settings to nonstandardized. commit be0324fd01d70c58a9eefd84ccb23d06a42ab57c Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 28 12:44:25 2022 +0000 Fix some bugs and set categorical columns as categories dtypes. commit 99c2fab8f9ab9cf2ed40a952019f994299b78c05 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 16 09:50:18 2022 +0000 Fix a bug in the making of the individual model (when there is no target in the participants columns). commit 286de93bfd55710d77c2e4bab899e73381f9a4a3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 11:21:51 2022 +0000 Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic. commit ab803ee49c2898d2dd4d49de64f763f549c077e3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 10:14:07 2022 +0000 Add additional appraisal targets. commit 621f11b2d98cb3e17d86c3be902ebd40f94d3079 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 09:53:31 2022 +0000 Fix a bug related to wrong user input (duplicated events). commit bd41f42a5da7e28b9de190a53b5f2195fad0920d Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:07:36 2022 +0000 Rename target_ to segmenting_ method. commit a543ce372f1fd6cdd402be8ebdbe54610e449ce2 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:04:16 2022 +0000 Add comments for event_related_script understanding. commit 74b454b07bf69bdcd0517a940c5296e5f77c492e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 11 09:15:12 2022 +0000 Apply changes to string answers to make them language-generic. commit 6ebe83e47ea4da0066f4cd9dedbdb726cef5d06c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 12:42:52 2022 +0000 Improve the ERS extract method with a couple of validations. commit 00350ef8ca2ef43aed71f76609917021ce920f31 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:32:58 2022 +0000 Change config for stressfulness event target method. commit e4985c91214ac6ecd43501d52b67816d26d4fdef Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:29:11 2022 +0000 Override stressfulness event target with extracted values from csv. commit a668b6e8dad4dd393802ed4d5e948d6d42d60a01 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 09:37:27 2022 +0000 Extract ERS and stress event targets to csv files (completed). commit 9199b53ded1c5d858882d9826aa15e5e2102ab08 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 9 15:11:51 2022 +0000 Get, join and start processing required ERS stress event data. commit f3c6a66da9a7ce92d4296436927f48b3d1a467b8 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 15:53:43 2022 +0000 Begin with stress events in the ERS script. commit 0b3e9226b3c683e87ef758756f0d83350642a716 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 14:44:24 2022 +0000 Make small corrections in ERS file. commit 2d83f7ddecbc3880e8d901fc2aae25621a280f75 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 11:32:05 2022 +0000 Begin the ERS logic for 90-minutes events. commit 1da72a7cbe3178ef911ddb263ea30e5da79407ad Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 09:45:37 2022 +0000 Rename targets method in config. commit 9f441afc16ff9b75e131eb47d41edb570b51190c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 15:09:04 2022 +0000 Begin ERS logic for 90-minutes events. commit c1c9f4d05ac8bdf03f4759623165f8e795eaa5a9 Merge: 62f46ea3 7ab0280d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:58 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 62f46ea3763ba47af2a7c62d6b0b453cfd549929 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:53 2022 +0000 Prepare method-based logic for ERS generating. commit 7ab0280d7ed23022a4d2de0caa7bba3a43dff9d4 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 08:58:08 2022 +0000 Correctly rename stressful event target variable. commit eefa9f3f4d4c95374dd31907787ed767c636fe37 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 14:49:54 2022 +0000 Add new target: stressfulness_event. commit 5e8174dd41f5a4c2aa35c74fb4bd9b19a918d1c4 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:52:45 2022 +0000 Add new target: stressfulness_period. commit 35c1a762e7179c7b11f8f1154c1a4f4133402324 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:51:18 2022 +0000 Improve filtering by esm_session and device_id. commit 02264b21fd43212dd4636d300321e254da392149 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 09:30:12 2022 +0000 Add logic for target selection in ERS processing. commit 0ce8723bdb72bafa40924ff4fd3a2328e81808eb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 2 14:01:21 2022 +0000 Extend imputation logic within the cleaning script. commit 30b38bfc028b6e3261701feb915f9e3820a77c75 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 28 09:00:13 2022 +0000 Fix the generating procedure of ERS file for participants with multiple devices. commit cd137af15a9f03724593595a152f34a24323088f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:20:15 2022 +0000 Config for 30 minute EMA segments. commit 3c0585a566ede91dd97e2ba0a6617a4f42e72617 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:12:56 2022 +0000 Remove obsolete comments. commit 6b487fcf7b64a722e9c5486764155764332ba73c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:11:42 2022 +0000 Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script. commit 5d17c92e54427cc70a7f747be398ad59af98c5bf Merge: a31fdd14 0d143e6a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:20 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit a31fdd1479193a67b6a6985cc42fdc66ac7be1a4 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:08 2022 +0000 Start to test empatica_data_yield precieved error. commit 936324d234b6636366b1a569793452a4cca54847 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:17:27 2022 +0000 Switch config for 30 minutes event related segments. commit da0a4596f814a40997efe782239cb296e89fe606 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:16:25 2022 +0000 Add additional ESM processing logic for ERS csv extraction. commit d4d74818e69eab2755f988391978400096902b5d Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:14:32 2022 +0000 Fix a bug - missing time_segment column when df is empty commit 14ff59914b4b3071ff7a40bf9daaba558ff66746 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:59:46 2022 +0000 Fix to correct dtypes. commit 6ab0ac5329d0be06bbe8357203422c7d981c325a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:57:26 2022 +0000 Optimize memory consumption with dtype definition while reading csv file. commit 0d143e6aadaf9b67b2fbfd6cdf8c218d5720f157 Merge: 8acac501 b92a3aa3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:28:27 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 8acac501251105332d1d3d4863e88744b9528844 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:26:43 2022 +0000 Add safenet when features dataframe is empty. commit b92a3aa37a1968b7129cdb2b7ebaf9beda981428 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:25:22 2022 +0000 Remove unwanted output or other error producing code. commit bfd637eb9c40872b954b608aef420b24393d3e6f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 08:53:44 2022 +0000 Improve strings formatting in straw_events file. commit 0d81ad5756c54f03b2b200b801672b9eb39f27d5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 19 13:35:04 2022 +0000 Debug assignment of segments to rows commit cea451d344e3b0bcc110c77f2845a9077bbe5d75 Merge: e88bbd54 cf38d9f1 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:06 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit e88bbd548fcd2bb1f9057b27b572afa5a6d028a5 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:00 2022 +0000 Add new daily segment and filter by segment in the cleaning script. commit cf38d9f175c5bcc9d0f8c70f49e59d2b56d8ada7 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 17 15:07:33 2022 +0000 Implement ERS generating logic. commit f3ca56cdbf22d7eed38f920889c4b19f49da7760 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 14 14:46:28 2022 +0000 Start with ERS logic integration within Snakemake. commit 797aa98f4fe2faf411c5130d27c51c5c606e5c0e Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:50 2022 +0000 Config for ERS testing. commit 9baff159cd1a61019410838efefa4b59a6c4981c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:23 2022 +0000 Changes needed for testing and starting of the Event-Related Segments. commit 0f21273508654133a51d1e20e485c3de33dc2779 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:32:51 2022 +0000 Bugs fix commit 55517eb737463e21c6f6ad18f4711d38bd02fec5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:23:11 2022 +0000 Necessary commit before proceeding. commit de15a52dba43325c171584464995fa4311403e7e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:36:23 2022 +0000 Bug fix commit 1ad25bb5727d30affd2ee063386f2f5ca52e0d63 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:26:17 2022 +0000 Few modifications of some imputation values in cleaning script and feature extraction. commit 9884b383cf6e1b339738deea8cc54a6d264e5c87 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 10 16:45:38 2022 +0000 Testing new data with AutoML. commit 2dc89c083c99d43da5e1eb9cbc1c07d39901f27d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 7 08:52:12 2022 +0000 Small changes in cleaning overall commit 001d40072973797f159b94b48ac3add10138f58e Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 14:28:12 2022 +0000 Clean features and create input files based on all possible targets. commit 1e38d9bf1e4d1caa10ff8c5245a59a9b20d4d7f9 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 13:27:38 2022 +0000 Standardization and correlation visualization in overall cleaning script. commit a34412a18dbd75aafa9f3bba9303ab6a962cec03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 14:16:55 2022 +0000 E4 data yield corrections. Changes in overal cs - standardization. commit 437459648f16f71acec6794a07404bfeb781f907 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 13:35:05 2022 +0000 Errors fix: individual script - treat participants missing data. commit 53f6cc60d5d8262a3bbb3cad82e2ebf49cb9e2a5 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 13:06:39 2022 +0000 Config and cleaning script necessary changes ... commit bbeabeee6ff7e3f8cc429470404c2c4b246b6a22 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 12:53:31 2022 +0000 Last changes before processing on the server. commit 44531c6d94705757110df6d087f3762699d7211a Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 30 10:04:07 2022 +0000 Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds. commit 7ac7cd5a3714521fc9a36a8371554a921df132fe Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 14:33:21 2022 +0000 Preparation of the overall cleaning script. commit 68fd69dadab8c7e14095469d5ed1d9921b4c0ce7 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:55:25 2022 +0000 Cleaning script for individuals: corrections and comments. commit a4f0d056a047aaf3458b043eba5e98df76da039a Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:44:27 2022 +0000 Fillna for app foreground and activity recognition commit 6286e7a44c7e2e99116b83fc3c06ce4398d022e5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:47:08 2022 +0000 firstuseafter column removed from contextual imputation commit 9b3447febd075f4dc5ede6a4071f72821835e7a2 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:40:05 2022 +0000 Contextual imputation correction commit d6adda30cf95e6d9660e6001225dee461bbe3704 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:37:51 2022 +0000 Contextual imputation on time(first/last) features. commit 8af4ef11dc711dffd86c71c99b15e9451aa94ecd Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 10:02:47 2022 +0000 Contextual imputation by feature type. commit 536b9494cdfbc6b31d41a74126ac6af1d8fe62e0 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 14:12:08 2022 +0000 Cleaning script corrections commit f0b87c9dd02d31223c2b69c2586221ffe202e21f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 09:54:15 2022 +0000 Debugging of the empatica data yield integration. commit 7fcdb873fe910f7243fb71ffe56abfdd9ebb81e3 Merge: 5c7bb0f4 bd53dc16 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:50:29 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 5c7bb0f4c14ab4413ed3682268bb7e65ac56fc83 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:48:32 2022 +0000 Config changes commit bd53dc1684b2b6fadf5653e2a9cc00c953410149 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 26 15:54:00 2022 +0000 Empatica data yield usage in the cleaning script. commit d9a574c550f8beb1cf5662e164ffa66048106dc9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 23 13:24:50 2022 +0000 Changes in the cleaning script and preparation of empatica data yield method. commit 19aa8707c0b61790d9d4c1834944c1711d8777aa Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 22 13:45:51 2022 +0000 Redefined cleaning steps after revision commit 247d758cb7eaa93ed9c7df2b0711325ffa27d985 Merge: 90ee99e4 7493aaa6 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:18:01 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 90ee99e4b99eeb32650df06d60e43c0ee1e66a87 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:16:00 2022 +0000 Remove TODO comments commit 7493aaa64368f81adbf478b43411063f56a9a87e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 12:57:55 2022 +0000 Small changes in cleaning scrtipt and missing vals testing. commit eaf4340afd7db8a43174a4789cfb9ba5a831dac4 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 08:03:48 2022 +0000 Small imputation and cleaning corrections. commit a96ea508c628d8c8c736126b65772c06c7cf4ddc Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:34:02 2022 +0000 Fill NaN of Empatica's SD second order feature (must be tested). commit 52e11cdcab51ec8ef97d379304e9297dd233773f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:54 2022 +0000 Configurations for new standardization path. commit 92aff93e65f765ca531bf414c2bdb2e6d7ca1240 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:16 2022 +0000 Remove standardization script. commit 18b63127deefb7cee0061ed741af179a4d6fdb01 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 06:16:26 2022 +0000 Removed all standardizaton rules and configurations. commit 62982866cd9f3f45a335d26b67c3fdf3035c6d1e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 13:24:21 2022 +0000 Phone wifi visible inspection (WIP) commit 0ce6da5444b7d0e3a30c8f6ca73422dc88d928b2 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 11:30:08 2022 +0000 kNN imputation relocation and execution only on specific columns. commit e3b78c8a85084b4cd873350df5bc2b75009fae83 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 10:58:57 2022 +0000 Impute selected phone features with 0. Wifi visible, screen, and light. commit 7d85f75d218ef9b3af5ae077343a58e62bb5fa2c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 09:03:30 2022 +0000 Changes in phone features NaN values script. commit 385e21409d1d3978588fea56cc26a8d241e3af35 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 14:16:58 2022 +0000 Changes in NaN values testing script. commit 18002f59e1c0e161f68b2a4cc217e62a6a86e467 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 10:48:59 2022 +0000 Doryab bluetooth and locations features fill in NaN values. commit 3cf7ca41aac7772c89ac90ad0a26e938d39f3f34 Merge: d27a4a71 d5ab5a03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 15:38:32 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit d5ab5a0394cdd395088723ff80d78f2257f8e37c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 14:13:03 2022 +0000 Writing testing scripts to determine the point of manual imputation. commit dfbb758902bebdbe86b42753b0252b96ec6e791f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 13:54:06 2022 +0000 Changes in AutoML params and environment.yml commit 4ec371ed96102d4b1f3b85557cb5fc3c388c1cef Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 09:51:03 2022 +0000 Testing auto-sklearn commit d27a4a71c81a50f4d30e5eb5bd9b664610da268a Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 12 13:44:17 2022 +0000 Reorganisation and reordering of the cleaning script. commit 15d792089d3b37dd381b1cb02b11f1106920d304 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:33:36 2022 +0000 Changes in cleaning script: - target extracted from config to remove rows where target is nan - prepared sns.heatmap for further missing values analysis - necessary changes in config and participant p01 - picture of heatmap which shows the values state after cleaning commit cb351e0ff6f6325e86fb2867116a44505a44eae1 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:06:57 2022 +0000 Unnecessary line (rows with no target value will be removed in cleaning script). commit 86299d346b5c3d706190db0dc14555309d17629f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 09:57:21 2022 +0000 Impute phone and sms NAs with 0 commit 3f7ec80c18b1237c49dfdd9a6736cdf518e0b7fb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Aug 31 10:18:50 2022 +0000 Preparation a) phone_calls 0 imputation b) remove rows with NaN target
2022-12-08 17:04:39 +01:00
STANDARDIZATION: True
Squashed commit of the following: commit 31a47a5ee4569264e39d7c445525a6e64bb7700a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Jul 20 13:49:22 2022 +0000 Environment version change. commit 5b274ed8993f58e783bda6d82fce936764209c28 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 16:10:07 2022 +0000 Enabled cleaning for all participants + standardization files. commit 203fdb31e0f3c647ef8c8a60cb9531831b7ab924 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 14:14:51 2022 +0000 Features cleaning fixes after testing. Visualization script for phone features values. commit 176178d73b154c30b9eb9eb4a67514f00d6a924e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 09:05:14 2022 +0000 Revert "Necessary config changes." This reverts commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0. commit 26ea6512c9d512f95837e7b047fe510c1d196403 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 13:19:47 2022 +0000 Adding cleaning function condition and cleaning functionality. commit 575c29eef9c21e6f2d7832871e73bc0941643734 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:51:56 2022 +0000 Translation of the cleaning individual RAPIDS function from R to py. commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:02:18 2022 +0000 Necessary config changes. commit b5669f51612fbd8378848615d639677851ab032f Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 15:26:00 2022 +0000 Modified snakemake rule to dynamically choose script extention. commit 66636be1e8ae4828228b37c59b9df1faf3fc3d3d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 14:43:08 2022 +0000 Trying to modify the snakefile rule to execute scripts in two languages depended on the provider. commit 574778b00f3cbb368ef4bc74de15cf5070c65ea9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 09:49:41 2022 +0000 gitignore: adding required files so that RAPIDS can be run successfully. commit 71018ab178256970535e78961602ab8c7f0ebb14 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 08:34:19 2022 +0000 Standardization bug fixes commit 6253c470a624e6bfbb02e0c453b652452eb2dbbc Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 14 15:28:02 2022 +0000 Seperate rules for empatica vs. nonempatica standardization. Parameter in config that controls the creation of standardized merged files for individual and all participants.. commit 90f902778565e0896d3bae22ae8551be8b487e67 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 12 14:23:03 2022 +0000 Preparing for final csvs' standardization. commit d25dde3998786a9a582f5cda544ee104386778f9 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:47 2022 +0000 Revert "Changes in config to be reverted." This reverts commit bea7608e7095021fb7c53a9afa07074448fe4313. commit 6b23e70857e63deda98eb98d190af9090626c84b Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:26 2022 +0000 Enabled standardization for rest (previously active) phone features. Testing still needed. commit 8ec58a6f34ba3d42e5cc71d26e6d91837472ca5f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 09:07:55 2022 +0000 Enabled standardization for phone calls. All steps completed and tested. commit bea7608e7095021fb7c53a9afa07074448fe4313 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 07:47:51 2022 +0000 Changes in config to be reverted. commit 4e84ca0e51bf709bff56fd09437b95310ec6bedd Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:24 2022 +0000 Standardization for the rest of the features. commit cc581aa788e3d5c17131af8f3d5dd6b0c3b5aff7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:08 2022 +0000 README update again
2022-07-20 15:51:22 +02:00
SRC_SCRIPT: src/features/all_cleaning_individual/straw/main.py
ALL_CLEANING_OVERALL:
PROVIDERS:
RAPIDS:
Squashed commit of the following: commit 8a6b52a97c95dcd8b70b980b4f46421b1a847905 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:35:49 2022 +0000 Switch to 30_before ERS with corresponding targets. commit 244a05373014b14bc4c75db8ceb68a04dc5328df Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:19:43 2022 +0000 Change output files settings to nonstandardized. commit be0324fd01d70c58a9eefd84ccb23d06a42ab57c Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 28 12:44:25 2022 +0000 Fix some bugs and set categorical columns as categories dtypes. commit 99c2fab8f9ab9cf2ed40a952019f994299b78c05 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 16 09:50:18 2022 +0000 Fix a bug in the making of the individual model (when there is no target in the participants columns). commit 286de93bfd55710d77c2e4bab899e73381f9a4a3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 11:21:51 2022 +0000 Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic. commit ab803ee49c2898d2dd4d49de64f763f549c077e3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 10:14:07 2022 +0000 Add additional appraisal targets. commit 621f11b2d98cb3e17d86c3be902ebd40f94d3079 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 09:53:31 2022 +0000 Fix a bug related to wrong user input (duplicated events). commit bd41f42a5da7e28b9de190a53b5f2195fad0920d Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:07:36 2022 +0000 Rename target_ to segmenting_ method. commit a543ce372f1fd6cdd402be8ebdbe54610e449ce2 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:04:16 2022 +0000 Add comments for event_related_script understanding. commit 74b454b07bf69bdcd0517a940c5296e5f77c492e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 11 09:15:12 2022 +0000 Apply changes to string answers to make them language-generic. commit 6ebe83e47ea4da0066f4cd9dedbdb726cef5d06c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 12:42:52 2022 +0000 Improve the ERS extract method with a couple of validations. commit 00350ef8ca2ef43aed71f76609917021ce920f31 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:32:58 2022 +0000 Change config for stressfulness event target method. commit e4985c91214ac6ecd43501d52b67816d26d4fdef Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:29:11 2022 +0000 Override stressfulness event target with extracted values from csv. commit a668b6e8dad4dd393802ed4d5e948d6d42d60a01 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 09:37:27 2022 +0000 Extract ERS and stress event targets to csv files (completed). commit 9199b53ded1c5d858882d9826aa15e5e2102ab08 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 9 15:11:51 2022 +0000 Get, join and start processing required ERS stress event data. commit f3c6a66da9a7ce92d4296436927f48b3d1a467b8 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 15:53:43 2022 +0000 Begin with stress events in the ERS script. commit 0b3e9226b3c683e87ef758756f0d83350642a716 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 14:44:24 2022 +0000 Make small corrections in ERS file. commit 2d83f7ddecbc3880e8d901fc2aae25621a280f75 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 11:32:05 2022 +0000 Begin the ERS logic for 90-minutes events. commit 1da72a7cbe3178ef911ddb263ea30e5da79407ad Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 09:45:37 2022 +0000 Rename targets method in config. commit 9f441afc16ff9b75e131eb47d41edb570b51190c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 15:09:04 2022 +0000 Begin ERS logic for 90-minutes events. commit c1c9f4d05ac8bdf03f4759623165f8e795eaa5a9 Merge: 62f46ea3 7ab0280d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:58 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 62f46ea3763ba47af2a7c62d6b0b453cfd549929 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:53 2022 +0000 Prepare method-based logic for ERS generating. commit 7ab0280d7ed23022a4d2de0caa7bba3a43dff9d4 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 08:58:08 2022 +0000 Correctly rename stressful event target variable. commit eefa9f3f4d4c95374dd31907787ed767c636fe37 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 14:49:54 2022 +0000 Add new target: stressfulness_event. commit 5e8174dd41f5a4c2aa35c74fb4bd9b19a918d1c4 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:52:45 2022 +0000 Add new target: stressfulness_period. commit 35c1a762e7179c7b11f8f1154c1a4f4133402324 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:51:18 2022 +0000 Improve filtering by esm_session and device_id. commit 02264b21fd43212dd4636d300321e254da392149 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 09:30:12 2022 +0000 Add logic for target selection in ERS processing. commit 0ce8723bdb72bafa40924ff4fd3a2328e81808eb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 2 14:01:21 2022 +0000 Extend imputation logic within the cleaning script. commit 30b38bfc028b6e3261701feb915f9e3820a77c75 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 28 09:00:13 2022 +0000 Fix the generating procedure of ERS file for participants with multiple devices. commit cd137af15a9f03724593595a152f34a24323088f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:20:15 2022 +0000 Config for 30 minute EMA segments. commit 3c0585a566ede91dd97e2ba0a6617a4f42e72617 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:12:56 2022 +0000 Remove obsolete comments. commit 6b487fcf7b64a722e9c5486764155764332ba73c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:11:42 2022 +0000 Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script. commit 5d17c92e54427cc70a7f747be398ad59af98c5bf Merge: a31fdd14 0d143e6a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:20 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit a31fdd1479193a67b6a6985cc42fdc66ac7be1a4 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:08 2022 +0000 Start to test empatica_data_yield precieved error. commit 936324d234b6636366b1a569793452a4cca54847 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:17:27 2022 +0000 Switch config for 30 minutes event related segments. commit da0a4596f814a40997efe782239cb296e89fe606 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:16:25 2022 +0000 Add additional ESM processing logic for ERS csv extraction. commit d4d74818e69eab2755f988391978400096902b5d Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:14:32 2022 +0000 Fix a bug - missing time_segment column when df is empty commit 14ff59914b4b3071ff7a40bf9daaba558ff66746 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:59:46 2022 +0000 Fix to correct dtypes. commit 6ab0ac5329d0be06bbe8357203422c7d981c325a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:57:26 2022 +0000 Optimize memory consumption with dtype definition while reading csv file. commit 0d143e6aadaf9b67b2fbfd6cdf8c218d5720f157 Merge: 8acac501 b92a3aa3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:28:27 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 8acac501251105332d1d3d4863e88744b9528844 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:26:43 2022 +0000 Add safenet when features dataframe is empty. commit b92a3aa37a1968b7129cdb2b7ebaf9beda981428 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:25:22 2022 +0000 Remove unwanted output or other error producing code. commit bfd637eb9c40872b954b608aef420b24393d3e6f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 08:53:44 2022 +0000 Improve strings formatting in straw_events file. commit 0d81ad5756c54f03b2b200b801672b9eb39f27d5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 19 13:35:04 2022 +0000 Debug assignment of segments to rows commit cea451d344e3b0bcc110c77f2845a9077bbe5d75 Merge: e88bbd54 cf38d9f1 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:06 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit e88bbd548fcd2bb1f9057b27b572afa5a6d028a5 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:00 2022 +0000 Add new daily segment and filter by segment in the cleaning script. commit cf38d9f175c5bcc9d0f8c70f49e59d2b56d8ada7 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 17 15:07:33 2022 +0000 Implement ERS generating logic. commit f3ca56cdbf22d7eed38f920889c4b19f49da7760 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 14 14:46:28 2022 +0000 Start with ERS logic integration within Snakemake. commit 797aa98f4fe2faf411c5130d27c51c5c606e5c0e Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:50 2022 +0000 Config for ERS testing. commit 9baff159cd1a61019410838efefa4b59a6c4981c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:23 2022 +0000 Changes needed for testing and starting of the Event-Related Segments. commit 0f21273508654133a51d1e20e485c3de33dc2779 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:32:51 2022 +0000 Bugs fix commit 55517eb737463e21c6f6ad18f4711d38bd02fec5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:23:11 2022 +0000 Necessary commit before proceeding. commit de15a52dba43325c171584464995fa4311403e7e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:36:23 2022 +0000 Bug fix commit 1ad25bb5727d30affd2ee063386f2f5ca52e0d63 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:26:17 2022 +0000 Few modifications of some imputation values in cleaning script and feature extraction. commit 9884b383cf6e1b339738deea8cc54a6d264e5c87 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 10 16:45:38 2022 +0000 Testing new data with AutoML. commit 2dc89c083c99d43da5e1eb9cbc1c07d39901f27d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 7 08:52:12 2022 +0000 Small changes in cleaning overall commit 001d40072973797f159b94b48ac3add10138f58e Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 14:28:12 2022 +0000 Clean features and create input files based on all possible targets. commit 1e38d9bf1e4d1caa10ff8c5245a59a9b20d4d7f9 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 13:27:38 2022 +0000 Standardization and correlation visualization in overall cleaning script. commit a34412a18dbd75aafa9f3bba9303ab6a962cec03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 14:16:55 2022 +0000 E4 data yield corrections. Changes in overal cs - standardization. commit 437459648f16f71acec6794a07404bfeb781f907 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 13:35:05 2022 +0000 Errors fix: individual script - treat participants missing data. commit 53f6cc60d5d8262a3bbb3cad82e2ebf49cb9e2a5 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 13:06:39 2022 +0000 Config and cleaning script necessary changes ... commit bbeabeee6ff7e3f8cc429470404c2c4b246b6a22 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 12:53:31 2022 +0000 Last changes before processing on the server. commit 44531c6d94705757110df6d087f3762699d7211a Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 30 10:04:07 2022 +0000 Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds. commit 7ac7cd5a3714521fc9a36a8371554a921df132fe Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 14:33:21 2022 +0000 Preparation of the overall cleaning script. commit 68fd69dadab8c7e14095469d5ed1d9921b4c0ce7 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:55:25 2022 +0000 Cleaning script for individuals: corrections and comments. commit a4f0d056a047aaf3458b043eba5e98df76da039a Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:44:27 2022 +0000 Fillna for app foreground and activity recognition commit 6286e7a44c7e2e99116b83fc3c06ce4398d022e5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:47:08 2022 +0000 firstuseafter column removed from contextual imputation commit 9b3447febd075f4dc5ede6a4071f72821835e7a2 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:40:05 2022 +0000 Contextual imputation correction commit d6adda30cf95e6d9660e6001225dee461bbe3704 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:37:51 2022 +0000 Contextual imputation on time(first/last) features. commit 8af4ef11dc711dffd86c71c99b15e9451aa94ecd Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 10:02:47 2022 +0000 Contextual imputation by feature type. commit 536b9494cdfbc6b31d41a74126ac6af1d8fe62e0 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 14:12:08 2022 +0000 Cleaning script corrections commit f0b87c9dd02d31223c2b69c2586221ffe202e21f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 09:54:15 2022 +0000 Debugging of the empatica data yield integration. commit 7fcdb873fe910f7243fb71ffe56abfdd9ebb81e3 Merge: 5c7bb0f4 bd53dc16 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:50:29 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 5c7bb0f4c14ab4413ed3682268bb7e65ac56fc83 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:48:32 2022 +0000 Config changes commit bd53dc1684b2b6fadf5653e2a9cc00c953410149 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 26 15:54:00 2022 +0000 Empatica data yield usage in the cleaning script. commit d9a574c550f8beb1cf5662e164ffa66048106dc9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 23 13:24:50 2022 +0000 Changes in the cleaning script and preparation of empatica data yield method. commit 19aa8707c0b61790d9d4c1834944c1711d8777aa Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 22 13:45:51 2022 +0000 Redefined cleaning steps after revision commit 247d758cb7eaa93ed9c7df2b0711325ffa27d985 Merge: 90ee99e4 7493aaa6 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:18:01 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 90ee99e4b99eeb32650df06d60e43c0ee1e66a87 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:16:00 2022 +0000 Remove TODO comments commit 7493aaa64368f81adbf478b43411063f56a9a87e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 12:57:55 2022 +0000 Small changes in cleaning scrtipt and missing vals testing. commit eaf4340afd7db8a43174a4789cfb9ba5a831dac4 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 08:03:48 2022 +0000 Small imputation and cleaning corrections. commit a96ea508c628d8c8c736126b65772c06c7cf4ddc Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:34:02 2022 +0000 Fill NaN of Empatica's SD second order feature (must be tested). commit 52e11cdcab51ec8ef97d379304e9297dd233773f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:54 2022 +0000 Configurations for new standardization path. commit 92aff93e65f765ca531bf414c2bdb2e6d7ca1240 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:16 2022 +0000 Remove standardization script. commit 18b63127deefb7cee0061ed741af179a4d6fdb01 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 06:16:26 2022 +0000 Removed all standardizaton rules and configurations. commit 62982866cd9f3f45a335d26b67c3fdf3035c6d1e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 13:24:21 2022 +0000 Phone wifi visible inspection (WIP) commit 0ce6da5444b7d0e3a30c8f6ca73422dc88d928b2 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 11:30:08 2022 +0000 kNN imputation relocation and execution only on specific columns. commit e3b78c8a85084b4cd873350df5bc2b75009fae83 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 10:58:57 2022 +0000 Impute selected phone features with 0. Wifi visible, screen, and light. commit 7d85f75d218ef9b3af5ae077343a58e62bb5fa2c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 09:03:30 2022 +0000 Changes in phone features NaN values script. commit 385e21409d1d3978588fea56cc26a8d241e3af35 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 14:16:58 2022 +0000 Changes in NaN values testing script. commit 18002f59e1c0e161f68b2a4cc217e62a6a86e467 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 10:48:59 2022 +0000 Doryab bluetooth and locations features fill in NaN values. commit 3cf7ca41aac7772c89ac90ad0a26e938d39f3f34 Merge: d27a4a71 d5ab5a03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 15:38:32 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit d5ab5a0394cdd395088723ff80d78f2257f8e37c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 14:13:03 2022 +0000 Writing testing scripts to determine the point of manual imputation. commit dfbb758902bebdbe86b42753b0252b96ec6e791f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 13:54:06 2022 +0000 Changes in AutoML params and environment.yml commit 4ec371ed96102d4b1f3b85557cb5fc3c388c1cef Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 09:51:03 2022 +0000 Testing auto-sklearn commit d27a4a71c81a50f4d30e5eb5bd9b664610da268a Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 12 13:44:17 2022 +0000 Reorganisation and reordering of the cleaning script. commit 15d792089d3b37dd381b1cb02b11f1106920d304 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:33:36 2022 +0000 Changes in cleaning script: - target extracted from config to remove rows where target is nan - prepared sns.heatmap for further missing values analysis - necessary changes in config and participant p01 - picture of heatmap which shows the values state after cleaning commit cb351e0ff6f6325e86fb2867116a44505a44eae1 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:06:57 2022 +0000 Unnecessary line (rows with no target value will be removed in cleaning script). commit 86299d346b5c3d706190db0dc14555309d17629f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 09:57:21 2022 +0000 Impute phone and sms NAs with 0 commit 3f7ec80c18b1237c49dfdd9a6736cdf518e0b7fb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Aug 31 10:18:50 2022 +0000 Preparation a) phone_calls 0 imputation b) remove rows with NaN target
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COMPUTE: False
IMPUTE_SELECTED_EVENT_FEATURES:
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COMPUTE: False
MIN_DATA_YIELDED_MINUTES_TO_IMPUTE: 0.33
COLS_NAN_THRESHOLD: 1 # set to 1 to disable
COLS_VAR_THRESHOLD: True
ROWS_NAN_THRESHOLD: 1 # set to 1 to disable
DATA_YIELD_FEATURE: RATIO_VALID_YIELDED_HOURS # RATIO_VALID_YIELDED_HOURS or RATIO_VALID_YIELDED_MINUTES
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DATA_YIELD_RATIO_THRESHOLD: 0 # set to 0 to disable
DROP_HIGHLY_CORRELATED_FEATURES:
Squashed commit of the following: commit 43ecc243cb62bb31eed85cb477ca4131555c7fe7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 22 15:26:09 2022 +0000 Adding TODO comments commit 2df1ebf90c3a93812b112b8ed0ee4e23cd74533f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 21 13:59:23 2022 +0000 README update commit 5182c2b16dff3537aad42984b8ea5214743cdb32 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 21 11:03:01 2022 +0000 Few corrections for all_cleaning commit 3d9254c1b3bed6e95e631d4e0402548830a19534 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 21 10:28:05 2022 +0000 Adding the min overlap for corr threshold and preservation of esm cols. commit e27c49cc8fa4c51f9fe8e593a8d25e9a032ab393 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 21 09:02:00 2022 +0000 Commenting and cleaning. commit 31a47a5ee4569264e39d7c445525a6e64bb7700a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Jul 20 13:49:22 2022 +0000 Environment version change. commit 5b274ed8993f58e783bda6d82fce936764209c28 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 16:10:07 2022 +0000 Enabled cleaning for all participants + standardization files. commit 203fdb31e0f3c647ef8c8a60cb9531831b7ab924 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 14:14:51 2022 +0000 Features cleaning fixes after testing. Visualization script for phone features values. commit 176178d73b154c30b9eb9eb4a67514f00d6a924e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 09:05:14 2022 +0000 Revert "Necessary config changes." This reverts commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0. commit 26ea6512c9d512f95837e7b047fe510c1d196403 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 13:19:47 2022 +0000 Adding cleaning function condition and cleaning functionality. commit 575c29eef9c21e6f2d7832871e73bc0941643734 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:51:56 2022 +0000 Translation of the cleaning individual RAPIDS function from R to py. commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:02:18 2022 +0000 Necessary config changes. commit b5669f51612fbd8378848615d639677851ab032f Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 15:26:00 2022 +0000 Modified snakemake rule to dynamically choose script extention. commit 66636be1e8ae4828228b37c59b9df1faf3fc3d3d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 14:43:08 2022 +0000 Trying to modify the snakefile rule to execute scripts in two languages depended on the provider. commit 574778b00f3cbb368ef4bc74de15cf5070c65ea9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 09:49:41 2022 +0000 gitignore: adding required files so that RAPIDS can be run successfully. commit 71018ab178256970535e78961602ab8c7f0ebb14 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 08:34:19 2022 +0000 Standardization bug fixes commit 6253c470a624e6bfbb02e0c453b652452eb2dbbc Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 14 15:28:02 2022 +0000 Seperate rules for empatica vs. nonempatica standardization. Parameter in config that controls the creation of standardized merged files for individual and all participants.. commit 90f902778565e0896d3bae22ae8551be8b487e67 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 12 14:23:03 2022 +0000 Preparing for final csvs' standardization. commit d25dde3998786a9a582f5cda544ee104386778f9 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:47 2022 +0000 Revert "Changes in config to be reverted." This reverts commit bea7608e7095021fb7c53a9afa07074448fe4313. commit 6b23e70857e63deda98eb98d190af9090626c84b Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:26 2022 +0000 Enabled standardization for rest (previously active) phone features. Testing still needed. commit 8ec58a6f34ba3d42e5cc71d26e6d91837472ca5f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 09:07:55 2022 +0000 Enabled standardization for phone calls. All steps completed and tested. commit bea7608e7095021fb7c53a9afa07074448fe4313 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 07:47:51 2022 +0000 Changes in config to be reverted. commit 4e84ca0e51bf709bff56fd09437b95310ec6bedd Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:24 2022 +0000 Standardization for the rest of the features. commit cc581aa788e3d5c17131af8f3d5dd6b0c3b5aff7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:08 2022 +0000 README update again
2022-07-22 17:31:30 +02:00
COMPUTE: True
MIN_OVERLAP_FOR_CORR_THRESHOLD: 0.5
CORR_THRESHOLD: 0.95
SRC_SCRIPT: src/features/all_cleaning_overall/rapids/main.R
Squashed commit of the following: commit 8a6b52a97c95dcd8b70b980b4f46421b1a847905 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:35:49 2022 +0000 Switch to 30_before ERS with corresponding targets. commit 244a05373014b14bc4c75db8ceb68a04dc5328df Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:19:43 2022 +0000 Change output files settings to nonstandardized. commit be0324fd01d70c58a9eefd84ccb23d06a42ab57c Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 28 12:44:25 2022 +0000 Fix some bugs and set categorical columns as categories dtypes. commit 99c2fab8f9ab9cf2ed40a952019f994299b78c05 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 16 09:50:18 2022 +0000 Fix a bug in the making of the individual model (when there is no target in the participants columns). commit 286de93bfd55710d77c2e4bab899e73381f9a4a3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 11:21:51 2022 +0000 Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic. commit ab803ee49c2898d2dd4d49de64f763f549c077e3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 10:14:07 2022 +0000 Add additional appraisal targets. commit 621f11b2d98cb3e17d86c3be902ebd40f94d3079 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 09:53:31 2022 +0000 Fix a bug related to wrong user input (duplicated events). commit bd41f42a5da7e28b9de190a53b5f2195fad0920d Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:07:36 2022 +0000 Rename target_ to segmenting_ method. commit a543ce372f1fd6cdd402be8ebdbe54610e449ce2 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:04:16 2022 +0000 Add comments for event_related_script understanding. commit 74b454b07bf69bdcd0517a940c5296e5f77c492e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 11 09:15:12 2022 +0000 Apply changes to string answers to make them language-generic. commit 6ebe83e47ea4da0066f4cd9dedbdb726cef5d06c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 12:42:52 2022 +0000 Improve the ERS extract method with a couple of validations. commit 00350ef8ca2ef43aed71f76609917021ce920f31 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:32:58 2022 +0000 Change config for stressfulness event target method. commit e4985c91214ac6ecd43501d52b67816d26d4fdef Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:29:11 2022 +0000 Override stressfulness event target with extracted values from csv. commit a668b6e8dad4dd393802ed4d5e948d6d42d60a01 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 09:37:27 2022 +0000 Extract ERS and stress event targets to csv files (completed). commit 9199b53ded1c5d858882d9826aa15e5e2102ab08 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 9 15:11:51 2022 +0000 Get, join and start processing required ERS stress event data. commit f3c6a66da9a7ce92d4296436927f48b3d1a467b8 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 15:53:43 2022 +0000 Begin with stress events in the ERS script. commit 0b3e9226b3c683e87ef758756f0d83350642a716 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 14:44:24 2022 +0000 Make small corrections in ERS file. commit 2d83f7ddecbc3880e8d901fc2aae25621a280f75 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 11:32:05 2022 +0000 Begin the ERS logic for 90-minutes events. commit 1da72a7cbe3178ef911ddb263ea30e5da79407ad Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 09:45:37 2022 +0000 Rename targets method in config. commit 9f441afc16ff9b75e131eb47d41edb570b51190c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 15:09:04 2022 +0000 Begin ERS logic for 90-minutes events. commit c1c9f4d05ac8bdf03f4759623165f8e795eaa5a9 Merge: 62f46ea3 7ab0280d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:58 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 62f46ea3763ba47af2a7c62d6b0b453cfd549929 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:53 2022 +0000 Prepare method-based logic for ERS generating. commit 7ab0280d7ed23022a4d2de0caa7bba3a43dff9d4 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 08:58:08 2022 +0000 Correctly rename stressful event target variable. commit eefa9f3f4d4c95374dd31907787ed767c636fe37 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 14:49:54 2022 +0000 Add new target: stressfulness_event. commit 5e8174dd41f5a4c2aa35c74fb4bd9b19a918d1c4 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:52:45 2022 +0000 Add new target: stressfulness_period. commit 35c1a762e7179c7b11f8f1154c1a4f4133402324 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:51:18 2022 +0000 Improve filtering by esm_session and device_id. commit 02264b21fd43212dd4636d300321e254da392149 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 09:30:12 2022 +0000 Add logic for target selection in ERS processing. commit 0ce8723bdb72bafa40924ff4fd3a2328e81808eb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 2 14:01:21 2022 +0000 Extend imputation logic within the cleaning script. commit 30b38bfc028b6e3261701feb915f9e3820a77c75 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 28 09:00:13 2022 +0000 Fix the generating procedure of ERS file for participants with multiple devices. commit cd137af15a9f03724593595a152f34a24323088f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:20:15 2022 +0000 Config for 30 minute EMA segments. commit 3c0585a566ede91dd97e2ba0a6617a4f42e72617 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:12:56 2022 +0000 Remove obsolete comments. commit 6b487fcf7b64a722e9c5486764155764332ba73c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:11:42 2022 +0000 Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script. commit 5d17c92e54427cc70a7f747be398ad59af98c5bf Merge: a31fdd14 0d143e6a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:20 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit a31fdd1479193a67b6a6985cc42fdc66ac7be1a4 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:08 2022 +0000 Start to test empatica_data_yield precieved error. commit 936324d234b6636366b1a569793452a4cca54847 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:17:27 2022 +0000 Switch config for 30 minutes event related segments. commit da0a4596f814a40997efe782239cb296e89fe606 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:16:25 2022 +0000 Add additional ESM processing logic for ERS csv extraction. commit d4d74818e69eab2755f988391978400096902b5d Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:14:32 2022 +0000 Fix a bug - missing time_segment column when df is empty commit 14ff59914b4b3071ff7a40bf9daaba558ff66746 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:59:46 2022 +0000 Fix to correct dtypes. commit 6ab0ac5329d0be06bbe8357203422c7d981c325a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:57:26 2022 +0000 Optimize memory consumption with dtype definition while reading csv file. commit 0d143e6aadaf9b67b2fbfd6cdf8c218d5720f157 Merge: 8acac501 b92a3aa3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:28:27 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 8acac501251105332d1d3d4863e88744b9528844 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:26:43 2022 +0000 Add safenet when features dataframe is empty. commit b92a3aa37a1968b7129cdb2b7ebaf9beda981428 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:25:22 2022 +0000 Remove unwanted output or other error producing code. commit bfd637eb9c40872b954b608aef420b24393d3e6f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 08:53:44 2022 +0000 Improve strings formatting in straw_events file. commit 0d81ad5756c54f03b2b200b801672b9eb39f27d5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 19 13:35:04 2022 +0000 Debug assignment of segments to rows commit cea451d344e3b0bcc110c77f2845a9077bbe5d75 Merge: e88bbd54 cf38d9f1 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:06 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit e88bbd548fcd2bb1f9057b27b572afa5a6d028a5 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:00 2022 +0000 Add new daily segment and filter by segment in the cleaning script. commit cf38d9f175c5bcc9d0f8c70f49e59d2b56d8ada7 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 17 15:07:33 2022 +0000 Implement ERS generating logic. commit f3ca56cdbf22d7eed38f920889c4b19f49da7760 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 14 14:46:28 2022 +0000 Start with ERS logic integration within Snakemake. commit 797aa98f4fe2faf411c5130d27c51c5c606e5c0e Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:50 2022 +0000 Config for ERS testing. commit 9baff159cd1a61019410838efefa4b59a6c4981c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:23 2022 +0000 Changes needed for testing and starting of the Event-Related Segments. commit 0f21273508654133a51d1e20e485c3de33dc2779 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:32:51 2022 +0000 Bugs fix commit 55517eb737463e21c6f6ad18f4711d38bd02fec5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:23:11 2022 +0000 Necessary commit before proceeding. commit de15a52dba43325c171584464995fa4311403e7e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:36:23 2022 +0000 Bug fix commit 1ad25bb5727d30affd2ee063386f2f5ca52e0d63 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:26:17 2022 +0000 Few modifications of some imputation values in cleaning script and feature extraction. commit 9884b383cf6e1b339738deea8cc54a6d264e5c87 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 10 16:45:38 2022 +0000 Testing new data with AutoML. commit 2dc89c083c99d43da5e1eb9cbc1c07d39901f27d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 7 08:52:12 2022 +0000 Small changes in cleaning overall commit 001d40072973797f159b94b48ac3add10138f58e Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 14:28:12 2022 +0000 Clean features and create input files based on all possible targets. commit 1e38d9bf1e4d1caa10ff8c5245a59a9b20d4d7f9 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 13:27:38 2022 +0000 Standardization and correlation visualization in overall cleaning script. commit a34412a18dbd75aafa9f3bba9303ab6a962cec03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 14:16:55 2022 +0000 E4 data yield corrections. Changes in overal cs - standardization. commit 437459648f16f71acec6794a07404bfeb781f907 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 13:35:05 2022 +0000 Errors fix: individual script - treat participants missing data. commit 53f6cc60d5d8262a3bbb3cad82e2ebf49cb9e2a5 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 13:06:39 2022 +0000 Config and cleaning script necessary changes ... commit bbeabeee6ff7e3f8cc429470404c2c4b246b6a22 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 12:53:31 2022 +0000 Last changes before processing on the server. commit 44531c6d94705757110df6d087f3762699d7211a Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 30 10:04:07 2022 +0000 Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds. commit 7ac7cd5a3714521fc9a36a8371554a921df132fe Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 14:33:21 2022 +0000 Preparation of the overall cleaning script. commit 68fd69dadab8c7e14095469d5ed1d9921b4c0ce7 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:55:25 2022 +0000 Cleaning script for individuals: corrections and comments. commit a4f0d056a047aaf3458b043eba5e98df76da039a Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:44:27 2022 +0000 Fillna for app foreground and activity recognition commit 6286e7a44c7e2e99116b83fc3c06ce4398d022e5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:47:08 2022 +0000 firstuseafter column removed from contextual imputation commit 9b3447febd075f4dc5ede6a4071f72821835e7a2 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:40:05 2022 +0000 Contextual imputation correction commit d6adda30cf95e6d9660e6001225dee461bbe3704 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:37:51 2022 +0000 Contextual imputation on time(first/last) features. commit 8af4ef11dc711dffd86c71c99b15e9451aa94ecd Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 10:02:47 2022 +0000 Contextual imputation by feature type. commit 536b9494cdfbc6b31d41a74126ac6af1d8fe62e0 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 14:12:08 2022 +0000 Cleaning script corrections commit f0b87c9dd02d31223c2b69c2586221ffe202e21f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 09:54:15 2022 +0000 Debugging of the empatica data yield integration. commit 7fcdb873fe910f7243fb71ffe56abfdd9ebb81e3 Merge: 5c7bb0f4 bd53dc16 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:50:29 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 5c7bb0f4c14ab4413ed3682268bb7e65ac56fc83 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:48:32 2022 +0000 Config changes commit bd53dc1684b2b6fadf5653e2a9cc00c953410149 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 26 15:54:00 2022 +0000 Empatica data yield usage in the cleaning script. commit d9a574c550f8beb1cf5662e164ffa66048106dc9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 23 13:24:50 2022 +0000 Changes in the cleaning script and preparation of empatica data yield method. commit 19aa8707c0b61790d9d4c1834944c1711d8777aa Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 22 13:45:51 2022 +0000 Redefined cleaning steps after revision commit 247d758cb7eaa93ed9c7df2b0711325ffa27d985 Merge: 90ee99e4 7493aaa6 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:18:01 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 90ee99e4b99eeb32650df06d60e43c0ee1e66a87 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:16:00 2022 +0000 Remove TODO comments commit 7493aaa64368f81adbf478b43411063f56a9a87e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 12:57:55 2022 +0000 Small changes in cleaning scrtipt and missing vals testing. commit eaf4340afd7db8a43174a4789cfb9ba5a831dac4 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 08:03:48 2022 +0000 Small imputation and cleaning corrections. commit a96ea508c628d8c8c736126b65772c06c7cf4ddc Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:34:02 2022 +0000 Fill NaN of Empatica's SD second order feature (must be tested). commit 52e11cdcab51ec8ef97d379304e9297dd233773f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:54 2022 +0000 Configurations for new standardization path. commit 92aff93e65f765ca531bf414c2bdb2e6d7ca1240 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:16 2022 +0000 Remove standardization script. commit 18b63127deefb7cee0061ed741af179a4d6fdb01 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 06:16:26 2022 +0000 Removed all standardizaton rules and configurations. commit 62982866cd9f3f45a335d26b67c3fdf3035c6d1e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 13:24:21 2022 +0000 Phone wifi visible inspection (WIP) commit 0ce6da5444b7d0e3a30c8f6ca73422dc88d928b2 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 11:30:08 2022 +0000 kNN imputation relocation and execution only on specific columns. commit e3b78c8a85084b4cd873350df5bc2b75009fae83 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 10:58:57 2022 +0000 Impute selected phone features with 0. Wifi visible, screen, and light. commit 7d85f75d218ef9b3af5ae077343a58e62bb5fa2c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 09:03:30 2022 +0000 Changes in phone features NaN values script. commit 385e21409d1d3978588fea56cc26a8d241e3af35 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 14:16:58 2022 +0000 Changes in NaN values testing script. commit 18002f59e1c0e161f68b2a4cc217e62a6a86e467 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 10:48:59 2022 +0000 Doryab bluetooth and locations features fill in NaN values. commit 3cf7ca41aac7772c89ac90ad0a26e938d39f3f34 Merge: d27a4a71 d5ab5a03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 15:38:32 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit d5ab5a0394cdd395088723ff80d78f2257f8e37c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 14:13:03 2022 +0000 Writing testing scripts to determine the point of manual imputation. commit dfbb758902bebdbe86b42753b0252b96ec6e791f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 13:54:06 2022 +0000 Changes in AutoML params and environment.yml commit 4ec371ed96102d4b1f3b85557cb5fc3c388c1cef Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 09:51:03 2022 +0000 Testing auto-sklearn commit d27a4a71c81a50f4d30e5eb5bd9b664610da268a Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 12 13:44:17 2022 +0000 Reorganisation and reordering of the cleaning script. commit 15d792089d3b37dd381b1cb02b11f1106920d304 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:33:36 2022 +0000 Changes in cleaning script: - target extracted from config to remove rows where target is nan - prepared sns.heatmap for further missing values analysis - necessary changes in config and participant p01 - picture of heatmap which shows the values state after cleaning commit cb351e0ff6f6325e86fb2867116a44505a44eae1 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:06:57 2022 +0000 Unnecessary line (rows with no target value will be removed in cleaning script). commit 86299d346b5c3d706190db0dc14555309d17629f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 09:57:21 2022 +0000 Impute phone and sms NAs with 0 commit 3f7ec80c18b1237c49dfdd9a6736cdf518e0b7fb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Aug 31 10:18:50 2022 +0000 Preparation a) phone_calls 0 imputation b) remove rows with NaN target
2022-12-08 17:04:39 +01:00
STRAW:
COMPUTE: True
Squashed commit of the following: commit 8a6b52a97c95dcd8b70b980b4f46421b1a847905 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:35:49 2022 +0000 Switch to 30_before ERS with corresponding targets. commit 244a05373014b14bc4c75db8ceb68a04dc5328df Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:19:43 2022 +0000 Change output files settings to nonstandardized. commit be0324fd01d70c58a9eefd84ccb23d06a42ab57c Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 28 12:44:25 2022 +0000 Fix some bugs and set categorical columns as categories dtypes. commit 99c2fab8f9ab9cf2ed40a952019f994299b78c05 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 16 09:50:18 2022 +0000 Fix a bug in the making of the individual model (when there is no target in the participants columns). commit 286de93bfd55710d77c2e4bab899e73381f9a4a3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 11:21:51 2022 +0000 Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic. commit ab803ee49c2898d2dd4d49de64f763f549c077e3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 10:14:07 2022 +0000 Add additional appraisal targets. commit 621f11b2d98cb3e17d86c3be902ebd40f94d3079 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 09:53:31 2022 +0000 Fix a bug related to wrong user input (duplicated events). commit bd41f42a5da7e28b9de190a53b5f2195fad0920d Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:07:36 2022 +0000 Rename target_ to segmenting_ method. commit a543ce372f1fd6cdd402be8ebdbe54610e449ce2 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:04:16 2022 +0000 Add comments for event_related_script understanding. commit 74b454b07bf69bdcd0517a940c5296e5f77c492e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 11 09:15:12 2022 +0000 Apply changes to string answers to make them language-generic. commit 6ebe83e47ea4da0066f4cd9dedbdb726cef5d06c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 12:42:52 2022 +0000 Improve the ERS extract method with a couple of validations. commit 00350ef8ca2ef43aed71f76609917021ce920f31 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:32:58 2022 +0000 Change config for stressfulness event target method. commit e4985c91214ac6ecd43501d52b67816d26d4fdef Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:29:11 2022 +0000 Override stressfulness event target with extracted values from csv. commit a668b6e8dad4dd393802ed4d5e948d6d42d60a01 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 09:37:27 2022 +0000 Extract ERS and stress event targets to csv files (completed). commit 9199b53ded1c5d858882d9826aa15e5e2102ab08 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 9 15:11:51 2022 +0000 Get, join and start processing required ERS stress event data. commit f3c6a66da9a7ce92d4296436927f48b3d1a467b8 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 15:53:43 2022 +0000 Begin with stress events in the ERS script. commit 0b3e9226b3c683e87ef758756f0d83350642a716 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 14:44:24 2022 +0000 Make small corrections in ERS file. commit 2d83f7ddecbc3880e8d901fc2aae25621a280f75 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 11:32:05 2022 +0000 Begin the ERS logic for 90-minutes events. commit 1da72a7cbe3178ef911ddb263ea30e5da79407ad Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 09:45:37 2022 +0000 Rename targets method in config. commit 9f441afc16ff9b75e131eb47d41edb570b51190c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 15:09:04 2022 +0000 Begin ERS logic for 90-minutes events. commit c1c9f4d05ac8bdf03f4759623165f8e795eaa5a9 Merge: 62f46ea3 7ab0280d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:58 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 62f46ea3763ba47af2a7c62d6b0b453cfd549929 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:53 2022 +0000 Prepare method-based logic for ERS generating. commit 7ab0280d7ed23022a4d2de0caa7bba3a43dff9d4 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 08:58:08 2022 +0000 Correctly rename stressful event target variable. commit eefa9f3f4d4c95374dd31907787ed767c636fe37 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 14:49:54 2022 +0000 Add new target: stressfulness_event. commit 5e8174dd41f5a4c2aa35c74fb4bd9b19a918d1c4 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:52:45 2022 +0000 Add new target: stressfulness_period. commit 35c1a762e7179c7b11f8f1154c1a4f4133402324 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:51:18 2022 +0000 Improve filtering by esm_session and device_id. commit 02264b21fd43212dd4636d300321e254da392149 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 09:30:12 2022 +0000 Add logic for target selection in ERS processing. commit 0ce8723bdb72bafa40924ff4fd3a2328e81808eb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 2 14:01:21 2022 +0000 Extend imputation logic within the cleaning script. commit 30b38bfc028b6e3261701feb915f9e3820a77c75 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 28 09:00:13 2022 +0000 Fix the generating procedure of ERS file for participants with multiple devices. commit cd137af15a9f03724593595a152f34a24323088f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:20:15 2022 +0000 Config for 30 minute EMA segments. commit 3c0585a566ede91dd97e2ba0a6617a4f42e72617 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:12:56 2022 +0000 Remove obsolete comments. commit 6b487fcf7b64a722e9c5486764155764332ba73c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:11:42 2022 +0000 Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script. commit 5d17c92e54427cc70a7f747be398ad59af98c5bf Merge: a31fdd14 0d143e6a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:20 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit a31fdd1479193a67b6a6985cc42fdc66ac7be1a4 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:08 2022 +0000 Start to test empatica_data_yield precieved error. commit 936324d234b6636366b1a569793452a4cca54847 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:17:27 2022 +0000 Switch config for 30 minutes event related segments. commit da0a4596f814a40997efe782239cb296e89fe606 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:16:25 2022 +0000 Add additional ESM processing logic for ERS csv extraction. commit d4d74818e69eab2755f988391978400096902b5d Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:14:32 2022 +0000 Fix a bug - missing time_segment column when df is empty commit 14ff59914b4b3071ff7a40bf9daaba558ff66746 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:59:46 2022 +0000 Fix to correct dtypes. commit 6ab0ac5329d0be06bbe8357203422c7d981c325a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:57:26 2022 +0000 Optimize memory consumption with dtype definition while reading csv file. commit 0d143e6aadaf9b67b2fbfd6cdf8c218d5720f157 Merge: 8acac501 b92a3aa3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:28:27 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 8acac501251105332d1d3d4863e88744b9528844 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:26:43 2022 +0000 Add safenet when features dataframe is empty. commit b92a3aa37a1968b7129cdb2b7ebaf9beda981428 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:25:22 2022 +0000 Remove unwanted output or other error producing code. commit bfd637eb9c40872b954b608aef420b24393d3e6f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 08:53:44 2022 +0000 Improve strings formatting in straw_events file. commit 0d81ad5756c54f03b2b200b801672b9eb39f27d5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 19 13:35:04 2022 +0000 Debug assignment of segments to rows commit cea451d344e3b0bcc110c77f2845a9077bbe5d75 Merge: e88bbd54 cf38d9f1 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:06 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit e88bbd548fcd2bb1f9057b27b572afa5a6d028a5 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:00 2022 +0000 Add new daily segment and filter by segment in the cleaning script. commit cf38d9f175c5bcc9d0f8c70f49e59d2b56d8ada7 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 17 15:07:33 2022 +0000 Implement ERS generating logic. commit f3ca56cdbf22d7eed38f920889c4b19f49da7760 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 14 14:46:28 2022 +0000 Start with ERS logic integration within Snakemake. commit 797aa98f4fe2faf411c5130d27c51c5c606e5c0e Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:50 2022 +0000 Config for ERS testing. commit 9baff159cd1a61019410838efefa4b59a6c4981c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:23 2022 +0000 Changes needed for testing and starting of the Event-Related Segments. commit 0f21273508654133a51d1e20e485c3de33dc2779 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:32:51 2022 +0000 Bugs fix commit 55517eb737463e21c6f6ad18f4711d38bd02fec5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:23:11 2022 +0000 Necessary commit before proceeding. commit de15a52dba43325c171584464995fa4311403e7e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:36:23 2022 +0000 Bug fix commit 1ad25bb5727d30affd2ee063386f2f5ca52e0d63 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:26:17 2022 +0000 Few modifications of some imputation values in cleaning script and feature extraction. commit 9884b383cf6e1b339738deea8cc54a6d264e5c87 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 10 16:45:38 2022 +0000 Testing new data with AutoML. commit 2dc89c083c99d43da5e1eb9cbc1c07d39901f27d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 7 08:52:12 2022 +0000 Small changes in cleaning overall commit 001d40072973797f159b94b48ac3add10138f58e Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 14:28:12 2022 +0000 Clean features and create input files based on all possible targets. commit 1e38d9bf1e4d1caa10ff8c5245a59a9b20d4d7f9 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 13:27:38 2022 +0000 Standardization and correlation visualization in overall cleaning script. commit a34412a18dbd75aafa9f3bba9303ab6a962cec03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 14:16:55 2022 +0000 E4 data yield corrections. Changes in overal cs - standardization. commit 437459648f16f71acec6794a07404bfeb781f907 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 13:35:05 2022 +0000 Errors fix: individual script - treat participants missing data. commit 53f6cc60d5d8262a3bbb3cad82e2ebf49cb9e2a5 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 13:06:39 2022 +0000 Config and cleaning script necessary changes ... commit bbeabeee6ff7e3f8cc429470404c2c4b246b6a22 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 12:53:31 2022 +0000 Last changes before processing on the server. commit 44531c6d94705757110df6d087f3762699d7211a Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 30 10:04:07 2022 +0000 Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds. commit 7ac7cd5a3714521fc9a36a8371554a921df132fe Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 14:33:21 2022 +0000 Preparation of the overall cleaning script. commit 68fd69dadab8c7e14095469d5ed1d9921b4c0ce7 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:55:25 2022 +0000 Cleaning script for individuals: corrections and comments. commit a4f0d056a047aaf3458b043eba5e98df76da039a Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:44:27 2022 +0000 Fillna for app foreground and activity recognition commit 6286e7a44c7e2e99116b83fc3c06ce4398d022e5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:47:08 2022 +0000 firstuseafter column removed from contextual imputation commit 9b3447febd075f4dc5ede6a4071f72821835e7a2 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:40:05 2022 +0000 Contextual imputation correction commit d6adda30cf95e6d9660e6001225dee461bbe3704 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:37:51 2022 +0000 Contextual imputation on time(first/last) features. commit 8af4ef11dc711dffd86c71c99b15e9451aa94ecd Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 10:02:47 2022 +0000 Contextual imputation by feature type. commit 536b9494cdfbc6b31d41a74126ac6af1d8fe62e0 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 14:12:08 2022 +0000 Cleaning script corrections commit f0b87c9dd02d31223c2b69c2586221ffe202e21f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 09:54:15 2022 +0000 Debugging of the empatica data yield integration. commit 7fcdb873fe910f7243fb71ffe56abfdd9ebb81e3 Merge: 5c7bb0f4 bd53dc16 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:50:29 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 5c7bb0f4c14ab4413ed3682268bb7e65ac56fc83 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:48:32 2022 +0000 Config changes commit bd53dc1684b2b6fadf5653e2a9cc00c953410149 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 26 15:54:00 2022 +0000 Empatica data yield usage in the cleaning script. commit d9a574c550f8beb1cf5662e164ffa66048106dc9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 23 13:24:50 2022 +0000 Changes in the cleaning script and preparation of empatica data yield method. commit 19aa8707c0b61790d9d4c1834944c1711d8777aa Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 22 13:45:51 2022 +0000 Redefined cleaning steps after revision commit 247d758cb7eaa93ed9c7df2b0711325ffa27d985 Merge: 90ee99e4 7493aaa6 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:18:01 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 90ee99e4b99eeb32650df06d60e43c0ee1e66a87 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:16:00 2022 +0000 Remove TODO comments commit 7493aaa64368f81adbf478b43411063f56a9a87e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 12:57:55 2022 +0000 Small changes in cleaning scrtipt and missing vals testing. commit eaf4340afd7db8a43174a4789cfb9ba5a831dac4 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 08:03:48 2022 +0000 Small imputation and cleaning corrections. commit a96ea508c628d8c8c736126b65772c06c7cf4ddc Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:34:02 2022 +0000 Fill NaN of Empatica's SD second order feature (must be tested). commit 52e11cdcab51ec8ef97d379304e9297dd233773f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:54 2022 +0000 Configurations for new standardization path. commit 92aff93e65f765ca531bf414c2bdb2e6d7ca1240 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:16 2022 +0000 Remove standardization script. commit 18b63127deefb7cee0061ed741af179a4d6fdb01 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 06:16:26 2022 +0000 Removed all standardizaton rules and configurations. commit 62982866cd9f3f45a335d26b67c3fdf3035c6d1e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 13:24:21 2022 +0000 Phone wifi visible inspection (WIP) commit 0ce6da5444b7d0e3a30c8f6ca73422dc88d928b2 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 11:30:08 2022 +0000 kNN imputation relocation and execution only on specific columns. commit e3b78c8a85084b4cd873350df5bc2b75009fae83 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 10:58:57 2022 +0000 Impute selected phone features with 0. Wifi visible, screen, and light. commit 7d85f75d218ef9b3af5ae077343a58e62bb5fa2c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 09:03:30 2022 +0000 Changes in phone features NaN values script. commit 385e21409d1d3978588fea56cc26a8d241e3af35 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 14:16:58 2022 +0000 Changes in NaN values testing script. commit 18002f59e1c0e161f68b2a4cc217e62a6a86e467 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 10:48:59 2022 +0000 Doryab bluetooth and locations features fill in NaN values. commit 3cf7ca41aac7772c89ac90ad0a26e938d39f3f34 Merge: d27a4a71 d5ab5a03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 15:38:32 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit d5ab5a0394cdd395088723ff80d78f2257f8e37c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 14:13:03 2022 +0000 Writing testing scripts to determine the point of manual imputation. commit dfbb758902bebdbe86b42753b0252b96ec6e791f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 13:54:06 2022 +0000 Changes in AutoML params and environment.yml commit 4ec371ed96102d4b1f3b85557cb5fc3c388c1cef Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 09:51:03 2022 +0000 Testing auto-sklearn commit d27a4a71c81a50f4d30e5eb5bd9b664610da268a Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 12 13:44:17 2022 +0000 Reorganisation and reordering of the cleaning script. commit 15d792089d3b37dd381b1cb02b11f1106920d304 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:33:36 2022 +0000 Changes in cleaning script: - target extracted from config to remove rows where target is nan - prepared sns.heatmap for further missing values analysis - necessary changes in config and participant p01 - picture of heatmap which shows the values state after cleaning commit cb351e0ff6f6325e86fb2867116a44505a44eae1 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:06:57 2022 +0000 Unnecessary line (rows with no target value will be removed in cleaning script). commit 86299d346b5c3d706190db0dc14555309d17629f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 09:57:21 2022 +0000 Impute phone and sms NAs with 0 commit 3f7ec80c18b1237c49dfdd9a6736cdf518e0b7fb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Aug 31 10:18:50 2022 +0000 Preparation a) phone_calls 0 imputation b) remove rows with NaN target
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PHONE_DATA_YIELD_FEATURE: RATIO_VALID_YIELDED_MINUTES # RATIO_VALID_YIELDED_HOURS or RATIO_VALID_YIELDED_MINUTES
PHONE_DATA_YIELD_RATIO_THRESHOLD: 0.5 # set to 0 to disable
EMPATICA_DATA_YIELD_RATIO_THRESHOLD: 0.5 # set to 0 to disable
ROWS_NAN_THRESHOLD: 0.33 # set to 1 to disable
COLS_NAN_THRESHOLD: 0.8 # set to 1 to remove only columns that contains all (100% of) NaN
Squashed commit of the following: commit 31a47a5ee4569264e39d7c445525a6e64bb7700a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Jul 20 13:49:22 2022 +0000 Environment version change. commit 5b274ed8993f58e783bda6d82fce936764209c28 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 16:10:07 2022 +0000 Enabled cleaning for all participants + standardization files. commit 203fdb31e0f3c647ef8c8a60cb9531831b7ab924 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 14:14:51 2022 +0000 Features cleaning fixes after testing. Visualization script for phone features values. commit 176178d73b154c30b9eb9eb4a67514f00d6a924e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 09:05:14 2022 +0000 Revert "Necessary config changes." This reverts commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0. commit 26ea6512c9d512f95837e7b047fe510c1d196403 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 13:19:47 2022 +0000 Adding cleaning function condition and cleaning functionality. commit 575c29eef9c21e6f2d7832871e73bc0941643734 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:51:56 2022 +0000 Translation of the cleaning individual RAPIDS function from R to py. commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:02:18 2022 +0000 Necessary config changes. commit b5669f51612fbd8378848615d639677851ab032f Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 15:26:00 2022 +0000 Modified snakemake rule to dynamically choose script extention. commit 66636be1e8ae4828228b37c59b9df1faf3fc3d3d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 14:43:08 2022 +0000 Trying to modify the snakefile rule to execute scripts in two languages depended on the provider. commit 574778b00f3cbb368ef4bc74de15cf5070c65ea9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 09:49:41 2022 +0000 gitignore: adding required files so that RAPIDS can be run successfully. commit 71018ab178256970535e78961602ab8c7f0ebb14 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 08:34:19 2022 +0000 Standardization bug fixes commit 6253c470a624e6bfbb02e0c453b652452eb2dbbc Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 14 15:28:02 2022 +0000 Seperate rules for empatica vs. nonempatica standardization. Parameter in config that controls the creation of standardized merged files for individual and all participants.. commit 90f902778565e0896d3bae22ae8551be8b487e67 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 12 14:23:03 2022 +0000 Preparing for final csvs' standardization. commit d25dde3998786a9a582f5cda544ee104386778f9 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:47 2022 +0000 Revert "Changes in config to be reverted." This reverts commit bea7608e7095021fb7c53a9afa07074448fe4313. commit 6b23e70857e63deda98eb98d190af9090626c84b Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:26 2022 +0000 Enabled standardization for rest (previously active) phone features. Testing still needed. commit 8ec58a6f34ba3d42e5cc71d26e6d91837472ca5f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 09:07:55 2022 +0000 Enabled standardization for phone calls. All steps completed and tested. commit bea7608e7095021fb7c53a9afa07074448fe4313 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 07:47:51 2022 +0000 Changes in config to be reverted. commit 4e84ca0e51bf709bff56fd09437b95310ec6bedd Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:24 2022 +0000 Standardization for the rest of the features. commit cc581aa788e3d5c17131af8f3d5dd6b0c3b5aff7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:08 2022 +0000 README update again
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COLS_VAR_THRESHOLD: True
DROP_HIGHLY_CORRELATED_FEATURES:
COMPUTE: True
MIN_OVERLAP_FOR_CORR_THRESHOLD: 0.5
CORR_THRESHOLD: 0.95
STANDARDIZATION: True
TARGET_STANDARDIZATION: False
Squashed commit of the following: commit 31a47a5ee4569264e39d7c445525a6e64bb7700a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Jul 20 13:49:22 2022 +0000 Environment version change. commit 5b274ed8993f58e783bda6d82fce936764209c28 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 16:10:07 2022 +0000 Enabled cleaning for all participants + standardization files. commit 203fdb31e0f3c647ef8c8a60cb9531831b7ab924 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 14:14:51 2022 +0000 Features cleaning fixes after testing. Visualization script for phone features values. commit 176178d73b154c30b9eb9eb4a67514f00d6a924e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 09:05:14 2022 +0000 Revert "Necessary config changes." This reverts commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0. commit 26ea6512c9d512f95837e7b047fe510c1d196403 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 13:19:47 2022 +0000 Adding cleaning function condition and cleaning functionality. commit 575c29eef9c21e6f2d7832871e73bc0941643734 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:51:56 2022 +0000 Translation of the cleaning individual RAPIDS function from R to py. commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:02:18 2022 +0000 Necessary config changes. commit b5669f51612fbd8378848615d639677851ab032f Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 15:26:00 2022 +0000 Modified snakemake rule to dynamically choose script extention. commit 66636be1e8ae4828228b37c59b9df1faf3fc3d3d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 14:43:08 2022 +0000 Trying to modify the snakefile rule to execute scripts in two languages depended on the provider. commit 574778b00f3cbb368ef4bc74de15cf5070c65ea9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 09:49:41 2022 +0000 gitignore: adding required files so that RAPIDS can be run successfully. commit 71018ab178256970535e78961602ab8c7f0ebb14 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 08:34:19 2022 +0000 Standardization bug fixes commit 6253c470a624e6bfbb02e0c453b652452eb2dbbc Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 14 15:28:02 2022 +0000 Seperate rules for empatica vs. nonempatica standardization. Parameter in config that controls the creation of standardized merged files for individual and all participants.. commit 90f902778565e0896d3bae22ae8551be8b487e67 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 12 14:23:03 2022 +0000 Preparing for final csvs' standardization. commit d25dde3998786a9a582f5cda544ee104386778f9 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:47 2022 +0000 Revert "Changes in config to be reverted." This reverts commit bea7608e7095021fb7c53a9afa07074448fe4313. commit 6b23e70857e63deda98eb98d190af9090626c84b Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:26 2022 +0000 Enabled standardization for rest (previously active) phone features. Testing still needed. commit 8ec58a6f34ba3d42e5cc71d26e6d91837472ca5f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 09:07:55 2022 +0000 Enabled standardization for phone calls. All steps completed and tested. commit bea7608e7095021fb7c53a9afa07074448fe4313 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 07:47:51 2022 +0000 Changes in config to be reverted. commit 4e84ca0e51bf709bff56fd09437b95310ec6bedd Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:24 2022 +0000 Standardization for the rest of the features. commit cc581aa788e3d5c17131af8f3d5dd6b0c3b5aff7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:08 2022 +0000 README update again
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SRC_SCRIPT: src/features/all_cleaning_overall/straw/main.py
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########################################################################################################################
# Baseline #
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########################################################################################################################
PARAMS_FOR_ANALYSIS:
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BASELINE:
COMPUTE: True
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FOLDER: data/external/baseline
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CONTAINER: [results-survey637813_final.csv, # Slovenia
results-survey358134_final.csv, # Belgium 1
results-survey413767_final.csv # Belgium 2
]
QUESTION_LIST: survey637813+question_text.csv
FEATURES: [age, gender, startlanguage, limesurvey_demand, limesurvey_control, limesurvey_demand_control_ratio, limesurvey_demand_control_ratio_quartile]
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CATEGORICAL_FEATURES: [gender]
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TARGET:
COMPUTE: True
Squashed commit of the following: commit 8a6b52a97c95dcd8b70b980b4f46421b1a847905 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:35:49 2022 +0000 Switch to 30_before ERS with corresponding targets. commit 244a05373014b14bc4c75db8ceb68a04dc5328df Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:19:43 2022 +0000 Change output files settings to nonstandardized. commit be0324fd01d70c58a9eefd84ccb23d06a42ab57c Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 28 12:44:25 2022 +0000 Fix some bugs and set categorical columns as categories dtypes. commit 99c2fab8f9ab9cf2ed40a952019f994299b78c05 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 16 09:50:18 2022 +0000 Fix a bug in the making of the individual model (when there is no target in the participants columns). commit 286de93bfd55710d77c2e4bab899e73381f9a4a3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 11:21:51 2022 +0000 Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic. commit ab803ee49c2898d2dd4d49de64f763f549c077e3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 10:14:07 2022 +0000 Add additional appraisal targets. commit 621f11b2d98cb3e17d86c3be902ebd40f94d3079 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 09:53:31 2022 +0000 Fix a bug related to wrong user input (duplicated events). commit bd41f42a5da7e28b9de190a53b5f2195fad0920d Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:07:36 2022 +0000 Rename target_ to segmenting_ method. commit a543ce372f1fd6cdd402be8ebdbe54610e449ce2 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:04:16 2022 +0000 Add comments for event_related_script understanding. commit 74b454b07bf69bdcd0517a940c5296e5f77c492e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 11 09:15:12 2022 +0000 Apply changes to string answers to make them language-generic. commit 6ebe83e47ea4da0066f4cd9dedbdb726cef5d06c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 12:42:52 2022 +0000 Improve the ERS extract method with a couple of validations. commit 00350ef8ca2ef43aed71f76609917021ce920f31 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:32:58 2022 +0000 Change config for stressfulness event target method. commit e4985c91214ac6ecd43501d52b67816d26d4fdef Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:29:11 2022 +0000 Override stressfulness event target with extracted values from csv. commit a668b6e8dad4dd393802ed4d5e948d6d42d60a01 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 09:37:27 2022 +0000 Extract ERS and stress event targets to csv files (completed). commit 9199b53ded1c5d858882d9826aa15e5e2102ab08 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 9 15:11:51 2022 +0000 Get, join and start processing required ERS stress event data. commit f3c6a66da9a7ce92d4296436927f48b3d1a467b8 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 15:53:43 2022 +0000 Begin with stress events in the ERS script. commit 0b3e9226b3c683e87ef758756f0d83350642a716 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 14:44:24 2022 +0000 Make small corrections in ERS file. commit 2d83f7ddecbc3880e8d901fc2aae25621a280f75 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 11:32:05 2022 +0000 Begin the ERS logic for 90-minutes events. commit 1da72a7cbe3178ef911ddb263ea30e5da79407ad Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 09:45:37 2022 +0000 Rename targets method in config. commit 9f441afc16ff9b75e131eb47d41edb570b51190c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 15:09:04 2022 +0000 Begin ERS logic for 90-minutes events. commit c1c9f4d05ac8bdf03f4759623165f8e795eaa5a9 Merge: 62f46ea3 7ab0280d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:58 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 62f46ea3763ba47af2a7c62d6b0b453cfd549929 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:53 2022 +0000 Prepare method-based logic for ERS generating. commit 7ab0280d7ed23022a4d2de0caa7bba3a43dff9d4 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 08:58:08 2022 +0000 Correctly rename stressful event target variable. commit eefa9f3f4d4c95374dd31907787ed767c636fe37 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 14:49:54 2022 +0000 Add new target: stressfulness_event. commit 5e8174dd41f5a4c2aa35c74fb4bd9b19a918d1c4 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:52:45 2022 +0000 Add new target: stressfulness_period. commit 35c1a762e7179c7b11f8f1154c1a4f4133402324 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:51:18 2022 +0000 Improve filtering by esm_session and device_id. commit 02264b21fd43212dd4636d300321e254da392149 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 09:30:12 2022 +0000 Add logic for target selection in ERS processing. commit 0ce8723bdb72bafa40924ff4fd3a2328e81808eb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 2 14:01:21 2022 +0000 Extend imputation logic within the cleaning script. commit 30b38bfc028b6e3261701feb915f9e3820a77c75 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 28 09:00:13 2022 +0000 Fix the generating procedure of ERS file for participants with multiple devices. commit cd137af15a9f03724593595a152f34a24323088f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:20:15 2022 +0000 Config for 30 minute EMA segments. commit 3c0585a566ede91dd97e2ba0a6617a4f42e72617 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:12:56 2022 +0000 Remove obsolete comments. commit 6b487fcf7b64a722e9c5486764155764332ba73c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:11:42 2022 +0000 Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script. commit 5d17c92e54427cc70a7f747be398ad59af98c5bf Merge: a31fdd14 0d143e6a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:20 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit a31fdd1479193a67b6a6985cc42fdc66ac7be1a4 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:08 2022 +0000 Start to test empatica_data_yield precieved error. commit 936324d234b6636366b1a569793452a4cca54847 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:17:27 2022 +0000 Switch config for 30 minutes event related segments. commit da0a4596f814a40997efe782239cb296e89fe606 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:16:25 2022 +0000 Add additional ESM processing logic for ERS csv extraction. commit d4d74818e69eab2755f988391978400096902b5d Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:14:32 2022 +0000 Fix a bug - missing time_segment column when df is empty commit 14ff59914b4b3071ff7a40bf9daaba558ff66746 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:59:46 2022 +0000 Fix to correct dtypes. commit 6ab0ac5329d0be06bbe8357203422c7d981c325a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:57:26 2022 +0000 Optimize memory consumption with dtype definition while reading csv file. commit 0d143e6aadaf9b67b2fbfd6cdf8c218d5720f157 Merge: 8acac501 b92a3aa3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:28:27 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 8acac501251105332d1d3d4863e88744b9528844 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:26:43 2022 +0000 Add safenet when features dataframe is empty. commit b92a3aa37a1968b7129cdb2b7ebaf9beda981428 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:25:22 2022 +0000 Remove unwanted output or other error producing code. commit bfd637eb9c40872b954b608aef420b24393d3e6f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 08:53:44 2022 +0000 Improve strings formatting in straw_events file. commit 0d81ad5756c54f03b2b200b801672b9eb39f27d5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 19 13:35:04 2022 +0000 Debug assignment of segments to rows commit cea451d344e3b0bcc110c77f2845a9077bbe5d75 Merge: e88bbd54 cf38d9f1 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:06 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit e88bbd548fcd2bb1f9057b27b572afa5a6d028a5 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:00 2022 +0000 Add new daily segment and filter by segment in the cleaning script. commit cf38d9f175c5bcc9d0f8c70f49e59d2b56d8ada7 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 17 15:07:33 2022 +0000 Implement ERS generating logic. commit f3ca56cdbf22d7eed38f920889c4b19f49da7760 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 14 14:46:28 2022 +0000 Start with ERS logic integration within Snakemake. commit 797aa98f4fe2faf411c5130d27c51c5c606e5c0e Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:50 2022 +0000 Config for ERS testing. commit 9baff159cd1a61019410838efefa4b59a6c4981c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:23 2022 +0000 Changes needed for testing and starting of the Event-Related Segments. commit 0f21273508654133a51d1e20e485c3de33dc2779 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:32:51 2022 +0000 Bugs fix commit 55517eb737463e21c6f6ad18f4711d38bd02fec5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:23:11 2022 +0000 Necessary commit before proceeding. commit de15a52dba43325c171584464995fa4311403e7e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:36:23 2022 +0000 Bug fix commit 1ad25bb5727d30affd2ee063386f2f5ca52e0d63 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:26:17 2022 +0000 Few modifications of some imputation values in cleaning script and feature extraction. commit 9884b383cf6e1b339738deea8cc54a6d264e5c87 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 10 16:45:38 2022 +0000 Testing new data with AutoML. commit 2dc89c083c99d43da5e1eb9cbc1c07d39901f27d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 7 08:52:12 2022 +0000 Small changes in cleaning overall commit 001d40072973797f159b94b48ac3add10138f58e Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 14:28:12 2022 +0000 Clean features and create input files based on all possible targets. commit 1e38d9bf1e4d1caa10ff8c5245a59a9b20d4d7f9 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 13:27:38 2022 +0000 Standardization and correlation visualization in overall cleaning script. commit a34412a18dbd75aafa9f3bba9303ab6a962cec03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 14:16:55 2022 +0000 E4 data yield corrections. Changes in overal cs - standardization. commit 437459648f16f71acec6794a07404bfeb781f907 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 13:35:05 2022 +0000 Errors fix: individual script - treat participants missing data. commit 53f6cc60d5d8262a3bbb3cad82e2ebf49cb9e2a5 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 13:06:39 2022 +0000 Config and cleaning script necessary changes ... commit bbeabeee6ff7e3f8cc429470404c2c4b246b6a22 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 12:53:31 2022 +0000 Last changes before processing on the server. commit 44531c6d94705757110df6d087f3762699d7211a Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 30 10:04:07 2022 +0000 Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds. commit 7ac7cd5a3714521fc9a36a8371554a921df132fe Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 14:33:21 2022 +0000 Preparation of the overall cleaning script. commit 68fd69dadab8c7e14095469d5ed1d9921b4c0ce7 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:55:25 2022 +0000 Cleaning script for individuals: corrections and comments. commit a4f0d056a047aaf3458b043eba5e98df76da039a Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:44:27 2022 +0000 Fillna for app foreground and activity recognition commit 6286e7a44c7e2e99116b83fc3c06ce4398d022e5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:47:08 2022 +0000 firstuseafter column removed from contextual imputation commit 9b3447febd075f4dc5ede6a4071f72821835e7a2 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:40:05 2022 +0000 Contextual imputation correction commit d6adda30cf95e6d9660e6001225dee461bbe3704 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:37:51 2022 +0000 Contextual imputation on time(first/last) features. commit 8af4ef11dc711dffd86c71c99b15e9451aa94ecd Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 10:02:47 2022 +0000 Contextual imputation by feature type. commit 536b9494cdfbc6b31d41a74126ac6af1d8fe62e0 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 14:12:08 2022 +0000 Cleaning script corrections commit f0b87c9dd02d31223c2b69c2586221ffe202e21f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 09:54:15 2022 +0000 Debugging of the empatica data yield integration. commit 7fcdb873fe910f7243fb71ffe56abfdd9ebb81e3 Merge: 5c7bb0f4 bd53dc16 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:50:29 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 5c7bb0f4c14ab4413ed3682268bb7e65ac56fc83 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:48:32 2022 +0000 Config changes commit bd53dc1684b2b6fadf5653e2a9cc00c953410149 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 26 15:54:00 2022 +0000 Empatica data yield usage in the cleaning script. commit d9a574c550f8beb1cf5662e164ffa66048106dc9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 23 13:24:50 2022 +0000 Changes in the cleaning script and preparation of empatica data yield method. commit 19aa8707c0b61790d9d4c1834944c1711d8777aa Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 22 13:45:51 2022 +0000 Redefined cleaning steps after revision commit 247d758cb7eaa93ed9c7df2b0711325ffa27d985 Merge: 90ee99e4 7493aaa6 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:18:01 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 90ee99e4b99eeb32650df06d60e43c0ee1e66a87 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:16:00 2022 +0000 Remove TODO comments commit 7493aaa64368f81adbf478b43411063f56a9a87e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 12:57:55 2022 +0000 Small changes in cleaning scrtipt and missing vals testing. commit eaf4340afd7db8a43174a4789cfb9ba5a831dac4 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 08:03:48 2022 +0000 Small imputation and cleaning corrections. commit a96ea508c628d8c8c736126b65772c06c7cf4ddc Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:34:02 2022 +0000 Fill NaN of Empatica's SD second order feature (must be tested). commit 52e11cdcab51ec8ef97d379304e9297dd233773f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:54 2022 +0000 Configurations for new standardization path. commit 92aff93e65f765ca531bf414c2bdb2e6d7ca1240 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:16 2022 +0000 Remove standardization script. commit 18b63127deefb7cee0061ed741af179a4d6fdb01 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 06:16:26 2022 +0000 Removed all standardizaton rules and configurations. commit 62982866cd9f3f45a335d26b67c3fdf3035c6d1e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 13:24:21 2022 +0000 Phone wifi visible inspection (WIP) commit 0ce6da5444b7d0e3a30c8f6ca73422dc88d928b2 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 11:30:08 2022 +0000 kNN imputation relocation and execution only on specific columns. commit e3b78c8a85084b4cd873350df5bc2b75009fae83 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 10:58:57 2022 +0000 Impute selected phone features with 0. Wifi visible, screen, and light. commit 7d85f75d218ef9b3af5ae077343a58e62bb5fa2c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 09:03:30 2022 +0000 Changes in phone features NaN values script. commit 385e21409d1d3978588fea56cc26a8d241e3af35 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 14:16:58 2022 +0000 Changes in NaN values testing script. commit 18002f59e1c0e161f68b2a4cc217e62a6a86e467 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 10:48:59 2022 +0000 Doryab bluetooth and locations features fill in NaN values. commit 3cf7ca41aac7772c89ac90ad0a26e938d39f3f34 Merge: d27a4a71 d5ab5a03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 15:38:32 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit d5ab5a0394cdd395088723ff80d78f2257f8e37c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 14:13:03 2022 +0000 Writing testing scripts to determine the point of manual imputation. commit dfbb758902bebdbe86b42753b0252b96ec6e791f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 13:54:06 2022 +0000 Changes in AutoML params and environment.yml commit 4ec371ed96102d4b1f3b85557cb5fc3c388c1cef Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 09:51:03 2022 +0000 Testing auto-sklearn commit d27a4a71c81a50f4d30e5eb5bd9b664610da268a Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 12 13:44:17 2022 +0000 Reorganisation and reordering of the cleaning script. commit 15d792089d3b37dd381b1cb02b11f1106920d304 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:33:36 2022 +0000 Changes in cleaning script: - target extracted from config to remove rows where target is nan - prepared sns.heatmap for further missing values analysis - necessary changes in config and participant p01 - picture of heatmap which shows the values state after cleaning commit cb351e0ff6f6325e86fb2867116a44505a44eae1 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:06:57 2022 +0000 Unnecessary line (rows with no target value will be removed in cleaning script). commit 86299d346b5c3d706190db0dc14555309d17629f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 09:57:21 2022 +0000 Impute phone and sms NAs with 0 commit 3f7ec80c18b1237c49dfdd9a6736cdf518e0b7fb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Aug 31 10:18:50 2022 +0000 Preparation a) phone_calls 0 imputation b) remove rows with NaN target
2022-12-08 17:04:39 +01:00
LABEL: appraisal_stressfulness_event_mean
ALL_LABELS: [appraisal_stressfulness_event_mean, appraisal_threat_mean, appraisal_challenge_mean]
Squashed commit of the following: commit 8a6b52a97c95dcd8b70b980b4f46421b1a847905 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:35:49 2022 +0000 Switch to 30_before ERS with corresponding targets. commit 244a05373014b14bc4c75db8ceb68a04dc5328df Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:19:43 2022 +0000 Change output files settings to nonstandardized. commit be0324fd01d70c58a9eefd84ccb23d06a42ab57c Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 28 12:44:25 2022 +0000 Fix some bugs and set categorical columns as categories dtypes. commit 99c2fab8f9ab9cf2ed40a952019f994299b78c05 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 16 09:50:18 2022 +0000 Fix a bug in the making of the individual model (when there is no target in the participants columns). commit 286de93bfd55710d77c2e4bab899e73381f9a4a3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 11:21:51 2022 +0000 Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic. commit ab803ee49c2898d2dd4d49de64f763f549c077e3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 10:14:07 2022 +0000 Add additional appraisal targets. commit 621f11b2d98cb3e17d86c3be902ebd40f94d3079 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 09:53:31 2022 +0000 Fix a bug related to wrong user input (duplicated events). commit bd41f42a5da7e28b9de190a53b5f2195fad0920d Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:07:36 2022 +0000 Rename target_ to segmenting_ method. commit a543ce372f1fd6cdd402be8ebdbe54610e449ce2 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:04:16 2022 +0000 Add comments for event_related_script understanding. commit 74b454b07bf69bdcd0517a940c5296e5f77c492e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 11 09:15:12 2022 +0000 Apply changes to string answers to make them language-generic. commit 6ebe83e47ea4da0066f4cd9dedbdb726cef5d06c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 12:42:52 2022 +0000 Improve the ERS extract method with a couple of validations. commit 00350ef8ca2ef43aed71f76609917021ce920f31 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:32:58 2022 +0000 Change config for stressfulness event target method. commit e4985c91214ac6ecd43501d52b67816d26d4fdef Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:29:11 2022 +0000 Override stressfulness event target with extracted values from csv. commit a668b6e8dad4dd393802ed4d5e948d6d42d60a01 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 09:37:27 2022 +0000 Extract ERS and stress event targets to csv files (completed). commit 9199b53ded1c5d858882d9826aa15e5e2102ab08 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 9 15:11:51 2022 +0000 Get, join and start processing required ERS stress event data. commit f3c6a66da9a7ce92d4296436927f48b3d1a467b8 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 15:53:43 2022 +0000 Begin with stress events in the ERS script. commit 0b3e9226b3c683e87ef758756f0d83350642a716 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 14:44:24 2022 +0000 Make small corrections in ERS file. commit 2d83f7ddecbc3880e8d901fc2aae25621a280f75 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 11:32:05 2022 +0000 Begin the ERS logic for 90-minutes events. commit 1da72a7cbe3178ef911ddb263ea30e5da79407ad Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 09:45:37 2022 +0000 Rename targets method in config. commit 9f441afc16ff9b75e131eb47d41edb570b51190c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 15:09:04 2022 +0000 Begin ERS logic for 90-minutes events. commit c1c9f4d05ac8bdf03f4759623165f8e795eaa5a9 Merge: 62f46ea3 7ab0280d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:58 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 62f46ea3763ba47af2a7c62d6b0b453cfd549929 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:53 2022 +0000 Prepare method-based logic for ERS generating. commit 7ab0280d7ed23022a4d2de0caa7bba3a43dff9d4 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 08:58:08 2022 +0000 Correctly rename stressful event target variable. commit eefa9f3f4d4c95374dd31907787ed767c636fe37 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 14:49:54 2022 +0000 Add new target: stressfulness_event. commit 5e8174dd41f5a4c2aa35c74fb4bd9b19a918d1c4 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:52:45 2022 +0000 Add new target: stressfulness_period. commit 35c1a762e7179c7b11f8f1154c1a4f4133402324 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:51:18 2022 +0000 Improve filtering by esm_session and device_id. commit 02264b21fd43212dd4636d300321e254da392149 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 09:30:12 2022 +0000 Add logic for target selection in ERS processing. commit 0ce8723bdb72bafa40924ff4fd3a2328e81808eb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 2 14:01:21 2022 +0000 Extend imputation logic within the cleaning script. commit 30b38bfc028b6e3261701feb915f9e3820a77c75 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 28 09:00:13 2022 +0000 Fix the generating procedure of ERS file for participants with multiple devices. commit cd137af15a9f03724593595a152f34a24323088f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:20:15 2022 +0000 Config for 30 minute EMA segments. commit 3c0585a566ede91dd97e2ba0a6617a4f42e72617 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:12:56 2022 +0000 Remove obsolete comments. commit 6b487fcf7b64a722e9c5486764155764332ba73c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:11:42 2022 +0000 Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script. commit 5d17c92e54427cc70a7f747be398ad59af98c5bf Merge: a31fdd14 0d143e6a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:20 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit a31fdd1479193a67b6a6985cc42fdc66ac7be1a4 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:08 2022 +0000 Start to test empatica_data_yield precieved error. commit 936324d234b6636366b1a569793452a4cca54847 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:17:27 2022 +0000 Switch config for 30 minutes event related segments. commit da0a4596f814a40997efe782239cb296e89fe606 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:16:25 2022 +0000 Add additional ESM processing logic for ERS csv extraction. commit d4d74818e69eab2755f988391978400096902b5d Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:14:32 2022 +0000 Fix a bug - missing time_segment column when df is empty commit 14ff59914b4b3071ff7a40bf9daaba558ff66746 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:59:46 2022 +0000 Fix to correct dtypes. commit 6ab0ac5329d0be06bbe8357203422c7d981c325a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:57:26 2022 +0000 Optimize memory consumption with dtype definition while reading csv file. commit 0d143e6aadaf9b67b2fbfd6cdf8c218d5720f157 Merge: 8acac501 b92a3aa3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:28:27 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 8acac501251105332d1d3d4863e88744b9528844 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:26:43 2022 +0000 Add safenet when features dataframe is empty. commit b92a3aa37a1968b7129cdb2b7ebaf9beda981428 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:25:22 2022 +0000 Remove unwanted output or other error producing code. commit bfd637eb9c40872b954b608aef420b24393d3e6f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 08:53:44 2022 +0000 Improve strings formatting in straw_events file. commit 0d81ad5756c54f03b2b200b801672b9eb39f27d5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 19 13:35:04 2022 +0000 Debug assignment of segments to rows commit cea451d344e3b0bcc110c77f2845a9077bbe5d75 Merge: e88bbd54 cf38d9f1 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:06 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit e88bbd548fcd2bb1f9057b27b572afa5a6d028a5 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:00 2022 +0000 Add new daily segment and filter by segment in the cleaning script. commit cf38d9f175c5bcc9d0f8c70f49e59d2b56d8ada7 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 17 15:07:33 2022 +0000 Implement ERS generating logic. commit f3ca56cdbf22d7eed38f920889c4b19f49da7760 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 14 14:46:28 2022 +0000 Start with ERS logic integration within Snakemake. commit 797aa98f4fe2faf411c5130d27c51c5c606e5c0e Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:50 2022 +0000 Config for ERS testing. commit 9baff159cd1a61019410838efefa4b59a6c4981c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:23 2022 +0000 Changes needed for testing and starting of the Event-Related Segments. commit 0f21273508654133a51d1e20e485c3de33dc2779 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:32:51 2022 +0000 Bugs fix commit 55517eb737463e21c6f6ad18f4711d38bd02fec5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:23:11 2022 +0000 Necessary commit before proceeding. commit de15a52dba43325c171584464995fa4311403e7e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:36:23 2022 +0000 Bug fix commit 1ad25bb5727d30affd2ee063386f2f5ca52e0d63 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:26:17 2022 +0000 Few modifications of some imputation values in cleaning script and feature extraction. commit 9884b383cf6e1b339738deea8cc54a6d264e5c87 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 10 16:45:38 2022 +0000 Testing new data with AutoML. commit 2dc89c083c99d43da5e1eb9cbc1c07d39901f27d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 7 08:52:12 2022 +0000 Small changes in cleaning overall commit 001d40072973797f159b94b48ac3add10138f58e Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 14:28:12 2022 +0000 Clean features and create input files based on all possible targets. commit 1e38d9bf1e4d1caa10ff8c5245a59a9b20d4d7f9 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 13:27:38 2022 +0000 Standardization and correlation visualization in overall cleaning script. commit a34412a18dbd75aafa9f3bba9303ab6a962cec03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 14:16:55 2022 +0000 E4 data yield corrections. Changes in overal cs - standardization. commit 437459648f16f71acec6794a07404bfeb781f907 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 13:35:05 2022 +0000 Errors fix: individual script - treat participants missing data. commit 53f6cc60d5d8262a3bbb3cad82e2ebf49cb9e2a5 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 13:06:39 2022 +0000 Config and cleaning script necessary changes ... commit bbeabeee6ff7e3f8cc429470404c2c4b246b6a22 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 12:53:31 2022 +0000 Last changes before processing on the server. commit 44531c6d94705757110df6d087f3762699d7211a Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 30 10:04:07 2022 +0000 Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds. commit 7ac7cd5a3714521fc9a36a8371554a921df132fe Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 14:33:21 2022 +0000 Preparation of the overall cleaning script. commit 68fd69dadab8c7e14095469d5ed1d9921b4c0ce7 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:55:25 2022 +0000 Cleaning script for individuals: corrections and comments. commit a4f0d056a047aaf3458b043eba5e98df76da039a Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:44:27 2022 +0000 Fillna for app foreground and activity recognition commit 6286e7a44c7e2e99116b83fc3c06ce4398d022e5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:47:08 2022 +0000 firstuseafter column removed from contextual imputation commit 9b3447febd075f4dc5ede6a4071f72821835e7a2 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:40:05 2022 +0000 Contextual imputation correction commit d6adda30cf95e6d9660e6001225dee461bbe3704 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:37:51 2022 +0000 Contextual imputation on time(first/last) features. commit 8af4ef11dc711dffd86c71c99b15e9451aa94ecd Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 10:02:47 2022 +0000 Contextual imputation by feature type. commit 536b9494cdfbc6b31d41a74126ac6af1d8fe62e0 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 14:12:08 2022 +0000 Cleaning script corrections commit f0b87c9dd02d31223c2b69c2586221ffe202e21f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 09:54:15 2022 +0000 Debugging of the empatica data yield integration. commit 7fcdb873fe910f7243fb71ffe56abfdd9ebb81e3 Merge: 5c7bb0f4 bd53dc16 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:50:29 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 5c7bb0f4c14ab4413ed3682268bb7e65ac56fc83 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:48:32 2022 +0000 Config changes commit bd53dc1684b2b6fadf5653e2a9cc00c953410149 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 26 15:54:00 2022 +0000 Empatica data yield usage in the cleaning script. commit d9a574c550f8beb1cf5662e164ffa66048106dc9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 23 13:24:50 2022 +0000 Changes in the cleaning script and preparation of empatica data yield method. commit 19aa8707c0b61790d9d4c1834944c1711d8777aa Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 22 13:45:51 2022 +0000 Redefined cleaning steps after revision commit 247d758cb7eaa93ed9c7df2b0711325ffa27d985 Merge: 90ee99e4 7493aaa6 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:18:01 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 90ee99e4b99eeb32650df06d60e43c0ee1e66a87 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:16:00 2022 +0000 Remove TODO comments commit 7493aaa64368f81adbf478b43411063f56a9a87e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 12:57:55 2022 +0000 Small changes in cleaning scrtipt and missing vals testing. commit eaf4340afd7db8a43174a4789cfb9ba5a831dac4 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 08:03:48 2022 +0000 Small imputation and cleaning corrections. commit a96ea508c628d8c8c736126b65772c06c7cf4ddc Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:34:02 2022 +0000 Fill NaN of Empatica's SD second order feature (must be tested). commit 52e11cdcab51ec8ef97d379304e9297dd233773f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:54 2022 +0000 Configurations for new standardization path. commit 92aff93e65f765ca531bf414c2bdb2e6d7ca1240 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:16 2022 +0000 Remove standardization script. commit 18b63127deefb7cee0061ed741af179a4d6fdb01 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 06:16:26 2022 +0000 Removed all standardizaton rules and configurations. commit 62982866cd9f3f45a335d26b67c3fdf3035c6d1e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 13:24:21 2022 +0000 Phone wifi visible inspection (WIP) commit 0ce6da5444b7d0e3a30c8f6ca73422dc88d928b2 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 11:30:08 2022 +0000 kNN imputation relocation and execution only on specific columns. commit e3b78c8a85084b4cd873350df5bc2b75009fae83 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 10:58:57 2022 +0000 Impute selected phone features with 0. Wifi visible, screen, and light. commit 7d85f75d218ef9b3af5ae077343a58e62bb5fa2c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 09:03:30 2022 +0000 Changes in phone features NaN values script. commit 385e21409d1d3978588fea56cc26a8d241e3af35 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 14:16:58 2022 +0000 Changes in NaN values testing script. commit 18002f59e1c0e161f68b2a4cc217e62a6a86e467 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 10:48:59 2022 +0000 Doryab bluetooth and locations features fill in NaN values. commit 3cf7ca41aac7772c89ac90ad0a26e938d39f3f34 Merge: d27a4a71 d5ab5a03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 15:38:32 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit d5ab5a0394cdd395088723ff80d78f2257f8e37c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 14:13:03 2022 +0000 Writing testing scripts to determine the point of manual imputation. commit dfbb758902bebdbe86b42753b0252b96ec6e791f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 13:54:06 2022 +0000 Changes in AutoML params and environment.yml commit 4ec371ed96102d4b1f3b85557cb5fc3c388c1cef Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 09:51:03 2022 +0000 Testing auto-sklearn commit d27a4a71c81a50f4d30e5eb5bd9b664610da268a Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 12 13:44:17 2022 +0000 Reorganisation and reordering of the cleaning script. commit 15d792089d3b37dd381b1cb02b11f1106920d304 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:33:36 2022 +0000 Changes in cleaning script: - target extracted from config to remove rows where target is nan - prepared sns.heatmap for further missing values analysis - necessary changes in config and participant p01 - picture of heatmap which shows the values state after cleaning commit cb351e0ff6f6325e86fb2867116a44505a44eae1 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:06:57 2022 +0000 Unnecessary line (rows with no target value will be removed in cleaning script). commit 86299d346b5c3d706190db0dc14555309d17629f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 09:57:21 2022 +0000 Impute phone and sms NAs with 0 commit 3f7ec80c18b1237c49dfdd9a6736cdf518e0b7fb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Aug 31 10:18:50 2022 +0000 Preparation a) phone_calls 0 imputation b) remove rows with NaN target
2022-12-08 17:04:39 +01:00
# PANAS_positive_affect_mean, PANAS_negative_affect_mean, JCQ_job_demand_mean, JCQ_job_control_mean, JCQ_supervisor_support_mean,
# JCQ_coworker_support_mean, appraisal_stressfulness_period_mean, appraisal_stressfulness_event_mean, appraisal_threat_mean, appraisal_challenge_mean