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1407 Commits (master)

Author SHA1 Message Date
Primoz a620def209 Generate standardized model input files (NOTE: commented unstandardized sections!) 2022-08-24 13:42:39 +00:00
Primoz c498ecb742 Include baseline models (+corrections), disable columns drop in cleaning function. 2022-08-23 14:12:14 +00:00
Primoz f088e9586f Handle empty ACC.csv 2022-08-22 14:20:47 +00:00
Primoz 0aa0e82673 Handle empty Empatica csv files. 2022-08-22 14:18:12 +00:00
Primoz 4cfe5a3a98 Disable discarding rows if DATA_YIELD_RATIO_THRESHOLD==0. 2022-08-19 13:10:56 +00:00
Primoz 607da820f2 Configuration and cleaning changes 2022-08-18 14:21:05 +00:00
Primoz fb577bc9ad 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 15:31:30 +00:00
Primoz 6ba4a66deb 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 13:51:22 +00:00
Primoz 788ac31190 Bug fix: if df has no rows write an empty zscore file. 2022-07-08 10:40:45 +00:00
Primoz 21eb2665d7 README: few changes. 2022-07-08 10:40:08 +00:00
Primoz a65a85cce9 Merge branch 'empatica_calculating_features' 2022-07-07 15:35:47 +00:00
Primoz fa961fe2f5 gitignore 2022-07-07 15:34:31 +00:00
Primoz 6c8014ba8e Updated R and Python package files. Updated README. 2022-07-07 15:30:07 +00:00
Primoz 5a777ac79f Working version that integrates both phone and empatica feature calculations. 2022-07-07 15:00:47 +00:00
Primoz 0425403951 Merge branch 'master' of https://repo.ijs.si/junoslukan/rapids 2022-07-06 11:53:31 +00:00
Primoz 887fd7dc72 Merge branch 'empatica_calculating_features' 2022-07-06 11:53:21 +00:00
Primoz 5a4696c548 Misc. changes 2022-07-06 11:30:18 +00:00
Primoz d2758eef46 Set not NaN sum insted of 0 sum for HRV features windows. 2022-07-06 07:36:35 +00:00
Primoz 2d5d23b615 Testing files change and remove standardization from hrv sensors main files. 2022-07-06 07:35:39 +00:00
Primoz a5480f1369 Few changes during addition to file structure. 2022-07-04 13:00:47 +00:00
Primoz 505c3a86b9 Testing different EDA findPeaks parameters. 2022-06-30 15:15:37 +00:00
junos ce04394679 Merge commit 'c05b047c2d9452151553961928c846c01d7395bc' 2022-06-25 20:06:24 +02:00
Primoz c851ab0763 Fill EDA NaN values where numPeak is zero. Other small changes. 2022-06-21 14:09:49 +00:00
Primoz a8cd16f88c Debugging eda_explorer 2022-06-16 11:32:59 +00:00
Primoz dda4554d46 Various small changes. 2022-06-15 13:57:46 +00:00
Primoz 212cf300f8 Debugging EDA signal - preliminary step for imputation. 2022-06-14 15:09:14 +00:00
Primoz 9ea39dc557 Standardization as a Snakefile's rule enabled for all E4 sensors. 2022-06-13 18:17:30 +00:00
Primoz 402059871f Making standardization as a rule. WIP: done only for BVP. 2022-06-13 14:12:03 +00:00
Primoz 094743244d Added SO feature for sum all rows that are non zero for BVP and IBI sensors. 2022-06-13 10:51:22 +00:00
primoz e1d7607de4 Extraction of additional SO features. Min/max has been changed to nsmallest/nlargest means. 2022-06-10 12:34:48 +00:00
primoz f371249b99 First order features standardization WIP 2022-06-09 13:35:15 +00:00
primoz 64e41cfa35 Second order features standardization in config.yaml. 2022-06-07 10:39:48 +00:00
primoz 2c7ac21465 Added standardization on SO features. 2022-06-06 13:51:15 +00:00
primoz 2acf6ff9fb Exception handling in case of empty ibi. Changes of the method EDA uses in main.py. Other small corrections. 2022-06-03 12:34:36 +00:00
primoz d300f0f8f0 Fixed RAPIDS bug: error when IBI.csv is empty. 2022-06-02 11:43:49 +00:00
Primoz fbf6a77dfc Small misc changes 2022-06-02 06:41:53 +00:00
Primoz 5532043b1f Patching IBI with BVP - completed. 2022-05-25 19:39:47 +00:00
Primoz bb62497ba6 Patching IBI with BVP - selecting appropriate pipeline entry point. WIP 2022-05-24 11:07:18 +00:00
Primoz 2a8f58f5c8 Patching IBI with BVP. WIP 2022-05-20 13:18:45 +00:00
Primoz 1471c86c62 Cr-features version update in rapids venv. 2022-05-13 13:37:12 +00:00
Primoz 6864cfe775 Changes after thorough testing with available data. 2022-05-13 13:35:34 +00:00
Primoz c1564f0cae Changed wrapper method calculate_feature to its newest version (for TEMP and ACC). 2022-05-11 14:21:21 +00:00
Primoz 31e36e7400 Alternating Second order and full segment features corresponding to config settings. 2022-05-11 08:50:15 +00:00
Primoz 9cf9e1fe14 Testing and modifying the code with different E4 data. 2022-05-10 11:36:49 +00:00
Primoz f62a1302dd Cr-features corrections for ACC and TEMP sensors 2022-05-09 11:01:52 +00:00
Primoz 5638367999 Implementation of the second order features. 2022-04-25 13:07:03 +00:00
Primoz 66451160e9 Calculating HRV features with IBI.csv. 2022-04-20 10:44:51 +00:00
= 8c8fe1fec7 Modifications, mostly imports, after changes in cr-features module. 2022-04-19 13:24:46 +00:00
= 075c64d1e5 HRV: changed wrapper calcFeat method with specialized one. 2022-04-14 11:51:53 +00:00
junos c05b047c2d Correct outstanding baseline feature mistake. 2022-04-13 17:05:16 +02:00