rapids/src/features/all_cleaning_individual/straw/main.py

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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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import pandas as pd
import numpy as np
import math, sys
import yaml
from sklearn.impute import KNNImputer
from sklearn.preprocessing import StandardScaler
import matplotlib.pyplot as plt
import seaborn as sns
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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def straw_cleaning(sensor_data_files, provider):
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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features = pd.read_csv(sensor_data_files["sensor_data"][0])
esm_cols = features.loc[:, features.columns.str.startswith('phone_esm_straw')] # Get target (esm) columns
with open('config.yaml', 'r') as stream:
config = yaml.load(stream, Loader=yaml.FullLoader)
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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# (1) FILTER_OUT THE ROWS THAT DO NOT HAVE THE TARGET COLUMN AVAILABLE
if config['PARAMS_FOR_ANALYSIS']['TARGET']['COMPUTE']:
target = config['PARAMS_FOR_ANALYSIS']['TARGET']['LABEL'] # get target label from config
features = features[features['phone_esm_straw_' + target].notna()].reset_index()
test_cols = [col for col in features.columns if 'phone_calls' in col or 'phone_messages' in col]
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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# TODO: reorder the cleaning steps so it makes sense for the analysis
# TODO: add conditions that differentiates cleaning steps for standardized and nonstandardized features, for this
# the snakemake rules will also have to come with additional parameter (in rules/features.smk)
# TODO: imputate the rows where the participants have at least 2 rows (2 time segments) - error prevention (has to be tested)
# TODO: because of different imputation logic (e.g., the phone_data_yield parameter for phone features) the imputation has to
# be planned accordingly. Should the phone features first be imputated with 0 and only then general kNN imputation is executed
# i.e., on the rows that are missing when E4 and phone features availability is not synchronized. CHECK phone_data_yield feat.
# A lot of imputation types/levels (1) imputation related to feature's content (2) imputation related to phone / empatica
# structual specifics (3) general imputation which is needed when types of features desynchronization is present (row is not full)
# because of the lack of the availability. Secondly, there's a high importance that features data frame is checked if and NaN
# values still exist.
# (2) PARTIAL IMPUTATION: IMPUTE DATA DEPENDEND ON THE FEATURES GROUP (e.g., phone or E4 features)
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
impute_phone_features = provider["IMPUTE_PHONE_SELECTED_EVENT_FEATURES"]
if impute_phone_features["COMPUTE"]:
if not 'phone_data_yield_rapids_ratiovalidyieldedminutes' in features.columns:
raise KeyError("RAPIDS provider needs to impute the selected event features based on phone_data_yield_rapids_ratiovalidyieldedminutes column, please set config[PHONE_DATA_YIELD][PROVIDERS][RAPIDS][COMPUTE] to True and include 'ratiovalidyieldedminutes' in [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
# TODO: if the type of the imputation will vary for different groups of features make conditional imputations here
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
phone_cols = [col for col in features if \
col.startswith('phone_applications_foreground_rapids_') or
col.startswith('phone_battery_rapids_') or
col.startswith('phone_calls_rapids_') or
col.startswith('phone_keyboard_rapids_') or
col.startswith('phone_messages_rapids_') or
col.startswith('phone_screen_rapids_') or
col.startswith('phone_wifi_')]
mask = features['phone_data_yield_rapids_ratiovalidyieldedminutes'] > impute_phone_features['MIN_DATA_YIELDED_MINUTES_TO_IMPUTE']
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
features.loc[mask, phone_cols] = impute(features[mask][phone_cols], method=impute_phone_features["TYPE"].lower())
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
# ??? Drop rows with the value of data_yield_column less than data_yield_ratio_threshold ???
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
data_yield_unit = provider["DATA_YIELD_FEATURE"].split("_")[3].lower()
data_yield_column = "phone_data_yield_rapids_ratiovalidyielded" + data_yield_unit
if not data_yield_column in features.columns:
raise KeyError(f"RAPIDS provider needs to impute the selected event features based on {data_yield_column} column, please set config[PHONE_DATA_YIELD][PROVIDERS][RAPIDS][COMPUTE] to True and include 'ratiovalidyielded{data_yield_unit}' in [FEATURES].")
if provider["DATA_YIELD_RATIO_THRESHOLD"]:
features = features[features[data_yield_column] >= provider["DATA_YIELD_RATIO_THRESHOLD"]]
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
# (3) REMOVE COLS IF THEIR NAN THRESHOLD IS PASSED (should be <= if even all NaN columns must be preserved)
features = features.loc[:, features.isna().sum() < provider["COLS_NAN_THRESHOLD"] * features.shape[0]]
# (4) REMOVE COLS WHERE VARIANCE IS 0
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
if provider["COLS_VAR_THRESHOLD"]:
features.drop(features.std()[features.std() == 0].index.values, axis=1, inplace=True)
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
# Preserve esm cols if deleted (has to come after drop cols operations)
for esm in esm_cols:
if esm not in features:
features[esm] = esm_cols[esm]
# (5) DROP HIGHLY CORRELATED FEATURES
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
drop_corr_features = provider["DROP_HIGHLY_CORRELATED_FEATURES"]
if drop_corr_features["COMPUTE"]:
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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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
numerical_cols = features.select_dtypes(include=np.number).columns.tolist()
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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# Remove columns where NaN count threshold is passed
valid_features = features[numerical_cols].loc[:, features[numerical_cols].isna().sum() < drop_corr_features['MIN_OVERLAP_FOR_CORR_THRESHOLD'] * features[numerical_cols].shape[0]]
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
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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cor_matrix = valid_features.corr(method='spearman').abs()
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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upper_tri = cor_matrix.where(np.triu(np.ones(cor_matrix.shape), k=1).astype(np.bool))
to_drop = [column for column in upper_tri.columns if any(upper_tri[column] > drop_corr_features["CORR_THRESHOLD"])]
features.drop(to_drop, axis=1, inplace=True)
# Remove rows if threshold of NaN values is passed
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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min_count = math.ceil((1 - provider["ROWS_NAN_THRESHOLD"]) * features.shape[1]) # minimal not nan values in row
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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features.dropna(axis=0, thresh=min_count, inplace=True)
sns.set(rc={"figure.figsize":(16, 8)})
sns.heatmap(features.isna(), cbar=False)
plt.savefig(f'features_nans_bf_knn.png', bbox_inches='tight')
# KNN IMPUTATION
features = impute(features, method="knn")
sns.set(rc={"figure.figsize":(16, 8)})
sns.heatmap(features.isna(), cbar=False)
plt.savefig(f'features_nans_af_knn.png', bbox_inches='tight')
## STANDARDIZATION - should it happen before or after kNN imputation?
# TODO: check if there are additional columns that need to be excluded from the standardization
excluded_columns = ['local_segment', 'local_segment_label', 'local_segment_start_datetime', 'local_segment_end_datetime']
excluded_columns += [col for col in features.columns if "level_1" in col]
features.loc[:, ~features.columns.isin(excluded_columns)] = StandardScaler().fit_transform(features.loc[:, ~features.columns.isin(excluded_columns)])
# VERIFY IF THERE ARE ANY NANS LEFT IN THE DATAFRAME
if features.isna.any().any():
raise ValueError
sys.exit()
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return features
def impute(df, method='zero'):
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def k_nearest(df):
imputer = KNNImputer(n_neighbors=3)
return pd.DataFrame(imputer.fit_transform(df), columns=df.columns)
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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return {
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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'zero': df.fillna(0),
'mean': df.fillna(df.mean()),
'median': df.fillna(df.median()),
'knn': k_nearest(df)
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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}[method]