rapids/Snakefile

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from snakemake.utils import validate
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configfile: "config.yaml"
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validate(config, "tools/config.schema.yaml")
include: "rules/common.smk"
include: "rules/renv.smk"
include: "rules/preprocessing.smk"
include: "rules/features.smk"
include: "rules/models.smk"
include: "rules/reports.smk"
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import itertools
files_to_compute = []
if len(config["PIDS"]) == 0:
raise ValueError("Add participants IDs to PIDS in config.yaml. Remember to create their participant files in data/external")
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for provider in config["PHONE_DATA_YIELD"]["PROVIDERS"].keys():
if config["PHONE_DATA_YIELD"]["PROVIDERS"][provider]["COMPUTE"]:
allowed_phone_sensors = get_phone_sensor_names()
if not (set(config["PHONE_DATA_YIELD"]["SENSORS"]) <= set(allowed_phone_sensors)):
raise ValueError('\nInvalid sensor(s) for PHONE_DATA_YIELD. config["PHONE_DATA_YIELD"]["SENSORS"] can have '
'one or more of the following phone sensors: {}.\nInstead you provided "{}".\n'
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'Keep in mind that the sensors\' CONTAINER attribute must point to a valid database table or file'\
.format(', '.join(allowed_phone_sensors),
', '.join(set(config["PHONE_DATA_YIELD"]["SENSORS"]) - set(allowed_phone_sensors))))
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=map(str.lower, config["PHONE_DATA_YIELD"]["SENSORS"])))
files_to_compute.extend(expand("data/interim/{pid}/phone_yielded_timestamps.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_yielded_timestamps_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_data_yield_features/phone_data_yield_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_DATA_YIELD"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_data_yield.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_MESSAGES"]["PROVIDERS"].keys():
if config["PHONE_MESSAGES"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_messages_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_messages_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_messages_features/phone_messages_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_MESSAGES"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_messages.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_CALLS"]["PROVIDERS"].keys():
if config["PHONE_CALLS"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_calls_raw.csv", pid=config["PIDS"]))
if (provider == "RAPIDS") and (config["PHONE_CALLS"]["PROVIDERS"][provider]["FEATURES_TYPE"] == "EPISODES"):
files_to_compute.extend(expand("data/interim/{pid}/phone_calls_episodes.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_calls_episodes_resampled.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_calls_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
else:
files_to_compute.extend(expand("data/raw/{pid}/phone_calls_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_calls_features/phone_calls_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_CALLS"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_calls.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_BLUETOOTH"]["PROVIDERS"].keys():
if config["PHONE_BLUETOOTH"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_bluetooth_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_bluetooth_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_bluetooth_features/phone_bluetooth_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_BLUETOOTH"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_bluetooth.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"].keys():
if config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_activity_recognition_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_activity_recognition_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_activity_recognition_episodes.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_activity_recognition_episodes_resampled.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_activity_recognition_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_activity_recognition_features/phone_activity_recognition_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_activity_recognition.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_BATTERY"]["PROVIDERS"].keys():
if config["PHONE_BATTERY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_battery_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_battery_episodes.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_battery_episodes_resampled.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_battery_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_battery_features/phone_battery_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_BATTERY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_battery.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_SCREEN"]["PROVIDERS"].keys():
if config["PHONE_SCREEN"]["PROVIDERS"][provider]["COMPUTE"]:
# if "PHONE_SCREEN" in config["PHONE_DATA_YIELD"]["SENSORS"]:# not used for now because we took episodepersensedminutes out of the list of supported features
# files_to_compute.extend(expand("data/interim/{pid}/phone_yielded_timestamps.csv", pid=config["PIDS"]))
# else:
# raise ValueError("Error: Add PHONE_SCREEN (and as many PHONE_SENSORS as you have in your database) to [PHONE_DATA_YIELD][SENSORS] in config.yaml. This is necessary to compute phone_yielded_timestamps (time when the smartphone was sensing data)")
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files_to_compute.extend(expand("data/raw/{pid}/phone_screen_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_screen_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_screen_episodes.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_screen_episodes_resampled.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_screen_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_screen_features/phone_screen_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_SCREEN"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_screen.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_LIGHT"]["PROVIDERS"].keys():
if config["PHONE_LIGHT"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_light_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_light_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_light_features/phone_light_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_LIGHT"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_light.csv", pid=config["PIDS"],))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_ACCELEROMETER"]["PROVIDERS"].keys():
if config["PHONE_ACCELEROMETER"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_accelerometer_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_accelerometer_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_accelerometer_features/phone_accelerometer_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_ACCELEROMETER"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_accelerometer.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"].keys():
if config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_foreground_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_foreground_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_foreground_with_datetime_with_categories.csv", pid=config["PIDS"]))
if config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"][provider]["INCLUDE_EPISODE_FEATURES"]:
files_to_compute.extend(expand("data/interim/{pid}/phone_app_episodes.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_app_episodes_resampled.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_app_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_applications_foreground_features/phone_applications_foreground_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_applications_foreground.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_WIFI_VISIBLE"]["PROVIDERS"].keys():
if config["PHONE_WIFI_VISIBLE"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_wifi_visible_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_wifi_visible_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_wifi_visible_features/phone_wifi_visible_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_WIFI_VISIBLE"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_wifi_visible.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_WIFI_CONNECTED"]["PROVIDERS"].keys():
if config["PHONE_WIFI_CONNECTED"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_wifi_connected_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_wifi_connected_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_wifi_connected_features/phone_wifi_connected_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_WIFI_CONNECTED"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_wifi_connected.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_CONVERSATION"]["PROVIDERS"].keys():
if config["PHONE_CONVERSATION"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_conversation_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_conversation_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_conversation_features/phone_conversation_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_CONVERSATION"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_conversation.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_ESM"]["PROVIDERS"].keys():
if config["PHONE_ESM"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_esm_raw.csv",pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_esm_with_datetime.csv",pid=config["PIDS"]))
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files_to_compute.extend(expand("data/interim/{pid}/phone_esm_clean.csv",pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_esm_features/phone_esm_{language}_{provider_key}.csv",pid=config["PIDS"],language=get_script_language(config["PHONE_ESM"]["PROVIDERS"][provider]["SRC_SCRIPT"]),provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_esm.csv", pid=config["PIDS"]))
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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# files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv",pid=config["PIDS"]))
# files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
# We can delete these if's as soon as we add feature PROVIDERS to any of these sensors
if isinstance(config["PHONE_APPLICATIONS_CRASHES"]["PROVIDERS"], dict):
for provider in config["PHONE_APPLICATIONS_CRASHES"]["PROVIDERS"].keys():
if config["PHONE_APPLICATIONS_CRASHES"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_crashes_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_crashes_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_crashes_with_datetime_with_categories.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_applications_crashes_features/phone_applications_crashes_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_APPLICATIONS_CRASHES"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_applications_crashes.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if isinstance(config["PHONE_APPLICATIONS_NOTIFICATIONS"]["PROVIDERS"], dict):
for provider in config["PHONE_APPLICATIONS_NOTIFICATIONS"]["PROVIDERS"].keys():
if config["PHONE_APPLICATIONS_NOTIFICATIONS"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_notifications_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_notifications_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_notifications_with_datetime_with_categories.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_applications_notifications_features/phone_applications_notifications_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_APPLICATIONS_NOTIFICATIONS"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_applications_notifications.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if isinstance(config["PHONE_KEYBOARD"]["PROVIDERS"], dict):
for provider in config["PHONE_KEYBOARD"]["PROVIDERS"].keys():
if config["PHONE_KEYBOARD"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_keyboard_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_keyboard_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_keyboard_features/phone_keyboard_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_KEYBOARD"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_keyboard.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if isinstance(config["PHONE_LOG"]["PROVIDERS"], dict):
for provider in config["PHONE_LOG"]["PROVIDERS"].keys():
if config["PHONE_LOG"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_log_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_log_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_log_features/phone_log_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_LOG"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_log.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
2020-10-19 21:07:12 +02:00
for provider in config["PHONE_LOCATIONS"]["PROVIDERS"].keys():
if config["PHONE_LOCATIONS"]["PROVIDERS"][provider]["COMPUTE"]:
if config["PHONE_LOCATIONS"]["LOCATIONS_TO_USE"] in ["FUSED_RESAMPLED","ALL_RESAMPLED"]:
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if "PHONE_LOCATIONS" in config["PHONE_DATA_YIELD"]["SENSORS"]:
files_to_compute.extend(expand("data/interim/{pid}/phone_yielded_timestamps.csv", pid=config["PIDS"]))
else:
raise ValueError("Error: Add PHONE_LOCATIONS (and as many PHONE_SENSORS as you have) to [PHONE_DATA_YIELD][SENSORS] in config.yaml. This is necessary to compute phone_yielded_timestamps (time when the smartphone was sensing data) which is used to resample fused location data (ALL_RESAMPLED and RESAMPLED_FUSED)")
2020-10-19 21:07:12 +02:00
if provider == "BARNETT":
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_barnett_daily.csv", pid=config["PIDS"]))
if provider == "DORYAB":
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_processed_with_datetime_with_doryab_columns_episodes.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_processed_with_datetime_with_doryab_columns_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
2020-10-19 21:07:12 +02:00
files_to_compute.extend(expand("data/raw/{pid}/phone_locations_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_processed.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_processed_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_features/phone_locations_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["PHONE_LOCATIONS"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_locations.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["FITBIT_CALORIES_INTRADAY"]["PROVIDERS"].keys():
if config["FITBIT_CALORIES_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_calories_intraday_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_calories_intraday_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_calories_intraday_features/fitbit_calories_intraday_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["FITBIT_CALORIES_INTRADAY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_calories_intraday.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_DATA_YIELD"]["PROVIDERS"].keys():
if config["FITBIT_DATA_YIELD"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_intraday_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_intraday_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_data_yield.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_HEARTRATE_SUMMARY"]["PROVIDERS"].keys():
if config["FITBIT_HEARTRATE_SUMMARY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_summary_raw.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_summary_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_heartrate_summary_features/fitbit_heartrate_summary_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["FITBIT_HEARTRATE_SUMMARY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_heartrate_summary.csv", pid=config["PIDS"]))
2020-11-25 22:34:05 +01:00
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_HEARTRATE_INTRADAY"]["PROVIDERS"].keys():
if config["FITBIT_HEARTRATE_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_intraday_raw.csv", pid=config["PIDS"]))
2021-03-10 19:31:56 +01:00
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_intraday_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_heartrate_intraday_features/fitbit_heartrate_intraday_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["FITBIT_HEARTRATE_INTRADAY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_heartrate_intraday.csv", pid=config["PIDS"]))
2020-11-25 22:34:05 +01:00
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_SLEEP_SUMMARY"]["PROVIDERS"].keys():
if config["FITBIT_SLEEP_SUMMARY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_summary_raw.csv", pid=config["PIDS"]))
2021-03-10 23:22:26 +01:00
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_summary_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_sleep_summary_features/fitbit_sleep_summary_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["FITBIT_SLEEP_SUMMARY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_sleep_summary.csv", pid=config["PIDS"]))
2020-11-25 22:34:05 +01:00
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_SLEEP_INTRADAY"]["PROVIDERS"].keys():
if config["FITBIT_SLEEP_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_intraday_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_intraday_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_sleep_intraday_episodes.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_sleep_intraday_episodes_resampled.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_sleep_intraday_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_sleep_intraday_features/fitbit_sleep_intraday_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["FITBIT_SLEEP_INTRADAY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_sleep_intraday.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_STEPS_SUMMARY"]["PROVIDERS"].keys():
if config["FITBIT_STEPS_SUMMARY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_summary_raw.csv", pid=config["PIDS"]))
2021-03-09 17:20:21 +01:00
files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_summary_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_steps_summary_features/fitbit_steps_summary_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["FITBIT_STEPS_SUMMARY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_steps_summary.csv", pid=config["PIDS"]))
2020-11-25 22:34:05 +01:00
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"].keys():
if config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
if config["FITBIT_STEPS_INTRADAY"]["EXCLUDE_SLEEP"]["TIME_BASED"]["EXCLUDE"] or config["FITBIT_STEPS_INTRADAY"]["EXCLUDE_SLEEP"]["FITBIT_BASED"]["EXCLUDE"]:
if config["FITBIT_STEPS_INTRADAY"]["EXCLUDE_SLEEP"]["FITBIT_BASED"]["EXCLUDE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_summary_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_steps_intraday_with_datetime_exclude_sleep.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_intraday_raw.csv", pid=config["PIDS"]))
2021-03-10 16:07:52 +01:00
files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_intraday_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_steps_intraday_features/fitbit_steps_intraday_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_steps_intraday.csv", pid=config["PIDS"]))
2020-11-25 22:34:05 +01:00
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
2020-10-22 19:08:52 +02:00
2020-11-25 22:34:05 +01:00
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for provider in config["EMPATICA_ACCELEROMETER"]["PROVIDERS"].keys():
if config["EMPATICA_ACCELEROMETER"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/empatica_accelerometer_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_accelerometer_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/empatica_accelerometer_features/empatica_accelerometer_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["EMPATICA_ACCELEROMETER"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_accelerometer.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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
2020-12-15 02:30:34 +01:00
for provider in config["EMPATICA_HEARTRATE"]["PROVIDERS"].keys():
if config["EMPATICA_HEARTRATE"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/empatica_heartrate_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_heartrate_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/empatica_heartrate_features/empatica_heartrate_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["EMPATICA_HEARTRATE"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_heartrate.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
2020-12-15 02:30:34 +01:00
for provider in config["EMPATICA_TEMPERATURE"]["PROVIDERS"].keys():
if config["EMPATICA_TEMPERATURE"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/empatica_temperature_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_temperature_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/empatica_temperature_features/empatica_temperature_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["EMPATICA_TEMPERATURE"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_temperature.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["EMPATICA_ELECTRODERMAL_ACTIVITY"]["PROVIDERS"].keys():
if config["EMPATICA_ELECTRODERMAL_ACTIVITY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/empatica_electrodermal_activity_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_electrodermal_activity_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["EMPATICA_ELECTRODERMAL_ACTIVITY"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_electrodermal_activity.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["EMPATICA_BLOOD_VOLUME_PULSE"]["PROVIDERS"].keys():
if config["EMPATICA_BLOOD_VOLUME_PULSE"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/empatica_blood_volume_pulse_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_blood_volume_pulse_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["EMPATICA_BLOOD_VOLUME_PULSE"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_blood_volume_pulse.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"].keys():
if config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/empatica_inter_beat_interval_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_inter_beat_interval_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_inter_beat_interval.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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 isinstance(config["EMPATICA_TAGS"]["PROVIDERS"], dict):
for provider in config["EMPATICA_TAGS"]["PROVIDERS"].keys():
if config["EMPATICA_TAGS"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/empatica_tags_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_tags_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/empatica_tags_features/empatica_tags_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["EMPATICA_TAGS"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_tags.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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# Visualization for Data Exploration
if config["HISTOGRAM_PHONE_DATA_YIELD"]["PLOT"]:
files_to_compute.append("reports/data_exploration/histogram_phone_data_yield.html")
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if config["HEATMAP_SENSORS_PER_MINUTE_PER_TIME_SEGMENT"]["PLOT"]:
files_to_compute.extend(expand("reports/interim/{pid}/heatmap_sensors_per_minute_per_time_segment.html", pid=config["PIDS"]))
files_to_compute.append("reports/data_exploration/heatmap_sensors_per_minute_per_time_segment.html")
if config["HEATMAP_SENSOR_ROW_COUNT_PER_TIME_SEGMENT"]["PLOT"]:
files_to_compute.extend(expand("reports/interim/{pid}/heatmap_sensor_row_count_per_time_segment.html", pid=config["PIDS"]))
files_to_compute.append("reports/data_exploration/heatmap_sensor_row_count_per_time_segment.html")
if config["HEATMAP_PHONE_DATA_YIELD_PER_PARTICIPANT_PER_TIME_SEGMENT"]["PLOT"]:
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if not config["PHONE_DATA_YIELD"]["PROVIDERS"]["RAPIDS"]["COMPUTE"]:
raise ValueError("Error: [PHONE_DATA_YIELD][PROVIDERS][RAPIDS][COMPUTE] must be True in config.yaml to get heatmaps of overall data yield.")
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files_to_compute.append("reports/data_exploration/heatmap_phone_data_yield_per_participant_per_time_segment.html")
if config["HEATMAP_FEATURE_CORRELATION_MATRIX"]["PLOT"]:
files_to_compute.append("reports/data_exploration/heatmap_feature_correlation_matrix.html")
2020-07-22 22:47:32 +02:00
# Data Cleaning
for provider in config["ALL_CLEANING_INDIVIDUAL"]["PROVIDERS"].keys():
if config["ALL_CLEANING_INDIVIDUAL"]["PROVIDERS"][provider]["COMPUTE"]:
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 == "STRAW":
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features_cleaned_" + provider.lower() + "_py.csv", pid=config["PIDS"]))
else:
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features_cleaned_" + provider.lower() + "_R.csv", pid=config["PIDS"]))
for provider in config["ALL_CLEANING_OVERALL"]["PROVIDERS"].keys():
if config["ALL_CLEANING_OVERALL"]["PROVIDERS"][provider]["COMPUTE"]:
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 == "STRAW":
Squashed commit of the following: commit 8a6b52a97c95dcd8b70b980b4f46421b1a847905 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:35:49 2022 +0000 Switch to 30_before ERS with corresponding targets. commit 244a05373014b14bc4c75db8ceb68a04dc5328df Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:19:43 2022 +0000 Change output files settings to nonstandardized. commit be0324fd01d70c58a9eefd84ccb23d06a42ab57c Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 28 12:44:25 2022 +0000 Fix some bugs and set categorical columns as categories dtypes. commit 99c2fab8f9ab9cf2ed40a952019f994299b78c05 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 16 09:50:18 2022 +0000 Fix a bug in the making of the individual model (when there is no target in the participants columns). commit 286de93bfd55710d77c2e4bab899e73381f9a4a3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 11:21:51 2022 +0000 Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic. commit ab803ee49c2898d2dd4d49de64f763f549c077e3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 10:14:07 2022 +0000 Add additional appraisal targets. commit 621f11b2d98cb3e17d86c3be902ebd40f94d3079 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 09:53:31 2022 +0000 Fix a bug related to wrong user input (duplicated events). commit bd41f42a5da7e28b9de190a53b5f2195fad0920d Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:07:36 2022 +0000 Rename target_ to segmenting_ method. commit a543ce372f1fd6cdd402be8ebdbe54610e449ce2 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:04:16 2022 +0000 Add comments for event_related_script understanding. commit 74b454b07bf69bdcd0517a940c5296e5f77c492e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 11 09:15:12 2022 +0000 Apply changes to string answers to make them language-generic. commit 6ebe83e47ea4da0066f4cd9dedbdb726cef5d06c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 12:42:52 2022 +0000 Improve the ERS extract method with a couple of validations. commit 00350ef8ca2ef43aed71f76609917021ce920f31 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:32:58 2022 +0000 Change config for stressfulness event target method. commit e4985c91214ac6ecd43501d52b67816d26d4fdef Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:29:11 2022 +0000 Override stressfulness event target with extracted values from csv. commit a668b6e8dad4dd393802ed4d5e948d6d42d60a01 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 09:37:27 2022 +0000 Extract ERS and stress event targets to csv files (completed). commit 9199b53ded1c5d858882d9826aa15e5e2102ab08 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 9 15:11:51 2022 +0000 Get, join and start processing required ERS stress event data. commit f3c6a66da9a7ce92d4296436927f48b3d1a467b8 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 15:53:43 2022 +0000 Begin with stress events in the ERS script. commit 0b3e9226b3c683e87ef758756f0d83350642a716 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 14:44:24 2022 +0000 Make small corrections in ERS file. commit 2d83f7ddecbc3880e8d901fc2aae25621a280f75 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 11:32:05 2022 +0000 Begin the ERS logic for 90-minutes events. commit 1da72a7cbe3178ef911ddb263ea30e5da79407ad Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 09:45:37 2022 +0000 Rename targets method in config. commit 9f441afc16ff9b75e131eb47d41edb570b51190c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 15:09:04 2022 +0000 Begin ERS logic for 90-minutes events. commit c1c9f4d05ac8bdf03f4759623165f8e795eaa5a9 Merge: 62f46ea3 7ab0280d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:58 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 62f46ea3763ba47af2a7c62d6b0b453cfd549929 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:53 2022 +0000 Prepare method-based logic for ERS generating. commit 7ab0280d7ed23022a4d2de0caa7bba3a43dff9d4 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 08:58:08 2022 +0000 Correctly rename stressful event target variable. commit eefa9f3f4d4c95374dd31907787ed767c636fe37 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 14:49:54 2022 +0000 Add new target: stressfulness_event. commit 5e8174dd41f5a4c2aa35c74fb4bd9b19a918d1c4 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:52:45 2022 +0000 Add new target: stressfulness_period. commit 35c1a762e7179c7b11f8f1154c1a4f4133402324 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:51:18 2022 +0000 Improve filtering by esm_session and device_id. commit 02264b21fd43212dd4636d300321e254da392149 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 09:30:12 2022 +0000 Add logic for target selection in ERS processing. commit 0ce8723bdb72bafa40924ff4fd3a2328e81808eb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 2 14:01:21 2022 +0000 Extend imputation logic within the cleaning script. commit 30b38bfc028b6e3261701feb915f9e3820a77c75 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 28 09:00:13 2022 +0000 Fix the generating procedure of ERS file for participants with multiple devices. commit cd137af15a9f03724593595a152f34a24323088f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:20:15 2022 +0000 Config for 30 minute EMA segments. commit 3c0585a566ede91dd97e2ba0a6617a4f42e72617 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:12:56 2022 +0000 Remove obsolete comments. commit 6b487fcf7b64a722e9c5486764155764332ba73c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:11:42 2022 +0000 Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script. commit 5d17c92e54427cc70a7f747be398ad59af98c5bf Merge: a31fdd14 0d143e6a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:20 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit a31fdd1479193a67b6a6985cc42fdc66ac7be1a4 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:08 2022 +0000 Start to test empatica_data_yield precieved error. commit 936324d234b6636366b1a569793452a4cca54847 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:17:27 2022 +0000 Switch config for 30 minutes event related segments. commit da0a4596f814a40997efe782239cb296e89fe606 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:16:25 2022 +0000 Add additional ESM processing logic for ERS csv extraction. commit d4d74818e69eab2755f988391978400096902b5d Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:14:32 2022 +0000 Fix a bug - missing time_segment column when df is empty commit 14ff59914b4b3071ff7a40bf9daaba558ff66746 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:59:46 2022 +0000 Fix to correct dtypes. commit 6ab0ac5329d0be06bbe8357203422c7d981c325a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:57:26 2022 +0000 Optimize memory consumption with dtype definition while reading csv file. commit 0d143e6aadaf9b67b2fbfd6cdf8c218d5720f157 Merge: 8acac501 b92a3aa3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:28:27 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 8acac501251105332d1d3d4863e88744b9528844 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:26:43 2022 +0000 Add safenet when features dataframe is empty. commit b92a3aa37a1968b7129cdb2b7ebaf9beda981428 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:25:22 2022 +0000 Remove unwanted output or other error producing code. commit bfd637eb9c40872b954b608aef420b24393d3e6f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 08:53:44 2022 +0000 Improve strings formatting in straw_events file. commit 0d81ad5756c54f03b2b200b801672b9eb39f27d5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 19 13:35:04 2022 +0000 Debug assignment of segments to rows commit cea451d344e3b0bcc110c77f2845a9077bbe5d75 Merge: e88bbd54 cf38d9f1 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:06 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit e88bbd548fcd2bb1f9057b27b572afa5a6d028a5 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:00 2022 +0000 Add new daily segment and filter by segment in the cleaning script. commit cf38d9f175c5bcc9d0f8c70f49e59d2b56d8ada7 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 17 15:07:33 2022 +0000 Implement ERS generating logic. commit f3ca56cdbf22d7eed38f920889c4b19f49da7760 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 14 14:46:28 2022 +0000 Start with ERS logic integration within Snakemake. commit 797aa98f4fe2faf411c5130d27c51c5c606e5c0e Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:50 2022 +0000 Config for ERS testing. commit 9baff159cd1a61019410838efefa4b59a6c4981c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:23 2022 +0000 Changes needed for testing and starting of the Event-Related Segments. commit 0f21273508654133a51d1e20e485c3de33dc2779 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:32:51 2022 +0000 Bugs fix commit 55517eb737463e21c6f6ad18f4711d38bd02fec5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:23:11 2022 +0000 Necessary commit before proceeding. commit de15a52dba43325c171584464995fa4311403e7e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:36:23 2022 +0000 Bug fix commit 1ad25bb5727d30affd2ee063386f2f5ca52e0d63 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:26:17 2022 +0000 Few modifications of some imputation values in cleaning script and feature extraction. commit 9884b383cf6e1b339738deea8cc54a6d264e5c87 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 10 16:45:38 2022 +0000 Testing new data with AutoML. commit 2dc89c083c99d43da5e1eb9cbc1c07d39901f27d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 7 08:52:12 2022 +0000 Small changes in cleaning overall commit 001d40072973797f159b94b48ac3add10138f58e Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 14:28:12 2022 +0000 Clean features and create input files based on all possible targets. commit 1e38d9bf1e4d1caa10ff8c5245a59a9b20d4d7f9 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 13:27:38 2022 +0000 Standardization and correlation visualization in overall cleaning script. commit a34412a18dbd75aafa9f3bba9303ab6a962cec03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 14:16:55 2022 +0000 E4 data yield corrections. Changes in overal cs - standardization. commit 437459648f16f71acec6794a07404bfeb781f907 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 13:35:05 2022 +0000 Errors fix: individual script - treat participants missing data. commit 53f6cc60d5d8262a3bbb3cad82e2ebf49cb9e2a5 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 13:06:39 2022 +0000 Config and cleaning script necessary changes ... commit bbeabeee6ff7e3f8cc429470404c2c4b246b6a22 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 12:53:31 2022 +0000 Last changes before processing on the server. commit 44531c6d94705757110df6d087f3762699d7211a Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 30 10:04:07 2022 +0000 Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds. commit 7ac7cd5a3714521fc9a36a8371554a921df132fe Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 14:33:21 2022 +0000 Preparation of the overall cleaning script. commit 68fd69dadab8c7e14095469d5ed1d9921b4c0ce7 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:55:25 2022 +0000 Cleaning script for individuals: corrections and comments. commit a4f0d056a047aaf3458b043eba5e98df76da039a Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:44:27 2022 +0000 Fillna for app foreground and activity recognition commit 6286e7a44c7e2e99116b83fc3c06ce4398d022e5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:47:08 2022 +0000 firstuseafter column removed from contextual imputation commit 9b3447febd075f4dc5ede6a4071f72821835e7a2 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:40:05 2022 +0000 Contextual imputation correction commit d6adda30cf95e6d9660e6001225dee461bbe3704 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:37:51 2022 +0000 Contextual imputation on time(first/last) features. commit 8af4ef11dc711dffd86c71c99b15e9451aa94ecd Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 10:02:47 2022 +0000 Contextual imputation by feature type. commit 536b9494cdfbc6b31d41a74126ac6af1d8fe62e0 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 14:12:08 2022 +0000 Cleaning script corrections commit f0b87c9dd02d31223c2b69c2586221ffe202e21f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 09:54:15 2022 +0000 Debugging of the empatica data yield integration. commit 7fcdb873fe910f7243fb71ffe56abfdd9ebb81e3 Merge: 5c7bb0f4 bd53dc16 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:50:29 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 5c7bb0f4c14ab4413ed3682268bb7e65ac56fc83 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:48:32 2022 +0000 Config changes commit bd53dc1684b2b6fadf5653e2a9cc00c953410149 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 26 15:54:00 2022 +0000 Empatica data yield usage in the cleaning script. commit d9a574c550f8beb1cf5662e164ffa66048106dc9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 23 13:24:50 2022 +0000 Changes in the cleaning script and preparation of empatica data yield method. commit 19aa8707c0b61790d9d4c1834944c1711d8777aa Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 22 13:45:51 2022 +0000 Redefined cleaning steps after revision commit 247d758cb7eaa93ed9c7df2b0711325ffa27d985 Merge: 90ee99e4 7493aaa6 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:18:01 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 90ee99e4b99eeb32650df06d60e43c0ee1e66a87 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:16:00 2022 +0000 Remove TODO comments commit 7493aaa64368f81adbf478b43411063f56a9a87e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 12:57:55 2022 +0000 Small changes in cleaning scrtipt and missing vals testing. commit eaf4340afd7db8a43174a4789cfb9ba5a831dac4 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 08:03:48 2022 +0000 Small imputation and cleaning corrections. commit a96ea508c628d8c8c736126b65772c06c7cf4ddc Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:34:02 2022 +0000 Fill NaN of Empatica's SD second order feature (must be tested). commit 52e11cdcab51ec8ef97d379304e9297dd233773f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:54 2022 +0000 Configurations for new standardization path. commit 92aff93e65f765ca531bf414c2bdb2e6d7ca1240 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:16 2022 +0000 Remove standardization script. commit 18b63127deefb7cee0061ed741af179a4d6fdb01 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 06:16:26 2022 +0000 Removed all standardizaton rules and configurations. commit 62982866cd9f3f45a335d26b67c3fdf3035c6d1e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 13:24:21 2022 +0000 Phone wifi visible inspection (WIP) commit 0ce6da5444b7d0e3a30c8f6ca73422dc88d928b2 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 11:30:08 2022 +0000 kNN imputation relocation and execution only on specific columns. commit e3b78c8a85084b4cd873350df5bc2b75009fae83 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 10:58:57 2022 +0000 Impute selected phone features with 0. Wifi visible, screen, and light. commit 7d85f75d218ef9b3af5ae077343a58e62bb5fa2c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 09:03:30 2022 +0000 Changes in phone features NaN values script. commit 385e21409d1d3978588fea56cc26a8d241e3af35 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 14:16:58 2022 +0000 Changes in NaN values testing script. commit 18002f59e1c0e161f68b2a4cc217e62a6a86e467 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 10:48:59 2022 +0000 Doryab bluetooth and locations features fill in NaN values. commit 3cf7ca41aac7772c89ac90ad0a26e938d39f3f34 Merge: d27a4a71 d5ab5a03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 15:38:32 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit d5ab5a0394cdd395088723ff80d78f2257f8e37c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 14:13:03 2022 +0000 Writing testing scripts to determine the point of manual imputation. commit dfbb758902bebdbe86b42753b0252b96ec6e791f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 13:54:06 2022 +0000 Changes in AutoML params and environment.yml commit 4ec371ed96102d4b1f3b85557cb5fc3c388c1cef Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 09:51:03 2022 +0000 Testing auto-sklearn commit d27a4a71c81a50f4d30e5eb5bd9b664610da268a Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 12 13:44:17 2022 +0000 Reorganisation and reordering of the cleaning script. commit 15d792089d3b37dd381b1cb02b11f1106920d304 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:33:36 2022 +0000 Changes in cleaning script: - target extracted from config to remove rows where target is nan - prepared sns.heatmap for further missing values analysis - necessary changes in config and participant p01 - picture of heatmap which shows the values state after cleaning commit cb351e0ff6f6325e86fb2867116a44505a44eae1 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:06:57 2022 +0000 Unnecessary line (rows with no target value will be removed in cleaning script). commit 86299d346b5c3d706190db0dc14555309d17629f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 09:57:21 2022 +0000 Impute phone and sms NAs with 0 commit 3f7ec80c18b1237c49dfdd9a6736cdf518e0b7fb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Aug 31 10:18:50 2022 +0000 Preparation a) phone_calls 0 imputation b) remove rows with NaN target
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for target in config["PARAMS_FOR_ANALYSIS"]["TARGET"]["ALL_LABELS"]:
files_to_compute.extend(expand("data/processed/features/all_participants/all_sensor_features_cleaned_" + provider.lower() +"_py_(" + target + ").csv"))
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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else:
Squashed commit of the following: commit 8a6b52a97c95dcd8b70b980b4f46421b1a847905 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:35:49 2022 +0000 Switch to 30_before ERS with corresponding targets. commit 244a05373014b14bc4c75db8ceb68a04dc5328df Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:19:43 2022 +0000 Change output files settings to nonstandardized. commit be0324fd01d70c58a9eefd84ccb23d06a42ab57c Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 28 12:44:25 2022 +0000 Fix some bugs and set categorical columns as categories dtypes. commit 99c2fab8f9ab9cf2ed40a952019f994299b78c05 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 16 09:50:18 2022 +0000 Fix a bug in the making of the individual model (when there is no target in the participants columns). commit 286de93bfd55710d77c2e4bab899e73381f9a4a3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 11:21:51 2022 +0000 Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic. commit ab803ee49c2898d2dd4d49de64f763f549c077e3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 10:14:07 2022 +0000 Add additional appraisal targets. commit 621f11b2d98cb3e17d86c3be902ebd40f94d3079 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 09:53:31 2022 +0000 Fix a bug related to wrong user input (duplicated events). commit bd41f42a5da7e28b9de190a53b5f2195fad0920d Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:07:36 2022 +0000 Rename target_ to segmenting_ method. commit a543ce372f1fd6cdd402be8ebdbe54610e449ce2 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:04:16 2022 +0000 Add comments for event_related_script understanding. commit 74b454b07bf69bdcd0517a940c5296e5f77c492e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 11 09:15:12 2022 +0000 Apply changes to string answers to make them language-generic. commit 6ebe83e47ea4da0066f4cd9dedbdb726cef5d06c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 12:42:52 2022 +0000 Improve the ERS extract method with a couple of validations. commit 00350ef8ca2ef43aed71f76609917021ce920f31 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:32:58 2022 +0000 Change config for stressfulness event target method. commit e4985c91214ac6ecd43501d52b67816d26d4fdef Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:29:11 2022 +0000 Override stressfulness event target with extracted values from csv. commit a668b6e8dad4dd393802ed4d5e948d6d42d60a01 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 09:37:27 2022 +0000 Extract ERS and stress event targets to csv files (completed). commit 9199b53ded1c5d858882d9826aa15e5e2102ab08 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 9 15:11:51 2022 +0000 Get, join and start processing required ERS stress event data. commit f3c6a66da9a7ce92d4296436927f48b3d1a467b8 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 15:53:43 2022 +0000 Begin with stress events in the ERS script. commit 0b3e9226b3c683e87ef758756f0d83350642a716 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 14:44:24 2022 +0000 Make small corrections in ERS file. commit 2d83f7ddecbc3880e8d901fc2aae25621a280f75 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 11:32:05 2022 +0000 Begin the ERS logic for 90-minutes events. commit 1da72a7cbe3178ef911ddb263ea30e5da79407ad Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 09:45:37 2022 +0000 Rename targets method in config. commit 9f441afc16ff9b75e131eb47d41edb570b51190c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 15:09:04 2022 +0000 Begin ERS logic for 90-minutes events. commit c1c9f4d05ac8bdf03f4759623165f8e795eaa5a9 Merge: 62f46ea3 7ab0280d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:58 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 62f46ea3763ba47af2a7c62d6b0b453cfd549929 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:53 2022 +0000 Prepare method-based logic for ERS generating. commit 7ab0280d7ed23022a4d2de0caa7bba3a43dff9d4 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 08:58:08 2022 +0000 Correctly rename stressful event target variable. commit eefa9f3f4d4c95374dd31907787ed767c636fe37 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 14:49:54 2022 +0000 Add new target: stressfulness_event. commit 5e8174dd41f5a4c2aa35c74fb4bd9b19a918d1c4 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:52:45 2022 +0000 Add new target: stressfulness_period. commit 35c1a762e7179c7b11f8f1154c1a4f4133402324 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:51:18 2022 +0000 Improve filtering by esm_session and device_id. commit 02264b21fd43212dd4636d300321e254da392149 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 09:30:12 2022 +0000 Add logic for target selection in ERS processing. commit 0ce8723bdb72bafa40924ff4fd3a2328e81808eb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 2 14:01:21 2022 +0000 Extend imputation logic within the cleaning script. commit 30b38bfc028b6e3261701feb915f9e3820a77c75 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 28 09:00:13 2022 +0000 Fix the generating procedure of ERS file for participants with multiple devices. commit cd137af15a9f03724593595a152f34a24323088f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:20:15 2022 +0000 Config for 30 minute EMA segments. commit 3c0585a566ede91dd97e2ba0a6617a4f42e72617 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:12:56 2022 +0000 Remove obsolete comments. commit 6b487fcf7b64a722e9c5486764155764332ba73c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:11:42 2022 +0000 Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script. commit 5d17c92e54427cc70a7f747be398ad59af98c5bf Merge: a31fdd14 0d143e6a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:20 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit a31fdd1479193a67b6a6985cc42fdc66ac7be1a4 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:08 2022 +0000 Start to test empatica_data_yield precieved error. commit 936324d234b6636366b1a569793452a4cca54847 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:17:27 2022 +0000 Switch config for 30 minutes event related segments. commit da0a4596f814a40997efe782239cb296e89fe606 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:16:25 2022 +0000 Add additional ESM processing logic for ERS csv extraction. commit d4d74818e69eab2755f988391978400096902b5d Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:14:32 2022 +0000 Fix a bug - missing time_segment column when df is empty commit 14ff59914b4b3071ff7a40bf9daaba558ff66746 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:59:46 2022 +0000 Fix to correct dtypes. commit 6ab0ac5329d0be06bbe8357203422c7d981c325a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:57:26 2022 +0000 Optimize memory consumption with dtype definition while reading csv file. commit 0d143e6aadaf9b67b2fbfd6cdf8c218d5720f157 Merge: 8acac501 b92a3aa3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:28:27 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 8acac501251105332d1d3d4863e88744b9528844 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:26:43 2022 +0000 Add safenet when features dataframe is empty. commit b92a3aa37a1968b7129cdb2b7ebaf9beda981428 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:25:22 2022 +0000 Remove unwanted output or other error producing code. commit bfd637eb9c40872b954b608aef420b24393d3e6f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 08:53:44 2022 +0000 Improve strings formatting in straw_events file. commit 0d81ad5756c54f03b2b200b801672b9eb39f27d5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 19 13:35:04 2022 +0000 Debug assignment of segments to rows commit cea451d344e3b0bcc110c77f2845a9077bbe5d75 Merge: e88bbd54 cf38d9f1 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:06 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit e88bbd548fcd2bb1f9057b27b572afa5a6d028a5 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:00 2022 +0000 Add new daily segment and filter by segment in the cleaning script. commit cf38d9f175c5bcc9d0f8c70f49e59d2b56d8ada7 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 17 15:07:33 2022 +0000 Implement ERS generating logic. commit f3ca56cdbf22d7eed38f920889c4b19f49da7760 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 14 14:46:28 2022 +0000 Start with ERS logic integration within Snakemake. commit 797aa98f4fe2faf411c5130d27c51c5c606e5c0e Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:50 2022 +0000 Config for ERS testing. commit 9baff159cd1a61019410838efefa4b59a6c4981c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:23 2022 +0000 Changes needed for testing and starting of the Event-Related Segments. commit 0f21273508654133a51d1e20e485c3de33dc2779 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:32:51 2022 +0000 Bugs fix commit 55517eb737463e21c6f6ad18f4711d38bd02fec5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:23:11 2022 +0000 Necessary commit before proceeding. commit de15a52dba43325c171584464995fa4311403e7e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:36:23 2022 +0000 Bug fix commit 1ad25bb5727d30affd2ee063386f2f5ca52e0d63 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:26:17 2022 +0000 Few modifications of some imputation values in cleaning script and feature extraction. commit 9884b383cf6e1b339738deea8cc54a6d264e5c87 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 10 16:45:38 2022 +0000 Testing new data with AutoML. commit 2dc89c083c99d43da5e1eb9cbc1c07d39901f27d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 7 08:52:12 2022 +0000 Small changes in cleaning overall commit 001d40072973797f159b94b48ac3add10138f58e Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 14:28:12 2022 +0000 Clean features and create input files based on all possible targets. commit 1e38d9bf1e4d1caa10ff8c5245a59a9b20d4d7f9 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 13:27:38 2022 +0000 Standardization and correlation visualization in overall cleaning script. commit a34412a18dbd75aafa9f3bba9303ab6a962cec03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 14:16:55 2022 +0000 E4 data yield corrections. Changes in overal cs - standardization. commit 437459648f16f71acec6794a07404bfeb781f907 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 13:35:05 2022 +0000 Errors fix: individual script - treat participants missing data. commit 53f6cc60d5d8262a3bbb3cad82e2ebf49cb9e2a5 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 13:06:39 2022 +0000 Config and cleaning script necessary changes ... commit bbeabeee6ff7e3f8cc429470404c2c4b246b6a22 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 12:53:31 2022 +0000 Last changes before processing on the server. commit 44531c6d94705757110df6d087f3762699d7211a Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 30 10:04:07 2022 +0000 Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds. commit 7ac7cd5a3714521fc9a36a8371554a921df132fe Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 14:33:21 2022 +0000 Preparation of the overall cleaning script. commit 68fd69dadab8c7e14095469d5ed1d9921b4c0ce7 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:55:25 2022 +0000 Cleaning script for individuals: corrections and comments. commit a4f0d056a047aaf3458b043eba5e98df76da039a Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:44:27 2022 +0000 Fillna for app foreground and activity recognition commit 6286e7a44c7e2e99116b83fc3c06ce4398d022e5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:47:08 2022 +0000 firstuseafter column removed from contextual imputation commit 9b3447febd075f4dc5ede6a4071f72821835e7a2 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:40:05 2022 +0000 Contextual imputation correction commit d6adda30cf95e6d9660e6001225dee461bbe3704 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:37:51 2022 +0000 Contextual imputation on time(first/last) features. commit 8af4ef11dc711dffd86c71c99b15e9451aa94ecd Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 10:02:47 2022 +0000 Contextual imputation by feature type. commit 536b9494cdfbc6b31d41a74126ac6af1d8fe62e0 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 14:12:08 2022 +0000 Cleaning script corrections commit f0b87c9dd02d31223c2b69c2586221ffe202e21f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 09:54:15 2022 +0000 Debugging of the empatica data yield integration. commit 7fcdb873fe910f7243fb71ffe56abfdd9ebb81e3 Merge: 5c7bb0f4 bd53dc16 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:50:29 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 5c7bb0f4c14ab4413ed3682268bb7e65ac56fc83 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:48:32 2022 +0000 Config changes commit bd53dc1684b2b6fadf5653e2a9cc00c953410149 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 26 15:54:00 2022 +0000 Empatica data yield usage in the cleaning script. commit d9a574c550f8beb1cf5662e164ffa66048106dc9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 23 13:24:50 2022 +0000 Changes in the cleaning script and preparation of empatica data yield method. commit 19aa8707c0b61790d9d4c1834944c1711d8777aa Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 22 13:45:51 2022 +0000 Redefined cleaning steps after revision commit 247d758cb7eaa93ed9c7df2b0711325ffa27d985 Merge: 90ee99e4 7493aaa6 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:18:01 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 90ee99e4b99eeb32650df06d60e43c0ee1e66a87 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:16:00 2022 +0000 Remove TODO comments commit 7493aaa64368f81adbf478b43411063f56a9a87e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 12:57:55 2022 +0000 Small changes in cleaning scrtipt and missing vals testing. commit eaf4340afd7db8a43174a4789cfb9ba5a831dac4 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 08:03:48 2022 +0000 Small imputation and cleaning corrections. commit a96ea508c628d8c8c736126b65772c06c7cf4ddc Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:34:02 2022 +0000 Fill NaN of Empatica's SD second order feature (must be tested). commit 52e11cdcab51ec8ef97d379304e9297dd233773f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:54 2022 +0000 Configurations for new standardization path. commit 92aff93e65f765ca531bf414c2bdb2e6d7ca1240 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:16 2022 +0000 Remove standardization script. commit 18b63127deefb7cee0061ed741af179a4d6fdb01 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 06:16:26 2022 +0000 Removed all standardizaton rules and configurations. commit 62982866cd9f3f45a335d26b67c3fdf3035c6d1e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 13:24:21 2022 +0000 Phone wifi visible inspection (WIP) commit 0ce6da5444b7d0e3a30c8f6ca73422dc88d928b2 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 11:30:08 2022 +0000 kNN imputation relocation and execution only on specific columns. commit e3b78c8a85084b4cd873350df5bc2b75009fae83 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 10:58:57 2022 +0000 Impute selected phone features with 0. Wifi visible, screen, and light. commit 7d85f75d218ef9b3af5ae077343a58e62bb5fa2c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 09:03:30 2022 +0000 Changes in phone features NaN values script. commit 385e21409d1d3978588fea56cc26a8d241e3af35 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 14:16:58 2022 +0000 Changes in NaN values testing script. commit 18002f59e1c0e161f68b2a4cc217e62a6a86e467 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 10:48:59 2022 +0000 Doryab bluetooth and locations features fill in NaN values. commit 3cf7ca41aac7772c89ac90ad0a26e938d39f3f34 Merge: d27a4a71 d5ab5a03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 15:38:32 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit d5ab5a0394cdd395088723ff80d78f2257f8e37c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 14:13:03 2022 +0000 Writing testing scripts to determine the point of manual imputation. commit dfbb758902bebdbe86b42753b0252b96ec6e791f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 13:54:06 2022 +0000 Changes in AutoML params and environment.yml commit 4ec371ed96102d4b1f3b85557cb5fc3c388c1cef Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 09:51:03 2022 +0000 Testing auto-sklearn commit d27a4a71c81a50f4d30e5eb5bd9b664610da268a Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 12 13:44:17 2022 +0000 Reorganisation and reordering of the cleaning script. commit 15d792089d3b37dd381b1cb02b11f1106920d304 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:33:36 2022 +0000 Changes in cleaning script: - target extracted from config to remove rows where target is nan - prepared sns.heatmap for further missing values analysis - necessary changes in config and participant p01 - picture of heatmap which shows the values state after cleaning commit cb351e0ff6f6325e86fb2867116a44505a44eae1 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:06:57 2022 +0000 Unnecessary line (rows with no target value will be removed in cleaning script). commit 86299d346b5c3d706190db0dc14555309d17629f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 09:57:21 2022 +0000 Impute phone and sms NAs with 0 commit 3f7ec80c18b1237c49dfdd9a6736cdf518e0b7fb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Aug 31 10:18:50 2022 +0000 Preparation a) phone_calls 0 imputation b) remove rows with NaN target
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files_to_compute.extend(expand("data/processed/features/all_participants/all_sensor_features_cleaned_" + provider.lower() +"_R.csv"))
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# Baseline features
if config["PARAMS_FOR_ANALYSIS"]["BASELINE"]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/baseline_merged.csv"))
files_to_compute.extend(expand("data/raw/{pid}/participant_baseline_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/baseline_questionnaires.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/baseline_features.csv", pid=config["PIDS"]))
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# Targets (labels)
if config["PARAMS_FOR_ANALYSIS"]["TARGET"]["COMPUTE"]:
Squashed commit of the following: commit 8a6b52a97c95dcd8b70b980b4f46421b1a847905 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:35:49 2022 +0000 Switch to 30_before ERS with corresponding targets. commit 244a05373014b14bc4c75db8ceb68a04dc5328df Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 29 11:19:43 2022 +0000 Change output files settings to nonstandardized. commit be0324fd01d70c58a9eefd84ccb23d06a42ab57c Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 28 12:44:25 2022 +0000 Fix some bugs and set categorical columns as categories dtypes. commit 99c2fab8f9ab9cf2ed40a952019f994299b78c05 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 16 09:50:18 2022 +0000 Fix a bug in the making of the individual model (when there is no target in the participants columns). commit 286de93bfd55710d77c2e4bab899e73381f9a4a3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 11:21:51 2022 +0000 Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic. commit ab803ee49c2898d2dd4d49de64f763f549c077e3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 10:14:07 2022 +0000 Add additional appraisal targets. commit 621f11b2d98cb3e17d86c3be902ebd40f94d3079 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 15 09:53:31 2022 +0000 Fix a bug related to wrong user input (duplicated events). commit bd41f42a5da7e28b9de190a53b5f2195fad0920d Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:07:36 2022 +0000 Rename target_ to segmenting_ method. commit a543ce372f1fd6cdd402be8ebdbe54610e449ce2 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Nov 14 15:04:16 2022 +0000 Add comments for event_related_script understanding. commit 74b454b07bf69bdcd0517a940c5296e5f77c492e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 11 09:15:12 2022 +0000 Apply changes to string answers to make them language-generic. commit 6ebe83e47ea4da0066f4cd9dedbdb726cef5d06c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 12:42:52 2022 +0000 Improve the ERS extract method with a couple of validations. commit 00350ef8ca2ef43aed71f76609917021ce920f31 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:32:58 2022 +0000 Change config for stressfulness event target method. commit e4985c91214ac6ecd43501d52b67816d26d4fdef Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 10:29:11 2022 +0000 Override stressfulness event target with extracted values from csv. commit a668b6e8dad4dd393802ed4d5e948d6d42d60a01 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 10 09:37:27 2022 +0000 Extract ERS and stress event targets to csv files (completed). commit 9199b53ded1c5d858882d9826aa15e5e2102ab08 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 9 15:11:51 2022 +0000 Get, join and start processing required ERS stress event data. commit f3c6a66da9a7ce92d4296436927f48b3d1a467b8 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 15:53:43 2022 +0000 Begin with stress events in the ERS script. commit 0b3e9226b3c683e87ef758756f0d83350642a716 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 14:44:24 2022 +0000 Make small corrections in ERS file. commit 2d83f7ddecbc3880e8d901fc2aae25621a280f75 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 11:32:05 2022 +0000 Begin the ERS logic for 90-minutes events. commit 1da72a7cbe3178ef911ddb263ea30e5da79407ad Author: Primoz <sisko.primoz@gmail.com> Date: Tue Nov 8 09:45:37 2022 +0000 Rename targets method in config. commit 9f441afc16ff9b75e131eb47d41edb570b51190c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 15:09:04 2022 +0000 Begin ERS logic for 90-minutes events. commit c1c9f4d05ac8bdf03f4759623165f8e795eaa5a9 Merge: 62f46ea3 7ab0280d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:58 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 62f46ea3763ba47af2a7c62d6b0b453cfd549929 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 09:11:53 2022 +0000 Prepare method-based logic for ERS generating. commit 7ab0280d7ed23022a4d2de0caa7bba3a43dff9d4 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Nov 4 08:58:08 2022 +0000 Correctly rename stressful event target variable. commit eefa9f3f4d4c95374dd31907787ed767c636fe37 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 14:49:54 2022 +0000 Add new target: stressfulness_event. commit 5e8174dd41f5a4c2aa35c74fb4bd9b19a918d1c4 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:52:45 2022 +0000 Add new target: stressfulness_period. commit 35c1a762e7179c7b11f8f1154c1a4f4133402324 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 13:51:18 2022 +0000 Improve filtering by esm_session and device_id. commit 02264b21fd43212dd4636d300321e254da392149 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Nov 3 09:30:12 2022 +0000 Add logic for target selection in ERS processing. commit 0ce8723bdb72bafa40924ff4fd3a2328e81808eb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Nov 2 14:01:21 2022 +0000 Extend imputation logic within the cleaning script. commit 30b38bfc028b6e3261701feb915f9e3820a77c75 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 28 09:00:13 2022 +0000 Fix the generating procedure of ERS file for participants with multiple devices. commit cd137af15a9f03724593595a152f34a24323088f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:20:15 2022 +0000 Config for 30 minute EMA segments. commit 3c0585a566ede91dd97e2ba0a6617a4f42e72617 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:12:56 2022 +0000 Remove obsolete comments. commit 6b487fcf7b64a722e9c5486764155764332ba73c Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 27 14:11:42 2022 +0000 Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script. commit 5d17c92e54427cc70a7f747be398ad59af98c5bf Merge: a31fdd14 0d143e6a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:20 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit a31fdd1479193a67b6a6985cc42fdc66ac7be1a4 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:18:08 2022 +0000 Start to test empatica_data_yield precieved error. commit 936324d234b6636366b1a569793452a4cca54847 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:17:27 2022 +0000 Switch config for 30 minutes event related segments. commit da0a4596f814a40997efe782239cb296e89fe606 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:16:25 2022 +0000 Add additional ESM processing logic for ERS csv extraction. commit d4d74818e69eab2755f988391978400096902b5d Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 14:14:32 2022 +0000 Fix a bug - missing time_segment column when df is empty commit 14ff59914b4b3071ff7a40bf9daaba558ff66746 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:59:46 2022 +0000 Fix to correct dtypes. commit 6ab0ac5329d0be06bbe8357203422c7d981c325a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 26 09:57:26 2022 +0000 Optimize memory consumption with dtype definition while reading csv file. commit 0d143e6aadaf9b67b2fbfd6cdf8c218d5720f157 Merge: 8acac501 b92a3aa3 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:28:27 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 8acac501251105332d1d3d4863e88744b9528844 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:26:43 2022 +0000 Add safenet when features dataframe is empty. commit b92a3aa37a1968b7129cdb2b7ebaf9beda981428 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 15:25:22 2022 +0000 Remove unwanted output or other error producing code. commit bfd637eb9c40872b954b608aef420b24393d3e6f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 25 08:53:44 2022 +0000 Improve strings formatting in straw_events file. commit 0d81ad5756c54f03b2b200b801672b9eb39f27d5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 19 13:35:04 2022 +0000 Debug assignment of segments to rows commit cea451d344e3b0bcc110c77f2845a9077bbe5d75 Merge: e88bbd54 cf38d9f1 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:06 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit e88bbd548fcd2bb1f9057b27b572afa5a6d028a5 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 18 09:15:00 2022 +0000 Add new daily segment and filter by segment in the cleaning script. commit cf38d9f175c5bcc9d0f8c70f49e59d2b56d8ada7 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 17 15:07:33 2022 +0000 Implement ERS generating logic. commit f3ca56cdbf22d7eed38f920889c4b19f49da7760 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 14 14:46:28 2022 +0000 Start with ERS logic integration within Snakemake. commit 797aa98f4fe2faf411c5130d27c51c5c606e5c0e Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:50 2022 +0000 Config for ERS testing. commit 9baff159cd1a61019410838efefa4b59a6c4981c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 15:51:23 2022 +0000 Changes needed for testing and starting of the Event-Related Segments. commit 0f21273508654133a51d1e20e485c3de33dc2779 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:32:51 2022 +0000 Bugs fix commit 55517eb737463e21c6f6ad18f4711d38bd02fec5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 12 12:23:11 2022 +0000 Necessary commit before proceeding. commit de15a52dba43325c171584464995fa4311403e7e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:36:23 2022 +0000 Bug fix commit 1ad25bb5727d30affd2ee063386f2f5ca52e0d63 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Oct 11 08:26:17 2022 +0000 Few modifications of some imputation values in cleaning script and feature extraction. commit 9884b383cf6e1b339738deea8cc54a6d264e5c87 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 10 16:45:38 2022 +0000 Testing new data with AutoML. commit 2dc89c083c99d43da5e1eb9cbc1c07d39901f27d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Oct 7 08:52:12 2022 +0000 Small changes in cleaning overall commit 001d40072973797f159b94b48ac3add10138f58e Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 14:28:12 2022 +0000 Clean features and create input files based on all possible targets. commit 1e38d9bf1e4d1caa10ff8c5245a59a9b20d4d7f9 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Oct 6 13:27:38 2022 +0000 Standardization and correlation visualization in overall cleaning script. commit a34412a18dbd75aafa9f3bba9303ab6a962cec03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 14:16:55 2022 +0000 E4 data yield corrections. Changes in overal cs - standardization. commit 437459648f16f71acec6794a07404bfeb781f907 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Oct 5 13:35:05 2022 +0000 Errors fix: individual script - treat participants missing data. commit 53f6cc60d5d8262a3bbb3cad82e2ebf49cb9e2a5 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 13:06:39 2022 +0000 Config and cleaning script necessary changes ... commit bbeabeee6ff7e3f8cc429470404c2c4b246b6a22 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Oct 3 12:53:31 2022 +0000 Last changes before processing on the server. commit 44531c6d94705757110df6d087f3762699d7211a Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 30 10:04:07 2022 +0000 Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds. commit 7ac7cd5a3714521fc9a36a8371554a921df132fe Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 14:33:21 2022 +0000 Preparation of the overall cleaning script. commit 68fd69dadab8c7e14095469d5ed1d9921b4c0ce7 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:55:25 2022 +0000 Cleaning script for individuals: corrections and comments. commit a4f0d056a047aaf3458b043eba5e98df76da039a Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 29 11:44:27 2022 +0000 Fillna for app foreground and activity recognition commit 6286e7a44c7e2e99116b83fc3c06ce4398d022e5 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:47:08 2022 +0000 firstuseafter column removed from contextual imputation commit 9b3447febd075f4dc5ede6a4071f72821835e7a2 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:40:05 2022 +0000 Contextual imputation correction commit d6adda30cf95e6d9660e6001225dee461bbe3704 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 12:37:51 2022 +0000 Contextual imputation on time(first/last) features. commit 8af4ef11dc711dffd86c71c99b15e9451aa94ecd Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 28 10:02:47 2022 +0000 Contextual imputation by feature type. commit 536b9494cdfbc6b31d41a74126ac6af1d8fe62e0 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 14:12:08 2022 +0000 Cleaning script corrections commit f0b87c9dd02d31223c2b69c2586221ffe202e21f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 09:54:15 2022 +0000 Debugging of the empatica data yield integration. commit 7fcdb873fe910f7243fb71ffe56abfdd9ebb81e3 Merge: 5c7bb0f4 bd53dc16 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:50:29 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 5c7bb0f4c14ab4413ed3682268bb7e65ac56fc83 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 27 07:48:32 2022 +0000 Config changes commit bd53dc1684b2b6fadf5653e2a9cc00c953410149 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 26 15:54:00 2022 +0000 Empatica data yield usage in the cleaning script. commit d9a574c550f8beb1cf5662e164ffa66048106dc9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 23 13:24:50 2022 +0000 Changes in the cleaning script and preparation of empatica data yield method. commit 19aa8707c0b61790d9d4c1834944c1711d8777aa Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 22 13:45:51 2022 +0000 Redefined cleaning steps after revision commit 247d758cb7eaa93ed9c7df2b0711325ffa27d985 Merge: 90ee99e4 7493aaa6 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:18:01 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit 90ee99e4b99eeb32650df06d60e43c0ee1e66a87 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 21 07:16:00 2022 +0000 Remove TODO comments commit 7493aaa64368f81adbf478b43411063f56a9a87e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 12:57:55 2022 +0000 Small changes in cleaning scrtipt and missing vals testing. commit eaf4340afd7db8a43174a4789cfb9ba5a831dac4 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 20 08:03:48 2022 +0000 Small imputation and cleaning corrections. commit a96ea508c628d8c8c736126b65772c06c7cf4ddc Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:34:02 2022 +0000 Fill NaN of Empatica's SD second order feature (must be tested). commit 52e11cdcab51ec8ef97d379304e9297dd233773f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:54 2022 +0000 Configurations for new standardization path. commit 92aff93e65f765ca531bf414c2bdb2e6d7ca1240 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 07:25:16 2022 +0000 Remove standardization script. commit 18b63127deefb7cee0061ed741af179a4d6fdb01 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 19 06:16:26 2022 +0000 Removed all standardizaton rules and configurations. commit 62982866cd9f3f45a335d26b67c3fdf3035c6d1e Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 13:24:21 2022 +0000 Phone wifi visible inspection (WIP) commit 0ce6da5444b7d0e3a30c8f6ca73422dc88d928b2 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 11:30:08 2022 +0000 kNN imputation relocation and execution only on specific columns. commit e3b78c8a85084b4cd873350df5bc2b75009fae83 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 10:58:57 2022 +0000 Impute selected phone features with 0. Wifi visible, screen, and light. commit 7d85f75d218ef9b3af5ae077343a58e62bb5fa2c Author: Primoz <sisko.primoz@gmail.com> Date: Fri Sep 16 09:03:30 2022 +0000 Changes in phone features NaN values script. commit 385e21409d1d3978588fea56cc26a8d241e3af35 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 14:16:58 2022 +0000 Changes in NaN values testing script. commit 18002f59e1c0e161f68b2a4cc217e62a6a86e467 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 15 10:48:59 2022 +0000 Doryab bluetooth and locations features fill in NaN values. commit 3cf7ca41aac7772c89ac90ad0a26e938d39f3f34 Merge: d27a4a71 d5ab5a03 Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 15:38:32 2022 +0000 Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning commit d5ab5a0394cdd395088723ff80d78f2257f8e37c Author: Primoz <sisko.primoz@gmail.com> Date: Wed Sep 14 14:13:03 2022 +0000 Writing testing scripts to determine the point of manual imputation. commit dfbb758902bebdbe86b42753b0252b96ec6e791f Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 13:54:06 2022 +0000 Changes in AutoML params and environment.yml commit 4ec371ed96102d4b1f3b85557cb5fc3c388c1cef Author: Primoz <sisko.primoz@gmail.com> Date: Tue Sep 13 09:51:03 2022 +0000 Testing auto-sklearn commit d27a4a71c81a50f4d30e5eb5bd9b664610da268a Author: Primoz <sisko.primoz@gmail.com> Date: Mon Sep 12 13:44:17 2022 +0000 Reorganisation and reordering of the cleaning script. commit 15d792089d3b37dd381b1cb02b11f1106920d304 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:33:36 2022 +0000 Changes in cleaning script: - target extracted from config to remove rows where target is nan - prepared sns.heatmap for further missing values analysis - necessary changes in config and participant p01 - picture of heatmap which shows the values state after cleaning commit cb351e0ff6f6325e86fb2867116a44505a44eae1 Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 10:06:57 2022 +0000 Unnecessary line (rows with no target value will be removed in cleaning script). commit 86299d346b5c3d706190db0dc14555309d17629f Author: Primoz <sisko.primoz@gmail.com> Date: Thu Sep 1 09:57:21 2022 +0000 Impute phone and sms NAs with 0 commit 3f7ec80c18b1237c49dfdd9a6736cdf518e0b7fb Author: Primoz <sisko.primoz@gmail.com> Date: Wed Aug 31 10:18:50 2022 +0000 Preparation a) phone_calls 0 imputation b) remove rows with NaN target
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files_to_compute.extend(expand("data/processed/models/individual_model/{pid}/input.csv", pid=config["PIDS"]))
for target in config["PARAMS_FOR_ANALYSIS"]["TARGET"]["ALL_LABELS"]:
files_to_compute.extend(expand("data/processed/models/population_model/input_" + target + ".csv"))
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rule all:
input:
files_to_compute
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rule clean:
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shell:
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"rm -rf data/raw/* && rm -rf data/interim/* && rm -rf data/processed/* && rm -rf reports/figures/* && rm -rf reports/*.zip && rm -rf reports/compliance/*"