diff --git a/Snakefile b/Snakefile index 538a5382..1e9a1fe8 100644 --- a/Snakefile +++ b/Snakefile @@ -410,14 +410,14 @@ for provider in config["ALL_CLEANING_INDIVIDUAL"]["PROVIDERS"].keys(): if config["ALL_CLEANING_INDIVIDUAL"]["PROVIDERS"][provider]["COMPUTE"]: if provider == "STRAW": files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features_cleaned_" + provider.lower() + "_py.csv", pid=config["PIDS"])) - else: + 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"]: if provider == "STRAW": files_to_compute.extend(expand("data/processed/features/all_participants/all_sensor_features_cleaned_" + provider.lower() +"_py.csv")) - else: + else: files_to_compute.extend(expand("data/processed/features/all_participants/all_sensor_features_cleaned_" + provider.lower() +"_R.csv")) # Baseline features @@ -429,10 +429,10 @@ if config["PARAMS_FOR_ANALYSIS"]["BASELINE"]["COMPUTE"]: # Targets (labels) if config["PARAMS_FOR_ANALYSIS"]["TARGET"]["COMPUTE"]: - # files_to_compute.extend(expand("data/processed/models/individual_model/{pid}/input.csv", pid=config["PIDS"])) - # files_to_compute.extend(expand("data/processed/models/population_model/input.csv")) - files_to_compute.extend(expand("data/processed/models/individual_model/{pid}/z_input.csv", pid=config["PIDS"])) - files_to_compute.extend(expand("data/processed/models/population_model/z_input.csv")) + files_to_compute.extend(expand("data/processed/models/individual_model/{pid}/input.csv", pid=config["PIDS"])) + files_to_compute.extend(expand("data/processed/models/population_model/input.csv")) + # files_to_compute.extend(expand("data/processed/models/individual_model/{pid}/z_input.csv", pid=config["PIDS"])) + # files_to_compute.extend(expand("data/processed/models/population_model/z_input.csv")) #files_to_compute.extend(expand("data/processed/models/individual_model/{pid}/output_{cv_method}/baselines.csv", pid=config["PIDS"], cv_method=config["PARAMS_FOR_ANALYSIS"]["CV_METHODS"])) diff --git a/config.yaml b/config.yaml index 4adddedb..3e6d43bd 100644 --- a/config.yaml +++ b/config.yaml @@ -3,7 +3,7 @@ ######################################################################################################################## # See https://www.rapids.science/latest/setup/configuration/#participant-files -PIDS: ['p01'] #['p031', 'p032', 'p033', 'p034', 'p035', 'p036', 'p037', 'p038', 'p039', 'p040', 'p042', 'p043', 'p044', 'p045', 'p046', 'p049', 'p050', 'p052', 'p053', 'p054', 'p055', 'p057', 'p058', 'p059', 'p060', 'p061', 'p062', 'p064', 'p067', 'p068', 'p069', 'p070', 'p071', 'p072', 'p073', 'p074', 'p075', 'p076', 'p077', 'p078', 'p079', 'p080', 'p081', 'p082', 'p083', 'p084', 'p085', 'p086', 'p088', 'p089', 'p090', 'p091', 'p092', 'p093', 'p106', 'p107'] +PIDS: ['p01', 'p02'] #['p031', 'p032', 'p033', 'p034', 'p035', 'p036', 'p037', 'p038', 'p039', 'p040', 'p042', 'p043', 'p044', 'p045', 'p046', 'p049', 'p050', 'p052', 'p053', 'p054', 'p055', 'p057', 'p058', 'p059', 'p060', 'p061', 'p062', 'p064', 'p067', 'p068', 'p069', 'p070', 'p071', 'p072', 'p073', 'p074', 'p075', 'p076', 'p077', 'p078', 'p079', 'p080', 'p081', 'p082', 'p083', 'p084', 'p085', 'p086', 'p088', 'p089', 'p090', 'p091', 'p092', 'p093', 'p106', 'p107'] # See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files CREATE_PARTICIPANT_FILES: @@ -70,7 +70,6 @@ PHONE_ACCELEROMETER: COMPUTE: False FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"] SRC_SCRIPT: src/features/phone_accelerometer/rapids/main.py - PANDA: COMPUTE: False VALID_SENSED_MINUTES: False diff --git a/rules/models.smk b/rules/models.smk index 3aade69a..cc9b406d 100644 --- a/rules/models.smk +++ b/rules/models.smk @@ -30,22 +30,22 @@ rule baseline_features: rule select_target: input: - cleaned_sensor_features = "data/processed/features/{pid}/z_all_sensor_features_cleaned_straw_py.csv" + cleaned_sensor_features = "data/processed/features/{pid}/all_sensor_features_cleaned_straw_py.csv" params: target_variable = config["PARAMS_FOR_ANALYSIS"]["TARGET"]["LABEL"] output: - "data/processed/models/individual_model/{pid}/z_input.csv" + "data/processed/models/individual_model/{pid}/input.csv" script: "../src/models/select_targets.py" rule merge_features_and_targets_for_population_model: input: - cleaned_sensor_features = "data/processed/features/all_participants/z_all_sensor_features_cleaned_straw_py.csv", + cleaned_sensor_features = "data/processed/features/all_participants/all_sensor_features_cleaned_straw_py.csv", demographic_features = expand("data/processed/features/{pid}/baseline_features.csv", pid=config["PIDS"]), params: target_variable=config["PARAMS_FOR_ANALYSIS"]["TARGET"]["LABEL"] output: - "data/processed/models/population_model/z_input.csv" + "data/processed/models/population_model/input.csv" script: "../src/models/merge_features_and_targets_for_population_model.py" diff --git a/src/features/all_cleaning_individual/straw/main.py b/src/features/all_cleaning_individual/straw/main.py index 55845c89..0b0259f7 100644 --- a/src/features/all_cleaning_individual/straw/main.py +++ b/src/features/all_cleaning_individual/straw/main.py @@ -116,7 +116,7 @@ def straw_cleaning(sensor_data_files, provider): plt.savefig(f'features_nans_af_knn.png', bbox_inches='tight') # VERIFY IF THERE ARE ANY NANS LEFT IN THE DATAFRAME - if features.isna.any().any(): + if features.isna().any().any(): raise ValueError sys.exit() diff --git a/src/features/phone_wifi_visible/rapids/main.R b/src/features/phone_wifi_visible/rapids/main.R index 03221d3a..a8a433fa 100644 --- a/src/features/phone_wifi_visible/rapids/main.R +++ b/src/features/phone_wifi_visible/rapids/main.R @@ -23,13 +23,6 @@ compute_wifi_feature <- function(data, feature, time_segment){ data <- data %>% filter_data_by_segment(time_segment) - print(data %>% - filter(bssid == mostuniquedevice) %>% - group_by(local_segment) %>% - summarise(!!feature := n())) - - raise - return(data %>% filter(bssid == mostuniquedevice) %>% group_by(local_segment) %>% @@ -55,6 +48,6 @@ rapids_features <- function(sensor_data_files, time_segment, provider){ feature <- compute_wifi_feature(wifi_data, feature_name, time_segment) features <- merge(features, feature, by="local_segment", all = TRUE) } - # features <- features %>% mutate_all(~replace(., is.na(.), 0)) + features <- features %>% mutate_all(~replace(., is.na(.), 0)) return(features) }