Arm swing quantification

docs/notebooks/gait/gait_analysis.ipynb

@@ -14,8 +14,11 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "from paradigma.gait.gait_analysis import extract_gait_features_io, detect_gait_io, extract_arm_activity_features_io, filter_gait_io\n",
-    "from paradigma.config import IMUConfig, GaitFeatureExtractionConfig, GaitDetectionConfig, ArmActivityFeatureExtractionConfig, FilteringGaitConfig\n",
+    "\n",
+    "from paradigma.config import IMUConfig, GaitFeatureExtractionConfig, GaitDetectionConfig, \\\n",
+    "    ArmActivityFeatureExtractionConfig, FilteringGaitConfig, ArmSwingQuantificationConfig\n",
+    "from paradigma.gait.gait_analysis import extract_gait_features_io, detect_gait_io, \\\n",
+    "    extract_arm_activity_features_io, filter_gait_io, quantify_arm_swing_io\n",
     "from paradigma.preprocessing import preprocess_imu_data_io"
    ]
   },
@@ -32,8 +35,21 @@
     "branch = 'gait'\n",
     "sensor = 'imu'\n",
     "\n",
+    "gait_detection_classifier_filename = 'gait_detection_classifier.pkl'\n",
+    "gait_detection_scaler_filename = 'gait_detection_scaler_params.json'\n",
+    "gait_detection_threshold_filename = 'gait_detection_threshold.txt'\n",
+    "\n",
+    "gait_filtering_classifier_filename = 'gait_filtering_classifier.pkl'\n",
+    "gait_filtering_scaler_filename = 'gait_filtering_scaler_params.json'\n",
+    "gait_filtering_threshold_filename = 'gait_filtering_threshold.txt'\n",
+    "\n",
     "path_to_data =  '../../../tests/data'\n",
-    "path_to_classifiers = os.path.join(path_to_data, '0.classification', branch)\n",
+    "\n",
+    "path_to_classifier_input = os.path.join(path_to_data, '0.classification', branch)\n",
+    "path_to_classifiers = os.path.join(path_to_classifier_input, 'classifiers')\n",
+    "path_to_scalers = os.path.join(path_to_classifier_input, 'scalers')\n",
+    "path_to_thresholds = os.path.join(path_to_classifier_input, 'thresholds')\n",
+    "\n",
     "path_to_sensor_data = os.path.join(path_to_data, '1.prepared_data', sensor)\n",
     "path_to_preprocessed_data = os.path.join(path_to_data, '2.preprocessed_data', sensor)\n",
     "path_to_extracted_features = os.path.join(path_to_data, '3.extracted_features', branch)\n",
@@ -57,7 +73,13 @@
    "outputs": [],
    "source": [
     "config = IMUConfig()\n",
-    "preprocess_imu_data_io(path_to_sensor_data, path_to_preprocessed_data, config, sensor='both')"
+    "\n",
+    "preprocess_imu_data_io(\n",
+    "    input_path=path_to_sensor_data, \n",
+    "    output_path=path_to_preprocessed_data, \n",
+    "    config=config, \n",
+    "    sensor='both'\n",
+    ")"
    ]
   },
   {
@@ -74,7 +96,12 @@
    "outputs": [],
    "source": [
     "config = GaitFeatureExtractionConfig()\n",
-    "extract_gait_features_io(path_to_preprocessed_data, path_to_extracted_features, config)"
+    "\n",
+    "extract_gait_features_io(\n",
+    "        config=config,\n",
+    "        path_to_preprocessed_input=path_to_preprocessed_data, \n",
+    "        path_to_output=path_to_extracted_features, \n",
+    "    )"
    ]
   },
   {
@@ -91,7 +118,17 @@
    "outputs": [],
    "source": [
     "config = GaitDetectionConfig()\n",
-    "detect_gait_io(path_to_extracted_features, path_to_predictions, path_to_classifiers, config)"
+    "\n",
+    "full_path_to_classifier = os.path.join(path_to_classifiers, gait_detection_classifier_filename)\n",
+    "full_path_to_scaler = os.path.join(path_to_scalers, gait_detection_scaler_filename)\n",
+    "\n",
+    "detect_gait_io(\n",
+    "    config=config, \n",
+    "    path_to_input_features=path_to_extracted_features, \n",
+    "    path_to_output=path_to_predictions, \n",
+    "    full_path_to_classifier=full_path_to_classifier, \n",
+    "    full_path_to_scaler=full_path_to_scaler\n",
+    ")"
    ]
   },
   {
@@ -108,7 +145,15 @@
    "outputs": [],
    "source": [
     "config = ArmActivityFeatureExtractionConfig()\n",
-    "extract_arm_activity_features_io(path_to_preprocessed_data, path_to_predictions, path_to_classifiers, path_to_extracted_features, config)"
+    "full_path_to_threshold = os.path.join(path_to_thresholds, gait_detection_threshold_filename)\n",
+    "\n",
+    "extract_arm_activity_features_io(\n",
+    "        config=config,\n",
+    "        path_to_timestamp_input=path_to_preprocessed_data, \n",
+    "        path_to_prediction_input=path_to_predictions, \n",
+    "        full_path_to_threshold=full_path_to_threshold, \n",
+    "        path_to_output=path_to_extracted_features\n",
+    "    )"
    ]
   },
   {
@@ -125,7 +170,16 @@
    "outputs": [],
    "source": [
     "config = FilteringGaitConfig()\n",
-    "filter_gait_io(path_to_extracted_features, path_to_classifiers, path_to_predictions, config)"
+    "full_path_to_classifier = os.path.join(path_to_classifiers, gait_filtering_classifier_filename)\n",
+    "full_path_to_scaler = os.path.join(path_to_scalers, gait_filtering_scaler_filename)\n",
+    "\n",
+    "filter_gait_io(\n",
+    "    config=config,\n",
+    "    path_to_feature_input=path_to_extracted_features, \n",
+    "    path_to_output=path_to_predictions,\n",
+    "    full_path_to_classifier=full_path_to_classifier, \n",
+    "    full_path_to_scaler=full_path_to_scaler\n",
+    ")"
    ]
   },
   {
@@ -141,8 +195,19 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# config = ArmSwingQuantificationConfig()\n",
-    "# quantify_arm_swing_io(path_to_extracted_features, path_to_predictions, path_to_classifiers, path_to_quantification, config)"
+    "asq_config = ArmSwingQuantificationConfig()\n",
+    "imu_config = IMUConfig()\n",
+    "\n",
+    "imu_config.set_sensor('gyroscope')\n",
+    "\n",
+    "quantify_arm_swing_io(\n",
+    "    imu_config=imu_config,\n",
+    "    asq_config=asq_config,\n",
+    "    path_to_timestamp_input=path_to_preprocessed_data, \n",
+    "    path_to_prediction_input=path_to_predictions, \n",
+    "    full_path_to_threshold=full_path_to_threshold, \n",
+    "    path_to_output=path_to_quantification, \n",
+    ")"
    ]
   }
  ],

docs/tutorials/data_preparation.ipynb

@@ -184,6 +184,11 @@
     "\n",
     "watch_side = 'right'\n",
     "\n",
+    "df_imu[DataColumns.ACCELEROMETER_Y] *= -1\n",
+    "df_imu[DataColumns.ACCELEROMETER_Z] *= -1\n",
+    "df_imu[DataColumns.GYROSCOPE_Y] *= -1\n",
+    "df_imu[DataColumns.GYROSCOPE_Z] *= -1\n",
+    "\n",
     "df_imu = invert_watch_side(df_imu, watch_side)\n",
     "df_imu.head(5)"
    ]