Merge pull request #94 from biomarkersParkinson/arm-swing-quantification

Arm swing quantification
biomarkersParkinson · Jan 9, 2025 · 6137c24 · 6137c24
2 parents e11a17f + 2e34ec7
commit 6137c24
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diff --git a/docs/notebooks/gait/gait_analysis.ipynb b/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, aggregate_quantification_dict_io\n",
     "from paradigma.preprocessing import preprocess_imu_data_io"
    ]
   },
@@ -32,13 +35,30 @@
     "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",
     "path_to_predictions = os.path.join(path_to_data, '4.predictions', branch)\n",
     "path_to_quantification = os.path.join(path_to_data, '5.quantification', branch)\n",
+    "path_to_aggregation = os.path.join(path_to_data, '6.aggregation', branch)\n",
+    "\n",
+    "quantification_filename = 'arm_swing_quantification.json'\n",
+    "aggregation_filename = 'arm_swing_aggregates.json'\n",
     "\n",
     "# Cell has the tag 'parameters', so it won't overwrite the parameters when running the notebook in tests"
    ]
@@ -57,7 +77,13 @@
    "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",
+    "    path_to_input=path_to_sensor_data, \n",
+    "    path_to_output=path_to_preprocessed_data, \n",
+    "    config=config, \n",
+    "    sensor='both'\n",
+    ")"
    ]
   },
   {
@@ -74,7 +100,12 @@
    "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_input=path_to_preprocessed_data, \n",
+    "        path_to_output=path_to_extracted_features, \n",
+    "    )"
    ]
   },
   {
@@ -91,7 +122,17 @@
    "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=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 +149,15 @@
    "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",
+    "        path_to_output=path_to_extracted_features,\n",
+    "        full_path_to_threshold=full_path_to_threshold\n",
+    "    )"
    ]
   },
   {
@@ -125,7 +174,16 @@
    "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_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 +199,44 @@
    "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",
+    "full_path_to_output = os.path.join(path_to_quantification, quantification_filename)\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_output=full_path_to_output, \n",
+    "    full_path_to_threshold=full_path_to_threshold, \n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Aggregate quantification"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "full_path_to_input = os.path.join(path_to_quantification, quantification_filename)\n",
+    "full_path_to_output = os.path.join(path_to_aggregation, aggregation_filename)\n",
+    "\n",
+    "aggregate_quantification_dict_io(\n",
+    "    full_path_to_input=full_path_to_input,\n",
+    "    full_path_to_output=full_path_to_output,\n",
+    "    aggregates=['median', '95p']\n",
+    ")"
    ]
   }
  ],

diff --git a/docs/notebooks/ppg/ppg_analysis.ipynb b/docs/notebooks/ppg/ppg_analysis.ipynb
@@ -117,7 +117,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "paradigma-8ps1bg0Z-py3.12",
+   "display_name": "paradigma-Fn6RLG4_-py3.11",
    "language": "python",
    "name": "python3"
   },
@@ -131,7 +131,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.6"
+   "version": "3.11.5"
   }
  },
  "nbformat": 4,

diff --git a/docs/tutorials/data_preparation.ipynb b/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)"
    ]