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Merge pull request #64 from biomarkersParkinson/gait_paper
Gait paper
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| @@ -1,173 +1,175 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# Gait analysis" | ||
| ] | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# Gait analysis" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# Automatically reload modules\n", | ||
| "%load_ext autoreload\n", | ||
| "%autoreload 2\n", | ||
| "\n", | ||
| "import os\n", | ||
| "from paradigma.preprocessing_config import IMUPreprocessingConfig\n", | ||
| "from paradigma.gait.gait_analysis import extract_gait_features_io, detect_gait_io, extract_arm_swing_features_io, detect_arm_swing_io, quantify_arm_swing_io\n", | ||
| "from paradigma.gait.gait_analysis_config import GaitFeatureExtractionConfig, GaitDetectionConfig, ArmSwingFeatureExtractionConfig, ArmSwingDetectionConfig, ArmSwingQuantificationConfig\n", | ||
| "from paradigma.imu_preprocessing import preprocess_imu_data_io" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 13, | ||
| "metadata": { | ||
| "tags": [ | ||
| "parameters" | ||
| ] | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "branch = 'gait'\n", | ||
| "sensor = 'imu'\n", | ||
| "\n", | ||
| "path_to_data = '../../../tests/data'\n", | ||
| "path_to_classifier = os.path.join(path_to_data, '0.classifiers', branch)\n", | ||
| "path_to_sensor_data = os.path.join(path_to_data, '1.sensor_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", | ||
| "\n", | ||
| "# Cell has the tag 'parameters', so it won't overwrite the parameters when running the notebook in tests" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Preprocessing" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 14, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "config = IMUPreprocessingConfig()\n", | ||
| "preprocess_imu_data_io(path_to_sensor_data, path_to_preprocessed_data, config)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Extract gait features" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 15, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "config = GaitFeatureExtractionConfig()\n", | ||
| "extract_gait_features_io(path_to_preprocessed_data, path_to_extracted_features, config)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Detect gait" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 16, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "config = GaitDetectionConfig()\n", | ||
| "detect_gait_io(path_to_extracted_features, path_to_predictions, path_to_classifier, config)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Extract arm swing features" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 17, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "config = ArmSwingFeatureExtractionConfig()\n", | ||
| "extract_arm_swing_features_io(path_to_preprocessed_data, path_to_extracted_features, config)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Detect arm swing" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 18, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "config = ArmSwingDetectionConfig()\n", | ||
| "detect_arm_swing_io(path_to_extracted_features, path_to_predictions, path_to_classifier, config)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Quantify arm swing" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 19, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "config = ArmSwingQuantificationConfig()\n", | ||
| "quantify_arm_swing_io(path_to_extracted_features, path_to_predictions, path_to_quantification, config)" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "paradigma-Fn6RLG4_-py3.11", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.11.5" | ||
| } | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# Automatically reload modules\n", | ||
| "%load_ext autoreload\n", | ||
| "%autoreload 2\n", | ||
| "\n", | ||
| "import os\n", | ||
| "from paradigma.preprocessing_config import IMUPreprocessingConfig\n", | ||
| "from paradigma.gait.gait_analysis import extract_gait_features_io, detect_gait_io, extract_arm_swing_features_io, detect_arm_swing_io, quantify_arm_swing_io\n", | ||
| "from paradigma.gait.gait_analysis_config import GaitFeatureExtractionConfig, GaitDetectionConfig, ArmSwingFeatureExtractionConfig, ArmSwingDetectionConfig, ArmSwingQuantificationConfig\n", | ||
| "from paradigma.imu_preprocessing import preprocess_imu_data_io" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 5, | ||
| "metadata": { | ||
| "tags": [ | ||
| "parameters" | ||
| ] | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "path_to_data = '../../../tests/data'\n", | ||
| "path_to_classifier = os.path.join(path_to_data, '0.classifiers', 'gait')\n", | ||
| "path_to_sensor_data = os.path.join(path_to_data, '1.sensor_data', 'imu')\n", | ||
| "path_to_preprocessed_data = os.path.join(path_to_data, '2.preprocessed_data', 'gait')\n", | ||
| "path_to_extracted_features = os.path.join(path_to_data, '3.extracted_features', 'gait')\n", | ||
| "path_to_predictions = os.path.join(path_to_data, '4.predictions', 'gait')\n", | ||
| "path_to_quantification = os.path.join(path_to_data, '5.quantification', 'gait')\n", | ||
| "\n", | ||
| "# Cell has the tag 'parameters', so it won't overwrite the parameters when running the notebook in tests" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Preprocessing" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 6, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "config = IMUPreprocessingConfig()\n", | ||
| "preprocess_imu_data_io(path_to_sensor_data, path_to_preprocessed_data, config)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Extract gait features" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 8, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "config = GaitFeatureExtractionConfig()\n", | ||
| "#config.set_sampling_frequency(50)\n", | ||
| "extract_gait_features_io(path_to_preprocessed_data, path_to_extracted_features, config)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Detect gait" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 11, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "config = GaitDetectionConfig()\n", | ||
| "detect_gait_io(path_to_extracted_features, path_to_predictions, path_to_classifier, config)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Extract arm swing features" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 13, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "config = ArmSwingFeatureExtractionConfig()\n", | ||
| "extract_arm_swing_features_io(path_to_preprocessed_data, path_to_extracted_features, config)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Detect arm swing" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 14, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "config = ArmSwingDetectionConfig()\n", | ||
| "detect_arm_swing_io(path_to_extracted_features, path_to_predictions, path_to_classifier, config)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Quantify arm swing" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 16, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "config = ArmSwingQuantificationConfig()\n", | ||
| "quantify_arm_swing_io(path_to_extracted_features, path_to_predictions, path_to_quantification, config)" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "paradigma-8ps1bg0Z-py3.12", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.12.6" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 2 | ||
| "nbformat": 4, | ||
| "nbformat_minor": 2 | ||
| } |
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