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.. _examples-index:

========
Examples
========


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Full pipelines
==============
Gait analysis examples from raw data to final parameters.



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    <div class="sphx-glr-thumbcontainer" tooltip="This pipeline showcases the current gait analysis pipeline used by the MaD-Lab with all require...">

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  .. image:: /auto_examples/full_pipelines/images/thumb/sphx_glr_mad_gait_pipeline_thumb.png
    :alt: MaD DiGait Pipeline

  :ref:`sphx_glr_auto_examples_full_pipelines_mad_gait_pipeline.py`

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      <div class="sphx-glr-thumbnail-title">MaD DiGait Pipeline</div>
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Preprocessing
=============
Examples that demonstrate the recommended preprocessing steps for typical gait analysis tasks.



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    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates the preprocessing pipeline, to make sure that coordinate system conven...">

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  .. image:: /auto_examples/preprocessing/images/thumb/sphx_glr_manual_sensor_alignment_thumb.png
    :alt: Manual Sensor Alignment

  :ref:`sphx_glr_auto_examples_preprocessing_manual_sensor_alignment.py`

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      <div class="sphx-glr-thumbnail-title">Manual Sensor Alignment</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates a minimal version of an automatic sensor alignment pipeline, to make s...">

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  .. image:: /auto_examples/preprocessing/images/thumb/sphx_glr_automatic_sensor_alignment_compact_thumb.png
    :alt: Automatic sensor alignment

  :ref:`sphx_glr_auto_examples_preprocessing_automatic_sensor_alignment_compact.py`

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      <div class="sphx-glr-thumbnail-title">Automatic sensor alignment</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates all individual steps of an automatic sensor alignment pipeline, to mak...">

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  .. image:: /auto_examples/preprocessing/images/thumb/sphx_glr_automatic_sensor_alignment_details_thumb.png
    :alt: Automatic sensor alignment (detailed)

  :ref:`sphx_glr_auto_examples_preprocessing_automatic_sensor_alignment_details.py`

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      <div class="sphx-glr-thumbnail-title">Automatic sensor alignment (detailed)</div>
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Gait Detection
===============
Demonstrations of gait detection algorithms.



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    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates how the gait sequence detection by the UllrichGaitSequenceDetection ca...">

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  .. image:: /auto_examples/gait_detection/images/thumb/sphx_glr_ullrich_gait_sequence_detection_thumb.png
    :alt: Ullrich gait sequence detection

  :ref:`sphx_glr_auto_examples_gait_detection_ullrich_gait_sequence_detection.py`

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      <div class="sphx-glr-thumbnail-title">Ullrich gait sequence detection</div>
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Stride Segmentation
===================
Demonstrations of stride segmentation algorithms.



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    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates how subsequent DTW implemented by the BarthDtw can be used to detect s...">

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  .. image:: /auto_examples/stride_segmentation/images/thumb/sphx_glr_barth_dtw_stride_segmentation_thumb.png
    :alt: BarthDtw stride segmentation

  :ref:`sphx_glr_auto_examples_stride_segmentation_barth_dtw_stride_segmentation.py`

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      <div class="sphx-glr-thumbnail-title">BarthDtw stride segmentation</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates how subsequent DTW with local warping constraints can be more effectiv...">

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  .. image:: /auto_examples/stride_segmentation/images/thumb/sphx_glr_constrained_barth_dtw_stride_segmentation_thumb.png
    :alt: Constrained BarthDtw stride segmentation

  :ref:`sphx_glr_auto_examples_stride_segmentation_constrained_barth_dtw_stride_segmentation.py`

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      <div class="sphx-glr-thumbnail-title">Constrained BarthDtw stride segmentation</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="In long datasets it might be desirable to predefine regions of interest in which strides should...">

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  .. image:: /auto_examples/stride_segmentation/images/thumb/sphx_glr_barth_dtw_stride_segmentation_roi_thumb.png
    :alt: Stride segmentation with Regions of Interest

  :ref:`sphx_glr_auto_examples_stride_segmentation_barth_dtw_stride_segmentation_roi.py`

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      <div class="sphx-glr-thumbnail-title">Stride segmentation with Regions of Interest</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates how a Hidden Markov Model (HMM) implemented by the HmmStrideSegmentati...">

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  .. image:: /auto_examples/stride_segmentation/images/thumb/sphx_glr_roth_hmm_stride_segmentation_thumb.png
    :alt: HMM stride segmentation - Prediction with pre-trained model

  :ref:`sphx_glr_auto_examples_stride_segmentation_roth_hmm_stride_segmentation.py`

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      <div class="sphx-glr-thumbnail-title">HMM stride segmentation - Prediction with pre-trained model</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates how a Hidden Markov Model (HMM) implemented by the RothSegmentationHmm...">

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  .. image:: /auto_examples/stride_segmentation/images/thumb/sphx_glr_segmentation_hmm_training_thumb.png
    :alt: SegmentationModel Training

  :ref:`sphx_glr_auto_examples_stride_segmentation_segmentation_hmm_training.py`

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      <div class="sphx-glr-thumbnail-title">SegmentationModel Training</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates how to use BarthDtw with your own template extracted from the data. Fo...">

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  .. image:: /auto_examples/stride_segmentation/images/thumb/sphx_glr_barth_dtw_custom_template_thumb.png
    :alt: BarthDtw stride segmentation with Custom Template

  :ref:`sphx_glr_auto_examples_stride_segmentation_barth_dtw_custom_template.py`

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      <div class="sphx-glr-thumbnail-title">BarthDtw stride segmentation with Custom Template</div>
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Event Detection
===============
Demonstrations of event detection algorithms.



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    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates how the gait event detection by the HerzerEventDetection can be used t...">

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  .. image:: /auto_examples/event_detection/images/thumb/sphx_glr_herzer_event_detection_thumb.png
    :alt: Herzer event detection

  :ref:`sphx_glr_auto_examples_event_detection_herzer_event_detection.py`

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      <div class="sphx-glr-thumbnail-title">Herzer event detection</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates how the gait event detection by the RamppEventDetection or FilteredRam...">

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  .. image:: /auto_examples/event_detection/images/thumb/sphx_glr_rampp_event_detection_thumb.png
    :alt: Rampp event detection

  :ref:`sphx_glr_auto_examples_event_detection_rampp_event_detection.py`

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      <div class="sphx-glr-thumbnail-title">Rampp event detection</div>
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Trajectory Reconstruction
=========================
Demonstrations of trajectory reconstruction algorithms.



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    <div class="sphx-glr-thumbcontainer" tooltip="Gaitmap has two ways to reconstruct the trajectory (orientation and position) of an IMU. The fi...">

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  .. image:: /auto_examples/trajectory_reconstruction/images/thumb/sphx_glr_trajectory_reconstruction_thumb.png
    :alt: Stride Level Trajectory reconstruction

  :ref:`sphx_glr_auto_examples_trajectory_reconstruction_trajectory_reconstruction.py`

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      <div class="sphx-glr-thumbnail-title">Stride Level Trajectory reconstruction</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="While most algorithms in gaitmap are designed to only work with accelerometer and gyroscope dat...">

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  .. image:: /auto_examples/trajectory_reconstruction/images/thumb/sphx_glr_with_magnetometer_thumb.png
    :alt: Region Level Trajectory with Magnetometer

  :ref:`sphx_glr_auto_examples_trajectory_reconstruction_with_magnetometer.py`

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      <div class="sphx-glr-thumbnail-title">Region Level Trajectory with Magnetometer</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to calculate a IMU/foot trajectory_full over an entire gait sequence usi...">

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  .. image:: /auto_examples/trajectory_reconstruction/images/thumb/sphx_glr_trajectory_reconstruction_region_thumb.png
    :alt: Region Level Trajectory reconstruction

  :ref:`sphx_glr_auto_examples_trajectory_reconstruction_trajectory_reconstruction_region.py`

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      <div class="sphx-glr-thumbnail-title">Region Level Trajectory reconstruction</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="The estimation of the trajectory using the Kalman filter is heavily dependend on the ZUPT detec...">

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  .. image:: /auto_examples/trajectory_reconstruction/images/thumb/sphx_glr_zupt_dependency_thumb.png
    :alt: ZUPT Dependency of the Trajectory Estimation

  :ref:`sphx_glr_auto_examples_trajectory_reconstruction_zupt_dependency.py`

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      <div class="sphx-glr-thumbnail-title">ZUPT Dependency of the Trajectory Estimation</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="The RTS Kalman Filter is a powerful tool to estimate the trajectory of a sensor. However, it ha...">

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  .. image:: /auto_examples/trajectory_reconstruction/images/thumb/sphx_glr_advanced_kalman_filter_usage_thumb.png
    :alt: Advanced Kalman Filter Usage

  :ref:`sphx_glr_auto_examples_trajectory_reconstruction_advanced_kalman_filter_usage.py`

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      <div class="sphx-glr-thumbnail-title">Advanced Kalman Filter Usage</div>
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Parameter Calculations
======================
How to calculate spatial-temporal parameters from calculated events and trajectories.



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    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates how temporal parameters can be calculated for each stride  by the Temp...">

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  .. image:: /auto_examples/parameters/images/thumb/sphx_glr_temporal_parameters_thumb.png
    :alt: Temporal parameters calculation

  :ref:`sphx_glr_auto_examples_parameters_temporal_parameters.py`

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      <div class="sphx-glr-thumbnail-title">Temporal parameters calculation</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates illustrates how spatial parameters can be calculated for each stride  ...">

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  .. image:: /auto_examples/parameters/images/thumb/sphx_glr_spatial_parameters_thumb.png
    :alt: Spatial parameters calculation

  :ref:`sphx_glr_auto_examples_parameters_spatial_parameters.py`

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      <div class="sphx-glr-thumbnail-title">Spatial parameters calculation</div>
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Datasets and Pipelines
======================
Examples that show how to to use `tpcp` datasets and pipelines together with gaitmap.
These are basically the same examples you will find in the tpcp documentation, but adapted to work with gaitmap.


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    <div class="sphx-glr-thumbcontainer" tooltip="Grid Search optimal Algorithm Parameter">

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  .. image:: /auto_examples/datasets_and_pipelines/images/thumb/sphx_glr_gridsearch_thumb.png
    :alt: Grid Search optimal Algorithm Parameter

  :ref:`sphx_glr_auto_examples_datasets_and_pipelines_gridsearch.py`

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      <div class="sphx-glr-thumbnail-title">Grid Search optimal Algorithm Parameter</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Some gait analysis algorithms can actively be &quot;trained&quot; to improve their performance or adapt i...">

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  .. image:: /auto_examples/datasets_and_pipelines/images/thumb/sphx_glr_optimizable_pipelines_thumb.png
    :alt: Optimizable Pipelines

  :ref:`sphx_glr_auto_examples_datasets_and_pipelines_optimizable_pipelines.py`

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      <div class="sphx-glr-thumbnail-title">Optimizable Pipelines</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Whenever using some sort of trainable algorithm it is important to clearly separate the trainin...">

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  .. image:: /auto_examples/datasets_and_pipelines/images/thumb/sphx_glr_cross_validation_thumb.png
    :alt: Cross Validation

  :ref:`sphx_glr_auto_examples_datasets_and_pipelines_cross_validation.py`

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      <div class="sphx-glr-thumbnail-title">Cross Validation</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Gaitmap has the concept of Dataset. Datasets represent a set of recordings that should all be p...">

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  .. image:: /auto_examples/datasets_and_pipelines/images/thumb/sphx_glr_custom_dataset_thumb.png
    :alt: Custom Dataset

  :ref:`sphx_glr_auto_examples_datasets_and_pipelines_custom_dataset.py`

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      <div class="sphx-glr-thumbnail-title">Custom Dataset</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="When trying to optimize parameters for algorithms that have trainable components, it is require...">

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  .. image:: /auto_examples/datasets_and_pipelines/images/thumb/sphx_glr_gridsearch_cv_thumb.png
    :alt: GridSearchCV

  :ref:`sphx_glr_auto_examples_datasets_and_pipelines_gridsearch_cv.py`

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      <div class="sphx-glr-thumbnail-title">GridSearchCV</div>
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Advanced Features
=================
These examples cover some of the low-level functionality of gaitmap that can be helpfull for for more advanced tasks
and performance optimization.



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    <div class="sphx-glr-thumbcontainer" tooltip="When working on large datasets, it can dramatically speed up calculations if multiple processin...">

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  .. image:: /auto_examples/advanced_features/images/thumb/sphx_glr_multi_process_thumb.png
    :alt: Running multiple pipelines in parallel

  :ref:`sphx_glr_auto_examples_advanced_features_multi_process.py`

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      <div class="sphx-glr-thumbnail-title">Running multiple pipelines in parallel</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to save algorithms including their configuration to json and load...">

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  .. image:: /auto_examples/advanced_features/images/thumb/sphx_glr_algo_serialize_thumb.png
    :alt: Export Algorithms to JSON

  :ref:`sphx_glr_auto_examples_advanced_features_algo_serialize.py`

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      <div class="sphx-glr-thumbnail-title">Export Algorithms to JSON</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Many algorithms implemented in gaitmap have a runtime of multiple seconds on larger datasets. I...">

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  .. image:: /auto_examples/advanced_features/images/thumb/sphx_glr_caching_thumb.png
    :alt: Caching algorithm outputs

  :ref:`sphx_glr_auto_examples_advanced_features_caching.py`

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      <div class="sphx-glr-thumbnail-title">Caching algorithm outputs</div>
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Generic Algorithm
=================
Demonstrating the use of some gaitmap algorithms outside the context of gait analysis.



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    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates how subsequent DTW implemented by the BaseDtw can be used to find mult...">

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  .. image:: /auto_examples/generic_algorithms/images/thumb/sphx_glr_base_dtw_generic_thumb.png
    :alt: BaseDtw simple segmentation

  :ref:`sphx_glr_auto_examples_generic_algorithms_base_dtw_generic.py`

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      <div class="sphx-glr-thumbnail-title">BaseDtw simple segmentation</div>
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.. toctree::
   :hidden:
   :includehidden:

   /./auto_examples/full_pipelines/index.rst
   /./auto_examples/preprocessing/index.rst
   /./auto_examples/gait_detection/index.rst
   /./auto_examples/stride_segmentation/index.rst
   /./auto_examples/event_detection/index.rst
   /./auto_examples/trajectory_reconstruction/index.rst
   /./auto_examples/parameters/index.rst
   /./auto_examples/datasets_and_pipelines/index.rst
   /./auto_examples/advanced_features/index.rst
   /./auto_examples/generic_algorithms/index.rst


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      :download:`Download all examples in Python source code: auto_examples_python.zip </auto_examples/auto_examples_python.zip>`

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download all examples in Jupyter notebooks: auto_examples_jupyter.zip </auto_examples/auto_examples_jupyter.zip>`


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