biomechzoo 0.1.1__py3-none-any.whl

biomechzoo/utils/split_trial.py

@@ -0,0 +1,23 @@
+def split_trial(data, start_event_indx, end_event_indx):
+    # todo check index problem compared to matlab start at 0 or 1
+    data_new = data.copy()
+
+    for key, value in data_new.items():
+        if key == 'zoosystem':
+            continue
+
+        # Slice the line data
+        data_new[key]['line'] = value['line'][start_event_indx:end_event_indx]
+
+        # Update events if present
+        if 'event' in value:
+            new_events = {}
+            for evt_name, evt_val in value['event'].items():
+                event_frame = evt_val[0]
+                # Check if event falls within the new window
+                if start_event_indx <= event_frame < end_event_indx:
+                    # Adjust index relative to new start
+                    new_events[evt_name] = [event_frame - start_event_indx, 0, 0]
+            data_new[key]['event'] = new_events
+
+    return data_new

biomechzoo/utils/zload.py

@@ -0,0 +1,46 @@
+from scipy.io import loadmat
+import os
+
+
+def zload(filepath):
+    if not filepath.endswith('.zoo'):
+        raise ValueError(f"{filepath} is not a .zoo file")
+
+    if not os.path.exists(filepath):
+        raise FileNotFoundError(f"File not found: {filepath}")
+
+    mat_data = loadmat(filepath, struct_as_record=False, squeeze_me=True)
+
+    # Remove default MATLAB metadata fields
+    mat_data = {k: v for k, v in mat_data.items() if not k.startswith('__')}
+
+    # Convert MATLAB structs to Python dicts (recursively)
+    def mat_struct_to_dict(obj):
+        if isinstance(obj, dict):
+            return {k: mat_struct_to_dict(v) for k, v in obj.items()}
+        elif hasattr(obj, '_fieldnames'):
+            return {field: mat_struct_to_dict(getattr(obj, field)) for field in obj._fieldnames}
+        elif isinstance(obj, list):
+            return [mat_struct_to_dict(item) for item in obj]
+        else:
+            return obj
+    data = {k: mat_struct_to_dict(v) for k, v in mat_data.items()}
+
+    if 'data' in data:
+        data = data['data']
+
+    return data
+
+
+if __name__ == '__main__':
+    """ testing: load a single zoo file from the other subfolder in data"""
+    # -------TESTING--------
+    current_dir = os.path.dirname(os.path.abspath(__file__))
+    project_root = os.path.dirname(current_dir)
+    fl = os.path.join(project_root, 'data', 'other', 'HC030A05.zoo')
+    data = zload(fl)
+
+    channels = [k for k in data.keys()]
+    print('{} channels found'.format(len(channels)))
+    for ch in channels:
+        print({ch})

biomechzoo/utils/zplot.py

@@ -0,0 +1,61 @@
+import matplotlib.pyplot as plt
+
+
+def zplot(data, ch, xlabel='frames', ylabel='angles (deg)'):
+    """
+    Plot a single channel of a zoo file, along with any existing events.
+
+    Parameters
+    ----------
+    data : dict
+        Loaded zoo file.
+    ch : str
+        Name of the channel to plot, e.g., 'RkneeAngles'.
+    xlabel : str
+        Label for x-axis. Default is 'frames'.
+    ylabel : str
+        Label for y-axis. Default is 'angles (deg)'.
+
+    Returns
+    -------
+    None
+    """
+
+    if ch not in data:
+        raise KeyError(f"Channel '{ch}' not found in data.")
+
+    y = data[ch]['line']
+    x = range(len(y))
+
+    plt.figure(figsize=(10, 4))
+    plt.plot(x, y, label='Signal', linewidth=2)
+    plt.title(ch)
+    plt.xlabel(xlabel)
+    plt.ylabel(ylabel)
+    plt.grid(True)
+
+    # Plot events if available
+    events = data[ch].get('event', {})
+    for name, coords in events.items():
+        evtx, evty = coords[0], coords[1]
+        plt.plot(evtx, evty, 'ro')
+        plt.text(evtx, evty, name, fontsize=8, color='red', ha='left', va='bottom')
+
+    plt.tight_layout()
+    plt.show()
+
+
+if __name__ == '__main__':
+    # -------TESTING--------
+    import os
+    from biomechzoo.utils.zload import zload
+
+    # get path to sample zoo file
+    current_dir = os.path.dirname(os.path.abspath(__file__))
+    project_root = os.path.dirname(current_dir)
+    fl = os.path.join(project_root, 'data', 'other', 'HC030A05.zoo')
+
+    # load  zoo file
+    data = zload(fl)
+    ch = 'SACR'
+    zplot(data, ch)

biomechzoo/utils/zsave.py

@@ -0,0 +1,50 @@
+from scipy.io import savemat
+import inspect
+import os
+
+
+def zsave(fl, data, inplace=True, out_folder=None, root_folder=None):
+    """
+    Save zoo data to .zoo file (MAT format)
+
+    Arguments:
+        fl (str): Full path to original .zoo file
+        data (dict): Zoo data to save
+        inplace (bool): Whether to overwrite original file
+        out_folder (str or None): If not inplace, output folder name (relative to root_folder or file location)
+        root_folder (str or None): Optional base directory for saving when inplace=False
+    """
+    # Get caller function name for logging
+    caller_name = inspect.stack()[1].function
+
+    # Initialize zoosystem and processing history
+    zoosystem = data.get('zoosystem', {})
+    processing = zoosystem.get('Processing', [])
+    if not isinstance(processing, list):
+        processing = [processing]
+    processing.append(caller_name)
+    zoosystem['Processing'] = processing
+    data['zoosystem'] = zoosystem
+
+    # Determine save path
+    if inplace:
+        save_path = fl
+    else:
+        filename = os.path.basename(fl)
+        if out_folder is None:
+            out_folder = 'processed'
+
+        if root_folder is None:
+            root_folder = os.path.dirname(fl)
+
+        root_path = os.path.dirname(root_folder)
+        in_folder = os.path.basename(root_folder)
+        out_dir = os.path.join(root_path, out_folder)
+        os.makedirs(out_dir, exist_ok=True)
+        fl_new = fl.replace(in_folder, out_folder)
+        save_folder = os.path.dirname(fl_new)
+        os.makedirs(save_folder, exist_ok=True)
+
+    # Save the .zoo file
+    savemat(fl_new, data)
+

biomechzoo-0.1.1.dist-info/METADATA

@@ -0,0 +1,48 @@
+Metadata-Version: 2.4
+Name: biomechzoo
+Version: 0.1.1
+Summary: Python implementation of the biomechZoo Matlab toolbox
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo
+Requires-Python: >=3.13
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: ezc3d>=1.5.19
+Requires-Dist: matplotlib>=3.10.6
+Requires-Dist: numpy>=2.3.3
+Requires-Dist: pandas>=2.3.2
+Requires-Dist: scipy>=1.16.2
+Dynamic: license-file
+
+# Repository for the Python version of biomechZoo
+This is a development version of the biomechzoo toolbox for python. To use biomechzoo
+as a packagage alongside your code, follow the "How to install" instructions below
+
+## How to install 
+- make sure the local version of your code sits at the same level as biomechzoo. 
+e.g.
+code_root/
+code_root/biomechzoo/         ← the repo with the actual package
+code_root/student_code/       ← where your scripts or notebooks live
+    
+- open terminal or command window
+- create an environment for your research project: ``conda create -n name python=3.13 -c conda-forge``, where name is of your choice
+- activate your new environment: ``conda activate name``
+- navigate to parent directory where biomechzoo was cloned. e.g. ``code_root``
+- install biomechzoo: ``pip install -e biomechzoo``
+- install additional requirements: ``pip install -r biomechzoo/pip_requirements.txt``
+
+## Updates (not tested)
+- If updates are made to biomechzoo, simply pull the latest version 
+  from github, you won't need to reinstall (unless there are new dependencies)
+
+## Usage notes
+- To use biomechzoo in your project, you will need to import biomechzoo as: 
+``from biomechzoo.biomechzoo import BiomechZoo``
+- Then, you can create an object that is an instance of the BimechZoo class as:
+``bmech = BiomechZoo(fld)`` where ``fld`` is the path to your data
+
+
+# opencap users
+- opencap users should pre-process their data using ``https://github.com/stanfordnmbl/opencap-processing``
+- processed data could be saved to csv using pandas and then imported to biomechzoo using csv2zoo (not yet functional)

biomechzoo-0.1.1.dist-info/RECORD

@@ -0,0 +1,44 @@
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+biomechzoo/__main__.py,sha256=hSMHN1Rxn2367fSGTLHoOQ4_pocZw0IWI7HFxl-74oY,88
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+biomechzoo/biomech_ops/continuous_relative_phase_line.py,sha256=Fa1LFRuPlmGPLQLvln6HVnJy3zMSm9z5YeooHmTu0lc,1365
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+biomechzoo-0.1.1.dist-info/RECORD,,

biomechzoo-0.1.1.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

biomechzoo-0.1.1.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+biomechzoo = main:main

biomechzoo-0.1.1.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) [2025] McGill MOTION Lab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

biomechzoo-0.1.1.dist-info/top_level.txt

@@ -0,0 +1 @@
+biomechzoo