biomechzoo 0.4.8__tar.gz → 0.4.10__tar.gz

{biomechzoo-0.4.8/src/biomechzoo.egg-info → biomechzoo-0.4.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.4.8
+Version: 0.4.10
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo
@@ -37,6 +37,7 @@ See also http://www.github.com/mcgillmotionlab/biomechzoo or http://www.biomechz
 ### Installing a dev environment
 conda create -n biomechzoo-dev python=3.11
 conda activate biomechzoo-dev
+cd biomechzoo root folder
 pip install -e ".[dev]"
 
 ### import issues

{biomechzoo-0.4.8 → biomechzoo-0.4.10}/README.md

@@ -20,6 +20,7 @@ See also http://www.github.com/mcgillmotionlab/biomechzoo or http://www.biomechz
 ### Installing a dev environment
 conda create -n biomechzoo-dev python=3.11
 conda activate biomechzoo-dev
+cd biomechzoo root folder
 pip install -e ".[dev]"
 
 ### import issues

{biomechzoo-0.4.8 → biomechzoo-0.4.10}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "biomechzoo"
-version = "0.4.8"
+version = "0.4.10"
 description = "Python implementation of the biomechZoo toolbox"
 readme = "README.md"
 requires-python = ">=3.11,<3.12"   # max version for opencap-process tools is 3.11

{biomechzoo-0.4.8 → biomechzoo-0.4.10}/src/biomechzoo/biomechzoo.py

@@ -8,7 +8,7 @@ from biomechzoo.utils.batchdisp import batchdisp
 from biomechzoo.utils.get_split_events import get_split_events
 from biomechzoo.utils.split_trial import split_trial
 from biomechzoo.conversion.c3d2zoo_data import c3d2zoo_data
-from biomechzoo.conversion.csv2zoo_data import csv2zoo_data
+from biomechzoo.conversion.table2zoo_data import table2zoo_data
 from biomechzoo.conversion.mvnx2zoo_data import mvnx2zoo_data
 from biomechzoo.processing.removechannel_data import removechannel_data
 from biomechzoo.processing.renamechannel_data import renamechannel_data
@@ -99,36 +99,18 @@ class BiomechZoo:
         # Update self.folder after  processing
         self._update_folder(out_folder, inplace, in_folder)
 
-    def csv2zoo(self, out_folder=None, inplace=None, skip_rows=0):
+    def table2zoo(self, out_folder=None, inplace=None, skip_rows=0, extension='csv'):
         """ Converts generic .csv file in the folder to .zoo format """
         start_time = time.time()
         verbose = self.verbose
         in_folder = self.in_folder
         if inplace is None:
             inplace = self.inplace
-        fl = engine(in_folder, extension='.csv', name_contains=self.name_contains, subfolders=self.subfolders)
+        fl = engine(in_folder, extension=extension, name_contains=self.name_contains, subfolders=self.subfolders)
         for f in fl:
-            batchdisp('converting csv to zoo for {}'.format(f), level=2, verbose=verbose)
-            data = csv2zoo_data(f, type='csv', skip_rows=skip_rows)
-            f_zoo = f.replace('.csv', '.zoo')
-            zsave(f_zoo, data, inplace=inplace, out_folder=out_folder, root_folder=in_folder)
-        method_name = inspect.currentframe().f_code.co_name
-        batchdisp('{} process complete for {} file(s) in {:.2f} secs'.format(method_name, len(fl), time.time() - start_time), level=1, verbose=verbose)
-        # Update self.folder after  processing
-        self._update_folder(out_folder, inplace, in_folder)
-
-    def parquet2zoo(self, out_folder=None, inplace=None):
-        """ Converts generic .csv file in the folder to .zoo format """
-        start_time = time.time()
-        verbose = self.verbose
-        in_folder = self.in_folder
-        if inplace is None:
-            inplace = self.inplace
-        fl = engine(in_folder, extension='.parquet', name_contains=self.name_contains, subfolders=self.subfolders)
-        for f in fl:
-            batchdisp('converting parquet to zoo for {}'.format(f), level=2, verbose=verbose)
-            data = csv2zoo_data(f, type='parquet')
-            f_zoo = f.replace('.parquet', '.zoo')
+            batchdisp('converting {} to zoo for {}'.format(extension, f), level=2, verbose=verbose)
+            data = table2zoo_data(f, type=extension, skip_rows=skip_rows)
+            f_zoo = f.replace(extension, '.zoo')
             zsave(f_zoo, data, inplace=inplace, out_folder=out_folder, root_folder=in_folder)
         method_name = inspect.currentframe().f_code.co_name
         batchdisp('{} process complete for {} file(s) in {:.2f} secs'.format(method_name, len(fl), time.time() - start_time), level=1, verbose=verbose)
@@ -324,7 +306,7 @@ class BiomechZoo:
         # Update self.folder after  processing
         self._update_folder(out_folder, inplace, in_folder)
 
-    def addevent(self, ch, evt_type, evt_name, out_folder=None, inplace=None):
+    def addevent(self, ch, event_type, event_name, out_folder=None, inplace=None):
         """ adds events of type evt_type with name evt_name to channel ch """
         start_time = time.time()
         verbose = self.verbose
@@ -334,9 +316,9 @@ class BiomechZoo:
         fl = engine(in_folder, extension='.zoo', name_contains=self.name_contains, subfolders=self.subfolders)
         for f in fl:
             if verbose:
-                batchdisp('adding event {} to channel {} for {}'.format(evt_type, ch, f), level=2, verbose=verbose)
+                batchdisp('adding event {} to channel {} for {}'.format(event_type, ch, f), level=2, verbose=verbose)
             data = zload(f)
-            data = addevent_data(data, ch, evt_type, evt_name)
+            data = addevent_data(data, ch, event_type, event_name)
             zsave(f, data, inplace=inplace, out_folder=out_folder, root_folder=in_folder)
         method_name = inspect.currentframe().f_code.co_name
         batchdisp('{} process complete for {} file(s) in {:.2f} secs'.format(method_name, len(fl), time.time() - start_time), level=1, verbose=verbose)

biomechzoo-0.4.8/src/biomechzoo/conversion/csv2zoo_data.py → biomechzoo-0.4.10/src/biomechzoo/conversion/table2zoo_data.py

@@ -6,9 +6,12 @@ from biomechzoo.utils.set_zoosystem import set_zoosystem
 from biomechzoo.utils.compute_sampling_rate_from_time import compute_sampling_rate_from_time
 
 
-def csv2zoo_data(csv_path, type='csv', skip_rows=0, freq=None):
+def table2zoo_data(csv_path, type='csv', skip_rows=0, freq=None):
     # todo: check calculation for sampling rate
 
+    if type not in ['csv', 'parquet']:
+        raise NotImplementedError('Only csv and parquet currently supported')
+
     # Read header lines until 'endheader'
     metadata = {}
     if type == 'csv' and skip_rows > 0:
@@ -99,4 +102,4 @@ if __name__ == '__main__':
     project_root = os.path.dirname(current_dir)
     csv_file = os.path.join(project_root, 'data', 'other', 'opencap_walking1.csv')
 
-    data = csv2zoo_data(csv_file)
+    data = table2zoo_data(csv_file)

{biomechzoo-0.4.8 → biomechzoo-0.4.10}/src/biomechzoo/processing/addevent_data.py

@@ -37,6 +37,11 @@ def addevent_data(data, ch, ename, etype):
         elif etype == 'rom':
             eyd = float(np.max(yd) - np.min(yd))
             exd = 0  # dummy index (like MATLAB version)
+        elif etype == 'max_stance':
+            # special event for gait and running
+            exd = max_stance(yd)
+            eyd = float(yd[exd])
+            eyd = float(yd[exd])
         else:
             raise ValueError(f'Unknown event type: {etype}')
 
@@ -44,3 +49,8 @@ def addevent_data(data, ch, ename, etype):
         data[channel]['event'][ename] = [exd, eyd, 0]
 
     return data
+
+def max_stance(yd):
+    """ extracts max from first 40% of the gait cycle"""
+    raise NotImplementedError
+    return exd

{biomechzoo-0.4.8 → biomechzoo-0.4.10/src/biomechzoo.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.4.8
+Version: 0.4.10
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo
@@ -37,6 +37,7 @@ See also http://www.github.com/mcgillmotionlab/biomechzoo or http://www.biomechz
 ### Installing a dev environment
 conda create -n biomechzoo-dev python=3.11
 conda activate biomechzoo-dev
+cd biomechzoo root folder
 pip install -e ".[dev]"
 
 ### import issues

{biomechzoo-0.4.8 → biomechzoo-0.4.10}/src/biomechzoo.egg-info/SOURCES.txt

@@ -22,9 +22,9 @@ src/biomechzoo/biomech_ops/phase_angle_data.py
 src/biomechzoo/biomech_ops/phase_angle_line.py
 src/biomechzoo/conversion/__init__.py
 src/biomechzoo/conversion/c3d2zoo_data.py
-src/biomechzoo/conversion/csv2zoo_data.py
 src/biomechzoo/conversion/mvnx2zoo_data.py
 src/biomechzoo/conversion/opencap2zoo_data.py
+src/biomechzoo/conversion/table2zoo_data.py
 src/biomechzoo/mvn/__init__.py
 src/biomechzoo/mvn/load_mvnx.py
 src/biomechzoo/mvn/main_mvnx.py