biomechzoo 0.4.8__py3-none-any.whl → 0.4.10__py3-none-any.whl

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/conversion/{csv2zoo_data.py → 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/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.dist-info → biomechzoo-0.4.10.dist-info}/METADATA

@@ -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.dist-info → biomechzoo-0.4.10.dist-info}/RECORD

@@ -1,7 +1,7 @@
 __init__.py,sha256=Uy3ykqw4l_lZKiUWSUFPRZpkZajYUfZLBaQLVhKzxdI,772
 biomechzoo/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biomechzoo/__main__.py,sha256=hSMHN1Rxn2367fSGTLHoOQ4_pocZw0IWI7HFxl-74oY,88
-biomechzoo/biomechzoo.py,sha256=6YpqhUaMH76d9zjNAsnOvyU5zppbCMD1t72FIzA8VyI,20782
+biomechzoo/biomechzoo.py,sha256=A60kTUaMVWaKl-4ZUZpW8pOKLiZLEpbPYvHZe6urd5w,19800
 biomechzoo/biomech_ops/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biomechzoo/biomech_ops/continuous_relative_phase_data.py,sha256=RePbt6zyOI1iv74CWhxSrunIokTFYVfFmFnoW51781E,1300
 biomechzoo/biomech_ops/continuous_relative_phase_line.py,sha256=Fa1LFRuPlmGPLQLvln6HVnJy3zMSm9z5YeooHmTu0lc,1365
@@ -13,9 +13,9 @@ biomechzoo/biomech_ops/phase_angle_data.py,sha256=_ekUBW2v3iC4UawcDL38ZZLYJmQsAm
 biomechzoo/biomech_ops/phase_angle_line.py,sha256=p6osB17_3QQSyKLNojuc6nYhv-k0K6EUUH75EXu8ifc,1391
 biomechzoo/conversion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biomechzoo/conversion/c3d2zoo_data.py,sha256=gnSCw99Hg5JLdrGezZNVZ6EHqiD6i-mpsLRtWmEa-Mg,2855
-biomechzoo/conversion/csv2zoo_data.py,sha256=9FjlJjCSdT9d5n10Kc74hq5sXBmUdRA8CSIMWlPAk4o,3175
 biomechzoo/conversion/mvnx2zoo_data.py,sha256=O6WuKe_5fZJfd1gUe3oP9rND_i5P4WGEuu2MDvI3ypY,3560
 biomechzoo/conversion/opencap2zoo_data.py,sha256=n4bLsrJI0wTSzG5bgJcmxj1dp2plnUKFNRzcTIbmV1o,608
+biomechzoo/conversion/table2zoo_data.py,sha256=OLiRlYB8GqOwv4MAlmwhIkGLxgAvmrgUjTb-Irev4lU,3297
 biomechzoo/mvn/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biomechzoo/mvn/load_mvnx.py,sha256=B4VGuidQ-5G_5E1t5vpU51Nb_Lu85_EOS_FmGZYjfX8,22499
 biomechzoo/mvn/main_mvnx.py,sha256=e1LasJQ9icyzjWnRCEcAWQq_-L13-mIzf7PzYA3QYDg,2394
@@ -24,7 +24,7 @@ biomechzoo/mvn/mvnx_file_accessor.py,sha256=Gk2vKq9v_gPbnOS_12zgeJehjFz7v3ClTnN2
 biomechzoo/processing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biomechzoo/processing/add_channel_data.py,sha256=U1xLLBSnyJeeDWzgmHSxOz1hyguzuuDXxQCQ8IFoZkw,1955
 biomechzoo/processing/addchannel_data.py,sha256=rmnnlMRVkoMlQCR-nRg1jjh-hzMDt37Sx9fAmocrpqA,1953
-biomechzoo/processing/addevent_data.py,sha256=DyTfvjOWZIlsWfnT6XDwvsU1jOzSDf4HhLa1TaKIhwI,1325
+biomechzoo/processing/addevent_data.py,sha256=L9xaoP0yBvaGbseotxpGCVqjr-eSV-gpnQaeRTz4VKE,1631
 biomechzoo/processing/explodechannel_data.py,sha256=AC2BOEw1tXcgJ1WuYWSE-yToS-q9XGdgkOHS4D3iUFo,1490
 biomechzoo/processing/partition_data.py,sha256=XF8dSqvHGpqsT-Q4i6qpoOajAT4LYjP-PJ6KbpoCfFc,2018
 biomechzoo/processing/removechannel_data.py,sha256=ndZcbWJRDvd7drlahGaq8MseT-rsxiu7pgdMtA1cTlo,1218
@@ -43,9 +43,9 @@ biomechzoo/utils/version.py,sha256=JIXDUuOcaJiZv9ruMP6PtWvJBh4sP0D5kAvlqPiZK_I,1
 biomechzoo/utils/zload.py,sha256=FPT6_-gwaOOqOckjgPRfnKEVKMsmNVIcenmQZF2KOvo,1535
 biomechzoo/utils/zplot.py,sha256=WVA8aCy1Pqy_bo_HXab9AmW-cBd8J8MPX2LAOd6dznU,1512
 biomechzoo/utils/zsave.py,sha256=wnRNuDxQc8bwCji4UrfoGjYrSZmka4eaDxQ5rMa78pE,1759
-biomechzoo-0.4.8.dist-info/licenses/LICENSE,sha256=Fsz62nrgRORre3A1wNXUDISaHoostodMvocRPDdXc9w,1076
-biomechzoo-0.4.8.dist-info/METADATA,sha256=WllGPwbLIbr26wyfwv8ZYz_VjlCa9jskutlRuhMFV_A,1553
-biomechzoo-0.4.8.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-biomechzoo-0.4.8.dist-info/entry_points.txt,sha256=VdryUUiwwvx0WZxrgmMrsyfe5Z1jtyaxdXOi0zWHOqk,41
-biomechzoo-0.4.8.dist-info/top_level.txt,sha256=nJEtuEZ9UPoN3EOR-BJ6myevEu7B5quWsWhaM_YeQpw,20
-biomechzoo-0.4.8.dist-info/RECORD,,
+biomechzoo-0.4.10.dist-info/licenses/LICENSE,sha256=Fsz62nrgRORre3A1wNXUDISaHoostodMvocRPDdXc9w,1076
+biomechzoo-0.4.10.dist-info/METADATA,sha256=P1enuQWmGLcQUQ5Q_6jy1e8o641FncZId2M5wUs1P9Y,1580
+biomechzoo-0.4.10.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+biomechzoo-0.4.10.dist-info/entry_points.txt,sha256=VdryUUiwwvx0WZxrgmMrsyfe5Z1jtyaxdXOi0zWHOqk,41
+biomechzoo-0.4.10.dist-info/top_level.txt,sha256=nJEtuEZ9UPoN3EOR-BJ6myevEu7B5quWsWhaM_YeQpw,20
+biomechzoo-0.4.10.dist-info/RECORD,,