Merge branch 'release'

CHANGELOG.md

@@ -1,5 +1,22 @@
 # Changelog
 
+## [1.0.1] - 2024-04-16
+
+### Added
+
+- interpolation of IMP and FRC surface parameter maps (Robert Arnold)
+
+### Changed
+
+- export point impedance and contact force data only if data is available (Robert Arnold)
+- test data set (added point force and impedance data) (Robert Arnold)
+
+### Fixed
+
+- load .pyceps with no additional meshes (Robert Arnold)
+- load .pyceps with maps without points (Robert Arnold)
+- import of point impedance and contact force data (Robert Arnold)
+
 ## [1.0.0] - 2024-04-10
 
 ### Added
@@ -79,6 +96,7 @@ _This release was yanked on PyPi due to a missing file._
 
 _Initial release._
 
+[1.0.1]: https://github.com/medunigraz/pyCEPS/releases/tag/1.0.1
 [1.0.0]: https://github.com/medunigraz/pyCEPS/releases/tag/1.0.0
 [0.1.1]: https://github.com/medunigraz/pyCEPS/releases/tag/0.1.1
 [0.1.0]: https://github.com/medunigraz/pyCEPS/releases/tag/0.1.0

pyceps/datatypes/study.py

@@ -386,6 +386,7 @@ def save(self, filepath=''):
             points = ET.SubElement(proc, 'Points',
                                    count=str(len(cmap.points))
                                    )
+            # export data from EPPoint baseclass only
             for key in list(EPPoint('dummy', parent=cmap).__dict__):
                 if key == 'parent':
                     # don't save this
@@ -573,7 +574,8 @@ def interpolate_data(self, which):
 
         Parameters:
             which : str
-                parameter to interpolate, options: ['uni', 'bip', 'act']
+                parameter to interpolate
+                options: ['uni', 'bip', 'lat', 'imp', 'frc']
 
         Raises:
             KeyError : If parameter to interpolate is unknown
@@ -609,11 +611,29 @@ def interpolate_data(self, which):
             data = np.asarray([p.bipVoltage for p in valid_points])
         elif which.lower() == 'uni':
             data = np.asarray([p.uniVoltage for p in valid_points])
+        elif which.lower() == 'imp':
+            data = np.asarray([p.impedance for p in valid_points])
+        elif which.lower() == 'frc':
+            data = np.asarray([p.force for p in valid_points])
         else:
             raise KeyError()
 
+        # check if there is data for interpolation
+        if np.isnan(data).all():
+            log.debug('found only NaN in data, cannot interpolate map {}'
+                      .format(which.upper())
+                      )
+            return
+
+        # remove data for redundant points
+        data = data[unique_ids]
+        # remove any points with NaN's before interpolation
+        mask = ~np.isnan(data)
+        data = data[mask]
+        unique_points = unique_points[mask]
+
         interpolated = inverse_distance_weighting(unique_points,
-                                                  data[unique_ids],
+                                                  data,
                                                   mesh_points,
                                                   k=7)
 
@@ -838,15 +858,17 @@ def export_point_data(self, basename='', which=None, points=None):
 
         if "IMP" in which:
             data = [point.impedance for point in points]
-            dat_file = basename + '.ptdata.IMP.pc.dat'
-            writer.dump(dat_file, data)
-            log.info('exported point data to {}'.format(dat_file))
+            if not np.isnan(data).all():
+                dat_file = basename + '.ptdata.IMP.pc.dat'
+                writer.dump(dat_file, data)
+                log.info('exported point data to {}'.format(dat_file))
 
         if "FRC" in which:
             data = [point.force for point in points]
-            dat_file = basename + '.ptdata.FRC.pc.dat'
-            writer.dump(dat_file, data)
-            log.info('exported point data to {}'.format(dat_file))
+            if not np.isnan(data).all():
+                dat_file = basename + '.ptdata.FRC.pc.dat'
+                writer.dump(dat_file, data)
+                log.info('exported point data to {}'.format(dat_file))
 
         return
 

pyceps/fileio/cartoio.py

@@ -665,7 +665,7 @@ def load(self, file: str,  repo_path: str = ''):
 
         # load additional meshes
         mesh_item = root.find('AdditionalMeshes')
-        if int(mesh_item.get('count')) > 0:
+        if mesh_item:
             _, reg_matrix = xml_load_binary_data(
                 [x for x in mesh_item.findall('DataArray')
                  if x.get('name') == 'registrationMatrix'][0]
@@ -706,24 +706,25 @@ def load(self, file: str,  repo_path: str = ''):
             points_item = proc.find('Points')
             num_points = int(points_item.get('count'))
 
-            for arr in points_item.findall('DataArray'):
-                d_name, data = xml_load_binary_data(arr)
-                p_data[d_name] = data
-            for arr in points_item.findall('Traces'):
-                d_name, data = xml_load_binary_trace(arr)
-                p_data[d_name] = data
-
-            points = []
-            for i in range(num_points):
-                new_point = CartoPoint('dummy', parent=new_map)
-                for key, value in p_data.items():
-                    if hasattr(new_point, key):
-                        setattr(new_point, key, value[i])
-                    else:
-                        log.warning('cannot set attribute "{}" for CartoPoint'
-                                    .format(key))
-                points.append(new_point)
-            new_map.points = points
+            if num_points > 0:
+                for arr in points_item.findall('DataArray'):
+                    d_name, data = xml_load_binary_data(arr)
+                    p_data[d_name] = data
+                for arr in points_item.findall('Traces'):
+                    d_name, data = xml_load_binary_trace(arr)
+                    p_data[d_name] = data
+
+                points = []
+                for i in range(num_points):
+                    new_point = CartoPoint('dummy', parent=new_map)
+                    for key, value in p_data.items():
+                        if hasattr(new_point, key):
+                            setattr(new_point, key, value[i])
+                        else:
+                            log.warning('cannot set attribute "{}" for CartoPoint'
+                                        .format(key))
+                    points.append(new_point)
+                new_map.points = points
 
             # now we can add the procedure to the study
             self.maps[name] = new_map
@@ -1193,6 +1194,8 @@ def import_map(self, egm_names_from_pos=False):
         self.interpolate_data('lat')
         self.interpolate_data('bip')
         self.interpolate_data('uni')
+        self.interpolate_data('imp')
+        self.interpolate_data('frc')
         self.bsecg = self.get_map_ecg(method=['median', 'mse', 'ccf'])
 
     def load_mesh(self):
@@ -1955,8 +1958,10 @@ class CartoPoint(EPPoint):
         forceFile : str
             name of the points contact force file
             <map_name>_<point_name>_Contact_Force.txt
-        force : PointForce
-            contact force data for this point
+        forceData : PointForce
+            full contact force data for this point
+        impedanceData : PointImpedance
+            full impedance data for this point
 
     Methods:
         is_valid()
@@ -1997,10 +2002,11 @@ def __init__(self, name,
         self.pointFile = ''
         self.barDirection = None
         self.tags = tags
-        self.ecgFile = None
+        self.ecgFile = ''
         self.uniX = np.full(3, np.nan, dtype=np.float32)
-        self.forceFile = None
+        self.forceFile = ''
         self.forceData = None
+        self.impedanceData = None
 
     def import_point(self, point_file, egm_names_from_pos=False):
         """
@@ -2058,8 +2064,12 @@ def import_point(self, point_file, egm_names_from_pos=False):
                 impedance_time[i] = x.get('Time')
                 impedance_value[i] = x.get('Value')
 
-            self.impedance = PointImpedance(time=impedance_time,
-                                            value=impedance_value)
+            self.impedanceData = PointImpedance(time=impedance_time,
+                                                value=impedance_value)
+            # update base class impedance value with the one closest to LAT
+            self.impedance = impedance_value[
+                np.nanargmin(np.abs(impedance_time - self.latAnnotation))
+            ]
 
         self.ecgFile = root.find('ECG').get('FileName')
 
@@ -2125,19 +2135,20 @@ def import_point(self, point_file, egm_names_from_pos=False):
 
         # now get the force data for this point
         log.debug('reading force file for point {}'.format(self.name))
-        self.forceFile = (self.pointFile.split('_Point_Export')[0]
-                          + '_ContactForce.txt'
-                          )
-
-        if self.parent.parent.repository.is_file(self.forceFile):
-            with self.parent.parent.repository.open(self.forceFile) as fid:
-                self.forceData = read_force_file(
-                    fid, encoding=self.parent.parent.encoding
-                )
-            # update base class force value
-            self.force = self.forceData.force
-        else:
-            log.debug('No force file found for point {}'.format(self.name))
+        try:
+            self.forceFile = root.find('ContactForce').get('FileName')
+            force_file = self.parent.parent.repository.join(self.forceFile)
+            if self.parent.parent.repository.is_file(force_file):
+                with self.parent.parent.repository.open(force_file) as fid:
+                    self.forceData = read_force_file(
+                        fid, encoding=self.parent.parent.encoding
+                    )
+                # update base class force value with the one closest to LAT
+                self.force = self.forceData.force
+            else:
+                log.debug('No force file found for point {}'.format(self.name))
+        except AttributeError:
+            log.debug('No force data saved for point {}'.format(self.name))
 
     def is_valid(self):
         """

pyceps/fileio/cartoutils.py

@@ -526,7 +526,6 @@ def read_force_file(fid, encoding='cp1252'):
                   't_lateralAngle': np.empty(0),
                   'systemTime': np.empty(0)}
 
-
     # read file version
     version = fid.readline().decode(encoding=encoding).rstrip()
     if not version.lower().endswith('contactforce.txt_2.0'):

setup.py

@@ -39,6 +39,10 @@
 AUTHOR = 'Robert Arnold'
 REQUIRES_PYTHON = '>=3.8'
 VERSION = '{{VERSION_PLACEHOLDER}}'
+PROJECT_URLS = {
+    'Github': 'https://github.com/medunigraz/pyCEPS',
+    'Changelog': 'https://github.com/medunigraz/pyCEPS/blob/main/CHANGELOG.md',
+}
 CLASSIFIERS = [
     # Trove classifiers
     # Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers
@@ -95,6 +99,7 @@
     author_email=EMAIL,
     python_requires=REQUIRES_PYTHON,
     url=URL,
+    project_urls=PROJECT_URLS,
     packages=find_packages(exclude=["tests", "*.tests", "*.tests.*", "tests.*"]),
     # If your package is a single module, use this instead of 'packages':
     # py_modules=['pyceps'],