Updating the heatmap generation unit test, minor attributes renaming.

raidionicsmaps/Computation/heatmap_computation_processor.py

@@ -97,7 +97,7 @@ def setup(self, cohort) -> None:
         self.cohort = cohort
 
         for p in list(self.cohort.patients.keys()):
-            mask_fn = self.cohort.patients[p].registered_label_filepaths
+            mask_fn = self.cohort.patients[p].registered_label_filepath
             if mask_fn is None or not os.path.exists(mask_fn):
                 logging.warning("Registered annotation mask missing for {}".format(self.cohort.patients[p].patient_id))
             else:
@@ -192,7 +192,7 @@ def __run(self, dense_parameters=None, cat_parameters=None) -> None:
                     param_value = self.cohort.extra_patients_parameters.loc[self.cohort.extra_patients_parameters['Patient'] == pid][cat_parameters[0]].values[0]
                     if param_value != cat_parameters[1]:
                         continue
-            fl = patient.registered_label_filepaths
+            fl = patient.registered_label_filepath
             labels = None
             try:
                 labels_ni = nib.load(fl)

raidionicsmaps/Computation/registration_step.py

@@ -52,7 +52,7 @@ def setup(self, patient_parameters):
         """
         self.patient_parameters = patient_parameters
         try:
-            self._moving_volume_filepath = self.patient_parameters.volume_filepaths
+            self._moving_volume_filepath = self.patient_parameters.volume_filepath
             self._fixed_volume_filepath = SharedResources.getInstance().mni_atlas_filepath_T1
         except Exception as e:
             logging.error("[RegistrationStep] Setting up process failed with {}".format(traceback.format_exc()))
@@ -69,7 +69,7 @@ def execute(self):
                 self.__registration(self._fixed_volume_filepath, self._moving_volume_filepath)
 
             # Flag for skipping applying registration to annotation files if they exist already
-            if self.patient_parameters.registered_label_filepaths is None:
+            if self.patient_parameters.registered_label_filepath is None:
                 self.__apply_registration()
 
             self._registration_runner.clear_cache()
@@ -145,12 +145,12 @@ def __apply_registration(self):
             shutil.move(reg_input_fn, os.path.join(self.patient_parameters.output_folderpath, 'input_reg_mni.nii.gz'))
             self.patient_parameters.registered_volume_filepaths = os.path.join(self.patient_parameters.output_folderpath,
                                                                                'input_reg_mni.nii.gz')
-            moving_filepath = self.patient_parameters.label_filepaths
+            moving_filepath = self.patient_parameters.label_filepath
             reg_anno_fn = self._registration_runner.apply_registration_transform(fixed=self._fixed_volume_filepath,
                                                                                  moving=moving_filepath)
             reg_base_name = 'input_reg_mni_' + SharedResources.getInstance().maps_gt_files_suffix
             shutil.move(reg_anno_fn, os.path.join(self.patient_parameters.output_folderpath, reg_base_name))
-            self.patient_parameters.registered_label_filepaths = os.path.join(self.patient_parameters.output_folderpath,
+            self.patient_parameters.registered_label_filepath = os.path.join(self.patient_parameters.output_folderpath,
                                                                               reg_base_name)
         except Exception as e:
             logging.error("[RegistrationStep] Apply registration failed with: {}.".format(traceback.format_exc()))

raidionicsmaps/Structures/PatientStructure.py

@@ -79,35 +79,35 @@ def input_folderpath(self, input_folderpath: str) -> None:
         self._input_folderpath = input_folderpath
 
     @property
-    def volume_filepaths(self) -> str:
+    def volume_filepath(self) -> str:
         return self._volume_filepath
 
-    @volume_filepaths.setter
-    def volume_filepaths(self, volume_filepaths: str) -> None:
-        self._volume_filepath = volume_filepaths
+    @volume_filepath.setter
+    def volume_filepath(self, volume_filepath: str) -> None:
+        self._volume_filepath = volume_filepath
 
     @property
-    def label_filepaths(self) -> str:
+    def label_filepath(self) -> str:
         return self._label_filepath
 
-    @label_filepaths.setter
-    def label_filepaths(self, label_filepaths: str) -> None:
-        self._label_filepath = label_filepaths
+    @label_filepath.setter
+    def label_filepath(self, label_filepath: str) -> None:
+        self._label_filepath = label_filepath
 
     @property
-    def registered_volume_filepaths(self) -> str:
+    def registered_volume_filepath(self) -> str:
         return self._registered_volume_filepath
 
-    @registered_volume_filepaths.setter
-    def registered_volume_filepaths(self, filepath: str) -> None:
+    @registered_volume_filepath.setter
+    def registered_volume_filepath(self, filepath: str) -> None:
         self._registered_volume_filepath = filepath
 
     @property
-    def registered_label_filepaths(self) -> str:
+    def registered_label_filepath(self) -> str:
         return self._registered_label_filepath
 
-    @registered_label_filepaths.setter
-    def registered_label_filepaths(self, filepath: str) -> None:
+    @registered_label_filepath.setter
+    def registered_label_filepath(self, filepath: str) -> None:
         self._registered_label_filepath = filepath
 
     @property
@@ -132,8 +132,8 @@ def __init_from_disk(self) -> None:
                     volume_files.append(f)
             break
 
-        self.volume_filepaths = os.path.join(self.input_folderpath, volume_files[0])
-        self.label_filepaths = os.path.join(self.input_folderpath, label_files[0])
+        self.volume_filepath = os.path.join(self.input_folderpath, volume_files[0])
+        self.label_filepath = os.path.join(self.input_folderpath, label_files[0])
 
         res_patient_folder = os.path.join(SharedResources.getInstance().maps_output_folder, self.patient_id)
         if os.path.exists(res_patient_folder):
@@ -177,15 +177,15 @@ def __init_from_disk(self) -> None:
             reg_labels_fn = os.path.join(self.output_folderpath,
                                          'input_reg_mni_' + SharedResources.getInstance().maps_gt_files_suffix)
             if os.path.exists(reg_input_fn):
-                self.registered_volume_filepaths = reg_input_fn
+                self.registered_volume_filepath = reg_input_fn
             if os.path.exists(reg_labels_fn):
-                self.registered_label_filepaths = reg_labels_fn
+                self.registered_label_filepath = reg_labels_fn
 
         if SharedResources.getInstance().maps_use_registered_data:
-            if self.registered_volume_filepaths is None:
-                self.registered_volume_filepaths = self.volume_filepaths
-            if self.registered_label_filepaths is None:
-                self.registered_label_filepaths = self.label_filepaths
+            if self.registered_volume_filepath is None:
+                self.registered_volume_filepath = self.volume_filepath
+            if self.registered_label_filepath is None:
+                self.registered_label_filepath = self.label_filepath
 
     def include_registration(self, reg_uid: str, registration: Registration) -> None:
         self.registrations[reg_uid] = registration

tests/heatmap_generation_test.py

@@ -55,6 +55,7 @@ def heatmap_generation_test():
         unit_test_config.set('Default', 'output_folder', os.path.join(test_dir, 'Cohort_UnitTest1_Output'))
         unit_test_config.add_section('Maps')
         unit_test_config.set('Maps', 'input_folder', os.path.join(test_dir, 'label_tumor.nii.gz'))
+        unit_test_config.set('Maps', 'use_registered_data', 'true')
         config_filename = os.path.join(test_dir, 'config.ini')
         with open(config_filename, 'w') as outfile:
             unit_test_config.write(outfile)