Merge branch 'develop' into documentation

FZJ-INM1-BDA · Jul 14, 2023 · 2770b91 · 2770b91
2 parents 30e2898 + a1b7694
commit 2770b91
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Showing 3 changed files with 11 additions and 6 deletions.
diff --git a/requirements.txt b/requirements.txt
@@ -1,5 +1,5 @@
 git+https://github.com/MIC-DKFZ/HD-BET.git#egg=HD-BET
-git+https://github.com/JThoennissen/siibra-explorer-toolsuite.git#egg=siibra-explorer-toolsuite
+git+https://github.com/JThoennissen/siibra-explorer-toolsuite.git@v0.0.1#egg=siibra-explorer-toolsuite
 siibra==0.4a59
 tkfontawesome==0.2.0
 matplotlib==3.7.2

diff --git a/voluba_mriwarp/logic.py b/voluba_mriwarp/logic.py
@@ -579,6 +579,7 @@ def export_assignments(
         report = AssignmentReport(
             parcellation=self.__parcellation, filter=filter,
             progress=progress_indicator)
+        filename = os.path.basename(self.__in_path)
 
         # Transfer points to siibra.Point objects.
         if self.__image_type == 'unaligned':
@@ -602,5 +603,6 @@ def export_assignments(
                              subject_points=self.__saved_points,
                              mni_points=mni_points, labels=labels,
                              image=self.__nifti_image, features=features,
+                             image_filename=filename,
                              receptors=receptors, cohorts=cohorts,
                              output_file=output_file)
diff --git a/voluba_mriwarp/reports.py b/voluba_mriwarp/reports.py
@@ -79,7 +79,9 @@ def _filter_assignments(self, initial_assignments):
         """
         mapping = {
             '<': lambda column, value: column < value,
+            '<=': lambda column, value: column < value,
             '>': lambda column, value: column > value,
+            '>=': lambda column, value: column > value,
             '=': lambda column, value: column == value
         }
         column, sign, value = self.filter
@@ -94,14 +96,15 @@ def _filter_assignments(self, initial_assignments):
 
     def create_report(
             self, assignments, subject_points, mni_points, labels, image,
-            features, receptors, cohorts, output_file):
+            image_filename, features, receptors, cohorts, output_file):
         """Create a PDF report of assigned regions and linked features.
 
         :param list assignments: region assignments for multiple points
         :param list subject_points: points in subject's physical space
         :param list mni_points: points in MNI152 space
         :param list labels: labels for each point
         :param nibabel.Nifti1Image image: input image
+        :param str image_filename: filename of the input image
         :param list features: linked features to export for each region
         :param list receptors: receptors to plot a ReceptorDensityProfile for
         :param list cohorts: cohorts to plot connectivity plots for
@@ -156,7 +159,7 @@ def create_report(
         # Build the PDF report.
         self._build_pdf(
             assignments, input_plot, pmap_plots, feature_plots, labels,
-            subject_points, mni_points, image, output_file)
+            subject_points, mni_points, image_filename, output_file)
         matplotlib.use(backend)
 
     def _plot_input(self, image):
@@ -276,7 +279,7 @@ def __plot_features(self, region, feature, selected_receptors, cohorts):
 
     def _build_pdf(
             self, assignments, input_plot, pmap_plots, feature_plots, labels,
-            subject_points, mni_points, image, output_file):
+            subject_points, mni_points, image_filename, output_file):
         """Actually create a PDF report of assigned regions and linked features.
 
         :param list assignments: region assignments for multiple points
@@ -286,7 +289,7 @@ def _build_pdf(
         :param list labels: labels for each point
         :param list subject_points: points in subject's physical space
         :param list mni_points: points in MNI152 space
-        :param nibabel.Nifti1Image image: input image
+        :param str image_filename: filename of the input image
         :param str output_file: PDF file to export report to
         """
         logging.getLogger(mriwarp_name).info(
@@ -308,7 +311,7 @@ def _build_pdf(
         pdf.set_xy(left, top + 14)
         pdf.multi_cell(
             0, text_height, '\n'.join(
-                [f'Input scan: {os.path.basename(image.get_filename())}',
+                [f'Input scan: {image_filename}',
                  f'Parcellation: {self.pmaps.parcellation.name}', ' ',
                  f'For each point, regions with {self.filter[0]} '
                  f'{self.filter[1]} {self.filter[2]} are assigned.',