Merge branch 'master' of github.com:pylidc/pylidc

notmatthancock · Apr 22, 2020 · 5320a42 · 5320a42
2 parents 72e1f0b + f54d6d9
commit 5320a42
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Showing 2 changed files with 13 additions and 9 deletions.
diff --git a/pylidc/Annotation.py b/pylidc/Annotation.py
@@ -842,7 +842,7 @@ def visualize_in_scan(self, verbose=True):
         )
         # Remove the cell borders.
         # It Seems like there should be an easier way to do this...
-        for cell in scan_info_table.properties()['child_artists']:
+        for cell in scan_info_table.properties()['children']:
             cell.set_color('w')
 
         ax_scan_info.set_title('Scan Info')
@@ -873,7 +873,7 @@ def visualize_in_scan(self, verbose=True):
         )
 
         # Again, remove cell borders.
-        for cell in annotation_info_table.properties()['child_artists']:
+        for cell in annotation_info_table.properties()['children']:
             cell.set_color('w')
 
         ax_annotation_info.set_title('Annotation Info')

diff --git a/pylidc/Scan.py b/pylidc/Scan.py
@@ -277,9 +277,9 @@ def load_all_dicom_images(self, verbose=True):
 
             images = scan.load_all_dicom_images()
             zs = [float(img.ImagePositionPatient[2]) for img in images]
-            print(zs[1] - zs[0], img.SliceThickness, scan.slice_thickness)
+            print(zs[1] - zs[0], images[0].SliceThickness, scan.slice_thickness)
             
-            plt.imshow( images[0].pixel_array, cmap=plt.cm.gray )
+            plt.imshow(images[0].pixel_array, cmap=plt.cm.gray)
             plt.show()
 
         """
@@ -539,7 +539,7 @@ def visualize(self, annotation_groups=None):
             loc='center', cellLoc='left'
         )
         # Remove the table cell borders.
-        for cell in scan_info_table.properties()['child_artists']:
+        for cell in scan_info_table.properties()['children']:
             cell.set_color('w')
         # Add title, remove ticks from scan info.
         ax_scan_info.set_title('Scan Info')
@@ -561,7 +561,7 @@ def visualize(self, annotation_groups=None):
             ann_grps_table = ax_ann_grps.table(cellText=txt, loc='center',
                                                cellLoc='left')
             # Remove cell borders.
-            for cell in ann_grps_table.properties()['child_artists']:
+            for cell in ann_grps_table.properties()['children']:
                 cell.set_color('w')
             # Add title, remove ticks from scan info.
             ax_ann_grps.set_title('Nodule Info')
@@ -638,7 +638,11 @@ def to_volume(self, verbose=True):
         """
         images = self.load_all_dicom_images(verbose=verbose)
 
-        volume = np.zeros((512,512,len(images)))
-        for i in range(len(images)):
-           volume[:,:,i] = images[i].pixel_array
+        volume = np.stack(
+            [
+                x.pixel_array * x.RescaleSlope + x.RescaleIntercept
+                for x in images
+            ],
+            axis=-1,
+        ).astype(np.int16)
         return volume