Merge branch 'ThruSections' of https://github.com/simoneponcioni/spli…

…ne-mesher into ThruSections
artorg-unibe-ch · Jun 21, 2024 · a6b7ba3 · a6b7ba3
2 parents 2955772 + f031f51
commit a6b7ba3
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Showing 2 changed files with 17 additions and 11 deletions.
diff --git a/src/pyhexspline/spline_mesher.py b/src/pyhexspline/spline_mesher.py
@@ -315,7 +315,9 @@ def mesher(
         )
 
         cortical_v.plot_mhd_slice()
-        image_pad = cortical_v.binary_threshold()
+        print(f'Image size before entering binary_threshold(): {cortical_v.sitk_image.GetSize()}')
+        image_pad = cortical_v.binary_threshold(img_path=cortical_v.img_path)
+        print(f'Image size after entering binary_threshold(): {image_pad.GetSize()}')
         cortical_ext_split, cortical_int_split, cortical_int_sanity = (
             cortical_v.volume_spline_fast_implementation(image_pad)
         )

diff --git a/src/pyhexspline/spline_volume.py b/src/pyhexspline/spline_volume.py
@@ -6,7 +6,6 @@
 import gmsh
 import imutils
 import matplotlib
-
 # matplotlib.use("TkAgg")
 import matplotlib.pyplot as plt
 import numpy as np
@@ -306,8 +305,8 @@ def pad_image(self, image: Image, iso_pad_size: int) -> Image:
         constant = int(sitk.GetArrayFromImage(image).min())
         image_thr = sitk.ConstantPad(
             image,
-            (0, iso_pad_size, iso_pad_size),
-            (0, iso_pad_size, iso_pad_size),
+            (iso_pad_size, iso_pad_size, 0),
+            (iso_pad_size, iso_pad_size, 0),
             constant,
         )
         return image_thr
@@ -324,20 +323,22 @@ def binary_threshold(self, img_path: str) -> Tuple[ndarray, ndarray]:
             image = sitk.ReadImage(img_path)
         else:
             image = self.sitk_image
-            image = sitk.PermuteAxes(image, [2, 0, 1])
-            image.SetSpacing(self.sitk_image.GetSpacing())
+            # image = sitk.PermuteAxes(image, [2, 0, 1])
+            # image.SetSpacing(self.sitk_image.GetSpacing())
 
-        image_thr = self.exec_thresholding(image, THRESHOLD_PARAM)
+        # image_thr = self.exec_thresholding(image, THRESHOLD_PARAM)
 
-        image_thr = self.pad_image(image_thr, iso_pad_size=10)
+        image_pad = self.pad_image(image, iso_pad_size=10)
 
         if self.show_plots is True:
             self.plot_slice(
-                image_thr, SLICE, f"Padded Image on slice n. {SLICE}", ASPECT
+                image_pad, SLICE, f"Padded Image on slice n. {SLICE}", ASPECT
             )
         else:
             self.logger.info(f"Padded Image\t\t\tshow_plots:\t{self.show_plots}")
-        return image_thr
+
+        print(f'Image size after padding: {image_pad.GetSize()}')
+        return image_pad
 
         """
         img_thr_join = self.get_binary_contour(image_thr)
@@ -884,7 +885,7 @@ def process_slice(self, mask, slice_idx):
 
     def classify_contours(self, mask, slice_idx):
         """Classify and extract outer and inner contours from the mask."""
-        contours = find_contours(mask[:, :, slice_idx], level=0.5)
+        contours = find_contours(mask[:, :, slice_idx]) #, level=127)
         outer_contour = contours[0] if contours else None
         inner_contour = contours[1] if len(contours) > 1 else None
         return outer_contour, inner_contour
@@ -935,10 +936,13 @@ def volume_spline_fast_implementation(
         self, imsitk_pad: Image
     ) -> Tuple[ndarray, ndarray]:
         imnp = sitk.GetArrayFromImage(imsitk_pad)
+        self.spacing = imsitk_pad.GetSpacing()
         imnp = np.transpose(imnp, [2, 1, 0])
         imnp = np.flip(imnp, axis=1)
         height = imnp.shape[2]
         self.logger.debug(f"Height:\t{height}")
+
+        print(f'Image size of numpy array inside volume_spline_fast_implementation(): {imnp.shape}')
 
         # Get number of slices / ThruSections
         total_slices = np.linspace(0, height - 1, self.SLICING_COEFFICIENT, dtype=int)