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Commit 5723fa2be54ca74d5824b53743f452e9a673a49f

Authored by Thiago Franco de Moraes
1 parent 1b21bd9e
Exists in watershed

Marking the mask as edited when using watershed tool

Showing 3 changed files with 18 additions and 8 deletions   Show diff stats
invesalius/data/slice_.py
  Diff comments   View file @5723fa2
@@ -525,9 +525,7 @@ class Slice(object): @@ -525,9 +525,7 @@ class Slice(object):
525 self.buffer_slices[orientation].vtk_image = image 525 self.buffer_slices[orientation].vtk_image = image
526 self.buffer_slices[orientation].vtk_mask = mask 526 self.buffer_slices[orientation].vtk_mask = mask
527 527
528 - print self.qblend  
529 if self.qblend[orientation].get(slice_number, None) is not None: 528 if self.qblend[orientation].get(slice_number, None) is not None:
530 - print "BLENDING"  
531 final_image = self.do_blend(final_image, 529 final_image = self.do_blend(final_image,
532 self.qblend[orientation][slice_number]) 530 self.qblend[orientation][slice_number])
533 return final_image 531 return final_image
invesalius/data/styles.py
  Diff comments   View file @5723fa2
@@ -30,7 +30,9 @@ import converters @@ -30,7 +30,9 @@ import converters
30 import numpy as np 30 import numpy as np
31 31
32 from scipy import ndimage 32 from scipy import ndimage
  33 +from scipy.misc import imsave
33 from skimage.morphology import watershed 34 from skimage.morphology import watershed
  35 +from skimage import filter
34 36
35 ORIENTATIONS = { 37 ORIENTATIONS = {
36 "AXIAL": const.AXIAL, 38 "AXIAL": const.AXIAL,
@@ -815,6 +817,7 @@ class WaterShedInteractorStyle(DefaultInteractorStyle): @@ -815,6 +817,7 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
815 cvmask = do_colour_mask(vmask) 817 cvmask = do_colour_mask(vmask)
816 self.viewer.slice_.qblend[self.orientation][n] = cvmask 818 self.viewer.slice_.qblend[self.orientation][n] = cvmask
817 # TODO: To create a new function to reload images to viewer. 819 # TODO: To create a new function to reload images to viewer.
  820 + viewer._flush_buffer = True
818 viewer.OnScrollBar() 821 viewer.OnScrollBar()
819 822
820 def OnBrushMove(self, obj, evt): 823 def OnBrushMove(self, obj, evt):
@@ -898,16 +901,19 @@ class WaterShedInteractorStyle(DefaultInteractorStyle): @@ -898,16 +901,19 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
898 if self.orientation == 'AXIAL': 901 if self.orientation == 'AXIAL':
899 image = self.viewer.slice_.matrix[n] 902 image = self.viewer.slice_.matrix[n]
900 mask = self.viewer.slice_.current_mask.matrix[n+1, 1:, 1:] 903 mask = self.viewer.slice_.current_mask.matrix[n+1, 1:, 1:]
  904 + self.viewer.slice_.current_mask.matrix[n+1, 0, 0] = 1
901 markers = self.matrix[n] 905 markers = self.matrix[n]
902 906
903 elif self.orientation == 'CORONAL': 907 elif self.orientation == 'CORONAL':
904 image = self.viewer.slice_.matrix[:, n, :] 908 image = self.viewer.slice_.matrix[:, n, :]
905 mask = self.viewer.slice_.current_mask.matrix[1:, n+1, 1:] 909 mask = self.viewer.slice_.current_mask.matrix[1:, n+1, 1:]
  910 + self.viewer.slice_.current_mask.matrix[0, n+1, 0]
906 markers = self.matrix[:, n, :] 911 markers = self.matrix[:, n, :]
907 912
908 elif self.orientation == 'SAGITAL': 913 elif self.orientation == 'SAGITAL':
909 image = self.viewer.slice_.matrix[:, :, n] 914 image = self.viewer.slice_.matrix[:, :, n]
910 mask = self.viewer.slice_.current_mask.matrix[1: , 1:, n+1] 915 mask = self.viewer.slice_.current_mask.matrix[1: , 1:, n+1]
  916 + self.viewer.slice_.current_mask.matrix[0 , 0, n+1]
911 markers = self.matrix[:, :, n] 917 markers = self.matrix[:, :, n]
912 918
913 919
@@ -915,7 +921,8 @@ class WaterShedInteractorStyle(DefaultInteractorStyle): @@ -915,7 +921,8 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
915 wl = self.viewer.slice_.window_level 921 wl = self.viewer.slice_.window_level
916 922
917 #tmp_image = get_LUT_value(image, ww, wl).astype('uint16') 923 #tmp_image = get_LUT_value(image, ww, wl).astype('uint16')
918 - tmp_image = ndimage.morphological_gradient(get_LUT_value(image, ww, wl).astype('uint16'), 5) 924 + tmp_image = ndimage.morphological_gradient(get_LUT_value(image, ww, wl).astype('uint16'), 3)
  925 + imsave('/tmp/manolo.png', tmp_image)
919 print tmp_image.dtype, tmp_image.min(), tmp_image.max() 926 print tmp_image.dtype, tmp_image.min(), tmp_image.max()
920 tmp_mask = watershed(tmp_image, markers) 927 tmp_mask = watershed(tmp_image, markers)
921 928
@@ -926,7 +933,9 @@ class WaterShedInteractorStyle(DefaultInteractorStyle): @@ -926,7 +933,9 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
926 mask[(tmp_mask==2) & ((mask == 0) | (mask == 2) | (mask == 253))] = 2 933 mask[(tmp_mask==2) & ((mask == 0) | (mask == 2) | (mask == 253))] = 2
927 mask[(tmp_mask==1) & ((mask == 0) | (mask == 2) | (mask == 253))] = 253 934 mask[(tmp_mask==1) & ((mask == 0) | (mask == 2) | (mask == 253))] = 253
928 935
929 - self.viewer._flush_buffer = True 936 +
  937 + self.viewer.slice_.current_mask.was_edited = True
  938 + self.viewer._flush_buffer = False
930 self.viewer.OnScrollBar(update3D=False) 939 self.viewer.OnScrollBar(update3D=False)
931 940
932 def get_coordinate_cursor(self): 941 def get_coordinate_cursor(self):
@@ -1027,10 +1036,11 @@ class WaterShedInteractorStyle(DefaultInteractorStyle): @@ -1027,10 +1036,11 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
1027 tmp_mask = watershed(tmp_image, markers) 1036 tmp_mask = watershed(tmp_image, markers)
1028 1037
1029 mask[:] = 0 1038 mask[:] = 0
1030 - mask[(tmp_mask==1)] = 253  
1031 - mask[0] = 1  
1032 - mask[:, 0, :] = 1  
1033 - mask[:, :, 0] = 1 1039 + mask[(tmp_mask == 1)] = 253
  1040 + #mask[:] = tmp_mask
  1041 + self.viewer.slice_.current_mask.matrix[0] = 1
  1042 + self.viewer.slice_.current_mask.matrix[:, 0, :] = 1
  1043 + self.viewer.slice_.current_mask.matrix[:, :, 0] = 1
1034 1044
1035 self.viewer._flush_buffer = True 1045 self.viewer._flush_buffer = True
1036 self.viewer.slice_.discard_all_buffers() 1046 self.viewer.slice_.discard_all_buffers()
invesalius/data/viewer_slice.py
  Diff comments   View file @5723fa2
@@ -283,6 +283,8 @@ class Viewer(wx.Panel): @@ -283,6 +283,8 @@ class Viewer(wx.Panel):
283 if cleanup: 283 if cleanup:
284 self.style.CleanUp() 284 self.style.CleanUp()
285 285
  286 + del self.style
  287 +
286 style = styles.get_style(state)(self) 288 style = styles.get_style(state)(self)
287 289
288 setup = getattr(style, 'SetUp', None) 290 setup = getattr(style, 'SetUp', None)