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Commit 0052304757e61234439ed9e6bc740135621aad46

Authored by Thiago Franco de Moraes
1 parent bd862845
Exists in ffill_segmentation

Split 2D and 3D segmentation

Showing 1 changed file with 75 additions and 44 deletions   Show diff stats
invesalius/data/styles.py
  Diff comments   View file @0052304
@@ -1897,6 +1897,23 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle): @@ -1897,6 +1897,23 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle):
1897 if (self.viewer.slice_.buffer_slices[self.orientation].mask is None): 1897 if (self.viewer.slice_.buffer_slices[self.orientation].mask is None):
1898 return 1898 return
1899 1899
  1900 + if self.config.target == "3D":
  1901 + self.do_3d_seg()
  1902 + else:
  1903 + self.do_2d_seg()
  1904 +
  1905 + self.viewer.slice_.buffer_slices['AXIAL'].discard_mask()
  1906 + self.viewer.slice_.buffer_slices['CORONAL'].discard_mask()
  1907 + self.viewer.slice_.buffer_slices['SAGITAL'].discard_mask()
  1908 +
  1909 + self.viewer.slice_.buffer_slices['AXIAL'].discard_vtk_mask()
  1910 + self.viewer.slice_.buffer_slices['CORONAL'].discard_vtk_mask()
  1911 + self.viewer.slice_.buffer_slices['SAGITAL'].discard_vtk_mask()
  1912 +
  1913 + self.viewer.slice_.current_mask.was_edited = True
  1914 + Publisher.sendMessage('Reload actual slice')
  1915 +
  1916 + def do_2d_seg(self):
1900 viewer = self.viewer 1917 viewer = self.viewer
1901 iren = viewer.interactor 1918 iren = viewer.interactor
1902 mouse_x, mouse_y = iren.GetEventPosition() 1919 mouse_x, mouse_y = iren.GetEventPosition()
@@ -1905,7 +1922,6 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle): @@ -1905,7 +1922,6 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle):
1905 mask = self.viewer.slice_.current_mask.matrix[1:, 1:, 1:] 1922 mask = self.viewer.slice_.current_mask.matrix[1:, 1:, 1:]
1906 image = self.viewer.slice_.matrix 1923 image = self.viewer.slice_.matrix
1907 1924
1908 -  
1909 if self.config.method == 'threshold': 1925 if self.config.method == 'threshold':
1910 v = image[z, y, x] 1926 v = image[z, y, x]
1911 t0 = self.config.t0 1927 t0 = self.config.t0
@@ -1926,59 +1942,74 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle): @@ -1926,59 +1942,74 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle):
1926 if image[z, y, x] < t0 or image[z, y, x] > t1: 1942 if image[z, y, x] < t0 or image[z, y, x] > t1:
1927 return 1943 return
1928 1944
1929 - if self.config.target == "3D":  
1930 - bstruct = np.array(generate_binary_structure(3, CON3D[self.config.con_3d]), dtype='uint8')  
1931 - self.viewer.slice_.do_threshold_to_all_slices()  
1932 - cp_mask = self.viewer.slice_.current_mask.matrix.copy()  
1933 - else:  
1934 - _bstruct = generate_binary_structure(2, CON2D[self.config.con_2d])  
1935 - if self.orientation == 'AXIAL':  
1936 - bstruct = np.zeros((1, 3, 3), dtype='uint8')  
1937 - bstruct[0] = _bstruct  
1938 - elif self.orientation == 'CORONAL':  
1939 - bstruct = np.zeros((3, 1, 3), dtype='uint8')  
1940 - bstruct[:, 0, :] = _bstruct  
1941 - elif self.orientation == 'SAGITAL':  
1942 - bstruct = np.zeros((3, 3, 1), dtype='uint8')  
1943 - bstruct[:, :, 0] = _bstruct 1945 + _bstruct = generate_binary_structure(2, CON2D[self.config.con_2d])
  1946 + if self.orientation == 'AXIAL':
  1947 + bstruct = np.zeros((1, 3, 3), dtype='uint8')
  1948 + bstruct[0] = _bstruct
  1949 + elif self.orientation == 'CORONAL':
  1950 + bstruct = np.zeros((3, 1, 3), dtype='uint8')
  1951 + bstruct[:, 0, :] = _bstruct
  1952 + elif self.orientation == 'SAGITAL':
  1953 + bstruct = np.zeros((3, 3, 1), dtype='uint8')
  1954 + bstruct[:, :, 0] = _bstruct
1944 1955
1945 - if self.config.target == '2D':  
1946 - floodfill.floodfill_threshold(image, [[x, y, z]], t0, t1, self.config.fill_value, bstruct, mask)  
1947 - b_mask = self.viewer.slice_.buffer_slices[self.orientation].mask  
1948 - index = self.viewer.slice_.buffer_slices[self.orientation].index 1956 + floodfill.floodfill_threshold(image, [[x, y, z]], t0, t1, self.config.fill_value, bstruct, mask)
  1957 + b_mask = self.viewer.slice_.buffer_slices[self.orientation].mask
  1958 + index = self.viewer.slice_.buffer_slices[self.orientation].index
1949 1959
1950 - if self.orientation == 'AXIAL':  
1951 - p_mask = mask[index,:,:].copy()  
1952 - elif self.orientation == 'CORONAL':  
1953 - p_mask = mask[:, index, :].copy()  
1954 - elif self.orientation == 'SAGITAL':  
1955 - p_mask = mask[:, :, index].copy() 1960 + if self.orientation == 'AXIAL':
  1961 + p_mask = mask[index,:,:].copy()
  1962 + elif self.orientation == 'CORONAL':
  1963 + p_mask = mask[:, index, :].copy()
  1964 + elif self.orientation == 'SAGITAL':
  1965 + p_mask = mask[:, :, index].copy()
1956 1966
1957 - self.viewer.slice_.current_mask.save_history(index, self.orientation, p_mask, b_mask)  
1958 - else:  
1959 - with futures.ThreadPoolExecutor(max_workers=1) as executor:  
1960 - future = executor.submit(floodfill.floodfill_threshold, image, [[x, y, z]], t0, t1, self.config.fill_value, bstruct, mask) 1967 + self.viewer.slice_.current_mask.save_history(index, self.orientation, p_mask, b_mask)
1961 1968
1962 - dlg = wx.ProgressDialog(self._progr_title, self._progr_msg, parent=None, style=wx.PD_APP_MODAL)  
1963 - while not future.done():  
1964 - dlg.Pulse()  
1965 - time.sleep(0.1) 1969 + def do_3d_seg(self):
  1970 + viewer = self.viewer
  1971 + iren = viewer.interactor
  1972 + mouse_x, mouse_y = iren.GetEventPosition()
  1973 + x, y, z = self.viewer.get_voxel_coord_by_screen_pos(mouse_x, mouse_y, self.picker)
1966 1974
1967 - dlg.Destroy() 1975 + mask = self.viewer.slice_.current_mask.matrix[1:, 1:, 1:]
  1976 + image = self.viewer.slice_.matrix
1968 1977
1969 - self.viewer.slice_.current_mask.save_history(0, 'VOLUME', self.viewer.slice_.current_mask.matrix.copy(), cp_mask) 1978 + if self.config.method == 'threshold':
  1979 + v = image[z, y, x]
  1980 + t0 = self.config.t0
  1981 + t1 = self.config.t1
1970 1982
1971 - self.viewer.slice_.buffer_slices['AXIAL'].discard_mask()  
1972 - self.viewer.slice_.buffer_slices['CORONAL'].discard_mask()  
1973 - self.viewer.slice_.buffer_slices['SAGITAL'].discard_mask() 1983 + elif self.config.method == 'dynamic':
  1984 + if self.config.use_ww_wl:
  1985 + print "Using WW&WL"
  1986 + ww = self.viewer.slice_.window_width
  1987 + wl = self.viewer.slice_.window_level
  1988 + image = get_LUT_value(image, ww, wl)
1974 1989
1975 - self.viewer.slice_.buffer_slices['AXIAL'].discard_vtk_mask()  
1976 - self.viewer.slice_.buffer_slices['CORONAL'].discard_vtk_mask()  
1977 - self.viewer.slice_.buffer_slices['SAGITAL'].discard_vtk_mask() 1990 + v = image[z, y, x]
1978 1991
1979 - self.viewer.slice_.current_mask.was_edited = True  
1980 - Publisher.sendMessage('Reload actual slice') 1992 + t0 = v - self.config.dev_min
  1993 + t1 = v + self.config.dev_max
  1994 +
  1995 + if image[z, y, x] < t0 or image[z, y, x] > t1:
  1996 + return
  1997 +
  1998 + bstruct = np.array(generate_binary_structure(3, CON3D[self.config.con_3d]), dtype='uint8')
  1999 + self.viewer.slice_.do_threshold_to_all_slices()
  2000 + cp_mask = self.viewer.slice_.current_mask.matrix.copy()
  2001 +
  2002 + with futures.ThreadPoolExecutor(max_workers=1) as executor:
  2003 + future = executor.submit(floodfill.floodfill_threshold, image, [[x, y, z]], t0, t1, self.config.fill_value, bstruct, mask)
  2004 +
  2005 + dlg = wx.ProgressDialog(self._progr_title, self._progr_msg, parent=None, style=wx.PD_APP_MODAL)
  2006 + while not future.done():
  2007 + dlg.Pulse()
  2008 + time.sleep(0.1)
  2009 +
  2010 + dlg.Destroy()
1981 2011
  2012 + self.viewer.slice_.current_mask.save_history(0, 'VOLUME', self.viewer.slice_.current_mask.matrix.copy(), cp_mask)
1982 2013
1983 def get_style(style): 2014 def get_style(style):
1984 STYLES = { 2015 STYLES = {