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Commit f6fab930746412c08db88c49f27914f1af42cdf2

Authored by Thiago Franco de Moraes
1 parent c0352ef3
Exists in region_growing_confidence

created a separated function

Showing 2 changed files with 73 additions and 73 deletions   Show diff stats
invesalius/data/styles.py
  Diff comments   View file @f6fab93
@@ -2052,88 +2052,43 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle): @@ -2052,88 +2052,43 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle):
2052 mask = self.viewer.slice_.buffer_slices[self.orientation].mask.copy() 2052 mask = self.viewer.slice_.buffer_slices[self.orientation].mask.copy()
2053 image = self.viewer.slice_.buffer_slices[self.orientation].image 2053 image = self.viewer.slice_.buffer_slices[self.orientation].image
2054 2054
2055 - if self.config.method == 'threshold':  
2056 - v = image[y, x]  
2057 - t0 = self.config.t0  
2058 - t1 = self.config.t1  
2059 -  
2060 - elif self.config.method == 'dynamic1':  
2061 - if self.config.use_ww_wl:  
2062 - print "Using WW&WL"  
2063 - ww = self.viewer.slice_.window_width  
2064 - wl = self.viewer.slice_.window_level  
2065 - image = get_LUT_value_255(image, ww, wl)  
2066 -  
2067 - v = image[y, x]  
2068 -  
2069 - t0 = v - self.config.dev_min  
2070 - t1 = v + self.config.dev_max  
2071 -  
2072 - else: 2055 + if self.config.method == 'confidence':
2073 dy, dx = image.shape 2056 dy, dx = image.shape
2074 image = image.reshape((1, dy, dx)) 2057 image = image.reshape((1, dy, dx))
2075 mask = mask.reshape((1, dy, dx)) 2058 mask = mask.reshape((1, dy, dx))
2076 - if self.config.use_ww_wl:  
2077 - print "Using WW&WL"  
2078 - ww = self.viewer.slice_.window_width  
2079 - wl = self.viewer.slice_.window_level  
2080 - image = get_LUT_value_255(image, ww, wl)  
2081 - bool_mask = np.zeros_like(mask, dtype='bool')  
2082 - out_mask = np.zeros_like(mask)  
2083 - for i in xrange(int(x-1), int(x+2)):  
2084 - if i < 0 or i >= bool_mask.shape[2]:  
2085 - continue  
2086 - for j in xrange(int(y-1), int(y+2)):  
2087 - if j < 0 or j >= bool_mask.shape[1]:  
2088 - continue  
2089 - bool_mask[0, j, i] = True  
2090 -  
2091 -  
2092 - bstruct = np.array(generate_binary_structure(2, CON2D[self.config.con_2d]), dtype='uint8')  
2093 - bstruct = bstruct.reshape((1, 3, 3))  
2094 -  
2095 - for i in xrange(3):  
2096 - var = np.std(image[bool_mask])  
2097 - mean = np.mean(image[bool_mask])  
2098 -  
2099 - t0 = mean - var * 2.5  
2100 - t1 = mean + var * 2.5  
2101 - print var, mean, t0, t1  
2102 -  
2103 - floodfill.floodfill_threshold(image, [[x, y, 0]], t0, t1, 1, bstruct, out_mask)  
2104 -  
2105 - bool_mask[out_mask == 1] = True  
2106 -  
2107 - mask[out_mask.astype('bool')] = self.config.fill_value 2059 + out_mask = self.do_rg_confidence((x, y, 0), image, mask)
  2060 + else:
  2061 + if self.config.method == 'threshold':
  2062 + v = image[y, x]
  2063 + t0 = self.config.t0
  2064 + t1 = self.config.t1
2108 2065
2109 - index = self.viewer.slice_.buffer_slices[self.orientation].index  
2110 - b_mask = self.viewer.slice_.buffer_slices[self.orientation].mask  
2111 - vol_mask = self.viewer.slice_.current_mask.matrix[1:, 1:, 1:] 2066 + elif self.config.method == 'dynamic':
  2067 + if self.config.use_ww_wl:
  2068 + print "Using WW&WL"
  2069 + ww = self.viewer.slice_.window_width
  2070 + wl = self.viewer.slice_.window_level
  2071 + image = get_LUT_value_255(image, ww, wl)
2112 2072
2113 - if self.orientation == 'AXIAL':  
2114 - vol_mask[index, :, :] = mask  
2115 - elif self.orientation == 'CORONAL':  
2116 - vol_mask[:, index, :] = mask  
2117 - elif self.orientation == 'SAGITAL':  
2118 - vol_mask[:, :, index] = mask 2073 + v = image[y, x]
2119 2074
2120 - self.viewer.slice_.current_mask.save_history(index, self.orientation, mask, b_mask) 2075 + t0 = v - self.config.dev_min
  2076 + t1 = v + self.config.dev_max
2121 2077
2122 - return  
2123 2078
2124 - if image[y, x] < t0 or image[y, x] > t1:  
2125 - return 2079 + if image[y, x] < t0 or image[y, x] > t1:
  2080 + return
2126 2081
2127 - dy, dx = image.shape  
2128 - image = image.reshape((1, dy, dx))  
2129 - mask = mask.reshape((1, dy, dx)) 2082 + dy, dx = image.shape
  2083 + image = image.reshape((1, dy, dx))
  2084 + mask = mask.reshape((1, dy, dx))
2130 2085
2131 - out_mask = np.zeros_like(mask) 2086 + out_mask = np.zeros_like(mask)
2132 2087
2133 - bstruct = np.array(generate_binary_structure(2, CON2D[self.config.con_2d]), dtype='uint8')  
2134 - bstruct = bstruct.reshape((1, 3, 3)) 2088 + bstruct = np.array(generate_binary_structure(2, CON2D[self.config.con_2d]), dtype='uint8')
  2089 + bstruct = bstruct.reshape((1, 3, 3))
2135 2090
2136 - floodfill.floodfill_threshold(image, [[x, y, 0]], t0, t1, 1, bstruct, out_mask) 2091 + floodfill.floodfill_threshold(image, [[x, y, 0]], t0, t1, 1, bstruct, out_mask)
2137 2092
2138 mask[out_mask.astype('bool')] = self.config.fill_value 2093 mask[out_mask.astype('bool')] = self.config.fill_value
2139 2094
@@ -2199,6 +2154,41 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle): @@ -2199,6 +2154,41 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle):
2199 2154
2200 self.viewer.slice_.current_mask.save_history(0, 'VOLUME', self.viewer.slice_.current_mask.matrix.copy(), cp_mask) 2155 self.viewer.slice_.current_mask.save_history(0, 'VOLUME', self.viewer.slice_.current_mask.matrix.copy(), cp_mask)
2201 2156
  2157 + def do_rg_confidence(self, p, image, mask):
  2158 + x, y, z = p
  2159 + if self.config.use_ww_wl:
  2160 + print "Using WW&WL"
  2161 + ww = self.viewer.slice_.window_width
  2162 + wl = self.viewer.slice_.window_level
  2163 + image = get_LUT_value_255(image, ww, wl)
  2164 + bool_mask = np.zeros_like(mask, dtype='bool')
  2165 + out_mask = np.zeros_like(mask)
  2166 + for i in xrange(int(x-1), int(x+2)):
  2167 + if i < 0 or i >= bool_mask.shape[2]:
  2168 + continue
  2169 + for j in xrange(int(y-1), int(y+2)):
  2170 + if j < 0 or j >= bool_mask.shape[1]:
  2171 + continue
  2172 + bool_mask[0, j, i] = True
  2173 +
  2174 +
  2175 + bstruct = np.array(generate_binary_structure(2, CON2D[self.config.con_2d]), dtype='uint8')
  2176 + bstruct = bstruct.reshape((1, 3, 3))
  2177 +
  2178 + for i in xrange(3):
  2179 + var = np.std(image[bool_mask])
  2180 + mean = np.mean(image[bool_mask])
  2181 +
  2182 + t0 = mean - var * 2.5
  2183 + t1 = mean + var * 2.5
  2184 + print var, mean, t0, t1
  2185 +
  2186 + floodfill.floodfill_threshold(image, [[x, y, 0]], t0, t1, 1, bstruct, out_mask)
  2187 +
  2188 + bool_mask[out_mask == 1] = True
  2189 +
  2190 + return out_mask
  2191 +
2202 def get_style(style): 2192 def get_style(style):
2203 STYLES = { 2193 STYLES = {
2204 const.STATE_DEFAULT: DefaultInteractorStyle, 2194 const.STATE_DEFAULT: DefaultInteractorStyle,
invesalius/gui/dialogs.py
  Diff comments   View file @f6fab93
@@ -2273,13 +2273,14 @@ class FFillSegmentationOptionsDialog(wx.Dialog): @@ -2273,13 +2273,14 @@ class FFillSegmentationOptionsDialog(wx.Dialog):
2273 else: 2273 else:
2274 self.panel3dcon.conect3D_6.SetValue(1) 2274 self.panel3dcon.conect3D_6.SetValue(1)
2275 2275
2276 - self.cmb_method = wx.ComboBox(self, -1, choices=(_(u"Dynamic"), _(u"Threshold")), style=wx.CB_READONLY) 2276 + self.cmb_method = wx.ComboBox(self, -1, choices=(_(u"Dynamic"), _(u"Threshold"), _(u"Confidence")), style=wx.CB_READONLY)
2277 2277
2278 if self.config.method == 'dynamic': 2278 if self.config.method == 'dynamic':
2279 self.cmb_method.SetSelection(0) 2279 self.cmb_method.SetSelection(0)
2280 - else: 2280 + elif self.config.method == 'threshold':
2281 self.cmb_method.SetSelection(1) 2281 self.cmb_method.SetSelection(1)
2282 - self.config.method = 'threshold' 2282 + elif self.config.method == 'confidence':
  2283 + self.cmb_method.SetSelection(2)
2283 2284
2284 self.panel_ffill_threshold = PanelFFillThreshold(self, self.config, -1, style=border_style|wx.TAB_TRAVERSAL) 2285 self.panel_ffill_threshold = PanelFFillThreshold(self, self.config, -1, style=border_style|wx.TAB_TRAVERSAL)
2285 self.panel_ffill_threshold.SetMinSize((250, -1)) 2286 self.panel_ffill_threshold.SetMinSize((250, -1))
@@ -2313,6 +2314,10 @@ class FFillSegmentationOptionsDialog(wx.Dialog): @@ -2313,6 +2314,10 @@ class FFillSegmentationOptionsDialog(wx.Dialog):
2313 self.cmb_method.SetSelection(0) 2314 self.cmb_method.SetSelection(0)
2314 self.panel_ffill_dynamic.Show() 2315 self.panel_ffill_dynamic.Show()
2315 sizer.Add(self.panel_ffill_dynamic, (11, 0), (1, 6), flag=wx.LEFT|wx.RIGHT|wx.EXPAND, border=7) 2316 sizer.Add(self.panel_ffill_dynamic, (11, 0), (1, 6), flag=wx.LEFT|wx.RIGHT|wx.EXPAND, border=7)
  2317 + elif self.config.method == 'confidence':
  2318 + self.cmb_method.SetSelection(2)
  2319 + self.panel_ffill_dynamic.Show()
  2320 + sizer.Add(self.panel_ffill_dynamic, (11, 0), (1, 6), flag=wx.LEFT|wx.RIGHT|wx.EXPAND, border=7)
2316 else: 2321 else:
2317 self.cmb_method.SetSelection(1) 2322 self.cmb_method.SetSelection(1)
2318 self.panel_ffill_threshold.Show() 2323 self.panel_ffill_threshold.Show()
@@ -2363,6 +2368,11 @@ class FFillSegmentationOptionsDialog(wx.Dialog): @@ -2363,6 +2368,11 @@ class FFillSegmentationOptionsDialog(wx.Dialog):
2363 self.panel_ffill_threshold.Hide() 2368 self.panel_ffill_threshold.Hide()
2364 self.panel_ffill_dynamic.Show() 2369 self.panel_ffill_dynamic.Show()
2365 self.GetSizer().Replace(self.panel_ffill_threshold, self.panel_ffill_dynamic) 2370 self.GetSizer().Replace(self.panel_ffill_threshold, self.panel_ffill_dynamic)
  2371 + elif self.cmb_method.GetSelection() == 2:
  2372 + self.config.method = 'confidence'
  2373 + self.panel_ffill_threshold.Hide()
  2374 + self.panel_ffill_dynamic.Show()
  2375 + self.GetSizer().Replace(self.panel_ffill_threshold, self.panel_ffill_dynamic)
2366 else: 2376 else:
2367 self.config.method = 'threshold' 2377 self.config.method = 'threshold'
2368 self.panel_ffill_dynamic.Hide() 2378 self.panel_ffill_dynamic.Hide()