Add Region growing confidence segmentation tool (#57)

2D and 3D segmentation. Added a GUI to config this segmentation.

Add Region growing confidence segmentation tool (#57)
2D and 3D segmentation. Added a GUI to config this segmentation.
Thiago Franco de Moraes · GitHub
1 parent 6e437a17
Showing 2 changed files with 187 additions and 52 deletions Show diff stats
invesalius/data/styles.py
invesalius/gui/dialogs.py
@@ -1983,6 +1983,9 @@ class FFillSegmentationConfig(object):
         self.use_ww_wl = True
+        self.confid_mult = 2.5
+        self.confid_iters = 3
+
 class FloodFillSegmentInteractorStyle(DefaultInteractorStyle):
     def __init__(self, viewer):
@@ -2052,36 +2055,47 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle):
         mask = self.viewer.slice_.buffer_slices[self.orientation].mask.copy()
         image = self.viewer.slice_.buffer_slices[self.orientation].image
-        if self.config.method == 'threshold':
-            v = image[y, x]
-            t0 = self.config.t0
-            t1 = self.config.t1
+        if self.config.method == 'confidence':
+            dy, dx = image.shape
+            image = image.reshape((1, dy, dx))
+            mask = mask.reshape((1, dy, dx))
-        elif self.config.method == 'dynamic':
-            if self.config.use_ww_wl:
-                print "Using WW&WL"
-                ww = self.viewer.slice_.window_width
-                wl = self.viewer.slice_.window_level
-                image = get_LUT_value_255(image, ww, wl)
+            bstruct = np.array(generate_binary_structure(2, CON2D[self.config.con_2d]), dtype='uint8')
+            bstruct = bstruct.reshape((1, 3, 3))
-            v = image[y, x]
+            out_mask = self.do_rg_confidence(image, mask, (x, y, 0), bstruct)
+        else:
+            if self.config.method == 'threshold':
+                v = image[y, x]
+                t0 = self.config.t0
+                t1 = self.config.t1
-            t0 = v - self.config.dev_min
-            t1 = v + self.config.dev_max
+            elif self.config.method == 'dynamic':
+                if self.config.use_ww_wl:
+                    print "Using WW&WL"
+                    ww = self.viewer.slice_.window_width
+                    wl = self.viewer.slice_.window_level
+                    image = get_LUT_value_255(image, ww, wl)
-        if image[y, x] < t0 or image[y, x] > t1:
-            return
+                v = image[y, x]
-        dy, dx = image.shape
-        image = image.reshape((1, dy, dx))
-        mask = mask.reshape((1, dy, dx))
+                t0 = v - self.config.dev_min
+                t1 = v + self.config.dev_max
-        out_mask = np.zeros_like(mask)
-        bstruct = np.array(generate_binary_structure(2, CON2D[self.config.con_2d]), dtype='uint8')
-        bstruct = bstruct.reshape((1, 3, 3))
+            if image[y, x] < t0 or image[y, x] > t1:
+                return
+
+            dy, dx = image.shape
+            image = image.reshape((1, dy, dx))
+            mask = mask.reshape((1, dy, dx))
+
+            out_mask = np.zeros_like(mask)
+
+            bstruct = np.array(generate_binary_structure(2, CON2D[self.config.con_2d]), dtype='uint8')
+            bstruct = bstruct.reshape((1, 3, 3))
-        floodfill.floodfill_threshold(image, [[x, y, 0]], t0, t1, 1, bstruct, out_mask)
+            floodfill.floodfill_threshold(image, [[x, y, 0]], t0, t1, 1, bstruct, out_mask)
         mask[out_mask.astype('bool')] = self.config.fill_value
@@ -2107,46 +2121,91 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle):
         mask = self.viewer.slice_.current_mask.matrix[1:, 1:, 1:]
         image = self.viewer.slice_.matrix
-        if self.config.method == 'threshold':
-            v = image[z, y, x]
-            t0 = self.config.t0
-            t1 = self.config.t1
+        if self.config.method != 'confidence':
+            if self.config.method == 'threshold':
+                v = image[z, y, x]
+                t0 = self.config.t0
+                t1 = self.config.t1
-        elif self.config.method == 'dynamic':
-            if self.config.use_ww_wl:
-                print "Using WW&WL"
-                ww = self.viewer.slice_.window_width
-                wl = self.viewer.slice_.window_level
-                image = get_LUT_value_255(image, ww, wl)
+            elif self.config.method == 'dynamic':
+                if self.config.use_ww_wl:
+                    print "Using WW&WL"
+                    ww = self.viewer.slice_.window_width
+                    wl = self.viewer.slice_.window_level
+                    image = get_LUT_value_255(image, ww, wl)
-            v = image[z, y, x]
+                v = image[z, y, x]
-            t0 = v - self.config.dev_min
-            t1 = v + self.config.dev_max
+                t0 = v - self.config.dev_min
+                t1 = v + self.config.dev_max
-        if image[z, y, x] < t0 or image[z, y, x] > t1:
-            return
+            if image[z, y, x] < t0 or image[z, y, x] > t1:
+                return
-        out_mask = np.zeros_like(mask)
         bstruct = np.array(generate_binary_structure(3, CON3D[self.config.con_3d]), dtype='uint8')
         self.viewer.slice_.do_threshold_to_all_slices()
         cp_mask = self.viewer.slice_.current_mask.matrix.copy()
-        with futures.ThreadPoolExecutor(max_workers=1) as executor:
-            future = executor.submit(floodfill.floodfill_threshold, image, [[x, y, z]], t0, t1, 1, bstruct, out_mask)
+        if self.config.method == 'confidence':
+            with futures.ThreadPoolExecutor(max_workers=1) as executor:
+                future = executor.submit(self.do_rg_confidence, image, mask, (x, y, z), bstruct)
-            dlg = wx.ProgressDialog(self._progr_title, self._progr_msg, parent=None, style=wx.PD_APP_MODAL)
-            while not future.done():
-                dlg.Pulse()
-                time.sleep(0.1)
+                dlg = wx.ProgressDialog(self._progr_title, self._progr_msg, parent=None, style=wx.PD_APP_MODAL)
+                while not future.done():
+                    dlg.Pulse()
+                    time.sleep(0.1)
+                dlg.Destroy()
+                out_mask = future.result()
+        else:
+            out_mask = np.zeros_like(mask)
+            with futures.ThreadPoolExecutor(max_workers=1) as executor:
+                future = executor.submit(floodfill.floodfill_threshold, image, [[x, y, z]], t0, t1, 1, bstruct, out_mask)
-            dlg.Destroy()
+                dlg = wx.ProgressDialog(self._progr_title, self._progr_msg, parent=None, style=wx.PD_APP_MODAL)
+                while not future.done():
+                    dlg.Pulse()
+                    time.sleep(0.1)
+
+                dlg.Destroy()
         mask[out_mask.astype('bool')] = self.config.fill_value
         self.viewer.slice_.current_mask.save_history(0, 'VOLUME', self.viewer.slice_.current_mask.matrix.copy(), cp_mask)
+    def do_rg_confidence(self, image, mask, p, bstruct):
+        x, y, z = p
+        if self.config.use_ww_wl:
+            ww = self.viewer.slice_.window_width
+            wl = self.viewer.slice_.window_level
+            image = get_LUT_value_255(image, ww, wl)
+        bool_mask = np.zeros_like(mask, dtype='bool')
+        out_mask = np.zeros_like(mask)
+
+        for k in xrange(int(z-1), int(z+2)):
+            if k < 0 or k >= bool_mask.shape[0]:
+                continue
+            for j in xrange(int(y-1), int(y+2)):
+                if j < 0 or j >= bool_mask.shape[1]:
+                    continue
+                for i in xrange(int(x-1), int(x+2)):
+                    if i < 0 or i >= bool_mask.shape[2]:
+                        continue
+                    bool_mask[k, j, i] = True
+
+        for i in xrange(self.config.confid_iters):
+            var = np.std(image[bool_mask])
+            mean = np.mean(image[bool_mask])
+
+            t0 = mean - var * self.config.confid_mult
+            t1 = mean + var * self.config.confid_mult
+
+            floodfill.floodfill_threshold(image, [[x, y, z]], t0, t1, 1, bstruct, out_mask)
+
+            bool_mask[out_mask == 1] = True
+
+        return out_mask
+
 def get_style(style):
     STYLES = {
         const.STATE_DEFAULT: DefaultInteractorStyle,
@@ -2031,6 +2031,64 @@ class PanelFFillDynamic(wx.Panel):
         self.config.dev_min = self.deviation_min.GetValue()
+class PanelFFillConfidence(wx.Panel):
+    def __init__(self, parent, config, ID=-1, style=wx.TAB_TRAVERSAL|wx.NO_BORDER):
+        wx.Panel.__init__(self, parent, ID, style=style)
+
+        self.config = config
+
+        self._init_gui()
+
+    def _init_gui(self):
+        self.use_ww_wl = wx.CheckBox(self, -1,  _(u"Use WW&WL"))
+        self.use_ww_wl.SetValue(self.config.use_ww_wl)
+
+        self.spin_mult = floatspin.FloatSpin(self, -1,
+                                             value=self.config.confid_mult,
+                                             min_val=1.0, max_val=10.0,
+                                             increment=0.1, digits=1,
+                                             style=wx.TE_PROCESS_TAB|wx.TE_PROCESS_ENTER,
+                                             agwStyle=floatspin.FS_RIGHT)
+        w, h = self.spin_mult.GetTextExtent('M')
+        self.spin_mult.SetMinSize((w*7, -1))
+
+        self.spin_iters = wx.SpinCtrl(self, -1, value='%d' % self.config.confid_iters, min=0, max=100)
+        self.spin_iters.SetMinSize((w*7, -1))
+
+        sizer = wx.GridBagSizer(5, 5)
+
+        sizer.AddStretchSpacer((0, 0))
+
+        sizer.Add(self.use_ww_wl, (1, 0), (1, 6), flag=wx.LEFT, border=5)
+
+        sizer.AddStretchSpacer((2, 0))
+
+        sizer.Add(wx.StaticText(self, -1, _(u"Multiplier")), (3, 0), (1, 3), flag=wx.ALIGN_CENTER_VERTICAL|wx.LEFT, border=5)
+        sizer.Add(self.spin_mult, (3, 3), (1, 2))
+
+        sizer.Add(wx.StaticText(self, -1, _(u"Iterations")), (4, 0), (1, 3), flag=wx.ALIGN_CENTER_VERTICAL|wx.LEFT, border=5)
+        sizer.Add(self.spin_iters, (4, 3), (1, 2))
+
+        sizer.AddStretchSpacer((5, 0))
+
+        self.SetSizer(sizer)
+        sizer.Fit(self)
+        self.Layout()
+
+        self.use_ww_wl.Bind(wx.EVT_CHECKBOX, self.OnSetUseWWWL)
+        self.spin_mult.Bind(wx.EVT_SPINCTRL, self.OnSetMult)
+        self.spin_iters.Bind(wx.EVT_SPINCTRL, self.OnSetIters)
+
+    def OnSetUseWWWL(self, evt):
+        self.config.use_ww_wl = self.use_ww_wl.GetValue()
+
+    def OnSetMult(self, evt):
+        self.config.confid_mult = self.spin_mult.GetValue()
+
+    def OnSetIters(self, evt):
+        self.config.confid_iters = self.spin_iters.GetValue()
+
+
 class FFillOptionsDialog(wx.Dialog):
     def __init__(self, title, config):
         pre = wx.PreDialog()
@@ -2273,13 +2331,14 @@ class FFillSegmentationOptionsDialog(wx.Dialog):
         else:
             self.panel3dcon.conect3D_6.SetValue(1)
-        self.cmb_method = wx.ComboBox(self, -1, choices=(_(u"Dynamic"), _(u"Threshold")), style=wx.CB_READONLY)
+        self.cmb_method = wx.ComboBox(self, -1, choices=(_(u"Dynamic"), _(u"Threshold"), _(u"Confidence")), style=wx.CB_READONLY)
         if self.config.method == 'dynamic':
             self.cmb_method.SetSelection(0)
-        else:
+        elif self.config.method == 'threshold':
             self.cmb_method.SetSelection(1)
-            self.config.method = 'threshold'
+        elif self.config.method == 'confidence':
+            self.cmb_method.SetSelection(2)
         self.panel_ffill_threshold = PanelFFillThreshold(self, self.config, -1, style=border_style|wx.TAB_TRAVERSAL)
         self.panel_ffill_threshold.SetMinSize((250, -1))
@@ -2289,6 +2348,10 @@ class FFillSegmentationOptionsDialog(wx.Dialog):
         self.panel_ffill_dynamic.SetMinSize((250, -1))
         self.panel_ffill_dynamic.Hide()
+        self.panel_ffill_confidence = PanelFFillConfidence(self, self.config, -1, style=border_style|wx.TAB_TRAVERSAL)
+        self.panel_ffill_confidence.SetMinSize((250, -1))
+        self.panel_ffill_confidence.Hide()
+
         self.close_btn = wx.Button(self, wx.ID_CLOSE)
         # Sizer
@@ -2313,6 +2376,10 @@ class FFillSegmentationOptionsDialog(wx.Dialog):
             self.cmb_method.SetSelection(0)
             self.panel_ffill_dynamic.Show()
             sizer.Add(self.panel_ffill_dynamic, (11, 0), (1, 6), flag=wx.LEFT|wx.RIGHT|wx.EXPAND, border=7)
+        elif self.config.method == 'confidence':
+            self.cmb_method.SetSelection(2)
+            self.panel_ffill_confidence.Show()
+            sizer.Add(self.panel_ffill_confidence, (11, 0), (1, 6), flag=wx.LEFT|wx.RIGHT|wx.EXPAND, border=7)
         else:
             self.cmb_method.SetSelection(1)
             self.panel_ffill_threshold.Show()
@@ -2358,16 +2425,25 @@ class FFillSegmentationOptionsDialog(wx.Dialog):
             self.config.con_3d = 26
     def OnSetMethod(self, evt):
+        item_panel = self.GetSizer().FindItemAtPosition((11, 0)).GetWindow()
+
         if self.cmb_method.GetSelection() == 0:
             self.config.method = 'dynamic'
-            self.panel_ffill_threshold.Hide()
+            item_panel.Hide()
             self.panel_ffill_dynamic.Show()
-            self.GetSizer().Replace(self.panel_ffill_threshold, self.panel_ffill_dynamic)
+            self.GetSizer().Replace(item_panel, self.panel_ffill_dynamic)
+
+        elif self.cmb_method.GetSelection() == 2:
+            self.config.method = 'confidence'
+            item_panel.Hide()
+            self.panel_ffill_confidence.Show()
+            self.GetSizer().Replace(item_panel, self.panel_ffill_confidence)
+
         else:
             self.config.method = 'threshold'
-            self.panel_ffill_dynamic.Hide()
+            item_panel.Hide()
             self.panel_ffill_threshold.Show()
-            self.GetSizer().Replace(self.panel_ffill_dynamic, self.panel_ffill_threshold)
+            self.GetSizer().Replace(item_panel, self.panel_ffill_threshold)
         self.GetSizer().Fit(self)
         self.Layout()
	@@ -1983,6 +1983,9 @@ class FFillSegmentationConfig(object):		@@ -1983,6 +1983,9 @@ class FFillSegmentationConfig(object):
1983		1983
1984	self.use_ww_wl = True	1984	self.use_ww_wl = True
1985		1985
		1986	+ self.confid_mult = 2.5
		1987	+ self.confid_iters = 3
		1988	+
1986		1989
1987	class FloodFillSegmentInteractorStyle(DefaultInteractorStyle):	1990	class FloodFillSegmentInteractorStyle(DefaultInteractorStyle):
1988	def __init__(self, viewer):	1991	def __init__(self, viewer):
	@@ -2052,36 +2055,47 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle):		@@ -2052,36 +2055,47 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle):
2052	mask = self.viewer.slice_.buffer_slices[self.orientation].mask.copy()	2055	mask = self.viewer.slice_.buffer_slices[self.orientation].mask.copy()
2053	image = self.viewer.slice_.buffer_slices[self.orientation].image	2056	image = self.viewer.slice_.buffer_slices[self.orientation].image
2054		2057
2055	- if self.config.method == 'threshold':
2056	- v = image[y, x]
2057	- t0 = self.config.t0
2058	- t1 = self.config.t1	2058	+ if self.config.method == 'confidence':
		2059	+ dy, dx = image.shape
		2060	+ image = image.reshape((1, dy, dx))
		2061	+ mask = mask.reshape((1, dy, dx))
2059		2062
2060	- elif self.config.method == 'dynamic':
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)	2063	+ bstruct = np.array(generate_binary_structure(2, CON2D[self.config.con_2d]), dtype='uint8')
		2064	+ bstruct = bstruct.reshape((1, 3, 3))
2066		2065
2067	- v = image[y, x]	2066	+ out_mask = self.do_rg_confidence(image, mask, (x, y, 0), bstruct)
		2067	+ else:
		2068	+ if self.config.method == 'threshold':
		2069	+ v = image[y, x]
		2070	+ t0 = self.config.t0
		2071	+ t1 = self.config.t1
2068		2072
2069	- t0 = v - self.config.dev_min
2070	- t1 = v + self.config.dev_max	2073	+ elif self.config.method == 'dynamic':
		2074	+ if self.config.use_ww_wl:
		2075	+ print "Using WW&WL"
		2076	+ ww = self.viewer.slice_.window_width
		2077	+ wl = self.viewer.slice_.window_level
		2078	+ image = get_LUT_value_255(image, ww, wl)
2071		2079
2072	- if image[y, x] < t0 or image[y, x] > t1:
2073	- return	2080	+ v = image[y, x]
2074		2081
2075	- dy, dx = image.shape
2076	- image = image.reshape((1, dy, dx))
2077	- mask = mask.reshape((1, dy, dx))	2082	+ t0 = v - self.config.dev_min
		2083	+ t1 = v + self.config.dev_max
2078		2084
2079	- out_mask = np.zeros_like(mask)
2080		2085
2081	- bstruct = np.array(generate_binary_structure(2, CON2D[self.config.con_2d]), dtype='uint8')
2082	- bstruct = bstruct.reshape((1, 3, 3))	2086	+ if image[y, x] < t0 or image[y, x] > t1:
		2087	+ return
		2088	+
		2089	+ dy, dx = image.shape
		2090	+ image = image.reshape((1, dy, dx))
		2091	+ mask = mask.reshape((1, dy, dx))
		2092	+
		2093	+ out_mask = np.zeros_like(mask)
		2094	+
		2095	+ bstruct = np.array(generate_binary_structure(2, CON2D[self.config.con_2d]), dtype='uint8')
		2096	+ bstruct = bstruct.reshape((1, 3, 3))
2083		2097
2084	- floodfill.floodfill_threshold(image, [[x, y, 0]], t0, t1, 1, bstruct, out_mask)	2098	+ floodfill.floodfill_threshold(image, [[x, y, 0]], t0, t1, 1, bstruct, out_mask)
2085		2099
2086	mask[out_mask.astype('bool')] = self.config.fill_value	2100	mask[out_mask.astype('bool')] = self.config.fill_value
2087		2101
	@@ -2107,46 +2121,91 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle):		@@ -2107,46 +2121,91 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle):
2107	mask = self.viewer.slice_.current_mask.matrix[1:, 1:, 1:]	2121	mask = self.viewer.slice_.current_mask.matrix[1:, 1:, 1:]
2108	image = self.viewer.slice_.matrix	2122	image = self.viewer.slice_.matrix
2109		2123
2110	- if self.config.method == 'threshold':
2111	- v = image[z, y, x]
2112	- t0 = self.config.t0
2113	- t1 = self.config.t1	2124	+ if self.config.method != 'confidence':
		2125	+ if self.config.method == 'threshold':
		2126	+ v = image[z, y, x]
		2127	+ t0 = self.config.t0
		2128	+ t1 = self.config.t1
2114		2129
2115	- elif self.config.method == 'dynamic':
2116	- if self.config.use_ww_wl:
2117	- print "Using WW&WL"
2118	- ww = self.viewer.slice_.window_width
2119	- wl = self.viewer.slice_.window_level
2120	- image = get_LUT_value_255(image, ww, wl)	2130	+ elif self.config.method == 'dynamic':
		2131	+ if self.config.use_ww_wl:
		2132	+ print "Using WW&WL"
		2133	+ ww = self.viewer.slice_.window_width
		2134	+ wl = self.viewer.slice_.window_level
		2135	+ image = get_LUT_value_255(image, ww, wl)
2121		2136
2122	- v = image[z, y, x]	2137	+ v = image[z, y, x]
2123		2138
2124	- t0 = v - self.config.dev_min
2125	- t1 = v + self.config.dev_max	2139	+ t0 = v - self.config.dev_min
		2140	+ t1 = v + self.config.dev_max
2126		2141
2127	- if image[z, y, x] < t0 or image[z, y, x] > t1:
2128	- return	2142	+ if image[z, y, x] < t0 or image[z, y, x] > t1:
		2143	+ return
2129		2144
2130	- out_mask = np.zeros_like(mask)
2131		2145
2132	bstruct = np.array(generate_binary_structure(3, CON3D[self.config.con_3d]), dtype='uint8')	2146	bstruct = np.array(generate_binary_structure(3, CON3D[self.config.con_3d]), dtype='uint8')
2133	self.viewer.slice_.do_threshold_to_all_slices()	2147	self.viewer.slice_.do_threshold_to_all_slices()
2134	cp_mask = self.viewer.slice_.current_mask.matrix.copy()	2148	cp_mask = self.viewer.slice_.current_mask.matrix.copy()
2135		2149
2136	- with futures.ThreadPoolExecutor(max_workers=1) as executor:
2137	- future = executor.submit(floodfill.floodfill_threshold, image, [[x, y, z]], t0, t1, 1, bstruct, out_mask)	2150	+ if self.config.method == 'confidence':
		2151	+ with futures.ThreadPoolExecutor(max_workers=1) as executor:
		2152	+ future = executor.submit(self.do_rg_confidence, image, mask, (x, y, z), bstruct)
2138		2153
2139	- dlg = wx.ProgressDialog(self._progr_title, self._progr_msg, parent=None, style=wx.PD_APP_MODAL)
2140	- while not future.done():
2141	- dlg.Pulse()
2142	- time.sleep(0.1)	2154	+ dlg = wx.ProgressDialog(self._progr_title, self._progr_msg, parent=None, style=wx.PD_APP_MODAL)
		2155	+ while not future.done():
		2156	+ dlg.Pulse()
		2157	+ time.sleep(0.1)
		2158	+ dlg.Destroy()
		2159	+ out_mask = future.result()
		2160	+ else:
		2161	+ out_mask = np.zeros_like(mask)
		2162	+ with futures.ThreadPoolExecutor(max_workers=1) as executor:
		2163	+ future = executor.submit(floodfill.floodfill_threshold, image, [[x, y, z]], t0, t1, 1, bstruct, out_mask)
2143		2164
2144	- dlg.Destroy()	2165	+ dlg = wx.ProgressDialog(self._progr_title, self._progr_msg, parent=None, style=wx.PD_APP_MODAL)
		2166	+ while not future.done():
		2167	+ dlg.Pulse()
		2168	+ time.sleep(0.1)
		2169	+
		2170	+ dlg.Destroy()
2145		2171
2146	mask[out_mask.astype('bool')] = self.config.fill_value	2172	mask[out_mask.astype('bool')] = self.config.fill_value
2147		2173
2148	self.viewer.slice_.current_mask.save_history(0, 'VOLUME', self.viewer.slice_.current_mask.matrix.copy(), cp_mask)	2174	self.viewer.slice_.current_mask.save_history(0, 'VOLUME', self.viewer.slice_.current_mask.matrix.copy(), cp_mask)
2149		2175
		2176	+ def do_rg_confidence(self, image, mask, p, bstruct):
		2177	+ x, y, z = p
		2178	+ if self.config.use_ww_wl:
		2179	+ ww = self.viewer.slice_.window_width
		2180	+ wl = self.viewer.slice_.window_level
		2181	+ image = get_LUT_value_255(image, ww, wl)
		2182	+ bool_mask = np.zeros_like(mask, dtype='bool')
		2183	+ out_mask = np.zeros_like(mask)
		2184	+
		2185	+ for k in xrange(int(z-1), int(z+2)):
		2186	+ if k < 0 or k >= bool_mask.shape[0]:
		2187	+ continue
		2188	+ for j in xrange(int(y-1), int(y+2)):
		2189	+ if j < 0 or j >= bool_mask.shape[1]:
		2190	+ continue
		2191	+ for i in xrange(int(x-1), int(x+2)):
		2192	+ if i < 0 or i >= bool_mask.shape[2]:
		2193	+ continue
		2194	+ bool_mask[k, j, i] = True
		2195	+
		2196	+ for i in xrange(self.config.confid_iters):
		2197	+ var = np.std(image[bool_mask])
		2198	+ mean = np.mean(image[bool_mask])
		2199	+
		2200	+ t0 = mean - var * self.config.confid_mult
		2201	+ t1 = mean + var * self.config.confid_mult
		2202	+
		2203	+ floodfill.floodfill_threshold(image, [[x, y, z]], t0, t1, 1, bstruct, out_mask)
		2204	+
		2205	+ bool_mask[out_mask == 1] = True
		2206	+
		2207	+ return out_mask
		2208	+
2150	def get_style(style):	2209	def get_style(style):
2151	STYLES = {	2210	STYLES = {
2152	const.STATE_DEFAULT: DefaultInteractorStyle,	2211	const.STATE_DEFAULT: DefaultInteractorStyle,
	@@ -2031,6 +2031,64 @@ class PanelFFillDynamic(wx.Panel):		@@ -2031,6 +2031,64 @@ class PanelFFillDynamic(wx.Panel):
2031	self.config.dev_min = self.deviation_min.GetValue()	2031	self.config.dev_min = self.deviation_min.GetValue()
2032		2032
2033		2033
		2034	+class PanelFFillConfidence(wx.Panel):
		2035	+ def __init__(self, parent, config, ID=-1, style=wx.TAB_TRAVERSAL\|wx.NO_BORDER):
		2036	+ wx.Panel.__init__(self, parent, ID, style=style)
		2037	+
		2038	+ self.config = config
		2039	+
		2040	+ self._init_gui()
		2041	+
		2042	+ def _init_gui(self):
		2043	+ self.use_ww_wl = wx.CheckBox(self, -1, _(u"Use WW&WL"))
		2044	+ self.use_ww_wl.SetValue(self.config.use_ww_wl)
		2045	+
		2046	+ self.spin_mult = floatspin.FloatSpin(self, -1,
		2047	+ value=self.config.confid_mult,
		2048	+ min_val=1.0, max_val=10.0,
		2049	+ increment=0.1, digits=1,
		2050	+ style=wx.TE_PROCESS_TAB\|wx.TE_PROCESS_ENTER,
		2051	+ agwStyle=floatspin.FS_RIGHT)
		2052	+ w, h = self.spin_mult.GetTextExtent('M')
		2053	+ self.spin_mult.SetMinSize((w*7, -1))
		2054	+
		2055	+ self.spin_iters = wx.SpinCtrl(self, -1, value='%d' % self.config.confid_iters, min=0, max=100)
		2056	+ self.spin_iters.SetMinSize((w*7, -1))
		2057	+
		2058	+ sizer = wx.GridBagSizer(5, 5)
		2059	+
		2060	+ sizer.AddStretchSpacer((0, 0))
		2061	+
		2062	+ sizer.Add(self.use_ww_wl, (1, 0), (1, 6), flag=wx.LEFT, border=5)
		2063	+
		2064	+ sizer.AddStretchSpacer((2, 0))
		2065	+
		2066	+ sizer.Add(wx.StaticText(self, -1, _(u"Multiplier")), (3, 0), (1, 3), flag=wx.ALIGN_CENTER_VERTICAL\|wx.LEFT, border=5)
		2067	+ sizer.Add(self.spin_mult, (3, 3), (1, 2))
		2068	+
		2069	+ sizer.Add(wx.StaticText(self, -1, _(u"Iterations")), (4, 0), (1, 3), flag=wx.ALIGN_CENTER_VERTICAL\|wx.LEFT, border=5)
		2070	+ sizer.Add(self.spin_iters, (4, 3), (1, 2))
		2071	+
		2072	+ sizer.AddStretchSpacer((5, 0))
		2073	+
		2074	+ self.SetSizer(sizer)
		2075	+ sizer.Fit(self)
		2076	+ self.Layout()
		2077	+
		2078	+ self.use_ww_wl.Bind(wx.EVT_CHECKBOX, self.OnSetUseWWWL)
		2079	+ self.spin_mult.Bind(wx.EVT_SPINCTRL, self.OnSetMult)
		2080	+ self.spin_iters.Bind(wx.EVT_SPINCTRL, self.OnSetIters)
		2081	+
		2082	+ def OnSetUseWWWL(self, evt):
		2083	+ self.config.use_ww_wl = self.use_ww_wl.GetValue()
		2084	+
		2085	+ def OnSetMult(self, evt):
		2086	+ self.config.confid_mult = self.spin_mult.GetValue()
		2087	+
		2088	+ def OnSetIters(self, evt):
		2089	+ self.config.confid_iters = self.spin_iters.GetValue()
		2090	+
		2091	+
2034	class FFillOptionsDialog(wx.Dialog):	2092	class FFillOptionsDialog(wx.Dialog):
2035	def __init__(self, title, config):	2093	def __init__(self, title, config):
2036	pre = wx.PreDialog()	2094	pre = wx.PreDialog()
	@@ -2273,13 +2331,14 @@ class FFillSegmentationOptionsDialog(wx.Dialog):		@@ -2273,13 +2331,14 @@ class FFillSegmentationOptionsDialog(wx.Dialog):
2273	else:	2331	else:
2274	self.panel3dcon.conect3D_6.SetValue(1)	2332	self.panel3dcon.conect3D_6.SetValue(1)
2275		2333
2276	- self.cmb_method = wx.ComboBox(self, -1, choices=(_(u"Dynamic"), _(u"Threshold")), style=wx.CB_READONLY)	2334	+ self.cmb_method = wx.ComboBox(self, -1, choices=(_(u"Dynamic"), _(u"Threshold"), _(u"Confidence")), style=wx.CB_READONLY)
2277		2335
2278	if self.config.method == 'dynamic':	2336	if self.config.method == 'dynamic':
2279	self.cmb_method.SetSelection(0)	2337	self.cmb_method.SetSelection(0)
2280	- else:	2338	+ elif self.config.method == 'threshold':
2281	self.cmb_method.SetSelection(1)	2339	self.cmb_method.SetSelection(1)
2282	- self.config.method = 'threshold'	2340	+ elif self.config.method == 'confidence':
		2341	+ self.cmb_method.SetSelection(2)
2283		2342
2284	self.panel_ffill_threshold = PanelFFillThreshold(self, self.config, -1, style=border_style\|wx.TAB_TRAVERSAL)	2343	self.panel_ffill_threshold = PanelFFillThreshold(self, self.config, -1, style=border_style\|wx.TAB_TRAVERSAL)
2285	self.panel_ffill_threshold.SetMinSize((250, -1))	2344	self.panel_ffill_threshold.SetMinSize((250, -1))
	@@ -2289,6 +2348,10 @@ class FFillSegmentationOptionsDialog(wx.Dialog):		@@ -2289,6 +2348,10 @@ class FFillSegmentationOptionsDialog(wx.Dialog):
2289	self.panel_ffill_dynamic.SetMinSize((250, -1))	2348	self.panel_ffill_dynamic.SetMinSize((250, -1))
2290	self.panel_ffill_dynamic.Hide()	2349	self.panel_ffill_dynamic.Hide()
2291		2350
		2351	+ self.panel_ffill_confidence = PanelFFillConfidence(self, self.config, -1, style=border_style\|wx.TAB_TRAVERSAL)
		2352	+ self.panel_ffill_confidence.SetMinSize((250, -1))
		2353	+ self.panel_ffill_confidence.Hide()
		2354	+
2292	self.close_btn = wx.Button(self, wx.ID_CLOSE)	2355	self.close_btn = wx.Button(self, wx.ID_CLOSE)
2293		2356
2294	# Sizer	2357	# Sizer
	@@ -2313,6 +2376,10 @@ class FFillSegmentationOptionsDialog(wx.Dialog):		@@ -2313,6 +2376,10 @@ class FFillSegmentationOptionsDialog(wx.Dialog):
2313	self.cmb_method.SetSelection(0)	2376	self.cmb_method.SetSelection(0)
2314	self.panel_ffill_dynamic.Show()	2377	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)	2378	sizer.Add(self.panel_ffill_dynamic, (11, 0), (1, 6), flag=wx.LEFT\|wx.RIGHT\|wx.EXPAND, border=7)
		2379	+ elif self.config.method == 'confidence':
		2380	+ self.cmb_method.SetSelection(2)
		2381	+ self.panel_ffill_confidence.Show()
		2382	+ sizer.Add(self.panel_ffill_confidence, (11, 0), (1, 6), flag=wx.LEFT\|wx.RIGHT\|wx.EXPAND, border=7)
2316	else:	2383	else:
2317	self.cmb_method.SetSelection(1)	2384	self.cmb_method.SetSelection(1)
2318	self.panel_ffill_threshold.Show()	2385	self.panel_ffill_threshold.Show()
	@@ -2358,16 +2425,25 @@ class FFillSegmentationOptionsDialog(wx.Dialog):		@@ -2358,16 +2425,25 @@ class FFillSegmentationOptionsDialog(wx.Dialog):
2358	self.config.con_3d = 26	2425	self.config.con_3d = 26
2359		2426
2360	def OnSetMethod(self, evt):	2427	def OnSetMethod(self, evt):
		2428	+ item_panel = self.GetSizer().FindItemAtPosition((11, 0)).GetWindow()
		2429	+
2361	if self.cmb_method.GetSelection() == 0:	2430	if self.cmb_method.GetSelection() == 0:
2362	self.config.method = 'dynamic'	2431	self.config.method = 'dynamic'
2363	- self.panel_ffill_threshold.Hide()	2432	+ item_panel.Hide()
2364	self.panel_ffill_dynamic.Show()	2433	self.panel_ffill_dynamic.Show()
2365	- self.GetSizer().Replace(self.panel_ffill_threshold, self.panel_ffill_dynamic)	2434	+ self.GetSizer().Replace(item_panel, self.panel_ffill_dynamic)
		2435	+
		2436	+ elif self.cmb_method.GetSelection() == 2:
		2437	+ self.config.method = 'confidence'
		2438	+ item_panel.Hide()
		2439	+ self.panel_ffill_confidence.Show()
		2440	+ self.GetSizer().Replace(item_panel, self.panel_ffill_confidence)
		2441	+
2366	else:	2442	else:
2367	self.config.method = 'threshold'	2443	self.config.method = 'threshold'
2368	- self.panel_ffill_dynamic.Hide()	2444	+ item_panel.Hide()
2369	self.panel_ffill_threshold.Show()	2445	self.panel_ffill_threshold.Show()
2370	- self.GetSizer().Replace(self.panel_ffill_dynamic, self.panel_ffill_threshold)	2446	+ self.GetSizer().Replace(item_panel, self.panel_ffill_threshold)
2371		2447
2372	self.GetSizer().Fit(self)	2448	self.GetSizer().Fit(self)
2373	self.Layout()	2449	self.Layout()