starting to clean slice_.py

Thiago Franco de Moraes
1 parent c010bda2
Showing 1 changed file with 18 additions and 176 deletions Show diff stats
invesalius/data/slice_.py
@@ -16,7 +16,6 @@
 #    PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
 #    detalhes.
 #--------------------------------------------------------------------------
-import math
 import os
 import tempfile
@@ -79,7 +78,6 @@ class Slice(object):
     # Therefore, we use Singleton design pattern for implementing it.
     def __init__(self):
-        self.imagedata = None
         self.current_mask = None
         self.blend_filter = None
         self.histogram = None
@@ -249,7 +247,6 @@ class Slice(object):
         self.CloseProject()
     def CloseProject(self):
-        self.imagedata = None
         f = self._matrix.filename
         self._matrix._mmap.close()
         self._matrix  = None
@@ -836,19 +833,12 @@ class Slice(object):
     def SelectCurrentMask(self, index):
         "Insert mask data, based on given index, into pipeline."
-        # This condition is not necessary in Linux, only under mac and windows
-        # because combobox event is binded when the same item is selected again.
-        #if index != self.current_mask.index:
-        print "SelectCurrentMask"
-        print "index:", index
         proj = Project()
         future_mask = proj.GetMask(index)
         future_mask.is_shown = True
         self.current_mask = future_mask
         colour = future_mask.colour
-        #index = future_mask.index
-        print index
         self.SetMaskColour(index, colour, update=False)
         self.buffer_slices = {"AXIAL": SliceBuffer(),
@@ -871,18 +861,9 @@ class Slice(object):
         proj = Project()
         mask = proj.mask_dict[surface_parameters['options']['index']]
-        # This is very important. Do not use masks' imagedata. It would mess up
-        # surface quality event when using contour
-        #self.SetMaskThreshold(mask.index, threshold)
-        for n in xrange(1, mask.matrix.shape[0]):
-            if mask.matrix[n, 0, 0] == 0:
-                m = mask.matrix[n, 1:, 1:]
-                mask.matrix[n, 1:, 1:] = self.do_threshold_to_a_slice(self.matrix[n-1], m)
+        self.do_threshold_to_all_slices(mask)
+        Publisher.sendMessage('Create surface', (self, mask, surface_parameters))
-        mask.matrix.flush()
-
-        Publisher.sendMessage('Create surface', (self, mask,
-                                                 surface_parameters))
     def GetOutput(self):
         return self.blend_filter.GetOutput()
@@ -906,59 +887,6 @@ class Slice(object):
             Publisher.sendMessage('Check projection menu', tprojection)
-    def SetInput(self, imagedata, mask_dict):
-        print "SETINPUT!"
-        self.imagedata = imagedata
-        self.extent = imagedata.GetExtent()
-
-        imagedata_bg = self.__create_background(imagedata)
-
-        if not mask_dict:
-            imagedata_mask = self.__build_mask(imagedata, create=True)
-        else:
-            self.__load_masks(imagedata, mask_dict)
-            imagedata_mask = self.img_colours_mask.GetOutput()
-
-        mask_opacity = self.current_mask.opacity
-
-        # blend both imagedatas, so it can be inserted into viewer
-        blend_filter = vtk.vtkImageBlend()
-        blend_filter.SetBlendModeToNormal()
-        blend_filter.SetOpacity(0, 1)
-        if self.current_mask.is_shown:
-            blend_filter.SetOpacity(1, mask_opacity)
-        else:
-            blend_filter.SetOpacity(1, 0)
-        blend_filter.SetInput(0, imagedata_bg)
-        blend_filter.SetInput(1, imagedata_mask)
-        blend_filter.SetBlendModeToNormal()
-        blend_filter.GetOutput().ReleaseDataFlagOn()
-        self.blend_filter = blend_filter
-
-        self.window_level = vtk.vtkImageMapToWindowLevelColors()
-        self.window_level.SetInput(self.imagedata)
-
-    def __create_background(self, imagedata):
-        thresh_min, thresh_max = imagedata.GetScalarRange()
-        Publisher.sendMessage('Update threshold limits list', (thresh_min,
-                                    thresh_max))
-
-        # map scalar values into colors
-        lut_bg = self.lut_bg = vtk.vtkLookupTable()
-        lut_bg.SetTableRange(thresh_min, thresh_max)
-        lut_bg.SetSaturationRange(0, 0)
-        lut_bg.SetHueRange(0, 0)
-        lut_bg.SetValueRange(0, 1)
-        lut_bg.Build()
-
-        # map the input image through a lookup table
-        img_colours_bg = self.img_colours_bg = vtk.vtkImageMapToColors()
-        img_colours_bg.SetOutputFormatToRGBA()
-        img_colours_bg.SetLookupTable(lut_bg)
-        img_colours_bg.SetInput(imagedata)
-
-        return img_colours_bg.GetOutput()
-
     def UpdateWindowLevelBackground(self, pubsub_evt):
         window, level = pubsub_evt.data
         self.window_width = window
@@ -1030,15 +958,12 @@ class Slice(object):
         cast.ClampOverflowOn()
         cast.Update()
-        #if (original_orientation == const.AXIAL):
         flip = vtk.vtkImageFlip()
         flip.SetInput(cast.GetOutput())
         flip.SetFilteredAxis(1)
         flip.FlipAboutOriginOn()
         flip.Update()
         widget.SetInput(flip.GetOutput())
-        #else:
-            #widget.SetInput(cast.GetOutput())
     def UpdateSlice3D(self, pubsub_evt):
         widget, orientation = pubsub_evt.data
@@ -1111,27 +1036,6 @@ class Slice(object):
             Publisher.sendMessage('Change mask selected', mask.index)
             Publisher.sendMessage('Update slice viewer')
-    def __load_masks(self, imagedata, mask_dict):
-        keys = mask_dict.keys()
-        keys.sort()
-        for key in keys:
-            mask = mask_dict[key]
-
-            # update gui related to mask
-            utils.debug("__load_masks")
-            utils.debug('THRESHOLD_RANGE %s'% mask.threshold_range)
-            Publisher.sendMessage('Add mask',
-                                    (mask.index,
-                                     mask.name,
-                                     mask.threshold_range,
-                                     mask.colour))
-
-        self.current_mask = mask
-        self.__build_mask(imagedata, False)
-
-        Publisher.sendMessage('Change mask selected', mask.index)
-        Publisher.sendMessage('Update slice viewer')
-
     def do_ww_wl(self, image):
         if self.from_ == PLIST:
             lut = vtk.vtkWindowLevelLookupTable()
@@ -1212,12 +1116,16 @@ class Slice(object):
         m[mask == 254] = 254
         return m.astype('uint8')
-    def do_threshold_to_all_slices(self):
-        mask = self.current_mask
+    def do_threshold_to_all_slices(self, mask=None):
+        """
+        Apply threshold to all slices.
-        # This is very important. Do not use masks' imagedata. It would mess up
-        # surface quality event when using contour
-        #self.SetMaskThreshold(mask.index, threshold)
+        Params:
+            - mask: the mask where result of the threshold will be stored.If
+              None, it'll be the current mask.
+        """
+        if mask is None:
+            mask = self.current_mask
         for n in xrange(1, mask.matrix.shape[0]):
             if mask.matrix[n, 0, 0] == 0:
                 m = mask.matrix[n, 1:, 1:]
@@ -1390,76 +1298,9 @@ class Slice(object):
             self.buffer_slices[o].discard_vtk_mask()
         Publisher.sendMessage('Reload actual slice')
-    def __build_mask(self, imagedata, create=True):
-        # create new mask instance and insert it into project
-        if create:
-            self.CreateMask(imagedata=imagedata)
-        current_mask = self.current_mask
-
-        # properties to be inserted into pipeline
-        scalar_range = int(imagedata.GetScalarRange()[1])
-        r,g,b = current_mask.colour
-
-        # map scalar values into colors
-        lut_mask = vtk.vtkLookupTable()
-        lut_mask.SetNumberOfTableValues(1)
-        lut_mask.SetNumberOfColors(1)
-        lut_mask.SetHueRange(const.THRESHOLD_HUE_RANGE)
-        lut_mask.SetSaturationRange(1, 1)
-        lut_mask.SetValueRange(1, 1)
-        lut_mask.SetNumberOfTableValues(scalar_range)
-        lut_mask.SetTableValue(1, r, g, b, 1.0)
-        lut_mask.SetTableValue(scalar_range - 1, r, g, b, 1.0)
-        lut_mask.SetRampToLinear()
-        lut_mask.Build()
-        self.lut_mask = lut_mask
-
-        mask_thresh_imagedata = self.__create_mask_threshold(imagedata)
-
-        if create:
-            # threshold pipeline
-            current_mask.imagedata.DeepCopy(mask_thresh_imagedata)
-        else:
-            mask_thresh_imagedata = self.current_mask.imagedata
-
-        # map the input image through a lookup table
-        img_colours_mask = vtk.vtkImageMapToColors()
-        img_colours_mask.SetOutputFormatToRGBA()
-        img_colours_mask.SetLookupTable(lut_mask)
-
-        img_colours_mask.SetInput(mask_thresh_imagedata)
-
-        self.img_colours_mask = img_colours_mask
-
-        return img_colours_mask.GetOutput()
-
-    def __create_mask_threshold(self, imagedata, threshold_range=None):
-        if not threshold_range:
-            thresh_min, thresh_max = self.current_mask.threshold_range
-        else:
-            thresh_min, thresh_max = threshold_range
-
-        # flexible threshold
-        img_thresh_mask = vtk.vtkImageThreshold()
-        img_thresh_mask.SetInValue(const.THRESHOLD_INVALUE)
-        img_thresh_mask.SetInput(imagedata)
-        img_thresh_mask.SetOutValue(const.THRESHOLD_OUTVALUE)
-        img_thresh_mask.ThresholdBetween(float(thresh_min), float(thresh_max))
-        img_thresh_mask.Update()
-        self.img_thresh_mask = img_thresh_mask
-
-        # copy of threshold output
-        imagedata_mask = vtk.vtkImageData()
-        imagedata_mask.DeepCopy(img_thresh_mask.GetOutput())
-        imagedata_mask.Update()
-
-        return imagedata_mask
-
     def _open_image_matrix(self, filename, shape, dtype):
         self.matrix_filename = filename
-        print ">>>", filename
-        self.matrix = numpy.memmap(filename, shape=shape, dtype=dtype,
-                                   mode='r+')
+        self.matrix = numpy.memmap(filename, shape=shape, dtype=dtype, mode='r+')
     def OnFlipVolume(self, pubsub_evt):
         axis = pubsub_evt.data
@@ -1489,8 +1330,9 @@ class Slice(object):
         print type(self.matrix)
     def OnExportMask(self, pubsub_evt):
-        #imagedata = self.current_mask.imagedata
-        imagedata = self.imagedata
-        filename, filetype = pubsub_evt.data
-        if (filetype == const.FILETYPE_IMAGEDATA):
-            iu.Export(imagedata, filename)
+        pass
+        ##imagedata = self.current_mask.imagedata
+        #imagedata = self.imagedata
+        #filename, filetype = pubsub_evt.data
+        #if (filetype == const.FILETYPE_IMAGEDATA):
+            #iu.Export(imagedata, filename)
	@@ -16,7 +16,6 @@		@@ -16,7 +16,6 @@
16	# PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais	16	# PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
17	# detalhes.	17	# detalhes.
18	#--------------------------------------------------------------------------	18	#--------------------------------------------------------------------------
19	-import math
20	import os	19	import os
21	import tempfile	20	import tempfile
22		21
	@@ -79,7 +78,6 @@ class Slice(object):		@@ -79,7 +78,6 @@ class Slice(object):
79	# Therefore, we use Singleton design pattern for implementing it.	78	# Therefore, we use Singleton design pattern for implementing it.
80		79
81	def __init__(self):	80	def __init__(self):
82	- self.imagedata = None
83	self.current_mask = None	81	self.current_mask = None
84	self.blend_filter = None	82	self.blend_filter = None
85	self.histogram = None	83	self.histogram = None
	@@ -249,7 +247,6 @@ class Slice(object):		@@ -249,7 +247,6 @@ class Slice(object):
249	self.CloseProject()	247	self.CloseProject()
250		248
251	def CloseProject(self):	249	def CloseProject(self):
252	- self.imagedata = None
253	f = self._matrix.filename	250	f = self._matrix.filename
254	self._matrix._mmap.close()	251	self._matrix._mmap.close()
255	self._matrix = None	252	self._matrix = None
	@@ -836,19 +833,12 @@ class Slice(object):		@@ -836,19 +833,12 @@ class Slice(object):
836		833
837	def SelectCurrentMask(self, index):	834	def SelectCurrentMask(self, index):
838	"Insert mask data, based on given index, into pipeline."	835	"Insert mask data, based on given index, into pipeline."
839	- # This condition is not necessary in Linux, only under mac and windows
840	- # because combobox event is binded when the same item is selected again.
841	- #if index != self.current_mask.index:
842	- print "SelectCurrentMask"
843	- print "index:", index
844	proj = Project()	836	proj = Project()
845	future_mask = proj.GetMask(index)	837	future_mask = proj.GetMask(index)
846	future_mask.is_shown = True	838	future_mask.is_shown = True
847	self.current_mask = future_mask	839	self.current_mask = future_mask
848		840
849	colour = future_mask.colour	841	colour = future_mask.colour
850	- #index = future_mask.index
851	- print index
852	self.SetMaskColour(index, colour, update=False)	842	self.SetMaskColour(index, colour, update=False)
853		843
854	self.buffer_slices = {"AXIAL": SliceBuffer(),	844	self.buffer_slices = {"AXIAL": SliceBuffer(),
	@@ -871,18 +861,9 @@ class Slice(object):		@@ -871,18 +861,9 @@ class Slice(object):
871	proj = Project()	861	proj = Project()
872	mask = proj.mask_dict[surface_parameters['options']['index']]	862	mask = proj.mask_dict[surface_parameters['options']['index']]
873		863
874	- # This is very important. Do not use masks' imagedata. It would mess up
875	- # surface quality event when using contour
876	- #self.SetMaskThreshold(mask.index, threshold)
877	- for n in xrange(1, mask.matrix.shape[0]):
878	- if mask.matrix[n, 0, 0] == 0:
879	- m = mask.matrix[n, 1:, 1:]
880	- mask.matrix[n, 1:, 1:] = self.do_threshold_to_a_slice(self.matrix[n-1], m)	864	+ self.do_threshold_to_all_slices(mask)
		865	+ Publisher.sendMessage('Create surface', (self, mask, surface_parameters))
881		866
882	- mask.matrix.flush()
883	-
884	- Publisher.sendMessage('Create surface', (self, mask,
885	- surface_parameters))
886	def GetOutput(self):	867	def GetOutput(self):
887	return self.blend_filter.GetOutput()	868	return self.blend_filter.GetOutput()
888		869
	@@ -906,59 +887,6 @@ class Slice(object):		@@ -906,59 +887,6 @@ class Slice(object):
906		887
907	Publisher.sendMessage('Check projection menu', tprojection)	888	Publisher.sendMessage('Check projection menu', tprojection)
908		889
909	- def SetInput(self, imagedata, mask_dict):
910	- print "SETINPUT!"
911	- self.imagedata = imagedata
912	- self.extent = imagedata.GetExtent()
913	-
914	- imagedata_bg = self.__create_background(imagedata)
915	-
916	- if not mask_dict:
917	- imagedata_mask = self.__build_mask(imagedata, create=True)
918	- else:
919	- self.__load_masks(imagedata, mask_dict)
920	- imagedata_mask = self.img_colours_mask.GetOutput()
921	-
922	- mask_opacity = self.current_mask.opacity
923	-
924	- # blend both imagedatas, so it can be inserted into viewer
925	- blend_filter = vtk.vtkImageBlend()
926	- blend_filter.SetBlendModeToNormal()
927	- blend_filter.SetOpacity(0, 1)
928	- if self.current_mask.is_shown:
929	- blend_filter.SetOpacity(1, mask_opacity)
930	- else:
931	- blend_filter.SetOpacity(1, 0)
932	- blend_filter.SetInput(0, imagedata_bg)
933	- blend_filter.SetInput(1, imagedata_mask)
934	- blend_filter.SetBlendModeToNormal()
935	- blend_filter.GetOutput().ReleaseDataFlagOn()
936	- self.blend_filter = blend_filter
937	-
938	- self.window_level = vtk.vtkImageMapToWindowLevelColors()
939	- self.window_level.SetInput(self.imagedata)
940	-
941	- def __create_background(self, imagedata):
942	- thresh_min, thresh_max = imagedata.GetScalarRange()
943	- Publisher.sendMessage('Update threshold limits list', (thresh_min,
944	- thresh_max))
945	-
946	- # map scalar values into colors
947	- lut_bg = self.lut_bg = vtk.vtkLookupTable()
948	- lut_bg.SetTableRange(thresh_min, thresh_max)
949	- lut_bg.SetSaturationRange(0, 0)
950	- lut_bg.SetHueRange(0, 0)
951	- lut_bg.SetValueRange(0, 1)
952	- lut_bg.Build()
953	-
954	- # map the input image through a lookup table
955	- img_colours_bg = self.img_colours_bg = vtk.vtkImageMapToColors()
956	- img_colours_bg.SetOutputFormatToRGBA()
957	- img_colours_bg.SetLookupTable(lut_bg)
958	- img_colours_bg.SetInput(imagedata)
959	-
960	- return img_colours_bg.GetOutput()
961	-
962	def UpdateWindowLevelBackground(self, pubsub_evt):	890	def UpdateWindowLevelBackground(self, pubsub_evt):
963	window, level = pubsub_evt.data	891	window, level = pubsub_evt.data
964	self.window_width = window	892	self.window_width = window
	@@ -1030,15 +958,12 @@ class Slice(object):		@@ -1030,15 +958,12 @@ class Slice(object):
1030	cast.ClampOverflowOn()	958	cast.ClampOverflowOn()
1031	cast.Update()	959	cast.Update()
1032		960
1033	- #if (original_orientation == const.AXIAL):
1034	flip = vtk.vtkImageFlip()	961	flip = vtk.vtkImageFlip()
1035	flip.SetInput(cast.GetOutput())	962	flip.SetInput(cast.GetOutput())
1036	flip.SetFilteredAxis(1)	963	flip.SetFilteredAxis(1)
1037	flip.FlipAboutOriginOn()	964	flip.FlipAboutOriginOn()
1038	flip.Update()	965	flip.Update()
1039	widget.SetInput(flip.GetOutput())	966	widget.SetInput(flip.GetOutput())
1040	- #else:
1041	- #widget.SetInput(cast.GetOutput())
1042		967
1043	def UpdateSlice3D(self, pubsub_evt):	968	def UpdateSlice3D(self, pubsub_evt):
1044	widget, orientation = pubsub_evt.data	969	widget, orientation = pubsub_evt.data
	@@ -1111,27 +1036,6 @@ class Slice(object):		@@ -1111,27 +1036,6 @@ class Slice(object):
1111	Publisher.sendMessage('Change mask selected', mask.index)	1036	Publisher.sendMessage('Change mask selected', mask.index)
1112	Publisher.sendMessage('Update slice viewer')	1037	Publisher.sendMessage('Update slice viewer')
1113		1038
1114	- def __load_masks(self, imagedata, mask_dict):
1115	- keys = mask_dict.keys()
1116	- keys.sort()
1117	- for key in keys:
1118	- mask = mask_dict[key]
1119	-
1120	- # update gui related to mask
1121	- utils.debug("__load_masks")
1122	- utils.debug('THRESHOLD_RANGE %s'% mask.threshold_range)
1123	- Publisher.sendMessage('Add mask',
1124	- (mask.index,
1125	- mask.name,
1126	- mask.threshold_range,
1127	- mask.colour))
1128	-
1129	- self.current_mask = mask
1130	- self.__build_mask(imagedata, False)
1131	-
1132	- Publisher.sendMessage('Change mask selected', mask.index)
1133	- Publisher.sendMessage('Update slice viewer')
1134	-
1135	def do_ww_wl(self, image):	1039	def do_ww_wl(self, image):
1136	if self.from_ == PLIST:	1040	if self.from_ == PLIST:
1137	lut = vtk.vtkWindowLevelLookupTable()	1041	lut = vtk.vtkWindowLevelLookupTable()
	@@ -1212,12 +1116,16 @@ class Slice(object):		@@ -1212,12 +1116,16 @@ class Slice(object):
1212	m[mask == 254] = 254	1116	m[mask == 254] = 254
1213	return m.astype('uint8')	1117	return m.astype('uint8')
1214		1118
1215	- def do_threshold_to_all_slices(self):
1216	- mask = self.current_mask	1119	+ def do_threshold_to_all_slices(self, mask=None):
		1120	+ """
		1121	+ Apply threshold to all slices.
1217		1122
1218	- # This is very important. Do not use masks' imagedata. It would mess up
1219	- # surface quality event when using contour
1220	- #self.SetMaskThreshold(mask.index, threshold)	1123	+ Params:
		1124	+ - mask: the mask where result of the threshold will be stored.If
		1125	+ None, it'll be the current mask.
		1126	+ """
		1127	+ if mask is None:
		1128	+ mask = self.current_mask
1221	for n in xrange(1, mask.matrix.shape[0]):	1129	for n in xrange(1, mask.matrix.shape[0]):
1222	if mask.matrix[n, 0, 0] == 0:	1130	if mask.matrix[n, 0, 0] == 0:
1223	m = mask.matrix[n, 1:, 1:]	1131	m = mask.matrix[n, 1:, 1:]
	@@ -1390,76 +1298,9 @@ class Slice(object):		@@ -1390,76 +1298,9 @@ class Slice(object):
1390	self.buffer_slices[o].discard_vtk_mask()	1298	self.buffer_slices[o].discard_vtk_mask()
1391	Publisher.sendMessage('Reload actual slice')	1299	Publisher.sendMessage('Reload actual slice')
1392		1300
1393	- def __build_mask(self, imagedata, create=True):
1394	- # create new mask instance and insert it into project
1395	- if create:
1396	- self.CreateMask(imagedata=imagedata)
1397	- current_mask = self.current_mask
1398	-
1399	- # properties to be inserted into pipeline
1400	- scalar_range = int(imagedata.GetScalarRange()[1])
1401	- r,g,b = current_mask.colour
1402	-
1403	- # map scalar values into colors
1404	- lut_mask = vtk.vtkLookupTable()
1405	- lut_mask.SetNumberOfTableValues(1)
1406	- lut_mask.SetNumberOfColors(1)
1407	- lut_mask.SetHueRange(const.THRESHOLD_HUE_RANGE)
1408	- lut_mask.SetSaturationRange(1, 1)
1409	- lut_mask.SetValueRange(1, 1)
1410	- lut_mask.SetNumberOfTableValues(scalar_range)
1411	- lut_mask.SetTableValue(1, r, g, b, 1.0)
1412	- lut_mask.SetTableValue(scalar_range - 1, r, g, b, 1.0)
1413	- lut_mask.SetRampToLinear()
1414	- lut_mask.Build()
1415	- self.lut_mask = lut_mask
1416	-
1417	- mask_thresh_imagedata = self.__create_mask_threshold(imagedata)
1418	-
1419	- if create:
1420	- # threshold pipeline
1421	- current_mask.imagedata.DeepCopy(mask_thresh_imagedata)
1422	- else:
1423	- mask_thresh_imagedata = self.current_mask.imagedata
1424	-
1425	- # map the input image through a lookup table
1426	- img_colours_mask = vtk.vtkImageMapToColors()
1427	- img_colours_mask.SetOutputFormatToRGBA()
1428	- img_colours_mask.SetLookupTable(lut_mask)
1429	-
1430	- img_colours_mask.SetInput(mask_thresh_imagedata)
1431	-
1432	- self.img_colours_mask = img_colours_mask
1433	-
1434	- return img_colours_mask.GetOutput()
1435	-
1436	- def __create_mask_threshold(self, imagedata, threshold_range=None):
1437	- if not threshold_range:
1438	- thresh_min, thresh_max = self.current_mask.threshold_range
1439	- else:
1440	- thresh_min, thresh_max = threshold_range
1441	-
1442	- # flexible threshold
1443	- img_thresh_mask = vtk.vtkImageThreshold()
1444	- img_thresh_mask.SetInValue(const.THRESHOLD_INVALUE)
1445	- img_thresh_mask.SetInput(imagedata)
1446	- img_thresh_mask.SetOutValue(const.THRESHOLD_OUTVALUE)
1447	- img_thresh_mask.ThresholdBetween(float(thresh_min), float(thresh_max))
1448	- img_thresh_mask.Update()
1449	- self.img_thresh_mask = img_thresh_mask
1450	-
1451	- # copy of threshold output
1452	- imagedata_mask = vtk.vtkImageData()
1453	- imagedata_mask.DeepCopy(img_thresh_mask.GetOutput())
1454	- imagedata_mask.Update()
1455	-
1456	- return imagedata_mask
1457	-
1458	def _open_image_matrix(self, filename, shape, dtype):	1301	def _open_image_matrix(self, filename, shape, dtype):
1459	self.matrix_filename = filename	1302	self.matrix_filename = filename
1460	- print ">>>", filename
1461	- self.matrix = numpy.memmap(filename, shape=shape, dtype=dtype,
1462	- mode='r+')	1303	+ self.matrix = numpy.memmap(filename, shape=shape, dtype=dtype, mode='r+')
1463		1304
1464	def OnFlipVolume(self, pubsub_evt):	1305	def OnFlipVolume(self, pubsub_evt):
1465	axis = pubsub_evt.data	1306	axis = pubsub_evt.data
	@@ -1489,8 +1330,9 @@ class Slice(object):		@@ -1489,8 +1330,9 @@ class Slice(object):
1489	print type(self.matrix)	1330	print type(self.matrix)
1490		1331
1491	def OnExportMask(self, pubsub_evt):	1332	def OnExportMask(self, pubsub_evt):
1492	- #imagedata = self.current_mask.imagedata
1493	- imagedata = self.imagedata
1494	- filename, filetype = pubsub_evt.data
1495	- if (filetype == const.FILETYPE_IMAGEDATA):
1496	- iu.Export(imagedata, filename)	1333	+ pass
		1334	+ ##imagedata = self.current_mask.imagedata
		1335	+ #imagedata = self.imagedata
		1336	+ #filename, filetype = pubsub_evt.data
		1337	+ #if (filetype == const.FILETYPE_IMAGEDATA):
		1338	+ #iu.Export(imagedata, filename)