FIX: Fixed error in generate surface in the win32 and win64 ticket #271

Paulo Henrique Junqueira Amorim
1 parent e58244f7
Showing 4 changed files with 31 additions and 46 deletions Show diff stats
invesalius/data/imagedata_utils.py
invesalius/data/slice_.py
invesalius/data/surface_process.py
invesalius/session.py
@@ -546,39 +546,4 @@ def analyze2mmap(analyze):
     matrix.flush()
     return matrix, temp_file
  
-def to_vtk(n_array, spacing, slice_number, orientation):
-    try:
-        dz, dy, dx = n_array.shape
-    except ValueError:
-        dy, dx = n_array.shape
-        dz = 1
-
-    v_image = numpy_support.numpy_to_vtk(n_array.flat)
-
-    print orientation
-    if orientation == 'AXIAL':
-        extent = (0, dx -1, 0, dy -1, slice_number, slice_number + dz - 1)
-    elif orientation == 'SAGITAL':
-        dx, dy, dz = dz, dx, dy
-        extent = (slice_number, slice_number + dx - 1, 0, dy - 1, 0, dz - 1)
-    elif orientation == 'CORONAL':
-        dx, dy, dz = dx, dz, dy
-        extent = (0, dx - 1, slice_number, slice_number + dy - 1, 0, dz - 1)
-
-    # Generating the vtkImageData
-    image = vtk.vtkImageData()
-    image.SetOrigin(0, 0, 0)
-    image.SetSpacing(spacing)
-    image.SetNumberOfScalarComponents(1)
-    image.SetDimensions(dx, dy, dz)
-    image.SetExtent(extent)
-    image.SetScalarType(numpy_support.get_vtk_array_type(n_array.dtype))
-    image.AllocateScalars()
-    image.GetPointData().SetScalars(v_image)
-    image.Update()
-
-    image_copy = vtk.vtkImageData()
-    image_copy.DeepCopy(image)
-    image_copy.Update()
-
-    return image_copy
+
@@ -23,6 +23,7 @@ import vtk
 import wx.lib.pubsub as ps
  
 import constants as const
+import converters
 import imagedata_utils as iu
 import style as st
 import session as ses
@@ -358,7 +359,7 @@ class Slice(object):
                 image = self.buffer_slices[orientation].vtk_image
             else:
                 n_image = self.get_image_slice(orientation, slice_number)
-                image = iu.to_vtk(n_image, self.spacing, slice_number, orientation)
+                image = converters.to_vtk(n_image, self.spacing, slice_number, orientation)
                 ww_wl_image = self.do_ww_wl(image)
                 image = self.do_colour_image(ww_wl_image)
             if self.current_mask and self.current_mask.is_shown:
@@ -368,7 +369,7 @@ class Slice(object):
                 else:
                     print "Do not getting from buffer"
                     n_mask = self.get_mask_slice(orientation, slice_number)
-                    mask = iu.to_vtk(n_mask, self.spacing, slice_number, orientation)
+                    mask = converters.to_vtk(n_mask, self.spacing, slice_number, orientation)
                     mask = self.do_colour_mask(mask)
                     self.buffer_slices[orientation].mask = n_mask
                 final_image = self.do_blend(image, mask)
@@ -378,13 +379,13 @@ class Slice(object):
             self.buffer_slices[orientation].vtk_image = image
         else:
             n_image = self.get_image_slice(orientation, slice_number)
-            image = iu.to_vtk(n_image, self.spacing, slice_number, orientation)
+            image = converters.to_vtk(n_image, self.spacing, slice_number, orientation)
             ww_wl_image = self.do_ww_wl(image)
             image = self.do_colour_image(ww_wl_image)
  
             if self.current_mask and self.current_mask.is_shown:
                 n_mask = self.get_mask_slice(orientation, slice_number)
-                mask = iu.to_vtk(n_mask, self.spacing, slice_number, orientation)
+                mask = converters.to_vtk(n_mask, self.spacing, slice_number, orientation)
                 mask = self.do_colour_mask(mask)
                 final_image = self.do_blend(image, mask)
             else:
@@ -6,8 +6,7 @@ import numpy
 import vtk
  
 import i18n
-import imagedata_utils
-
+import converters
 from scipy import ndimage
  
 class SurfaceProcess(multiprocessing.Process):
@@ -33,11 +32,12 @@ class SurfaceProcess(multiprocessing.Process):
         self.flip_image = flip_image
         self.q_in = q_in
         self.q_out = q_out
-
-        self.mask = numpy.memmap(filename, mode='r', dtype=dtype,
-                                 shape=shape)
+        self.dtype = dtype
+        self.shape = shape
  
     def run(self):
+        self.mask = numpy.memmap(self.filename, mode='r', dtype=self.dtype,
+                                 shape=self.shape)
         while 1:
             roi = self.q_in.get()
             print roi
@@ -51,7 +51,7 @@ class SurfaceProcess(multiprocessing.Process):
  
     def CreateSurface(self, roi):
         smoothed = numpy.array(self.mask[roi])
-        image = imagedata_utils.to_vtk(smoothed, self.spacing, roi.start,
+        image =  converters.to_vtk(smoothed, self.spacing, roi.start,
                                        "AXIAL")
         flip = vtk.vtkImageFlip()
         flip.SetInput(image)
+#--------------------------------------------------------------------------
+# Software:     InVesalius - Software de Reconstrucao 3D de Imagens Medicas
+# Copyright:    (C) 2001  Centro de Pesquisas Renato Archer
+# Homepage:     http://www.softwarepublico.gov.br
+# Contact:      invesalius@cti.gov.br
+# License:      GNU - GPL 2 (LICENSE.txt/LICENCA.txt)
+#--------------------------------------------------------------------------
+#    Este programa e software livre; voce pode redistribui-lo e/ou
+#    modifica-lo sob os termos da Licenca Publica Geral GNU, conforme
+#    publicada pela Free Software Foundation; de acordo com a versao 2
+#    da Licenca.
+#
+#    Este programa eh distribuido na expectativa de ser util, mas SEM
+#    QUALQUER GARANTIA; sem mesmo a garantia implicita de
+#    COMERCIALIZACAO ou de ADEQUACAO A QUALQUER PROPOSITO EM
+#    PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
+#    detalhes.
+#--------------------------------------------------------------------------
+
 import ConfigParser
 import os
 import shutil
...	...	@@ -546,39 +546,4 @@ def analyze2mmap(analyze):
546	546	matrix.flush()
547	547	return matrix, temp_file
548	548
549		-def to_vtk(n_array, spacing, slice_number, orientation):
550		- try:
551		- dz, dy, dx = n_array.shape
552		- except ValueError:
553		- dy, dx = n_array.shape
554		- dz = 1
555		-
556		- v_image = numpy_support.numpy_to_vtk(n_array.flat)
557		-
558		- print orientation
559		- if orientation == 'AXIAL':
560		- extent = (0, dx -1, 0, dy -1, slice_number, slice_number + dz - 1)
561		- elif orientation == 'SAGITAL':
562		- dx, dy, dz = dz, dx, dy
563		- extent = (slice_number, slice_number + dx - 1, 0, dy - 1, 0, dz - 1)
564		- elif orientation == 'CORONAL':
565		- dx, dy, dz = dx, dz, dy
566		- extent = (0, dx - 1, slice_number, slice_number + dy - 1, 0, dz - 1)
567		-
568		- # Generating the vtkImageData
569		- image = vtk.vtkImageData()
570		- image.SetOrigin(0, 0, 0)
571		- image.SetSpacing(spacing)
572		- image.SetNumberOfScalarComponents(1)
573		- image.SetDimensions(dx, dy, dz)
574		- image.SetExtent(extent)
575		- image.SetScalarType(numpy_support.get_vtk_array_type(n_array.dtype))
576		- image.AllocateScalars()
577		- image.GetPointData().SetScalars(v_image)
578		- image.Update()
579		-
580		- image_copy = vtk.vtkImageData()
581		- image_copy.DeepCopy(image)
582		- image_copy.Update()
583		-
584		- return image_copy
	549	+
...	...
...	...	@@ -23,6 +23,7 @@ import vtk
23	23	import wx.lib.pubsub as ps
24	24
25	25	import constants as const
	26	+import converters
26	27	import imagedata_utils as iu
27	28	import style as st
28	29	import session as ses
...	...	@@ -358,7 +359,7 @@ class Slice(object):
358	359	image = self.buffer_slices[orientation].vtk_image
359	360	else:
360	361	n_image = self.get_image_slice(orientation, slice_number)
361		- image = iu.to_vtk(n_image, self.spacing, slice_number, orientation)
	362	+ image = converters.to_vtk(n_image, self.spacing, slice_number, orientation)
362	363	ww_wl_image = self.do_ww_wl(image)
363	364	image = self.do_colour_image(ww_wl_image)
364	365	if self.current_mask and self.current_mask.is_shown:
...	...	@@ -368,7 +369,7 @@ class Slice(object):
368	369	else:
369	370	print "Do not getting from buffer"
370	371	n_mask = self.get_mask_slice(orientation, slice_number)
371		- mask = iu.to_vtk(n_mask, self.spacing, slice_number, orientation)
	372	+ mask = converters.to_vtk(n_mask, self.spacing, slice_number, orientation)
372	373	mask = self.do_colour_mask(mask)
373	374	self.buffer_slices[orientation].mask = n_mask
374	375	final_image = self.do_blend(image, mask)
...	...	@@ -378,13 +379,13 @@ class Slice(object):
378	379	self.buffer_slices[orientation].vtk_image = image
379	380	else:
380	381	n_image = self.get_image_slice(orientation, slice_number)
381		- image = iu.to_vtk(n_image, self.spacing, slice_number, orientation)
	382	+ image = converters.to_vtk(n_image, self.spacing, slice_number, orientation)
382	383	ww_wl_image = self.do_ww_wl(image)
383	384	image = self.do_colour_image(ww_wl_image)
384	385
385	386	if self.current_mask and self.current_mask.is_shown:
386	387	n_mask = self.get_mask_slice(orientation, slice_number)
387		- mask = iu.to_vtk(n_mask, self.spacing, slice_number, orientation)
	388	+ mask = converters.to_vtk(n_mask, self.spacing, slice_number, orientation)
388	389	mask = self.do_colour_mask(mask)
389	390	final_image = self.do_blend(image, mask)
390	391	else:
...	...
...	...	@@ -6,8 +6,7 @@ import numpy
6	6	import vtk
7	7
8	8	import i18n
9		-import imagedata_utils
10		-
	9	+import converters
11	10	from scipy import ndimage
12	11
13	12	class SurfaceProcess(multiprocessing.Process):
...	...	@@ -33,11 +32,12 @@ class SurfaceProcess(multiprocessing.Process):
33	32	self.flip_image = flip_image
34	33	self.q_in = q_in
35	34	self.q_out = q_out
36		-
37		- self.mask = numpy.memmap(filename, mode='r', dtype=dtype,
38		- shape=shape)
	35	+ self.dtype = dtype
	36	+ self.shape = shape
39	37
40	38	def run(self):
	39	+ self.mask = numpy.memmap(self.filename, mode='r', dtype=self.dtype,
	40	+ shape=self.shape)
41	41	while 1:
42	42	roi = self.q_in.get()
43	43	print roi
...	...	@@ -51,7 +51,7 @@ class SurfaceProcess(multiprocessing.Process):
51	51
52	52	def CreateSurface(self, roi):
53	53	smoothed = numpy.array(self.mask[roi])
54		- image = imagedata_utils.to_vtk(smoothed, self.spacing, roi.start,
	54	+ image = converters.to_vtk(smoothed, self.spacing, roi.start,
55	55	"AXIAL")
56	56	flip = vtk.vtkImageFlip()
57	57	flip.SetInput(image)
...	...
	1	+#--------------------------------------------------------------------------
	2	+# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
	3	+# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
	4	+# Homepage: http://www.softwarepublico.gov.br
	5	+# Contact: invesalius@cti.gov.br
	6	+# License: GNU - GPL 2 (LICENSE.txt/LICENCA.txt)
	7	+#--------------------------------------------------------------------------
	8	+# Este programa e software livre; voce pode redistribui-lo e/ou
	9	+# modifica-lo sob os termos da Licenca Publica Geral GNU, conforme
	10	+# publicada pela Free Software Foundation; de acordo com a versao 2
	11	+# da Licenca.
	12	+#
	13	+# Este programa eh distribuido na expectativa de ser util, mas SEM
	14	+# QUALQUER GARANTIA; sem mesmo a garantia implicita de
	15	+# COMERCIALIZACAO ou de ADEQUACAO A QUALQUER PROPOSITO EM
	16	+# PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
	17	+# detalhes.
	18	+#--------------------------------------------------------------------------
	19	+
1	20	import ConfigParser
2	21	import os
3	22	import shutil
...	...