User can use the whitaker smoothing

Thiago Franco de Moraes
1 parent 8a446404
Showing 3 changed files with 26 additions and 5 deletions Show diff stats
invesalius/data/surface.py
invesalius/data/surface_process.py
invesalius/gui/dialogs.py
@@ -24,6 +24,7 @@ import random
 import tempfile
 import weakref
  
+import numpy as np
 import vtk
 import wx
 from wx.lib.pubsub import pub as Publisher
@@ -37,6 +38,8 @@ import surface_process
 import utils as utl
 import vtk_utils as vu
  
+from data import smooth_cy
+
 try:
     import ca_smoothing
 except ImportError:
@@ -465,13 +468,27 @@ class SurfaceManager():
         q_in = multiprocessing.Queue()
         q_out = multiprocessing.Queue()
  
+        if algorithm == 'Whitaker':
+            iteractions = 10
+            bsize = 4
+            mask_tfile = tempfile.mktemp()
+            mmask = np.memmap(mask_tfile, shape=mask.matrix.shape, dtype='float64', mode='w+')
+            smooth_cy.smooth(mask.matrix, iteractions, bsize, mmask)
+            mmask[0, :, :] = -1
+            mmask[:, 0, :] = -1
+            mmask[:, :, 0] = -1
+
+        else:
+            mask_tfile = mask.temp_file
+            mmask = mask.matrix
+
         p = []
         for i in xrange(n_processors):
             sp = surface_process.SurfaceProcess(pipe_in, filename_img,
                                                 matrix.shape, matrix.dtype,
-                                                mask.temp_file,
-                                                mask.matrix.shape,
-                                                mask.matrix.dtype,
+                                                mask_tfile,
+                                                mmask.shape,
+                                                mmask.dtype,
                                                 spacing,
                                                 mode, min_value, max_value,
                                                 decimate_reduction,
@@ -151,7 +151,10 @@ class SurfaceProcess(multiprocessing.Process):
         contour.SetInputData(image)
         #contour.SetInput(flip.GetOutput())
         if self.from_binary:
-            contour.SetValue(0, 127) # initial threshold
+            if self.algorithm == 'Whitaker':
+                contour.SetValue(0, 0.0) # initial threshold
+            else:
+                contour.SetValue(0, 127) # initial threshold
         else:
             contour.SetValue(0, self.min_value) # initial threshold
             contour.SetValue(1, self.max_value) # final threshold
@@ -1255,7 +1255,8 @@ class SurfaceMethodPanel(wx.Panel):
         self.mask_edited = mask_edited
         self.alg_types = {_(u'Default'): 'Default',
                           _(u'Context aware smoothing'): 'ca_smoothing',
-                          _(u'Binary'): 'Binary'}
+                          _(u'Binary'): 'Binary',
+                          _(u'Reducing Aliasing'): 'Whitaker'}
         self.edited_imp = [_(u'Default'), ]
  
         self._build_widgets()
...	...	@@ -24,6 +24,7 @@ import random
24	24	import tempfile
25	25	import weakref
26	26
	27	+import numpy as np
27	28	import vtk
28	29	import wx
29	30	from wx.lib.pubsub import pub as Publisher
...	...	@@ -37,6 +38,8 @@ import surface_process
37	38	import utils as utl
38	39	import vtk_utils as vu
39	40
	41	+from data import smooth_cy
	42	+
40	43	try:
41	44	import ca_smoothing
42	45	except ImportError:
...	...	@@ -465,13 +468,27 @@ class SurfaceManager():
465	468	q_in = multiprocessing.Queue()
466	469	q_out = multiprocessing.Queue()
467	470
	471	+ if algorithm == 'Whitaker':
	472	+ iteractions = 10
	473	+ bsize = 4
	474	+ mask_tfile = tempfile.mktemp()
	475	+ mmask = np.memmap(mask_tfile, shape=mask.matrix.shape, dtype='float64', mode='w+')
	476	+ smooth_cy.smooth(mask.matrix, iteractions, bsize, mmask)
	477	+ mmask[0, :, :] = -1
	478	+ mmask[:, 0, :] = -1
	479	+ mmask[:, :, 0] = -1
	480	+
	481	+ else:
	482	+ mask_tfile = mask.temp_file
	483	+ mmask = mask.matrix
	484	+
468	485	p = []
469	486	for i in xrange(n_processors):
470	487	sp = surface_process.SurfaceProcess(pipe_in, filename_img,
471	488	matrix.shape, matrix.dtype,
472		- mask.temp_file,
473		- mask.matrix.shape,
474		- mask.matrix.dtype,
	489	+ mask_tfile,
	490	+ mmask.shape,
	491	+ mmask.dtype,
475	492	spacing,
476	493	mode, min_value, max_value,
477	494	decimate_reduction,
...	...
...	...	@@ -151,7 +151,10 @@ class SurfaceProcess(multiprocessing.Process):
151	151	contour.SetInputData(image)
152	152	#contour.SetInput(flip.GetOutput())
153	153	if self.from_binary:
154		- contour.SetValue(0, 127) # initial threshold
	154	+ if self.algorithm == 'Whitaker':
	155	+ contour.SetValue(0, 0.0) # initial threshold
	156	+ else:
	157	+ contour.SetValue(0, 127) # initial threshold
155	158	else:
156	159	contour.SetValue(0, self.min_value) # initial threshold
157	160	contour.SetValue(1, self.max_value) # final threshold
...	...
...	...	@@ -1255,7 +1255,8 @@ class SurfaceMethodPanel(wx.Panel):
1255	1255	self.mask_edited = mask_edited
1256	1256	self.alg_types = {_(u'Default'): 'Default',
1257	1257	_(u'Context aware smoothing'): 'ca_smoothing',
1258		- _(u'Binary'): 'Binary'}
	1258	+ _(u'Binary'): 'Binary',
	1259	+ _(u'Reducing Aliasing'): 'Whitaker'}
1259	1260	self.edited_imp = [_(u'Default'), ]
1260	1261
1261	1262	self._build_widgets()
...	...