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Commit 8a4cf33657f213a7836d52fd3569daf38a955541

Authored by tfmoraes
1 parent a41b332c
Exists in master and in 67 other branches 3d_inter_style, MIPs, beta3, beta4, brush_pix, canvas_reeng, canvas_text, casmoothing_cython, clean, command-line, cython_threshold, debian_cython, editor_improvements, encoding, ff_mask, ff_mask_improv, ffill_gui, ffill_segmentation, fill_holes_auto, fixes_pre_beta5, floodfill, get_pixel, import_mesh, interactor_style, inv3.0.1, mactoolbar, mactoolbar_bkp, manual_v3.1, mask_boolean_op, mask_boolean_op_bkp, mask_copy, mask_greatest_component, measure, measure_canvas, measure_improvements, measure_placement_test, measure_spacing, orientation, phoenix, region_growing_confidence, remote, remove_local_wxpython, rmatsuda-fix_ref_MTC, rmatsuda-fix_remove_marker_bug, rmatsuda-trigger_bug_fix, rotvol, segmentation_menu, select_part, smoothing_bin, smoothing_bin_pll, surface_area, threshold_history, user_guide_en, usp-navegador, vti, vtk6, watershed, watershed_improvements, watershed_improvements_bkp, watershed_merge, workdir, wwwlgui, wx2.9_mac, wxgtk3, wxgtk3_b5, wxgtk3_bkp, xmartlabs-command-line

FIX: Resolved the problem with non-ascii characters in mask and surface name by … 

…not appending its name on the file used to mantain them
Showing 5 changed files with 228 additions and 201 deletions   Show diff stats
.gitattributes
  Diff comments   View file @8a4cf33
@@ -845,6 +845,7 @@ invesalius/.svnignore -text @@ -845,6 +845,7 @@ invesalius/.svnignore -text
845 invesalius/data/bases.py -text 845 invesalius/data/bases.py -text
846 invesalius/data/co_registration.py -text 846 invesalius/data/co_registration.py -text
847 invesalius/data/converters.py -text 847 invesalius/data/converters.py -text
  848 +invesalius/data/polydata_utils.py -text svneol=native#unset
848 invesalius/gui/import_network_panel.py -text 849 invesalius/gui/import_network_panel.py -text
849 invesalius/gui/preferences.py -text 850 invesalius/gui/preferences.py -text
850 invesalius/net/__init__.py -text 851 invesalius/net/__init__.py -text
invesalius/data/mask.py
  Diff comments   View file @8a4cf33
@@ -53,7 +53,7 @@ class Mask(): @@ -53,7 +53,7 @@ class Mask():
53 53
54 def SavePlist(self, dir_temp): 54 def SavePlist(self, dir_temp):
55 mask = {} 55 mask = {}
56 - filename = u'mask%d_%s' % (self.index, self.name) 56 + filename = u'mask_%d' % self.index
57 mask_filename = u'%s.dat' % filename 57 mask_filename = u'%s.dat' % filename
58 mask_filepath = os.path.join(dir_temp, mask_filename) 58 mask_filepath = os.path.join(dir_temp, mask_filename)
59 self._save_mask(mask_filepath) 59 self._save_mask(mask_filepath)
invesalius/data/polydata_utils.py
  Diff comments   View file @8a4cf33
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 -  
20 -import sys  
21 -  
22 -import vtk  
23 -import wx  
24 -from wx.lib.pubsub import pub as Publisher  
25 -  
26 -import vtk_utils as vu  
27 -  
28 -# Update progress value in GUI  
29 -UpdateProgress = vu.ShowProgress()  
30 -  
31 -def ApplyDecimationFilter(polydata, reduction_factor):  
32 - """  
33 - Reduce number of triangles of the given vtkPolyData, based on  
34 - reduction_factor.  
35 - """  
36 - # Important: vtkQuadricDecimation presented better results than  
37 - # vtkDecimatePro  
38 - decimation = vtk.vtkQuadricDecimation()  
39 - decimation.SetInput(polydata)  
40 - decimation.SetTargetReduction(reduction_factor)  
41 - decimation.GetOutput().ReleaseDataFlagOn()  
42 - decimation.AddObserver("ProgressEvent", lambda obj, evt:  
43 - UpdateProgress(decimation, "Reducing number of triangles..."))  
44 - return decimation.GetOutput()  
45 -  
46 -def ApplySmoothFilter(polydata, iterations, relaxation_factor):  
47 - """  
48 - Smooth given vtkPolyData surface, based on iteration and relaxation_factor.  
49 - """  
50 - smoother = vtk.vtkSmoothPolyDataFilter()  
51 - smoother.SetInput(polydata)  
52 - smoother.SetNumberOfIterations(iterations)  
53 - smoother.SetFeatureAngle(80)  
54 - smoother.SetRelaxationFactor(relaxation_factor)  
55 - smoother.FeatureEdgeSmoothingOn()  
56 - smoother.BoundarySmoothingOn()  
57 - smoother.GetOutput().ReleaseDataFlagOn()  
58 - smoother.AddObserver("ProgressEvent", lambda obj, evt:  
59 - UpdateProgress(smoother, "Smoothing surface..."))  
60 -  
61 - return smoother.GetOutput()  
62 -  
63 -  
64 -  
65 -def FillSurfaceHole(polydata):  
66 - """  
67 - Fill holes in the given polydata.  
68 - """  
69 - # Filter used to detect and fill holes. Only fill  
70 - print "Filling polydata"  
71 - filled_polydata = vtk.vtkFillHolesFilter()  
72 - filled_polydata.SetInput(polydata)  
73 - filled_polydata.SetHoleSize(500)  
74 - return filled_polydata.GetOutput()  
75 -  
76 -def CalculateSurfaceVolume(polydata):  
77 - """  
78 - Calculate the volume from the given polydata  
79 - """  
80 - # Filter used to calculate volume and area from a polydata  
81 - measured_polydata = vtk.vtkMassProperties()  
82 - measured_polydata.SetInput(polydata)  
83 - return measured_polydata.GetVolume()  
84 -  
85 -def CalculateSurfaceArea(polydata):  
86 - """  
87 - Calculate the volume from the given polydata  
88 - """  
89 - # Filter used to calculate volume and area from a polydata  
90 - measured_polydata = vtk.vtkMassProperties()  
91 - measured_polydata.SetInput(polydata)  
92 - return measured_polydata.GetSurfaceArea()  
93 -  
94 -def Merge(polydata_list):  
95 - append = vtk.vtkAppendPolyData()  
96 -  
97 - for polydata in polydata_list:  
98 - triangle = vtk.vtkTriangleFilter()  
99 - triangle.SetInput(polydata)  
100 - append.AddInput(triangle.GetOutput())  
101 -  
102 - clean = vtk.vtkCleanPolyData()  
103 - clean.SetInput(append.GetOutput())  
104 -  
105 - return append.GetOutput()  
106 -  
107 -def Export(polydata, filename, bin=False):  
108 - writer = vtk.vtkXMLPolyDataWriter()  
109 - print filename, type(filename)  
110 - writer.SetFileName(filename.encode('utf-8'))  
111 - if bin:  
112 - writer.SetDataModeToBinary()  
113 - else:  
114 - writer.SetDataModeToAscii()  
115 - writer.SetInput(polydata)  
116 - writer.Write()  
117 -  
118 -def Import(filename):  
119 - reader = vtk.vtkXMLPolyDataReader()  
120 - reader.SetFileName(filename.encode('utf-8'))  
121 - reader.Update()  
122 - return reader.GetOutput()  
123 -  
124 -def JoinSeedsParts(polydata, point_id_list):  
125 - """  
126 - The function require vtkPolyData and point id  
127 - from vtkPolyData.  
128 - """  
129 - conn = vtk.vtkPolyDataConnectivityFilter()  
130 - conn.SetInput(polydata)  
131 - conn.SetExtractionModeToPointSeededRegions()  
132 - UpdateProgress = vu.ShowProgress(1 + len(point_id_list))  
133 - pos = 1  
134 - for seed in point_id_list:  
135 - conn.AddSeed(seed)  
136 - UpdateProgress(pos, _("Analysing selected regions..."))  
137 - pos += 1  
138 -  
139 - conn.AddObserver("ProgressEvent", lambda obj, evt:  
140 - UpdateProgress(conn, "Getting selected parts"))  
141 - conn.Update()  
142 -  
143 - result = vtk.vtkPolyData()  
144 - result.DeepCopy(conn.GetOutput())  
145 - result.Update()  
146 - return result  
147 -  
148 -def SelectLargestPart(polydata):  
149 - """  
150 - """  
151 - UpdateProgress = vu.ShowProgress(1)  
152 - conn = vtk.vtkPolyDataConnectivityFilter()  
153 - conn.SetInput(polydata)  
154 - conn.SetExtractionModeToLargestRegion()  
155 - conn.AddObserver("ProgressEvent", lambda obj, evt:  
156 - UpdateProgress(conn, "Getting largest part..."))  
157 - conn.Update()  
158 -  
159 - result = vtk.vtkPolyData()  
160 - result.DeepCopy(conn.GetOutput())  
161 - result.Update()  
162 - return result  
163 -  
164 -def SplitDisconectedParts(polydata):  
165 - """  
166 - """  
167 - conn = vtk.vtkPolyDataConnectivityFilter()  
168 - conn.SetInput(polydata)  
169 - conn.SetExtractionModeToAllRegions()  
170 - conn.Update()  
171 -  
172 - nregions = conn.GetNumberOfExtractedRegions()  
173 -  
174 - conn.SetExtractionModeToSpecifiedRegions()  
175 - conn.Update()  
176 -  
177 - polydata_collection = []  
178 -  
179 - # Update progress value in GUI  
180 - progress = nregions -1  
181 - if progress:  
182 - UpdateProgress = vu.ShowProgress(progress)  
183 -  
184 - for region in xrange(nregions):  
185 - conn.InitializeSpecifiedRegionList()  
186 - conn.AddSpecifiedRegion(region)  
187 - conn.Update()  
188 -  
189 - p = vtk.vtkPolyData()  
190 - p.DeepCopy(conn.GetOutput())  
191 - p.Update()  
192 -  
193 - polydata_collection.append(p)  
194 - if progress:  
195 - UpdateProgress(region, _("Splitting disconnected regions..."))  
196 -  
197 - return polydata_collection 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 +
  20 +import sys
  21 +
  22 +import vtk
  23 +import wx
  24 +from wx.lib.pubsub import pub as Publisher
  25 +
  26 +import vtk_utils as vu
  27 +
  28 +# Update progress value in GUI
  29 +UpdateProgress = vu.ShowProgress()
  30 +
  31 +def ApplyDecimationFilter(polydata, reduction_factor):
  32 + """
  33 + Reduce number of triangles of the given vtkPolyData, based on
  34 + reduction_factor.
  35 + """
  36 + # Important: vtkQuadricDecimation presented better results than
  37 + # vtkDecimatePro
  38 + decimation = vtk.vtkQuadricDecimation()
  39 + decimation.SetInput(polydata)
  40 + decimation.SetTargetReduction(reduction_factor)
  41 + decimation.GetOutput().ReleaseDataFlagOn()
  42 + decimation.AddObserver("ProgressEvent", lambda obj, evt:
  43 + UpdateProgress(decimation, "Reducing number of triangles..."))
  44 + return decimation.GetOutput()
  45 +
  46 +def ApplySmoothFilter(polydata, iterations, relaxation_factor):
  47 + """
  48 + Smooth given vtkPolyData surface, based on iteration and relaxation_factor.
  49 + """
  50 + smoother = vtk.vtkSmoothPolyDataFilter()
  51 + smoother.SetInput(polydata)
  52 + smoother.SetNumberOfIterations(iterations)
  53 + smoother.SetFeatureAngle(80)
  54 + smoother.SetRelaxationFactor(relaxation_factor)
  55 + smoother.FeatureEdgeSmoothingOn()
  56 + smoother.BoundarySmoothingOn()
  57 + smoother.GetOutput().ReleaseDataFlagOn()
  58 + smoother.AddObserver("ProgressEvent", lambda obj, evt:
  59 + UpdateProgress(smoother, "Smoothing surface..."))
  60 +
  61 + return smoother.GetOutput()
  62 +
  63 +
  64 +
  65 +def FillSurfaceHole(polydata):
  66 + """
  67 + Fill holes in the given polydata.
  68 + """
  69 + # Filter used to detect and fill holes. Only fill
  70 + print "Filling polydata"
  71 + filled_polydata = vtk.vtkFillHolesFilter()
  72 + filled_polydata.SetInput(polydata)
  73 + filled_polydata.SetHoleSize(500)
  74 + return filled_polydata.GetOutput()
  75 +
  76 +def CalculateSurfaceVolume(polydata):
  77 + """
  78 + Calculate the volume from the given polydata
  79 + """
  80 + # Filter used to calculate volume and area from a polydata
  81 + measured_polydata = vtk.vtkMassProperties()
  82 + measured_polydata.SetInput(polydata)
  83 + return measured_polydata.GetVolume()
  84 +
  85 +def CalculateSurfaceArea(polydata):
  86 + """
  87 + Calculate the volume from the given polydata
  88 + """
  89 + # Filter used to calculate volume and area from a polydata
  90 + measured_polydata = vtk.vtkMassProperties()
  91 + measured_polydata.SetInput(polydata)
  92 + return measured_polydata.GetSurfaceArea()
  93 +
  94 +def Merge(polydata_list):
  95 + append = vtk.vtkAppendPolyData()
  96 +
  97 + for polydata in polydata_list:
  98 + triangle = vtk.vtkTriangleFilter()
  99 + triangle.SetInput(polydata)
  100 + append.AddInput(triangle.GetOutput())
  101 +
  102 + clean = vtk.vtkCleanPolyData()
  103 + clean.SetInput(append.GetOutput())
  104 +
  105 + return append.GetOutput()
  106 +
  107 +def Export(polydata, filename, bin=False):
  108 + writer = vtk.vtkXMLPolyDataWriter()
  109 + print filename, type(filename)
  110 + writer.SetFileName(filename.encode('utf-8'))
  111 + if bin:
  112 + writer.SetDataModeToBinary()
  113 + else:
  114 + writer.SetDataModeToAscii()
  115 + writer.SetInput(polydata)
  116 + writer.Write()
  117 +
  118 +def Import(filename):
  119 + reader = vtk.vtkXMLPolyDataReader()
  120 + if isinstance(filename, unicode):
  121 + reader.SetFileName(filename.encode(wx.GetDefaultPyEncoding()))
  122 + else:
  123 + reader.SetFileName(filename)
  124 + reader.Update()
  125 + return reader.GetOutput()
  126 +
  127 +def JoinSeedsParts(polydata, point_id_list):
  128 + """
  129 + The function require vtkPolyData and point id
  130 + from vtkPolyData.
  131 + """
  132 + conn = vtk.vtkPolyDataConnectivityFilter()
  133 + conn.SetInput(polydata)
  134 + conn.SetExtractionModeToPointSeededRegions()
  135 + UpdateProgress = vu.ShowProgress(1 + len(point_id_list))
  136 + pos = 1
  137 + for seed in point_id_list:
  138 + conn.AddSeed(seed)
  139 + UpdateProgress(pos, _("Analysing selected regions..."))
  140 + pos += 1
  141 +
  142 + conn.AddObserver("ProgressEvent", lambda obj, evt:
  143 + UpdateProgress(conn, "Getting selected parts"))
  144 + conn.Update()
  145 +
  146 + result = vtk.vtkPolyData()
  147 + result.DeepCopy(conn.GetOutput())
  148 + result.Update()
  149 + return result
  150 +
  151 +def SelectLargestPart(polydata):
  152 + """
  153 + """
  154 + UpdateProgress = vu.ShowProgress(1)
  155 + conn = vtk.vtkPolyDataConnectivityFilter()
  156 + conn.SetInput(polydata)
  157 + conn.SetExtractionModeToLargestRegion()
  158 + conn.AddObserver("ProgressEvent", lambda obj, evt:
  159 + UpdateProgress(conn, "Getting largest part..."))
  160 + conn.Update()
  161 +
  162 + result = vtk.vtkPolyData()
  163 + result.DeepCopy(conn.GetOutput())
  164 + result.Update()
  165 + return result
  166 +
  167 +def SplitDisconectedParts(polydata):
  168 + """
  169 + """
  170 + conn = vtk.vtkPolyDataConnectivityFilter()
  171 + conn.SetInput(polydata)
  172 + conn.SetExtractionModeToAllRegions()
  173 + conn.Update()
  174 +
  175 + nregions = conn.GetNumberOfExtractedRegions()
  176 +
  177 + conn.SetExtractionModeToSpecifiedRegions()
  178 + conn.Update()
  179 +
  180 + polydata_collection = []
  181 +
  182 + # Update progress value in GUI
  183 + progress = nregions -1
  184 + if progress:
  185 + UpdateProgress = vu.ShowProgress(progress)
  186 +
  187 + for region in xrange(nregions):
  188 + conn.InitializeSpecifiedRegionList()
  189 + conn.AddSpecifiedRegion(region)
  190 + conn.Update()
  191 +
  192 + p = vtk.vtkPolyData()
  193 + p.DeepCopy(conn.GetOutput())
  194 + p.Update()
  195 +
  196 + polydata_collection.append(p)
  197 + if progress:
  198 + UpdateProgress(region, _("Splitting disconnected regions..."))
  199 +
  200 + return polydata_collection
invesalius/data/surface.py
  Diff comments   View file @8a4cf33
@@ -63,7 +63,7 @@ class Surface(): @@ -63,7 +63,7 @@ class Surface():
63 self.name = name 63 self.name = name
64 64
65 def SavePlist(self, dir_temp): 65 def SavePlist(self, dir_temp):
66 - filename = 'surface_%d_%s' % (self.index, self.name) 66 + filename = 'surface_%d' % self.index
67 vtp_filename = filename + '.vtp' 67 vtp_filename = filename + '.vtp'
68 vtp_filepath = os.path.join(dir_temp, vtp_filename) 68 vtp_filepath = os.path.join(dir_temp, vtp_filename)
69 pu.Export(self.polydata, vtp_filepath, bin=True) 69 pu.Export(self.polydata, vtp_filepath, bin=True)
invesalius/project.py
  Diff comments   View file @8a4cf33
@@ -274,7 +274,7 @@ class Project(object): @@ -274,7 +274,7 @@ class Project(object):
274 ow.SetInstance(fow) 274 ow.SetInstance(fow)
275 275
276 filelist = Extract(filename, tempfile.mkdtemp()) 276 filelist = Extract(filename, tempfile.mkdtemp())
277 - dirpath = os.path.abspath(os.path.split(filelist[0])[0]).decode(wx.GetDefaultPyEncoding()) 277 + dirpath = os.path.abspath(os.path.split(filelist[0])[0])
278 278
279 # Opening the main file from invesalius 3 project 279 # Opening the main file from invesalius 3 project
280 main_plist = os.path.join(dirpath ,'main.plist') 280 main_plist = os.path.join(dirpath ,'main.plist')
@@ -335,9 +335,32 @@ def Compress(folder, filename): @@ -335,9 +335,32 @@ def Compress(folder, filename):
335 tar.close() 335 tar.close()
336 shutil.move(tmpdir_+ ".inv3", filename) 336 shutil.move(tmpdir_+ ".inv3", filename)
337 os.chdir(current_dir) 337 os.chdir(current_dir)
338 - 338 +
339 def Extract(filename, folder): 339 def Extract(filename, folder):
340 tar = tarfile.open(filename, "r:gz") 340 tar = tarfile.open(filename, "r:gz")
  341 + idir = os.path.split(tar.getnames()[0])[0]
  342 + os.mkdir(os.path.join(folder, idir.decode('utf8')))
  343 + filelist = []
  344 + for t in tar.getmembers():
  345 + fsrc = tar.extractfile(t)
  346 +
  347 + fname = os.path.join(folder, t.name.decode('utf-8'))
  348 + fdst = file(fname, 'wb')
  349 +
  350 + shutil.copyfileobj(fsrc, fdst)
  351 +
  352 + filelist.append(fname)
  353 + fsrc.close()
  354 + fdst.close()
  355 + del fsrc
  356 + del fdst
  357 + tar.close()
  358 + print filelist
  359 + return filelist
  360 +
  361 +
  362 +def Extract_(filename, folder):
  363 + tar = tarfile.open(filename, "r:gz")
341 #tar.list(verbose=True) 364 #tar.list(verbose=True)
342 tar.extractall(folder) 365 tar.extractall(folder)
343 filelist = [os.path.join(folder, i) for i in tar.getnames()] 366 filelist = [os.path.join(folder, i) for i in tar.getnames()]