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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
845 845 invesalius/data/bases.py -text
846 846 invesalius/data/co_registration.py -text
847 847 invesalius/data/converters.py -text
  848 +invesalius/data/polydata_utils.py -text svneol=native#unset
848 849 invesalius/gui/import_network_panel.py -text
849 850 invesalius/gui/preferences.py -text
850 851 invesalius/net/__init__.py -text
... ...
invesalius/data/mask.py
  Diff comments   View file @8a4cf33
... ... @@ -53,7 +53,7 @@ class Mask():
53 53  
54 54 def SavePlist(self, dir_temp):
55 55 mask = {}
56   - filename = u'mask%d_%s' % (self.index, self.name)
  56 + filename = u'mask_%d' % self.index
57 57 mask_filename = u'%s.dat' % filename
58 58 mask_filepath = os.path.join(dir_temp, mask_filename)
59 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 63 self.name = name
64 64  
65 65 def SavePlist(self, dir_temp):
66   - filename = 'surface_%d_%s' % (self.index, self.name)
  66 + filename = 'surface_%d' % self.index
67 67 vtp_filename = filename + '.vtp'
68 68 vtp_filepath = os.path.join(dir_temp, vtp_filename)
69 69 pu.Export(self.polydata, vtp_filepath, bin=True)
... ...
invesalius/project.py
  Diff comments   View file @8a4cf33
... ... @@ -274,7 +274,7 @@ class Project(object):
274 274 ow.SetInstance(fow)
275 275  
276 276 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  
279 279 # Opening the main file from invesalius 3 project
280 280 main_plist = os.path.join(dirpath ,'main.plist')
... ... @@ -335,9 +335,32 @@ def Compress(folder, filename):
335 335 tar.close()
336 336 shutil.move(tmpdir_+ ".inv3", filename)
337 337 os.chdir(current_dir)
338   -
  338 +
339 339 def Extract(filename, folder):
340 340 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")
341 364 #tar.list(verbose=True)
342 365 tar.extractall(folder)
343 366 filelist = [os.path.join(folder, i) for i in tar.getnames()]
... ...