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Commit 3aa03487ce9ce8290b8270beba82ef41eb27d4c9

Authored by Thiago Franco de Moraes
1 parent 76b791fa
Exists in workdir

saving and opening in the new way

Showing 4 changed files with 155 additions and 80 deletions   Show diff stats
invesalius/data/imagedata_utils.py
  Diff comments   View file @3aa0348
... ... @@ -32,6 +32,7 @@ from vtk.util import numpy_support
32 32  
33 33 import constants as const
34 34 from data import vtk_utils
  35 +
35 36 import utils
36 37  
37 38 # TODO: Test cases which are originally in sagittal/coronal orientation
... ... @@ -421,10 +422,12 @@ def dcm2memmap(files, slice_size, orientation, resolution_percentage):
421 422 From a list of dicom files it creates memmap file in the temp folder and
422 423 returns it and its related filename.
423 424 """
  425 + from project import Project
424 426 message = _("Generating multiplanar visualization...")
425 427 update_progress= vtk_utils.ShowProgress(len(files) - 1, dialog_type = "ProgressDialog")
426   -
427   - temp_file = tempfile.mktemp()
  428 + proj = Project()
  429 + wdir = proj.working_dir
  430 + temp_file = os.path.join(wdir, 'matrix.dat')
428 431  
429 432 if orientation == 'SAGITTAL':
430 433 if resolution_percentage == 1.0:
... ... @@ -496,7 +499,9 @@ def dcm2memmap(files, slice_size, orientation, resolution_percentage):
496 499 def analyze2mmap(analyze):
497 500 data = analyze.get_data()
498 501 header = analyze.get_header()
499   - temp_file = tempfile.mktemp()
  502 + proj = Project()
  503 + wdir = proj.working_dir
  504 + temp_file = os.path.join(wdir, 'matrix.dat')
500 505  
501 506 # Sagital
502 507 if header['orient'] == 2:
... ...
invesalius/data/mask.py
  Diff comments   View file @3aa0348
... ... @@ -33,6 +33,7 @@ import session as ses
33 33 from wx.lib.pubsub import pub as Publisher
34 34  
35 35  
  36 +
36 37 class EditionHistoryNode(object):
37 38 def __init__(self, index, orientation, array, clean=False):
38 39 self.index = index
... ... @@ -259,6 +260,26 @@ class Mask():
259 260 path = os.path.join(dirpath, mask_file)
260 261 self._open_mask(path, tuple(shape))
261 262  
  263 + def save_workdir(self):
  264 + mask = {}
  265 + filename = os.path.split(self.temp_file)[-1]
  266 +
  267 + mask['index'] = self.index
  268 + mask['name'] = self.name
  269 + mask['colour'] = self.colour
  270 + mask['opacity'] = self.opacity
  271 + mask['threshold_range'] = self.threshold_range
  272 + mask['edition_threshold_range'] = self.edition_threshold_range
  273 + mask['visible'] = self.is_shown
  274 + mask['mask_file'] = filename
  275 + mask['mask_shape'] = self.matrix.shape
  276 + mask['edited'] = self.was_edited
  277 +
  278 + plist_filename = os.path.splitext(self.temp_file)[0]+ '.plist'
  279 + plistlib.writePlist(mask, plist_filename)
  280 +
  281 + return os.path.split(plist_filename)[-1]
  282 +
262 283 def OnFlipVolume(self, pubsub_evt):
263 284 axis = pubsub_evt.data
264 285 submatrix = self.matrix[1:, 1:, 1:]
... ... @@ -289,10 +310,14 @@ class Mask():
289 310 Mask.general_index = index
290 311  
291 312 def create_mask(self, shape):
292   - print "Creating a mask"
293   - self.temp_file = tempfile.mktemp()
  313 + from project import Project
  314 + proj = Project()
  315 + wdir = proj.working_dir
  316 + self.temp_file = tempfile.mktemp(prefix='mask%d_' % self.index, dir=wdir)
  317 + print "Creating mask at", self.temp_file
294 318 shape = shape[0] + 1, shape[1] + 1, shape[2] + 1
295 319 self.matrix = numpy.memmap(self.temp_file, mode='w+', dtype='uint8', shape=shape)
  320 + proj.save_workdir()
296 321  
297 322 def clean(self):
298 323 self.matrix[1:, 1:, 1:] = 0
... ...
invesalius/data/surface.py
  Diff comments   View file @3aa0348
... ... @@ -59,6 +59,7 @@ class Surface():
59 59 self.transparency = const.SURFACE_TRANSPARENCY
60 60 self.volume = 0
61 61 self.is_shown = 1
  62 + self.temp_file = ''
62 63 if not name:
63 64 self.name = const.SURFACE_NAME_PATTERN %(self.index+1)
64 65 else:
... ... @@ -101,6 +102,19 @@ class Surface():
101 102 self.polydata = pu.Import(os.path.join(dirpath, sp['polydata']))
102 103 Surface.general_index = max(Surface.general_index, self.index)
103 104  
  105 + def save_workdir(self):
  106 + surface = {'colour': self.colour,
  107 + 'index': self.index,
  108 + 'name': self.name,
  109 + 'polydata': self.temp_file,
  110 + 'transparency': self.transparency,
  111 + 'visible': bool(self.is_shown),
  112 + 'volume': self.volume,
  113 + }
  114 + plist_filename = os.path.splitext(self.temp_file)[0] + '.plist'
  115 + plistlib.writePlist(surface, plist_filename)
  116 + return os.path.split(plist_filename)[-1]
  117 +
104 118 def _set_class_index(self, index):
105 119 Surface.general_index = index
106 120  
... ... @@ -278,6 +292,17 @@ class SurfaceManager():
278 292 surface.index = index
279 293 self.last_surface_index = index
280 294  
  295 + wdir = proj.working_dir
  296 + temp_file = tempfile.mktemp(prefix='surface%d_' % surface.index, suffix='.vtp', dir=wdir)
  297 +
  298 + writer = vtk.vtkXMLPolyDataWriter()
  299 + writer.SetInput(polydata)
  300 + writer.SetFileName(temp_file)
  301 + writer.Write()
  302 + del writer
  303 +
  304 + surface.temp_file = temp_file
  305 +
281 306 # Set actor colour and transparency
282 307 actor.GetProperty().SetColor(surface.colour)
283 308 actor.GetProperty().SetOpacity(1-surface.transparency)
... ... @@ -307,6 +332,7 @@ class SurfaceManager():
307 332 (surface.index, surface.name,
308 333 surface.colour, surface.volume,
309 334 surface.transparency))
  335 +
310 336 return surface.index
311 337  
312 338 def OnCloseProject(self, pubsub_evt):
... ... @@ -644,6 +670,8 @@ class SurfaceManager():
644 670 polydata.DebugOn()
645 671 del filled_polydata
646 672  
  673 + proj = prj.Project()
  674 +
647 675 normals = vtk.vtkPolyDataNormals()
648 676 normals.ReleaseDataFlagOn()
649 677 normals_ref = weakref.ref(normals)
... ... @@ -693,6 +721,17 @@ class SurfaceManager():
693 721 surface = Surface(index = self.last_surface_index)
694 722 else:
695 723 surface = Surface(name=surface_name)
  724 +
  725 + wdir = proj.working_dir
  726 + temp_file = tempfile.mktemp(prefix='surface%d_' % surface.index, suffix='.vtp', dir=wdir)
  727 +
  728 + writer = vtk.vtkXMLPolyDataWriter()
  729 + writer.SetInput(polydata)
  730 + writer.SetFileName(temp_file)
  731 + writer.Write()
  732 + del writer
  733 +
  734 + surface.temp_file = temp_file
696 735 surface.colour = colour
697 736 surface.polydata = polydata
698 737 del polydata
... ... @@ -707,7 +746,6 @@ class SurfaceManager():
707 746  
708 747 prop.SetInterpolation(interpolation)
709 748  
710   - proj = prj.Project()
711 749 if overwrite:
712 750 proj.ChangeSurface(surface)
713 751 else:
... ...
invesalius/project.py
  Diff comments   View file @3aa0348
... ... @@ -74,6 +74,7 @@ class Project(object):
74 74  
75 75 self.raycasting_preset = ''
76 76  
  77 + self.working_dir = tempfile.mkdtemp()
77 78  
78 79 #self.surface_quality_list = ["Low", "Medium", "High", "Optimal *",
79 80 # "Custom"i]
... ... @@ -84,6 +85,13 @@ class Project(object):
84 85 # Allow insertion of new surface quality modes
85 86  
86 87 def Close(self):
  88 + try:
  89 + print ">>>>> Trying to remove", self.working_dir
  90 + os.rmdir(self.working_dir)
  91 + print ">>>> done"
  92 + except OSError:
  93 + print ">>>> It was not possible"
  94 +
87 95 for name in self.__dict__:
88 96 attr = getattr(self, name)
89 97 del attr
... ... @@ -195,77 +203,10 @@ class Project(object):
195 203 return measures
196 204  
197 205 def SavePlistProject(self, dir_, filename):
198   - dir_temp = tempfile.mkdtemp()
199   - filename_tmp = os.path.join(dir_temp, 'matrix.dat')
200   - filelist = {}
201   -
202   - project = {
203   - # Format info
204   - "format_version": 1,
205   - "invesalius_version": const.INVESALIUS_VERSION,
206   - "date": datetime.datetime.now().isoformat(),
207   -
208   - # case info
209   - "name": self.name, # patient's name
210   - "modality": self.modality, # CT, RMI, ...
211   - "orientation": self.original_orientation,
212   - "window_width": self.window,
213   - "window_level": self.level,
214   - "scalar_range": self.threshold_range,
215   - "spacing": self.spacing,
216   - }
217   -
218   - # Saving the matrix containing the slices
219   - matrix = {'filename': u'matrix.dat',
220   - 'shape': self.matrix_shape,
221   - 'dtype': self.matrix_dtype,
222   - }
223   - project['matrix'] = matrix
224   - filelist[self.matrix_filename] = 'matrix.dat'
225   - #shutil.copyfile(self.matrix_filename, filename_tmp)
226   -
227   - # Saving the masks
228   - masks = {}
229   - for index in self.mask_dict:
230   - masks[str(index)] = self.mask_dict[index].SavePlist(dir_temp,
231   - filelist)
232   - project['masks'] = masks
233   -
234   - # Saving the surfaces
235   - surfaces = {}
236   - for index in self.surface_dict:
237   - surfaces[str(index)] = self.surface_dict[index].SavePlist(dir_temp,
238   - filelist)
239   - project['surfaces'] = surfaces
240   -
241   - # Saving the measurements
242   - measurements = self.GetMeasuresDict()
243   - measurements_filename = 'measurements.plist'
244   - temp_mplist = tempfile.mktemp()
245   - plistlib.writePlist(measurements,
246   - temp_mplist)
247   - filelist[temp_mplist] = measurements_filename
248   - project['measurements'] = measurements_filename
249   -
250   - # Saving the annotations (empty in this version)
251   - project['annotations'] = {}
252   -
253   - # Saving the main plist
254   - temp_plist = tempfile.mktemp()
255   - plistlib.writePlist(project, temp_plist)
256   - filelist[temp_plist] = 'main.plist'
257   -
258   - # Compressing and generating the .inv3 file
259 206 path = os.path.join(dir_,filename)
260   - Compress(dir_temp, path, filelist)
  207 + filelist = self.save_workdir()
  208 + Compress(self.working_dir, path, filelist)
261 209  
262   - # Removing the temp folder.
263   - shutil.rmtree(dir_temp)
264   -
265   - for f in filelist:
266   - if filelist[f].endswith('.plist'):
267   - print f
268   - os.remove(f)
269 210  
270 211 def OpenPlistProject(self, filename):
271 212 import data.measures as ms
... ... @@ -278,7 +219,9 @@ class Project(object):
278 219 ow.SetInstance(fow)
279 220  
280 221 filelist = Extract(filename, tempfile.mkdtemp())
  222 + print "@@@@", os.path.split(filelist[0])[0]
281 223 dirpath = os.path.abspath(os.path.split(filelist[0])[0])
  224 + self.working_dir = dirpath
282 225  
283 226 # Opening the main file from invesalius 3 project
284 227 main_plist = os.path.join(dirpath ,'main.plist')
... ... @@ -326,15 +269,77 @@ class Project(object):
326 269 measure.Load(measurements[index])
327 270 self.measurement_dict[int(index)] = measure
328 271  
  272 + def save_workdir(self):
  273 + filelist = []
  274 + project = {
  275 + # Format info
  276 + "format_version": 1,
  277 + "invesalius_version": const.INVESALIUS_VERSION,
  278 + "date": datetime.datetime.now().isoformat(),
  279 +
  280 + # case info
  281 + "name": self.name, # patient's name
  282 + "modality": self.modality, # CT, RMI, ...
  283 + "orientation": self.original_orientation,
  284 + "window_width": self.window,
  285 + "window_level": self.level,
  286 + "scalar_range": self.threshold_range,
  287 + "spacing": self.spacing,
  288 + }
  289 +
  290 + # Saving the matrix containing the slices
  291 + matrix = {'filename': u'matrix.dat',
  292 + 'shape': self.matrix_shape,
  293 + 'dtype': self.matrix_dtype,
  294 + }
  295 +
  296 + project['matrix'] = matrix
  297 + filelist.append(os.path.join(self.working_dir, 'matrix.dat'))
  298 + #shutil.copyfile(self.matrix_filename, filename_tmp)
  299 +
  300 + # Saving the masks
  301 + masks = {}
  302 + for index in self.mask_dict:
  303 + masks[str(index)] = self.mask_dict[index].save_workdir()
  304 + filelist.append(os.path.join(self.working_dir, masks[str(index)]))
  305 + filelist.append(os.path.join(self.working_dir, os.path.splitext(masks[str(index)])[0]))
  306 + project['masks'] = masks
  307 +
  308 + # # Saving the surfaces
  309 + surfaces = {}
  310 + for index in self.surface_dict:
  311 + surfaces[str(index)] = self.surface_dict[index].save_workdir()
  312 + filelist.append(os.path.join(self.working_dir, surfaces[str(index)]))
  313 + filelist.append(os.path.join(self.working_dir, os.path.splitext(surfaces[str(index)])[0]))
  314 + project['surfaces'] = surfaces
  315 +
  316 + # Saving the measurements
  317 + measurements = self.GetMeasuresDict()
  318 + measurements_filename = 'measurements.plist'
  319 + temp_mplist = os.path.join(self.working_dir, measurements_filename)
  320 + plistlib.writePlist(measurements, temp_mplist)
  321 + project['measurements'] = measurements_filename
  322 + filelist.append(os.path.join(self.working_dir, 'measurements.plist'))
  323 +
  324 + # Saving the annotations (empty in this version)
  325 + project['annotations'] = {}
  326 +
  327 + # Saving the main plist
  328 + pfname = os.path.join(self.working_dir, 'main.plist')
  329 + plistlib.writePlist(project, pfname)
  330 + filelist.append(os.path.join(self.working_dir, 'main.plist'))
  331 +
  332 + return filelist
  333 +
  334 +
329 335 def Compress(folder, filename, filelist):
330 336 tmpdir, tmpdir_ = os.path.split(folder)
331 337 current_dir = os.path.abspath(".")
332   - #os.chdir(tmpdir)
333   - #file_list = glob.glob(os.path.join(tmpdir_,"*"))
334   - tar_filename = tmpdir_ + ".inv3"
335 338 tar = tarfile.open(filename.encode(wx.GetDefaultPyEncoding()), "w:gz")
336 339 for name in filelist:
337   - tar.add(name, arcname=os.path.join(tmpdir_, filelist[name]))
  340 + sname = name.split(os.path.sep)
  341 + print ">>>>", sname
  342 + tar.add(name, arcname=os.path.join(sname[-2], sname[-1]))
338 343 tar.close()
339 344 #shutil.move(tmpdir_+ ".inv3", filename)
340 345 #os.chdir(current_dir)
... ... @@ -350,6 +355,8 @@ def Extract(filename, folder):
350 355 fname = os.path.join(folder, t.name.decode('utf-8'))
351 356 fdst = file(fname, 'wb')
352 357  
  358 + print fsrc, fdst
  359 +
353 360 shutil.copyfileobj(fsrc, fdst)
354 361  
355 362 filelist.append(fname)
... ... @@ -361,7 +368,7 @@ def Extract(filename, folder):
361 368 print filelist
362 369 return filelist
363 370  
364   -
  371 +
365 372 def Extract_(filename, folder):
366 373 tar = tarfile.open(filename, "r:gz")
367 374 #tar.list(verbose=True)
... ...