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Commit a724a203ef29718751ee50e146b33b2b9accc8ab

Authored by tfmoraes
1 parent a3614eda
Exists in master and in 5 other branches beta3, beta4, inv3.0.1, usp-navegador, wxgtk3_b5

ENH: Generating surface using multiprocessing and with memmap

Showing 4 changed files with 156 additions and 147 deletions   Show diff stats
invesalius/data/imagedata_utils.py
  Diff comments   View file @a724a20
... ... @@ -497,20 +497,23 @@ def dcm2memmap(files, slice_size, orientation):
497 497 return matrix, temp_file
498 498  
499 499 def to_vtk(n_array, spacing, slice_number, orientation):
500   - dy, dx = n_array.shape
  500 + try:
  501 + dz, dy, dx = n_array.shape
  502 + except ValueError:
  503 + dy, dx = n_array.shape
  504 + dz = 1
501 505  
502 506 v_image = numpy_support.numpy_to_vtk(n_array.flat)
503 507  
504 508 print orientation
505 509 if orientation == 'AXIAL':
506   - dz = 1
507   - extent = (0, dx -1, 0, dy -1, slice_number, slice_number)
  510 + extent = (0, dx -1, 0, dy -1, slice_number, slice_number + dz - 1)
508 511 elif orientation == 'SAGITAL':
509   - dx, dy, dz = 1, dx, dy
510   - extent = (slice_number, slice_number, 0, dy - 1, 0, dz - 1)
  512 + dx, dy, dz = dz, dx, dy
  513 + extent = (slice_number, slice_number + dx - 1, 0, dy - 1, 0, dz - 1)
511 514 elif orientation == 'CORONAL':
512   - dx, dy, dz = dx, 1, dy
513   - extent = (0, dx - 1, slice_number, slice_number, 0, dz - 1)
  515 + dx, dy, dz = dx, dz, dy
  516 + extent = (0, dx - 1, slice_number, slice_number + dy - 1, 0, dz - 1)
514 517  
515 518 # Generating the vtkImageData
516 519 image = vtk.vtkImageData()
... ...
invesalius/data/slice_.py
  Diff comments   View file @a724a20
... ... @@ -260,8 +260,8 @@ class Slice(object):
260 260 #---------------------------------------------------------------------------
261 261  
262 262 def GetSlices(self, orientation, slice_number):
263   - print "Getting slice", self.buffer_slices[orientation][0], slice_number
264 263 if self.buffer_slices[orientation][0] == slice_number:
  264 + print "From buffer"
265 265 image = self.buffer_slices[orientation][1]
266 266 if self.current_mask and self.current_mask.is_shown:
267 267 n_mask = self.buffer_slices[orientation][2]
... ... @@ -275,7 +275,6 @@ class Slice(object):
275 275 image = self.do_ww_wl(image)
276 276  
277 277 if self.current_mask and self.current_mask.is_shown:
278   - print "Mask"
279 278 n_mask = self.GetMaskSlice(orientation, slice_number)
280 279 mask = iu.to_vtk(n_mask, self.spacing, slice_number, orientation)
281 280 final_image = self.do_blend(image, self.do_colour_mask(mask))
... ... @@ -411,12 +410,12 @@ class Slice(object):
411 410 m[slice_ < thresh_min] = 0
412 411 m[slice_ > thresh_max] = 0
413 412 m[m == 1] = 255
414   - self.current_mask.matrix[n] = m
  413 + self.current_mask.matrix[n+1, 1:, 1:] = m
415 414 else:
416 415 print "Only one slice"
417 416 slice_ = self.buffer_slices[orientation][3]
418   - self.buffer_slices[orientation][2][:] = 0
419   - self.buffer_slices[orientation][2][numpy.logical_and(slice_ >= thresh_min,slice_ <= thresh_max)] = 255
  417 + self.buffer_slices[orientation][2] = 255 * ((slice_ >= thresh_min) & (slice_ <= thresh_max))
  418 + print self.buffer_slices[orientation][2].dtype
420 419  
421 420 # Update viewer
422 421 #ps.Publisher().sendMessage('Update slice viewer')
... ... @@ -521,15 +520,15 @@ class Slice(object):
521 520  
522 521 # This is very important. Do not use masks' imagedata. It would mess up
523 522 # surface quality event when using contour
524   - imagedata = self.imagedata
525   -
526 523 colour = mask.colour
527 524 threshold = mask.threshold_range
528 525 edited_points = mask.edited_points
529 526  
530   - ps.Publisher().sendMessage('Create surface',
531   - (imagedata,colour,threshold,
532   - edited_points, overwrite_surface))
  527 + self.SetMaskThreshold(mask.index, threshold)
  528 +
  529 + mask.matrix.flush()
  530 +
  531 + ps.Publisher().sendMessage('Create surface', (mask, self.spacing))
533 532  
534 533 def GetOutput(self):
535 534 return self.blend_filter.GetOutput()
... ...
invesalius/data/surface.py
  Diff comments   View file @a724a20
... ... @@ -376,29 +376,36 @@ class SurfaceManager():
376 376 Create surface actor, save into project and send it to viewer.
377 377 """
378 378 surface_data = pubsub_evt.data
379   -
380   - if len(surface_data) == 5:
381   - imagedata, colour, [min_value, max_value], \
382   - edited_points, overwrite = pubsub_evt.data
383   - quality=_('Optimal *')
384   - surface_name = ""
385   - fill_holes = True
386   - keep_largest = False
387   - else:
388   - imagedata, colour, [min_value, max_value],\
389   - edited_points, overwrite, surface_name,\
390   - quality, fill_holes, keep_largest =\
391   - pubsub_evt.data
  379 + mask, spacing = pubsub_evt.data
  380 + min_value, max_value = mask.threshold_range
  381 + fill_holes = True
  382 +
  383 + #if len(surface_data) == 5:
  384 + #imagedata, colour, [min_value, max_value], \
  385 + #edited_points, overwrite = pubsub_evt.data
  386 + #quality=_('Optimal *')
  387 + #surface_name = ""
  388 + #fill_holes = True
  389 + #keep_largest = False
  390 + #else:
  391 + #imagedata, colour, [min_value, max_value],\
  392 + #edited_points, overwrite, surface_name,\
  393 + #quality, fill_holes, keep_largest =\
  394 + #pubsub_evt.data
392 395  
393 396 mode = 'CONTOUR' # 'GRAYSCALE'
394   -
395   - ps.Publisher().sendMessage('Begin busy cursor')
396   - imagedata_tmp = None
397   - if (edited_points):
398   - imagedata_tmp = vtk.vtkImageData()
399   - imagedata_tmp.DeepCopy(imagedata)
400   - imagedata_tmp.Update()
401   - imagedata = iu.BuildEditedImage(imagedata_tmp, edited_points)
  397 + quality=_('Optimal *')
  398 + keep_largest = True
  399 + surface_name = ""
  400 + colour = mask.colour
  401 +
  402 + #ps.Publisher().sendMessage('Begin busy cursor')
  403 + #imagedata_tmp = None
  404 + #if (edited_points):
  405 + #imagedata_tmp = vtk.vtkImageData()
  406 + #imagedata_tmp.DeepCopy(imagedata)
  407 + #imagedata_tmp.Update()
  408 + #imagedata = iu.BuildEditedImage(imagedata_tmp, edited_points)
402 409  
403 410 if quality in const.SURFACE_QUALITY.keys():
404 411 imagedata_resolution = const.SURFACE_QUALITY[quality][0]
... ... @@ -406,61 +413,89 @@ class SurfaceManager():
406 413 smooth_relaxation_factor = const.SURFACE_QUALITY[quality][2]
407 414 decimate_reduction = const.SURFACE_QUALITY[quality][3]
408 415  
409   - if imagedata_resolution:
410   - imagedata = iu.ResampleImage3D(imagedata, imagedata_resolution)
  416 + #if imagedata_resolution:
  417 + #imagedata = iu.ResampleImage3D(imagedata, imagedata_resolution)
411 418  
412   - pipeline_size = 4
413   - if decimate_reduction:
414   - pipeline_size += 1
415   - if (smooth_iterations and smooth_relaxation_factor):
416   - pipeline_size += 1
417   - if fill_holes:
418   - pipeline_size += 1
419   - if keep_largest:
420   - pipeline_size += 1
  419 + #pipeline_size = 4
  420 + #if decimate_reduction:
  421 + #pipeline_size += 1
  422 + #if (smooth_iterations and smooth_relaxation_factor):
  423 + #pipeline_size += 1
  424 + #if fill_holes:
  425 + #pipeline_size += 1
  426 + #if keep_largest:
  427 + #pipeline_size += 1
421 428  
422   - # Update progress value in GUI
423   - UpdateProgress = vu.ShowProgress(pipeline_size)
424   - UpdateProgress(0, _("Generating 3D surface..."))
  429 + ## Update progress value in GUI
  430 + #UpdateProgress = vu.ShowProgress(pipeline_size)
  431 + #UpdateProgress(0, _("Generating 3D surface..."))
425 432  
426   - filename_img = tempfile.mktemp()
  433 + #filename_img = tempfile.mktemp()
427 434  
428   - writer = vtk.vtkXMLImageDataWriter()
429   - writer.SetFileName(filename_img)
430   - writer.SetInput(imagedata)
431   - writer.Write()
  435 + #writer = vtk.vtkXMLImageDataWriter()
  436 + #writer.SetFileName(filename_img)
  437 + #writer.SetInput(imagedata)
  438 + #writer.Write()
432 439  
433 440 language = ses.Session().language
  441 +
  442 + filename_img = mask.temp_file
  443 + overwrite = 0
434 444  
435 445 if (prj.Project().original_orientation == const.CORONAL):
436 446 flip_image = False
437 447 else:
438 448 flip_image = True
  449 +
  450 + n_processors = 1 # multiprocessing.cpu_count()
439 451  
440 452 pipe_in, pipe_out = multiprocessing.Pipe()
441   - sp = surface_process.SurfaceProcess(pipe_in, filename_img, mode, min_value, max_value,
442   - decimate_reduction, smooth_relaxation_factor,
443   - smooth_iterations, language, fill_holes, keep_largest, flip_image)
444   - sp.start()
445   -
446   - while 1:
447   - msg = pipe_out.recv()
448   - if(msg is None):
449   - break
450   - UpdateProgress(msg[0],msg[1])
451   -
452   - filename_polydata = pipe_out.recv()
453   -
454   - reader = vtk.vtkXMLPolyDataReader()
455   - reader.SetFileName(filename_polydata)
456   - reader.Update()
457   -
458   - polydata = reader.GetOutput()
  453 + o_piece = 2
  454 + piece_size = 40
  455 +
  456 + n_pieces = round(mask.matrix.shape[0] / piece_size + 0.5, 0)
  457 + print "n_pieces", n_pieces, mask.matrix.shape
  458 +
  459 + q_in = multiprocessing.Queue()
  460 + q_out = multiprocessing.Queue()
  461 +
  462 + p = []
  463 + for i in xrange(n_processors):
  464 + sp = surface_process.SurfaceProcess(pipe_in, filename_img,
  465 + mask.matrix.shape, mask.matrix.dtype, spacing,
  466 + mode, min_value, max_value,
  467 + decimate_reduction, smooth_relaxation_factor,
  468 + smooth_iterations, language, fill_holes, keep_largest,
  469 + flip_image, q_in, q_out)
  470 + p.append(sp)
  471 + sp.start()
  472 +
  473 + for i in xrange(n_pieces):
  474 + init = i * piece_size
  475 + end = init + piece_size + o_piece
  476 + roi = slice(init, end)
  477 + q_in.put(roi)
  478 + print "new_piece", roi
  479 +
  480 + for i in p:
  481 + q_in.put(None)
  482 +
  483 + polydata_append = vtk.vtkAppendPolyData()
  484 + t = n_pieces
  485 + while t:
  486 + filename_polydata = q_out.get()
  487 +
  488 + reader = vtk.vtkXMLPolyDataReader()
  489 + reader.SetFileName(filename_polydata)
  490 + reader.Update()
  491 + polydata_append.AddInput(reader.GetOutput())
  492 +
  493 + t -= 1
  494 +
  495 + polydata = polydata_append.GetOutput()
459 496  
460 497 # Orient normals from inside to outside
461 498 normals = vtk.vtkPolyDataNormals()
462   - normals.AddObserver("ProgressEvent", lambda obj,evt:
463   - UpdateProgress(obj, _("Generating 3D surface...")))
464 499 normals.SetInput(polydata)
465 500 normals.SetFeatureAngle(80)
466 501 normals.AutoOrientNormalsOn()
... ... @@ -468,8 +503,6 @@ class SurfaceManager():
468 503  
469 504 # Improve performance
470 505 stripper = vtk.vtkStripper()
471   - stripper.AddObserver("ProgressEvent", lambda obj,evt:
472   - UpdateProgress(obj, _("Generating 3D surface...")))
473 506 stripper.SetInput(normals.GetOutput())
474 507 stripper.PassThroughCellIdsOn()
475 508 stripper.PassThroughPointIdsOn()
... ... @@ -526,8 +559,6 @@ class SurfaceManager():
526 559  
527 560 # The following lines have to be here, otherwise all volumes disappear
528 561 measured_polydata = vtk.vtkMassProperties()
529   - measured_polydata.AddObserver("ProgressEvent", lambda obj,evt:
530   - UpdateProgress(obj, _("Generating 3D surface...")))
531 562 measured_polydata.SetInput(polydata)
532 563 volume = measured_polydata.GetVolume()
533 564 surface.volume = volume
... ... @@ -552,10 +583,6 @@ class SurfaceManager():
552 583 surface.colour, surface.volume,
553 584 surface.transparency))
554 585  
555   - #Destroy Copy original imagedata
556   - if(imagedata_tmp):
557   - del imagedata_tmp
558   -
559 586 ps.Publisher().sendMessage('End busy cursor')
560 587  
561 588 def RemoveActor(self, index):
... ...
invesalius/data/surface_process.py
  Diff comments   View file @a724a20
1   -import vtk
2 1 import multiprocessing
3 2 import tempfile
  3 +import time
  4 +
  5 +import numpy
  6 +import vtk
4 7  
5 8 import i18n
  9 +import imagedata_utils
  10 +
  11 +from scipy import ndimage
6 12  
7 13 class SurfaceProcess(multiprocessing.Process):
8 14  
9   - def __init__(self, pipe, filename, mode, min_value, max_value,
  15 + def __init__(self, pipe, filename, shape, dtype, spacing, mode, min_value, max_value,
10 16 decimate_reduction, smooth_relaxation_factor,
11 17 smooth_iterations, language, fill_holes, keep_largest,
12   - flip_image):
  18 + flip_image, q_in, q_out):
13 19  
14 20 multiprocessing.Process.__init__(self)
15 21 self.pipe = pipe
  22 + self.spacing = spacing
16 23 self.filename = filename
17 24 self.mode = mode
18 25 self.min_value = min_value
... ... @@ -24,64 +31,59 @@ class SurfaceProcess(multiprocessing.Process):
24 31 self.fill_holes = fill_holes
25 32 self.keep_largest = keep_largest
26 33 self.flip_image = flip_image
  34 + self.q_in = q_in
  35 + self.q_out = q_out
27 36  
  37 + self.mask = numpy.memmap(filename, mode='r', dtype=dtype,
  38 + shape=shape)
28 39  
29 40 def run(self):
30   - self.CreateSurface()
  41 + while 1:
  42 + roi = self.q_in.get()
  43 + print roi
  44 + if roi is None:
  45 + break
  46 + self.CreateSurface(roi)
31 47  
32 48 def SendProgress(self, obj, msg):
33 49 prog = obj.GetProgress()
34 50 self.pipe.send([prog, msg])
35 51  
36   - def CreateSurface(self):
37   - _ = i18n.InstallLanguage(self.language)
38   -
39   - reader = vtk.vtkXMLImageDataReader()
40   - reader.SetFileName(self.filename)
41   - reader.Update()
42   -
43   - image = reader.GetOutput()
44   -
45   - if (self.flip_image):
46   - # Flip original vtkImageData
47   - flip = vtk.vtkImageFlip()
48   - flip.SetInput(reader.GetOutput())
49   - flip.SetFilteredAxis(1)
50   - flip.FlipAboutOriginOn()
51   - image = flip.GetOutput()
52   -
  52 + def CreateSurface(self, roi):
  53 + smoothed = ndimage.gaussian_filter(self.mask[roi], (1, 1, 1))
  54 + image = imagedata_utils.to_vtk(smoothed, self.spacing, roi.start,
  55 + "AXIAL")
  56 +
53 57 # Create vtkPolyData from vtkImageData
  58 + print "Generating Polydata"
54 59 if self.mode == "CONTOUR":
  60 + print "Contour"
55 61 contour = vtk.vtkContourFilter()
56 62 contour.SetInput(image)
57   - contour.SetValue(0, self.min_value) # initial threshold
58   - contour.SetValue(1, self.max_value) # final threshold
59   - contour.GetOutput().ReleaseDataFlagOn()
60   - contour.AddObserver("ProgressEvent", lambda obj,evt:
61   - self.SendProgress(obj, _("Generating 3D surface...")))
  63 + contour.SetValue(0, 127.5) # initial threshold
  64 + contour.ComputeScalarsOn()
  65 + contour.ComputeGradientsOn()
  66 + contour.ComputeNormalsOn()
62 67 polydata = contour.GetOutput()
63 68 else: #mode == "GRAYSCALE":
64 69 mcubes = vtk.vtkMarchingCubes()
65 70 mcubes.SetInput(image)
66   - mcubes.SetValue(0, 255)
  71 + mcubes.SetValue(0, 127.5)
67 72 mcubes.ComputeScalarsOn()
68 73 mcubes.ComputeGradientsOn()
69 74 mcubes.ComputeNormalsOn()
70   - mcubes.ThresholdBetween(self.min_value, self.max_value)
71   - mcubes.GetOutput().ReleaseDataFlagOn()
72   - mcubes.AddObserver("ProgressEvent", lambda obj,evt:
73   - self.SendProgress(obj, _("Generating 3D surface...")))
74 75 polydata = mcubes.GetOutput()
75 76  
  77 + print "Decimating"
76 78 if self.decimate_reduction:
77   - decimation = vtk.vtkQuadricDecimation()
  79 + decimation = vtk.vtkDecimatePro()
78 80 decimation.SetInput(polydata)
79 81 decimation.SetTargetReduction(self.decimate_reduction)
80   - decimation.GetOutput().ReleaseDataFlagOn()
81   - decimation.AddObserver("ProgressEvent", lambda obj,evt:
82   - self.SendProgress(obj, _("Generating 3D surface...")))
  82 + decimation.PreserveTopologyOn()
  83 + decimation.SplittingOff()
83 84 polydata = decimation.GetOutput()
84 85  
  86 + print "Smoothing"
85 87 if self.smooth_iterations and self.smooth_relaxation_factor:
86 88 smoother = vtk.vtkSmoothPolyDataFilter()
87 89 smoother.SetInput(polydata)
... ... @@ -90,38 +92,16 @@ class SurfaceProcess(multiprocessing.Process):
90 92 smoother.SetRelaxationFactor(self.smooth_relaxation_factor)
91 93 smoother.FeatureEdgeSmoothingOn()
92 94 smoother.BoundarySmoothingOn()
93   - smoother.GetOutput().ReleaseDataFlagOn()
94   - smoother.AddObserver("ProgressEvent", lambda obj,evt:
95   - self.SendProgress(obj, _("Generating 3D surface...")))
96 95 polydata = smoother.GetOutput()
97 96  
98   -
99   - if self.keep_largest:
100   - conn = vtk.vtkPolyDataConnectivityFilter()
101   - conn.SetInput(polydata)
102   - conn.SetExtractionModeToLargestRegion()
103   - conn.AddObserver("ProgressEvent", lambda obj,evt:
104   - self.SendProgress(obj, _("Generating 3D surface...")))
105   - polydata = conn.GetOutput()
106   -
107   - # Filter used to detect and fill holes. Only fill boundary edges holes.
108   - #TODO: Hey! This piece of code is the same from
109   - # polydata_utils.FillSurfaceHole, we need to review this.
110   - if self.fill_holes:
111   - filled_polydata = vtk.vtkFillHolesFilter()
112   - filled_polydata.SetInput(polydata)
113   - filled_polydata.SetHoleSize(300)
114   - filled_polydata.AddObserver("ProgressEvent", lambda obj,evt:
115   - self.SendProgress(obj, _("Generating 3D surface...")))
116   - polydata = filled_polydata.GetOutput()
117   -
118   -
119   -
  97 + print "Saving"
120 98 filename = tempfile.mktemp()
121 99 writer = vtk.vtkXMLPolyDataWriter()
122 100 writer.SetInput(polydata)
123 101 writer.SetFileName(filename)
124 102 writer.Write()
  103 + print filename
  104 +
  105 + time.sleep(1)
125 106  
126   - self.pipe.send(None)
127   - self.pipe.send(filename)
  107 + self.q_out.put(filename)
... ...