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Commit a84bfc2023ffaaa389d599e862112e8e9c80b084

Authored by Paulo Henrique Junqueira Amorim
1 parent 5323e991
Exists in master and in 68 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, invesalius-libift, 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: Inverted 3D from Coronal Slice (#240)

Showing 3 changed files with 43 additions and 25 deletions   Show diff stats
invesalius/data/surface.py
  Diff comments   View file @a84bfc2
@@ -431,11 +431,16 @@ class SurfaceManager(): @@ -431,11 +431,16 @@ class SurfaceManager():
431 writer.Write() 431 writer.Write()
432 432
433 language = ses.Session().language 433 language = ses.Session().language
434 - 434 +
  435 + if (prj.Project().original_orientation == const.AXIAL):
  436 + flip_image = True
  437 + else:
  438 + flip_image = False
  439 +
435 pipe_in, pipe_out = multiprocessing.Pipe() 440 pipe_in, pipe_out = multiprocessing.Pipe()
436 sp = surface_process.SurfaceProcess(pipe_in, filename_img, mode, min_value, max_value, 441 sp = surface_process.SurfaceProcess(pipe_in, filename_img, mode, min_value, max_value,
437 decimate_reduction, smooth_relaxation_factor, 442 decimate_reduction, smooth_relaxation_factor,
438 - smooth_iterations, language, fill_holes, keep_largest) 443 + smooth_iterations, language, fill_holes, keep_largest, flip_image)
439 sp.start() 444 sp.start()
440 445
441 while 1: 446 while 1:
invesalius/data/surface_process.py
  Diff comments   View file @a84bfc2
@@ -8,7 +8,8 @@ class SurfaceProcess(multiprocessing.Process): @@ -8,7 +8,8 @@ class SurfaceProcess(multiprocessing.Process):
8 8
9 def __init__(self, pipe, filename, mode, min_value, max_value, 9 def __init__(self, pipe, filename, mode, min_value, max_value,
10 decimate_reduction, smooth_relaxation_factor, 10 decimate_reduction, smooth_relaxation_factor,
11 - smooth_iterations, language, fill_holes, keep_largest): 11 + smooth_iterations, language, fill_holes, keep_largest,
  12 + flip_image):
12 13
13 multiprocessing.Process.__init__(self) 14 multiprocessing.Process.__init__(self)
14 self.pipe = pipe 15 self.pipe = pipe
@@ -22,6 +23,7 @@ class SurfaceProcess(multiprocessing.Process): @@ -22,6 +23,7 @@ class SurfaceProcess(multiprocessing.Process):
22 self.language = language 23 self.language = language
23 self.fill_holes = fill_holes 24 self.fill_holes = fill_holes
24 self.keep_largest = keep_largest 25 self.keep_largest = keep_largest
  26 + self.flip_image = flip_image
25 27
26 28
27 def run(self): 29 def run(self):
@@ -37,17 +39,21 @@ class SurfaceProcess(multiprocessing.Process): @@ -37,17 +39,21 @@ class SurfaceProcess(multiprocessing.Process):
37 reader = vtk.vtkXMLImageDataReader() 39 reader = vtk.vtkXMLImageDataReader()
38 reader.SetFileName(self.filename) 40 reader.SetFileName(self.filename)
39 reader.Update() 41 reader.Update()
40 -  
41 - # Flip original vtkImageData  
42 - flip = vtk.vtkImageFlip()  
43 - flip.SetInput(reader.GetOutput())  
44 - flip.SetFilteredAxis(1)  
45 - flip.FlipAboutOriginOn()  
46 - 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 +
47 # Create vtkPolyData from vtkImageData 53 # Create vtkPolyData from vtkImageData
48 if self.mode == "CONTOUR": 54 if self.mode == "CONTOUR":
49 contour = vtk.vtkContourFilter() 55 contour = vtk.vtkContourFilter()
50 - contour.SetInput(flip.GetOutput()) 56 + contour.SetInput(image)
51 contour.SetValue(0, self.min_value) # initial threshold 57 contour.SetValue(0, self.min_value) # initial threshold
52 contour.SetValue(1, self.max_value) # final threshold 58 contour.SetValue(1, self.max_value) # final threshold
53 contour.GetOutput().ReleaseDataFlagOn() 59 contour.GetOutput().ReleaseDataFlagOn()
@@ -56,7 +62,7 @@ class SurfaceProcess(multiprocessing.Process): @@ -56,7 +62,7 @@ class SurfaceProcess(multiprocessing.Process):
56 polydata = contour.GetOutput() 62 polydata = contour.GetOutput()
57 else: #mode == "GRAYSCALE": 63 else: #mode == "GRAYSCALE":
58 mcubes = vtk.vtkMarchingCubes() 64 mcubes = vtk.vtkMarchingCubes()
59 - mcubes.SetInput(flip.GetOutput()) 65 + mcubes.SetInput(image)
60 mcubes.SetValue(0, 255) 66 mcubes.SetValue(0, 255)
61 mcubes.ComputeScalarsOn() 67 mcubes.ComputeScalarsOn()
62 mcubes.ComputeGradientsOn() 68 mcubes.ComputeGradientsOn()
invesalius/data/volume.py
  Diff comments   View file @a84bfc2
@@ -450,19 +450,26 @@ class Volume(): @@ -450,19 +450,26 @@ class Volume():
450 image = proj.imagedata 450 image = proj.imagedata
451 451
452 number_filters = len(self.config['convolutionFilters']) 452 number_filters = len(self.config['convolutionFilters'])
453 - update_progress= vtk_utils.ShowProgress(2 + number_filters)  
454 -  
455 - # Flip original vtkImageData  
456 - flip = vtk.vtkImageFlip()  
457 - flip.SetInput(image)  
458 - flip.SetFilteredAxis(1)  
459 - flip.FlipAboutOriginOn()  
460 - flip.AddObserver("ProgressEvent", lambda obj,evt:  
461 - update_progress(flip, "Rendering..."))  
462 - flip.Update()  
463 -  
464 - image = flip.GetOutput()  
465 - 453 +
  454 + if (prj.Project().original_orientation == const.AXIAL):
  455 + flip_image = True
  456 + else:
  457 + flip_image = False
  458 +
  459 + if (flip_image):
  460 + update_progress= vtk_utils.ShowProgress(2 + number_filters)
  461 + # Flip original vtkImageData
  462 + flip = vtk.vtkImageFlip()
  463 + flip.SetInput(image)
  464 + flip.SetFilteredAxis(1)
  465 + flip.FlipAboutOriginOn()
  466 + flip.AddObserver("ProgressEvent", lambda obj,evt:
  467 + update_progress(flip, "Rendering..."))
  468 + flip.Update()
  469 + image = flip.GetOutput()
  470 + else:
  471 + update_progress= vtk_utils.ShowProgress(1 + number_filters)
  472 +
466 scale = image.GetScalarRange() 473 scale = image.GetScalarRange()
467 self.scale = scale 474 self.scale = scale
468 475