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Commit 53c78d4feebe95a7a78f3c65d2629904a425eda4

Authored by Thiago Franco de Moraes
1 parent 08a3b8ee
Exists in master

Resizing image when creating surface with low and medium quality

Showing 3 changed files with 44 additions and 29 deletions   Show diff stats
invesalius/data/imagedata_utils.py
  Diff comments   View file @53c78d4
... ... @@ -125,6 +125,16 @@ def resize_slice(im_array, resolution_percentage):
125 125 return out
126 126  
127 127  
  128 +def resize_image_array(image, resolution_percentage, as_mmap=False):
  129 + out = zoom(image, resolution_percentage, image.dtype, order=2)
  130 + if as_mmap:
  131 + fname = tempfile.mktemp(suffix="_resized")
  132 + out_mmap = np.memmap(fname, shape=out.shape, dtype=out.dtype, mode='w+')
  133 + out_mmap[:] = out
  134 + return out_mmap
  135 + return out
  136 +
  137 +
128 138 def read_dcm_slice_as_np2(filename, resolution_percentage=1.0):
129 139 reader = gdcm.ImageReader()
130 140 reader.SetFileName(filename)
... ...
invesalius/data/surface.py
  Diff comments   View file @53c78d4
... ... @@ -598,6 +598,10 @@ class SurfaceManager():
598 598 filename_img = slice_.matrix_filename
599 599 spacing = slice_.spacing
600 600  
  601 + mask_temp_file = mask.temp_file
  602 + mask_shape = mask.matrix.shape
  603 + mask_dtype = mask.matrix.dtype
  604 +
601 605 algorithm = surface_parameters['method']['algorithm']
602 606 options = surface_parameters['method']['options']
603 607  
... ... @@ -608,6 +612,8 @@ class SurfaceManager():
608 612  
609 613 fill_border_holes = surface_parameters['options'].get('fill_border_holes', True)
610 614  
  615 + print(surface_parameters)
  616 +
611 617 mode = 'CONTOUR' # 'GRAYSCALE'
612 618 min_value, max_value = mask.threshold_range
613 619 colour = mask.colour[:3]
... ... @@ -641,6 +647,16 @@ class SurfaceManager():
641 647 else:
642 648 flip_image = True
643 649  
  650 + if imagedata_resolution > 0:
  651 + spacing = tuple([s * imagedata_resolution for s in spacing])
  652 + matrix = iu.resize_image_array(matrix, 1.0/imagedata_resolution, True)
  653 + mask = iu.resize_image_array(mask.matrix, 1.0/imagedata_resolution, True)
  654 +
  655 + filename_img = matrix.filename
  656 + mask_temp_file = mask.filename
  657 + mask_shape = mask.shape
  658 + mask_dtype = mask.dtype
  659 +
644 660 n_processors = multiprocessing.cpu_count()
645 661  
646 662 o_piece = 1
... ... @@ -653,6 +669,8 @@ class SurfaceManager():
653 669 manager = multiprocessing.Manager()
654 670 msg_queue = manager.Queue(1)
655 671  
  672 + print("Resolution", imagedata_resolution)
  673 +
656 674 # If InVesalius is running without GUI
657 675 if wx.GetApp() is None:
658 676 for i in range(n_pieces):
... ... @@ -662,8 +680,8 @@ class SurfaceManager():
662 680 print("new_piece", roi)
663 681 f = pool.apply_async(surface_process.create_surface_piece,
664 682 args = (filename_img, matrix.shape, matrix.dtype,
665   - mask.temp_file, mask.matrix.shape,
666   - mask.matrix.dtype, roi, spacing, mode,
  683 + mask_temp_file, mask_shape,
  684 + mask_dtype, roi, spacing, mode,
667 685 min_value, max_value, decimate_reduction,
668 686 smooth_relaxation_factor,
669 687 smooth_iterations, language, flip_image,
... ... @@ -720,31 +738,18 @@ class SurfaceManager():
720 738 end = init + piece_size + o_piece
721 739 roi = slice(init, end)
722 740 print("new_piece", roi)
723   - try:
724   - f = pool.apply_async(surface_process.create_surface_piece,
725   - args = (filename_img, matrix.shape, matrix.dtype,
726   - mask.temp_file, mask.matrix.shape,
727   - mask.matrix.dtype, roi, spacing, mode,
728   - min_value, max_value, decimate_reduction,
729   - smooth_relaxation_factor,
730   - smooth_iterations, language, flip_image,
731   - algorithm != 'Default', algorithm,
732   - imagedata_resolution, fill_border_holes),
733   - callback=lambda x: filenames.append(x),
734   - error_callback=functools.partial(self._on_callback_error,
735   - dialog=sp))
736   - # python2
737   - except TypeError:
738   - f = pool.apply_async(surface_process.create_surface_piece,
739   - args = (filename_img, matrix.shape, matrix.dtype,
740   - mask.temp_file, mask.matrix.shape,
741   - mask.matrix.dtype, roi, spacing, mode,
742   - min_value, max_value, decimate_reduction,
743   - smooth_relaxation_factor,
744   - smooth_iterations, language, flip_image,
745   - algorithm != 'Default', algorithm,
746   - imagedata_resolution, fill_border_holes),
747   - callback=lambda x: filenames.append(x))
  741 + f = pool.apply_async(surface_process.create_surface_piece,
  742 + args = (filename_img, matrix.shape, matrix.dtype,
  743 + mask_temp_file, mask_shape,
  744 + mask_dtype, roi, spacing, mode,
  745 + min_value, max_value, decimate_reduction,
  746 + smooth_relaxation_factor,
  747 + smooth_iterations, language, flip_image,
  748 + algorithm != 'Default', algorithm,
  749 + imagedata_resolution, fill_border_holes),
  750 + callback=lambda x: filenames.append(x),
  751 + error_callback=functools.partial(self._on_callback_error,
  752 + dialog=sp))
748 753  
749 754 while len(filenames) != n_pieces:
750 755 if sp.WasCancelled() or not sp.running:
... ...
invesalius/data/surface_process.py
  Diff comments   View file @53c78d4
... ... @@ -131,8 +131,8 @@ def create_surface_piece(filename, shape, dtype, mask_filename, mask_shape,
131 131 image = converters.to_vtk(a_image, spacing, roi.start, "AXIAL", padding=padding)
132 132 del a_image
133 133  
134   - if imagedata_resolution:
135   - image = ResampleImage3D(image, imagedata_resolution)
  134 + # if imagedata_resolution:
  135 + # image = ResampleImage3D(image, imagedata_resolution)
136 136  
137 137 flip = vtk.vtkImageFlip()
138 138 flip.SetInputData(image)
... ...