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Commit cd0cef0954f13add478e94eb9795808562db9a0c

Authored by Thiago Franco de Moraes
Committed by GitHub
1 parent 8ba6ba8d
Exists in master

Remove vtkgdcm (#201) 

* generating thumbs only using gdcm + numpy

* applying intercept slop

* generating thumbnails and slices without vtkgdcmreader

* Using numpy and gdcm in dicom_preview_panel

* loading multiframe dicom

* working with rgb dicoms

* little improvements

* removed all vtkgdcm importing

* getting spacing from gdcmimagereader
Showing 7 changed files with 114 additions and 318 deletions   Show diff stats
invesalius/control.py
  Diff comments   View file @cd0cef0
... ... @@ -824,7 +824,6 @@ class Controller():
824 824 self.matrix, scalar_range, self.filename = image_utils.dcm2memmap(filelist, size,
825 825 orientation, resolution_percentage)
826 826  
827   - print(xyspacing, zspacing)
828 827 if orientation == 'AXIAL':
829 828 spacing = xyspacing[0], xyspacing[1], zspacing
830 829 elif orientation == 'CORONAL':
... ... @@ -832,7 +831,10 @@ class Controller():
832 831 elif orientation == 'SAGITTAL':
833 832 spacing = zspacing, xyspacing[1], xyspacing[0]
834 833 else:
835   - self.matrix, spacing, scalar_range, self.filename = image_utils.dcmmf2memmap(filelist[0], orientation)
  834 + print(">>>>>> filelist", filelist)
  835 + self.matrix, scalar_range, spacing, self.filename = image_utils.dcmmf2memmap(filelist[0], orientation)
  836 +
  837 + print(">>>>>> spacing", spacing)
836 838  
837 839 self.Slice = sl.Slice()
838 840 self.Slice.matrix = self.matrix
... ...
invesalius/data/converters.py
  Diff comments   View file @cd0cef0
... ... @@ -17,10 +17,13 @@
17 17 # detalhes.
18 18 #--------------------------------------------------------------------------
19 19  
20   -import numpy
  20 +import gdcm
  21 +import numpy as np
21 22 import vtk
  23 +
22 24 from vtk.util import numpy_support
23 25  
  26 +
24 27 def to_vtk(n_array, spacing, slice_number, orientation, origin=(0, 0, 0), padding=(0, 0, 0)):
25 28  
26 29 if orientation == "SAGITTAL":
... ... @@ -84,3 +87,40 @@ def np_rgba_to_vtk(n_array, spacing=(1.0, 1.0, 1.0)):
84 87 image.GetPointData().SetScalars(v_image)
85 88  
86 89 return image
  90 +
  91 +
  92 +# Based on http://gdcm.sourceforge.net/html/ConvertNumpy_8py-example.html
  93 +def gdcm_to_numpy(image, apply_intercep_scale=True):
  94 + map_gdcm_np = {
  95 + gdcm.PixelFormat.UINT8 :np.uint8,
  96 + gdcm.PixelFormat.INT8 :np.int8,
  97 + #gdcm.PixelFormat.UINT12 :np.uint12,
  98 + #gdcm.PixelFormat.INT12 :np.int12,
  99 + gdcm.PixelFormat.UINT16 :np.uint16,
  100 + gdcm.PixelFormat.INT16 :np.int16,
  101 + gdcm.PixelFormat.UINT32 :np.uint32,
  102 + gdcm.PixelFormat.INT32 :np.int32,
  103 + #gdcm.PixelFormat.FLOAT16:np.float16,
  104 + gdcm.PixelFormat.FLOAT32:np.float32,
  105 + gdcm.PixelFormat.FLOAT64:np.float64,
  106 + }
  107 +
  108 + pf = image.GetPixelFormat()
  109 + if image.GetNumberOfDimensions() == 3:
  110 + shape = image.GetDimension(2), image.GetDimension(1), image.GetDimension(0), pf.GetSamplesPerPixel()
  111 + else:
  112 + shape = image.GetDimension(1), image.GetDimension(0), pf.GetSamplesPerPixel()
  113 + dtype = map_gdcm_np[pf.GetScalarType()]
  114 + gdcm_array = image.GetBuffer()
  115 + np_array = np.frombuffer(gdcm_array.encode('utf-8', errors="surrogateescape"), dtype=dtype)
  116 + np_array.shape = shape
  117 + np_array = np_array.squeeze()
  118 +
  119 + if apply_intercep_scale:
  120 + shift = image.GetIntercept()
  121 + scale = image.GetSlope()
  122 + output = np.empty_like(np_array, np.int16)
  123 + output[:] = scale * np_array + shift
  124 + return output
  125 + else:
  126 + return np_array
... ...
invesalius/data/imagedata_utils.py
  Diff comments   View file @cd0cef0
... ... @@ -23,9 +23,10 @@ import sys
23 23 import tempfile
24 24  
25 25 import gdcm
  26 +import imageio
26 27 import numpy
  28 +import numpy as np
27 29 import vtk
28   -import vtkgdcm
29 30 from wx.lib.pubsub import pub as Publisher
30 31  
31 32 from scipy.ndimage import shift, zoom
... ... @@ -124,20 +125,15 @@ def resize_slice(im_array, resolution_percentage):
124 125 return out
125 126  
126 127  
127   -def read_dcm_slice_as_np(filename, resolution_percentage=1.0):
128   - """
129   - read a dicom slice file and return the slice as numpy ndarray
130   - """
131   - dcm_reader = vtkgdcm.vtkGDCMImageReader()
132   - dcm_reader.SetFileName(filename)
133   - dcm_reader.Update()
134   - image = dcm_reader.GetOutput()
  128 +def read_dcm_slice_as_np2(filename, resolution_percentage=1.0):
  129 + reader = gdcm.ImageReader()
  130 + reader.SetFileName(filename)
  131 + reader.Read()
  132 + image = reader.GetImage()
  133 + output = converters.gdcm_to_numpy(image)
135 134 if resolution_percentage < 1.0:
136   - image = ResampleImage2D(image, resolution_percentage=resolution_percentage)
137   - dx, dy, dz = image.GetDimensions()
138   - im_array = numpy_support.vtk_to_numpy(image.GetPointData().GetScalars())
139   - im_array.shape = dy, dx
140   - return im_array
  135 + output = zoom(output, resolution_percentage)
  136 + return output
141 137  
142 138  
143 139 def FixGantryTilt(matrix, spacing, tilt):
... ... @@ -240,17 +236,6 @@ def View(imagedata):
240 236 import time
241 237 time.sleep(10)
242 238  
243   -def ViewGDCM(imagedata):
244   - viewer = vtkgdcm.vtkImageColorViewer()
245   - viewer.SetInput(reader.GetOutput())
246   - viewer.SetColorWindow(500.)
247   - viewer.SetColorLevel(50.)
248   - viewer.Render()
249   -
250   - import time
251   - time.sleep(5)
252   -
253   -
254 239  
255 240 def ExtractVOI(imagedata,xi,xf,yi,yf,zi,zf):
256 241 """
... ... @@ -265,267 +250,33 @@ def ExtractVOI(imagedata,xi,xf,yi,yf,zi,zf):
265 250 return voi.GetOutput()
266 251  
267 252  
268   -def create_dicom_thumbnails(filename, window=None, level=None):
269   - rvtk = vtkgdcm.vtkGDCMImageReader()
270   - rvtk.SetFileName(utils.encode(filename, const.FS_ENCODE))
271   - rvtk.Update()
272   -
273   - img = rvtk.GetOutput()
  253 +def create_dicom_thumbnails(image, window=None, level=None):
  254 + pf = image.GetPixelFormat()
  255 + np_image = converters.gdcm_to_numpy(image, pf.GetSamplesPerPixel() == 1)
274 256 if window is None or level is None:
275   - _min, _max = img.GetScalarRange()
  257 + _min, _max = np_image.min(), np_image.max()
276 258 window = _max - _min
277 259 level = _min + window / 2
278 260  
279   - dx, dy, dz = img.GetDimensions()
280   -
281   - if dz > 1:
  261 + if image.GetNumberOfDimensions() >= 3:
282 262 thumbnail_paths = []
283   - for i in range(dz):
284   - img_slice = ExtractVOI(img, 0, dx-1, 0, dy-1, i, i+1)
285   -
286   - colorer = vtk.vtkImageMapToWindowLevelColors()
287   - colorer.SetInputData(img_slice)
288   - colorer.SetWindow(window)
289   - colorer.SetLevel(level)
290   - colorer.SetOutputFormatToRGB()
291   - colorer.Update()
292   -
293   - resample = vtk.vtkImageResample()
294   - resample.SetInputData(colorer.GetOutput())
295   - resample.SetAxisMagnificationFactor ( 0, 0.25 )
296   - resample.SetAxisMagnificationFactor ( 1, 0.25 )
297   - resample.SetAxisMagnificationFactor ( 2, 1 )
298   - resample.Update()
299   -
300   - thumbnail_path = tempfile.mktemp()
301   -
302   - write_png = vtk.vtkPNGWriter()
303   - write_png.SetInputData(resample.GetOutput())
304   - write_png.SetFileName(thumbnail_path)
305   - write_png.Write()
306   -
  263 + for i in range(np_image.shape[0]):
  264 + thumb_image = zoom(np_image[i], 0.25)
  265 + thumb_image = np.array(get_LUT_value_255(thumb_image, window, level), dtype=np.uint8)
  266 + thumbnail_path = tempfile.mktemp(prefix='thumb_', suffix='.png')
  267 + imageio.imsave(thumbnail_path, thumb_image)
307 268 thumbnail_paths.append(thumbnail_path)
308   -
309 269 return thumbnail_paths
310 270 else:
311   - colorer = vtk.vtkImageMapToWindowLevelColors()
312   - colorer.SetInputData(img)
313   - colorer.SetWindow(window)
314   - colorer.SetLevel(level)
315   - colorer.SetOutputFormatToRGB()
316   - colorer.Update()
317   -
318   - resample = vtk.vtkImageResample()
319   - resample.SetInputData(colorer.GetOutput())
320   - resample.SetAxisMagnificationFactor ( 0, 0.25 )
321   - resample.SetAxisMagnificationFactor ( 1, 0.25 )
322   - resample.SetAxisMagnificationFactor ( 2, 1 )
323   - resample.Update()
324   -
325   - thumbnail_path = tempfile.mktemp()
326   -
327   - write_png = vtk.vtkPNGWriter()
328   - write_png.SetInputData(resample.GetOutput())
329   - write_png.SetFileName(thumbnail_path)
330   - write_png.Write()
331   -
332   - return thumbnail_path
333   -
334   -
335   -def CreateImageData(filelist, zspacing, xyspacing,size,
336   - bits, use_dcmspacing):
337   - message = _("Generating multiplanar visualization...")
338   -
339   - if not const.VTK_WARNING:
340   - log_path = os.path.join(inv_paths.USER_LOG_DIR, 'vtkoutput.txt')
341   - fow = vtk.vtkFileOutputWindow()
342   - fow.SetFileName(log_path)
343   - ow = vtk.vtkOutputWindow()
344   - ow.SetInstance(fow)
345   -
346   - x,y = size
347   - px, py = utils.predict_memory(len(filelist), x, y, bits)
348   -
349   - utils.debug("Image Resized to >>> %f x %f" % (px, py))
350   -
351   - if (x == px) and (y == py):
352   - const.REDUCE_IMAGEDATA_QUALITY = 0
353   - else:
354   - const.REDUCE_IMAGEDATA_QUALITY = 1
355   -
356   - if not(const.REDUCE_IMAGEDATA_QUALITY):
357   - update_progress= vtk_utils.ShowProgress(1, dialog_type = "ProgressDialog")
358   -
359   - array = vtk.vtkStringArray()
360   - for x in range(len(filelist)):
361   - array.InsertValue(x,filelist[x])
362   -
363   - reader = vtkgdcm.vtkGDCMImageReader()
364   - reader.SetFileNames(array)
365   - reader.AddObserver("ProgressEvent", lambda obj,evt:
366   - update_progress(reader,message))
367   - reader.Update()
368   -
369   - # The zpacing is a DicomGroup property, so we need to set it
370   - imagedata = vtk.vtkImageData()
371   - imagedata.DeepCopy(reader.GetOutput())
372   - if (use_dcmspacing):
373   - spacing = xyspacing
374   - spacing[2] = zspacing
375   - else:
376   - spacing = imagedata.GetSpacing()
377   -
378   - imagedata.SetSpacing(spacing[0], spacing[1], zspacing)
379   - else:
380   -
381   - update_progress= vtk_utils.ShowProgress(2*len(filelist),
382   - dialog_type = "ProgressDialog")
383   -
384   - # Reformat each slice and future append them
385   - appender = vtk.vtkImageAppend()
386   - appender.SetAppendAxis(2) #Define Stack in Z
387   -
388   -
389   - # Reformat each slice
390   - for x in range(len(filelist)):
391   - # TODO: We need to check this automatically according
392   - # to each computer's architecture
393   - # If the resolution of the matrix is too large
394   - reader = vtkgdcm.vtkGDCMImageReader()
395   - reader.SetFileName(filelist[x])
396   - reader.AddObserver("ProgressEvent", lambda obj,evt:
397   - update_progress(reader,message))
398   - reader.Update()
399   -
400   - if (use_dcmspacing):
401   - spacing = xyspacing
402   - spacing[2] = zspacing
403   - else:
404   - spacing = reader.GetOutput().GetSpacing()
405   -
406   - tmp_image = vtk.vtkImageData()
407   - tmp_image.DeepCopy(reader.GetOutput())
408   - tmp_image.SetSpacing(spacing[0], spacing[1], zspacing)
409   - tmp_image.Update()
410   -
411   - #Resample image in x,y dimension
412   - slice_imagedata = ResampleImage2D(tmp_image, px, py, update_progress)
413   - #Stack images in Z axes
414   - appender.AddInput(slice_imagedata)
415   - #appender.AddObserver("ProgressEvent", lambda obj,evt:update_progress(appender))
416   - appender.Update()
417   -
418   - spacing = appender.GetOutput().GetSpacing()
419   -
420   - # The zpacing is a DicomGroup property, so we need to set it
421   - imagedata = vtk.vtkImageData()
422   - imagedata.DeepCopy(appender.GetOutput())
423   - imagedata.SetSpacing(spacing[0], spacing[1], zspacing)
424   -
425   - imagedata.AddObserver("ProgressEvent", lambda obj,evt:
426   - update_progress(imagedata,message))
427   - imagedata.Update()
428   -
429   - return imagedata
430   -
431   -
432   -class ImageCreator:
433   - def __init__(self):
434   - self.running = True
435   - Publisher.subscribe(self.CancelImageDataLoad, "Cancel DICOM load")
436   -
437   - def CancelImageDataLoad(self, evt_pusub):
438   - utils.debug("Canceling")
439   - self.running = False
440   -
441   - def CreateImageData(self, filelist, zspacing, size, bits):
442   - message = _("Generating multiplanar visualization...")
443   -
444   - if not const.VTK_WARNING:
445   - log_path = os.path.join(inv_paths.USER_LOG_DIR, 'vtkoutput.txt')
446   - fow = vtk.vtkFileOutputWindow()
447   - fow.SetFileName(log_path)
448   - ow = vtk.vtkOutputWindow()
449   - ow.SetInstance(fow)
450   -
451   - x,y = size
452   - px, py = utils.predict_memory(len(filelist), x, y, bits)
453   - utils.debug("Image Resized to >>> %f x %f" % (px, py))
454   -
455   - if (x == px) and (y == py):
456   - const.REDUCE_IMAGEDATA_QUALITY = 0
  271 + thumbnail_path = tempfile.mktemp(prefix='thumb_', suffix='.png')
  272 + if pf.GetSamplesPerPixel() == 1:
  273 + thumb_image = zoom(np_image, 0.25)
  274 + thumb_image = np.array(get_LUT_value_255(thumb_image, window, level), dtype=np.uint8)
457 275 else:
458   - const.REDUCE_IMAGEDATA_QUALITY = 1
459   -
460   - if not(const.REDUCE_IMAGEDATA_QUALITY):
461   - update_progress= vtk_utils.ShowProgress(1, dialog_type = "ProgressDialog")
462   -
463   - array = vtk.vtkStringArray()
464   - for x in range(len(filelist)):
465   - if not self.running:
466   - return False
467   - array.InsertValue(x,filelist[x])
468   -
469   - if not self.running:
470   - return False
471   - reader = vtkgdcm.vtkGDCMImageReader()
472   - reader.SetFileNames(array)
473   - reader.AddObserver("ProgressEvent", lambda obj,evt:
474   - update_progress(reader,message))
475   - reader.Update()
476   -
477   - if not self.running:
478   - reader.AbortExecuteOn()
479   - return False
480   - # The zpacing is a DicomGroup property, so we need to set it
481   - imagedata = vtk.vtkImageData()
482   - imagedata.DeepCopy(reader.GetOutput())
483   - spacing = imagedata.GetSpacing()
484   - imagedata.SetSpacing(spacing[0], spacing[1], zspacing)
485   - else:
486   -
487   - update_progress= vtk_utils.ShowProgress(2*len(filelist),
488   - dialog_type = "ProgressDialog")
489   -
490   - # Reformat each slice and future append them
491   - appender = vtk.vtkImageAppend()
492   - appender.SetAppendAxis(2) #Define Stack in Z
493   -
494   -
495   - # Reformat each slice
496   - for x in range(len(filelist)):
497   - # TODO: We need to check this automatically according
498   - # to each computer's architecture
499   - # If the resolution of the matrix is too large
500   - if not self.running:
501   - return False
502   - reader = vtkgdcm.vtkGDCMImageReader()
503   - reader.SetFileName(filelist[x])
504   - reader.AddObserver("ProgressEvent", lambda obj,evt:
505   - update_progress(reader,message))
506   - reader.Update()
507   -
508   - #Resample image in x,y dimension
509   - slice_imagedata = ResampleImage2D(reader.GetOutput(), px, py, update_progress)
510   - #Stack images in Z axes
511   - appender.AddInput(slice_imagedata)
512   - #appender.AddObserver("ProgressEvent", lambda obj,evt:update_progress(appender))
513   - appender.Update()
514   -
515   - # The zpacing is a DicomGroup property, so we need to set it
516   - if not self.running:
517   - return False
518   - imagedata = vtk.vtkImageData()
519   - imagedata.DeepCopy(appender.GetOutput())
520   - spacing = imagedata.GetSpacing()
521   -
522   - imagedata.SetSpacing(spacing[0], spacing[1], zspacing)
523   -
524   - imagedata.AddObserver("ProgressEvent", lambda obj,evt:
525   - update_progress(imagedata,message))
526   - imagedata.Update()
  276 + thumb_image = zoom(np_image, (0.25, 0.25, 1))
  277 + imageio.imsave(thumbnail_path, thumb_image)
  278 + return thumbnail_path
527 279  
528   - return imagedata
529 280  
530 281 def bitmap2memmap(files, slice_size, orientation, spacing, resolution_percentage):
531 282 """
... ... @@ -626,7 +377,6 @@ def bitmap2memmap(files, slice_size, orientation, spacing, resolution_percentage
626 377 return matrix, scalar_range, temp_file
627 378  
628 379  
629   -
630 380 def dcm2memmap(files, slice_size, orientation, resolution_percentage):
631 381 """
632 382 From a list of dicom files it creates memmap file in the temp folder and
... ... @@ -635,7 +385,7 @@ def dcm2memmap(files, slice_size, orientation, resolution_percentage):
635 385 message = _("Generating multiplanar visualization...")
636 386 update_progress= vtk_utils.ShowProgress(len(files) - 1, dialog_type = "ProgressDialog")
637 387  
638   - first_slice = read_dcm_slice_as_np(files[0], resolution_percentage)
  388 + first_slice = read_dcm_slice_as_np2(files[0], resolution_percentage)
639 389 slice_size = first_slice.shape[::-1]
640 390  
641 391 temp_file = tempfile.mktemp()
... ... @@ -649,7 +399,7 @@ def dcm2memmap(files, slice_size, orientation, resolution_percentage):
649 399  
650 400 matrix = numpy.memmap(temp_file, mode='w+', dtype='int16', shape=shape)
651 401 for n, f in enumerate(files):
652   - im_array = read_dcm_slice_as_np(f, resolution_percentage)
  402 + im_array = read_dcm_slice_as_np2(f, resolution_percentage)[::-1]
653 403  
654 404 if orientation == 'CORONAL':
655 405 matrix[:, shape[1] - n - 1, :] = im_array
... ... @@ -669,37 +419,35 @@ def dcm2memmap(files, slice_size, orientation, resolution_percentage):
669 419  
670 420  
671 421 def dcmmf2memmap(dcm_file, orientation):
672   - r = vtkgdcm.vtkGDCMImageReader()
673   - r.SetFileName(dcm_file)
674   - r.Update()
675   -
  422 + reader = gdcm.ImageReader()
  423 + reader.SetFileName(dcm_file)
  424 + reader.Read()
  425 + image = reader.GetImage()
  426 + xs, ys, zs = image.GetSpacing()
  427 + pf = image.GetPixelFormat()
  428 + np_image = converters.gdcm_to_numpy(image, pf.GetSamplesPerPixel() == 1)
676 429 temp_file = tempfile.mktemp()
677   -
678   - o = r.GetOutput()
679   - x, y, z = o.GetDimensions()
680   - spacing = o.GetSpacing()
681   -
682   - matrix = numpy.memmap(temp_file, mode='w+', dtype='int16', shape=(z, y, x))
683   -
684   - d = numpy_support.vtk_to_numpy(o.GetPointData().GetScalars())
685   - d.shape = z, y, x
  430 + matrix = numpy.memmap(temp_file, mode='w+', dtype='int16', shape=np_image.shape)
  431 + print("Number of dimensions", np_image.shape)
  432 + z, y, x = np_image.shape
686 433 if orientation == 'CORONAL':
  434 + spacing = xs, zs, ys
687 435 matrix.shape = y, z, x
688 436 for n in range(z):
689   - matrix[:, n, :] = d[n]
  437 + matrix[:, n, :] = np_image[n][::-1]
690 438 elif orientation == 'SAGITTAL':
691   - matrix.shape = x, z, y
  439 + spacing = zs, ys, xs
  440 + matrix.shape = y, x, z
692 441 for n in range(z):
693   - matrix[:, :, n] = d[n]
  442 + matrix[:, :, n] = np_image[n][::-1]
694 443 else:
695   - matrix[:] = d
  444 + spacing = xs, ys, zs
  445 + matrix[:] = np_image[:, ::-1, :]
696 446  
697 447 matrix.flush()
698 448 scalar_range = matrix.min(), matrix.max()
699 449  
700   - print("ORIENTATION", orientation)
701   -
702   - return matrix, spacing, scalar_range, temp_file
  450 + return matrix, scalar_range, spacing, temp_file
703 451  
704 452  
705 453 def img2memmap(group):
... ... @@ -753,3 +501,14 @@ def imgnormalize(data, srange=(0, 255)):
753 501 datan = datan.astype(numpy.int16)
754 502  
755 503 return datan
  504 +
  505 +
  506 +def get_LUT_value_255(data, window, level):
  507 + shape = data.shape
  508 + data_ = data.ravel()
  509 + data = np.piecewise(data_,
  510 + [data_ <= (level - 0.5 - (window-1)/2),
  511 + data_ > (level - 0.5 + (window-1)/2)],
  512 + [0, 255, lambda data_: ((data_ - (level - 0.5))/(window-1) + 0.5)*(255)])
  513 + data.shape = shape
  514 + return data
... ...
invesalius/gui/bitmap_preview_panel.py
  Diff comments   View file @cd0cef0
1 1 import wx
2 2 import vtk
3   -import vtkgdcm
4 3 import time
5 4 import numpy
6 5  
... ...
invesalius/gui/dicom_preview_panel.py
  Diff comments   View file @cd0cef0
... ... @@ -35,7 +35,8 @@ import invesalius.constants as const
35 35 import invesalius.reader.dicom_reader as dicom_reader
36 36 import invesalius.data.vtk_utils as vtku
37 37 import invesalius.utils as utils
38   -import vtkgdcm
  38 +from invesalius.data import imagedata_utils
  39 +from invesalius.data import converters
39 40  
40 41 if sys.platform == 'win32':
41 42 try:
... ... @@ -890,20 +891,20 @@ class SingleImagePreview(wx.Panel):
890 891 reader.Update()
891 892  
892 893 image = reader.GetOutput()
893   -
894 894 else:
895   - rdicom = vtkgdcm.vtkGDCMImageReader()
  895 + filename = dicom.image.file
896 896 if _has_win32api:
897   - rdicom.SetFileName(win32api.GetShortPathName(dicom.image.file).encode(const.FS_ENCODE))
898   - else:
899   - rdicom.SetFileName(dicom.image.file)
900   - rdicom.Update()
  897 + filename = win32api.GetShortPathName(filename).encode(const.FS_ENCODE)
  898 +
  899 + np_image = imagedata_utils.read_dcm_slice_as_np2(filename)
  900 + print(">>> spacing", dicom.image.spacing)
  901 + vtk_image = converters.to_vtk(np_image, dicom.image.spacing, 0, 'AXIAL')
901 902  
902 903 # ADJUST CONTRAST
903 904 window_level = dicom.image.level
904 905 window_width = dicom.image.window
905 906 colorer = vtk.vtkImageMapToWindowLevelColors()
906   - colorer.SetInputConnection(rdicom.GetOutputPort())
  907 + colorer.SetInputData(vtk_image)
907 908 colorer.SetWindow(float(window_width))
908 909 colorer.SetLevel(float(window_level))
909 910 colorer.Update()
... ...
invesalius/reader/dicom.py
  Diff comments   View file @cd0cef0
... ... @@ -19,7 +19,6 @@
19 19 #---------------------------------------------------------------------
20 20 import time
21 21 #import gdcm
22   -#import vtkgdcm
23 22 import sys
24 23 import invesalius.utils as utils
25 24 import invesalius.constants as const
... ...
invesalius/reader/dicom_reader.py
  Diff comments   View file @cd0cef0
... ... @@ -24,7 +24,6 @@ import sys
24 24 from multiprocessing import cpu_count
25 25  
26 26 import vtk
27   -import vtkgdcm
28 27 import gdcm
29 28 from wx.lib.pubsub import pub as Publisher
30 29  
... ... @@ -202,14 +201,11 @@ class LoadDicom:
202 201 level = None
203 202 window = None
204 203  
205   - if _has_win32api:
206   - thumbnail_path = imagedata_utils.create_dicom_thumbnails(win32api.GetShortPathName(self.filepath), window, level)
207   - else:
208   - thumbnail_path = imagedata_utils.create_dicom_thumbnails(self.filepath, window, level)
  204 + img = reader.GetImage()
  205 + thumbnail_path = imagedata_utils.create_dicom_thumbnails(img, window, level)
209 206  
210 207 #------ Verify the orientation --------------------------------
211 208  
212   - img = reader.GetImage()
213 209 direc_cosines = img.GetDirectionCosines()
214 210 orientation = gdcm.Orientation()
215 211 try:
... ...