Commit e53432ed26858d8a2687631986a283bf433d8449
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ENH: Using vtkgdcmImageReader instead gdcm.ImageReader.
Because it was necessary to do some extra works, like some math to calculate the hounsfield units, now we are using vtkgdcmImageReader instead of gdcm.ImageReader.
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invesalius/data/imagedata_utils.py
| @@ -456,25 +456,6 @@ class ImageCreator: | @@ -456,25 +456,6 @@ class ImageCreator: | ||
| 456 | 456 | ||
| 457 | return imagedata | 457 | return imagedata |
| 458 | 458 | ||
| 459 | -def get_gdcm_to_numpy_typemap(): | ||
| 460 | - """Returns the GDCM Pixel Format to numpy array type mapping.""" | ||
| 461 | - _gdcm_np = {gdcm.PixelFormat.UINT8 :numpy.int8, | ||
| 462 | - gdcm.PixelFormat.INT8 :numpy.uint8, | ||
| 463 | - #gdcm.PixelFormat.UINT12 :numpy.uint12, | ||
| 464 | - #gdcm.PixelFormat.INT12 :numpy.int12, | ||
| 465 | - gdcm.PixelFormat.UINT16 :numpy.uint16, | ||
| 466 | - gdcm.PixelFormat.INT16 :numpy.int16, | ||
| 467 | - gdcm.PixelFormat.UINT32 :numpy.uint32, | ||
| 468 | - gdcm.PixelFormat.INT32 :numpy.int32, | ||
| 469 | - #gdcm.PixelFormat.FLOAT16:numpy.float16, | ||
| 470 | - gdcm.PixelFormat.FLOAT32:numpy.float32, | ||
| 471 | - gdcm.PixelFormat.FLOAT64:numpy.float64 } | ||
| 472 | - return _gdcm_np | ||
| 473 | - | ||
| 474 | -def get_numpy_array_type(gdcm_pixel_format): | ||
| 475 | - """Returns a numpy array typecode given a GDCM Pixel Format.""" | ||
| 476 | - return get_gdcm_to_numpy_typemap()[gdcm_pixel_format] | ||
| 477 | - | ||
| 478 | def dcm2memmap(files, slice_size): | 459 | def dcm2memmap(files, slice_size): |
| 479 | """ | 460 | """ |
| 480 | From a list of dicom files it creates memmap file in the temp folder and | 461 | From a list of dicom files it creates memmap file in the temp folder and |
| @@ -483,20 +464,16 @@ def dcm2memmap(files, slice_size): | @@ -483,20 +464,16 @@ def dcm2memmap(files, slice_size): | ||
| 483 | temp_file = tempfile.mktemp() | 464 | temp_file = tempfile.mktemp() |
| 484 | shape = len(files), slice_size[0], slice_size[1] | 465 | shape = len(files), slice_size[0], slice_size[1] |
| 485 | 466 | ||
| 486 | - matrix = numpy.memmap(temp_file, mode='w+', dtype='uint16', shape=shape) | 467 | + matrix = numpy.memmap(temp_file, mode='w+', dtype='int16', shape=shape) |
| 487 | 468 | ||
| 488 | for n, f in enumerate(files): | 469 | for n, f in enumerate(files): |
| 489 | - dcm_image = gdcm.ImageReader() | ||
| 490 | - dcm_image.SetFileName(f) | ||
| 491 | - dcm_image.Read() | ||
| 492 | - | ||
| 493 | - image = dcm_image.GetImage() | ||
| 494 | - pf = image.GetPixelFormat().GetScalarType() | ||
| 495 | - dtype = get_numpy_array_type(pf) | 470 | + dcm_reader = vtkgdcm.vtkGDCMImageReader() |
| 471 | + dcm_reader.SetFileName(f) | ||
| 472 | + dcm_reader.Update() | ||
| 496 | 473 | ||
| 497 | - dcm_array = image.GetBuffer() | ||
| 498 | - array = numpy.frombuffer(dcm_array, dtype) | ||
| 499 | - array.shape = slice_size | 474 | + image = dcm_reader.GetOutput() |
| 475 | + array = numpy_support.vtk_to_numpy(image.GetPointData().GetScalars()) | ||
| 476 | + array.shape = matrix.shape[1], matrix.shape[2] | ||
| 500 | matrix[n] = array | 477 | matrix[n] = array |
| 501 | 478 | ||
| 502 | matrix.flush() | 479 | matrix.flush() |