def dcmmf2memmap(dcm_file, orientation):
reader = gdcm.ImageReader()
reader.SetFileName(dcm_file)
reader.Read()
image = reader.GetImage()
xs, ys, zs = image.GetSpacing()
pf = image.GetPixelFormat()
samples_per_pixel = pf.GetSamplesPerPixel()
np_image = converters.gdcm_to_numpy(image, pf.GetSamplesPerPixel() == 1)
if samples_per_pixel == 3:
np_image = image_normalize(rgb2gray(np_image), 0, 255)
temp_file = tempfile.mktemp()
matrix = numpy.memmap(temp_file, mode="w+", dtype="int16", shape=np_image.shape)
z, y, x = np_image.shape
if orientation == "CORONAL":
spacing = xs, zs, ys
matrix.shape = y, z, x
for n in range(z):
matrix[:, n, :] = np_image[n][::-1]
elif orientation == "SAGITTAL":
spacing = zs, ys, xs
matrix.shape = y, x, z
for n in range(z):
matrix[:, :, n] = np_image[n][::-1]
else:
spacing = xs, ys, zs
matrix[:] = np_image[:, ::-1, :]
matrix.flush()
scalar_range = matrix.min(), matrix.max()
return matrix, scalar_range, spacing, temp_file
def create_dicom_thumbnails(image, window=None, level=None):
pf = image.GetPixelFormat()
np_image = converters.gdcm_to_numpy(image, pf.GetSamplesPerPixel() == 1)
if window is None or level is None:
_min, _max = np_image.min(), np_image.max()
window = _max - _min
level = _min + window / 2
if image.GetNumberOfDimensions() >= 3:
thumbnail_paths = []
for i in range(np_image.shape[0]):
thumb_image = zoom(np_image[i], 0.25)
thumb_image = np.array(
get_LUT_value_255(thumb_image, window, level), dtype=np.uint8
)
thumbnail_path = tempfile.mktemp(prefix="thumb_", suffix=".png")
imageio.imsave(thumbnail_path, thumb_image)
thumbnail_paths.append(thumbnail_path)
return thumbnail_paths
else:
thumbnail_path = tempfile.mktemp(prefix="thumb_", suffix=".png")
if pf.GetSamplesPerPixel() == 1:
thumb_image = zoom(np_image, 0.25)
thumb_image = np.array(
get_LUT_value_255(thumb_image, window, level), dtype=np.uint8
)
else:
thumb_image = zoom(np_image, (0.25, 0.25, 1))
imageio.imsave(thumbnail_path, thumb_image)
return thumbnail_path
def dcmmf2memmap(dcm_file, orientation):
reader = gdcm.ImageReader()
reader.SetFileName(dcm_file)
reader.Read()
image = reader.GetImage()
xs, ys, zs = image.GetSpacing()
pf = image.GetPixelFormat()
np_image = converters.gdcm_to_numpy(image, pf.GetSamplesPerPixel() == 1)
temp_file = tempfile.mktemp()
matrix = numpy.memmap(temp_file, mode='w+', dtype='int16', shape=np_image.shape)
print("Number of dimensions", np_image.shape)
z, y, x = np_image.shape
if orientation == 'CORONAL':
spacing = xs, zs, ys
matrix.shape = y, z, x
for n in range(z):
matrix[:, n, :] = np_image[n][::-1]
elif orientation == 'SAGITTAL':
spacing = zs, ys, xs
matrix.shape = y, x, z
for n in range(z):
matrix[:, :, n] = np_image[n][::-1]
else:
spacing = xs, ys, zs
matrix[:] = np_image[:, ::-1, :]
matrix.flush()
scalar_range = matrix.min(), matrix.max()
return matrix, scalar_range, spacing, temp_file
def read_dcm_slice_as_np2(filename, resolution_percentage=1.0):
reader = gdcm.ImageReader()
reader.SetFileName(filename)
reader.Read()
image = reader.GetImage()
output = converters.gdcm_to_numpy(image)
if resolution_percentage < 1.0:
output = zoom(output, resolution_percentage)
return output
