def test_3d_array(self):
'''Correctly convert 3D array'''
array = np.arange(2 * 3 * 4).reshape(2, 3, 4)
image = numpy_to_vtkImageData(array)
npt.assert_array_almost_equal(image.GetDimensions(), array.shape)
for index, x in np.ndenumerate(array):
self.assertAlmostEqual(array[index],
image.GetScalarComponentAsDouble(*index, 0))
def test_numpy_consistent(self):
'''Conversion is consistent with numpy'''
array = np.arange(2 * 3 * 4).reshape(2, 3, 4)
image = numpy_to_vtkImageData(array)
array2 = vtkImageData_to_numpy(image)
npt.assert_array_almost_equal(image.GetDimensions(), array.shape)
npt.assert_array_almost_equal(array2.shape, array.shape)
for index, x in np.ndenumerate(array):
self.assertAlmostEqual(array[index],
image.GetScalarComponentAsDouble(*index, 0))
self.assertAlmostEqual(array[index], array2[index])
def ExtractFields(input_model,
output_image,
field_name,
outside_value=0.0,
lower_threshold=0.0,
upper_threshold=0.0,
output_type='float'):
# Python 2/3 compatible input
from six.moves import input
# Check requested output type
output_type = output_type.lower()
if output_type not in EXTRACT_FIELDS_SUPPORTED_TYPES.keys():
print('Valid output types: {}'.format(', '.join(
EXTRACT_FIELDS_SUPPORTED_TYPES.keys())))
os.sys.exit(
'[ERROR] Requested type {} not supported'.format(output_type))
# Read input
if not os.path.isfile(input_model):
os.sys.exit('[ERROR] Cannot find file \"{}\"'.format(input_model))
# Test field name
if field_name not in valid_fields():
print('Valid field names: {}'.format(valid_fields()))
os.sys.exit('[ERROR] Please provide a valid field name')
print('Reading elements into image array')
image, spacing, origin, n_elements = field_to_image(
input_model, field_name, outside_value)
print(' Spacing: {}'.format(spacing))
print(' Origin: {}'.format(origin))
print(' Dimensions: {}'.format(image.shape))
print(' Number of elements: {}'.format(n_elements))
print('')
# Convert to VTK
print('Converting to vtkImageData')
vtkImage = numpy_to_vtkImageData(image, spacing, origin)
print('')
if output_type == 'float':
print('Not rescaling data')
else:
print('Rescaling data into {} dynamic range'.format(output_type))
# Hack to get data type range
source = vtk.vtkImageEllipsoidSource()
source.SetWholeExtent(0, 1, 0, 1, 0, 0)
source.SetCenter(0, 0, 0)
source.SetRadius(0, 0, 0)
source.SetOutputScalarType(EXTRACT_FIELDS_SUPPORTED_TYPES[output_type])
source.Update()
# Compute min/max
if lower_threshold == upper_threshold:
scalar_range = vtkImage.GetScalarRange()
else:
scalar_range = [lower_threshold, upper_threshold]
dtype_range = [0, source.GetOutput().GetScalarTypeMax()]
print(' Image range: {}'.format(vtkImage.GetScalarRange()))
print(' Input range: {}'.format(scalar_range))
print(' Output range: {}'.format(dtype_range))
# Note the equation for shift/scale:
# u = (v + ScalarShift)*ScalarScale
m = float(dtype_range[1] - dtype_range[0]) / float(scalar_range[1] -
scalar_range[0])
b = float(dtype_range[1] - m * scalar_range[1])
b = b / m
print(' Shift: {}'.format(b))
print(' Scale: {}'.format(m))
scaler = vtk.vtkImageShiftScale()
scaler.SetInputData(vtkImage)
scaler.SetShift(b)
scaler.SetScale(m)
scaler.ClampOverflowOn()
scaler.SetOutputScalarType(EXTRACT_FIELDS_SUPPORTED_TYPES[output_type])
scaler.Update()
vtkImage = scaler.GetOutput()
print(' Output image range: {}'.format(vtkImage.GetScalarRange()))
print('')
# Write image
print('Saving image ' + output_image)
writer = get_vtk_writer(output_image)
if writer is None:
os.sys.exit(
'[ERROR] Cannot find writer for file \"{}\"'.format(output_image))
writer.SetInputData(vtkImage)
writer.SetFileName(output_image)
writer.Update()
def test_3d_array_origin(self):
'''Correctly set origin'''
array = np.arange(2 * 3 * 4).reshape(2, 3, 4)
image = numpy_to_vtkImageData(array, origin=[-12.0, 33.0, 104.0])
npt.assert_array_almost_equal(image.GetOrigin(), [-12.0, 33.0, 104.0])
def test_3d_array_spacing(self):
'''Correctly set spacing'''
array = np.arange(2 * 3 * 4).reshape(2, 3, 4)
image = numpy_to_vtkImageData(array, spacing=[2.0, 3.0, 4.0])
npt.assert_array_almost_equal(image.GetSpacing(), [2.0, 3.0, 4.0])