def ImageConverter(input_filename,
output_filename,
processing_log='',
overwrite=False):
# Python 2/3 compatible input
from six.moves import input
# Check if output exists and should overwrite
if os.path.isfile(output_filename) and not overwrite:
result = input('File \"{}\" already exists. Overwrite? [y/n]: '.format(
output_filename))
if result.lower() not in ['y', 'yes']:
print('Not overwriting. Exiting...')
os.sys.exit()
# Read input
if not os.path.isfile(input_filename):
os.sys.exit('[ERROR] Cannot find file \"{}\"'.format(input_filename))
reader = get_vtk_reader(input_filename)
if reader is None:
os.sys.exit('[ERROR] Cannot find reader for file \"{}\"'.format(
input_filename))
print('Reading input image ' + input_filename)
reader.SetFileName(input_filename)
reader.Update()
# Create writer
writer = get_vtk_writer(output_filename)
if writer is None:
os.sys.exit('[ERROR] Cannot find writer for file \"{}\"'.format(
output_filename))
writer.SetInputConnection(reader.GetOutputPort())
writer.SetFileName(output_filename)
# Setup processing log
final_processing_log = ''
if len(processing_log) > 0 and type(reader) == type(
vtkbone.vtkboneAIMReader):
final_processing_log = reader.GetProcessingLog(
) + os.linesep + processing_log
elif type(reader) == type(vtkbone.vtkboneAIMReader):
final_processing_log = reader.GetProcessingLog()
elif len(processing_log) > 0:
final_processing_log = processing_log
# Handle edge cases for each output file type
handle_filetype_writing_special_cases(writer,
processing_log=final_processing_log)
print('Saving image ' + output_filename)
writer.Update()
def write_mask(reader, mask, mask_fn, label, software, version):
processing_log = (
reader.GetProcessingLog() + os.linesep +
f"[{datetime.now().strftime('%Y-%m-%d %H:%M:%S')}] {label} created by {software}, version {version}."
)
writer = get_vtk_writer(mask_fn)
if writer is None:
raise RuntimeError(f'Cannot find writer for file {mask_fn}')
writer.SetFileName(mask_fn)
writer.SetInputData(mask)
handle_filetype_writing_special_cases(writer,
processing_log=processing_log)
writer.Update()
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_get_tif(self):
'''tif filetype returns None'''
expected = type(vtk.vtkTIFFWriter())
self.assertEqual(type(get_vtk_writer('test.Tif')), expected)
def test_get_jpg(self):
'''jpg filetype returns None'''
expected = type(vtk.vtkJPEGWriter())
self.assertEqual(type(get_vtk_writer('test.jpG')), expected)
def test_get_png(self):
'''png filetype returns None'''
expected = type(vtk.vtkPNGWriter())
self.assertEqual(type(get_vtk_writer('test.pNg')), expected)
def test_get_mnc(self):
'''mnc filetype returns None'''
expected = type(vtk.vtkMINCImageWriter())
self.assertEqual(type(get_vtk_writer('test.mnC')), expected)
def test_get_bmp(self):
'''bmp filetype returns None'''
expected = type(vtk.vtkBMPWriter())
self.assertEqual(type(get_vtk_writer('test.Bmp')), expected)
def test_get_mhd(self):
'''mhd filetype returns None'''
expected = type(vtk.vtkMetaImageWriter())
self.assertEqual(type(get_vtk_writer('test.mHd')), expected)
def test_get_nii_gz(self):
'''nii.gz filetype returns None'''
expected = type(vtk.vtkNIFTIImageWriter())
self.assertEqual(type(get_vtk_writer('test.nIi.gZ')), expected)
def test_get_aim(self):
'''AIM filetype returns None'''
expected = type(vtkbone.vtkboneAIMWriter())
self.assertEqual(type(get_vtk_writer('test25a.AiM')), expected)
def test_get_unknown_filetype(self):
'''Unknown filetype returns None'''
expected = None
self.assertEqual(get_vtk_writer('fake_file.bad.type'), expected)
def test_get_empty(self):
'''Empty string returns None'''
expected = None
self.assertEqual(get_vtk_writer(''), expected)
