def bulk_apply_mask(image_dir,
mask_dir,
output_dir,
output_suffix,
skip_existing_images=True):
"""Find corresponding images between dirs and apply the second as a mask
Inputs:
image_dir -- Directory of images to-be-masked
mask_dir -- Directory of images that will be used as the mask
output_dir -- Directory where the masked images will be saved
ouptut_suffix -- Filename text after the core/sample name of the image file
"""
(image_path_list,
mask_path_list) = blk.find_shared_images(image_dir, mask_dir)
for i in range(np.size(image_path_list)):
masked_path = blk.create_new_image_path(image_path_list[i], output_dir,
output_suffix)
if masked_path.exists() and skip_existing_images:
continue
image = meta.setup_image(image_path_list[i])
mask = meta.setup_image(mask_path_list[i]) > 0
print('Masking ' + os.path.basename(image_path_list[i]) + ' with ' +
os.path.basename(mask_path_list[i]))
masked_image = sitk.Mask(image, mask)
meta.copy_relevant_metadata(masked_image, image)
meta.write_image(masked_image, masked_path)
def resize_image(itk_image, current_spacing, target_spacing):
"""Resize an image by an integer factor towards target spacing"""
if current_spacing < target_spacing:
scale = math.floor(target_spacing / current_spacing)
end_res = current_spacing * scale
resized_image = sitk.Shrink(itk_image, [scale, scale])
resized_image.SetSpacing([end_res, end_res])
resized_image.SetOrigin(itk_image.GetOrigin())
elif current_spacing > target_spacing:
scale = math.floor(current_spacing / target_spacing)
end_res = current_spacing / scale
resized_image = sitk.Expand(itk_image, [scale, scale])
resized_image.SetSpacing([end_res, end_res])
resized_image.SetOrigin(itk_image.GetOrigin())
else:
resized_image = itk_image
meta.copy_relevant_metadata(resized_image, itk_image)
return resized_image
def convert_intensity_to_retardance(itk_image,
ret_ceiling=35, wavelength=549,
nm_input=True, deg_output=True):
"""Convert retardance intensities that are scaled to the image input
(e.g., 16 bit int) into to actual retardance values.
:param itk_image: The image being converted, as an ITK _image object
:param ret_ceiling: The retardance value corresponding to max intensity
:param wavelength: The wavelength of light used to image, for converting between degrees and retardance.
:param nm_input: The input ret_ceiling is in nm if true, degrees if false
:param deg_output: The output is in degrees if true, nm if false
:return A new ITK image with retardance values either in degrees or in nm
"""
input_array = sitk.GetArrayFromImage(itk_image)
# todo: implement a check for pixel type
pixel_type_factor = ret_ceiling / 65535
if nm_input and deg_output:
wavelength_factor = 360 / wavelength
elif nm_input is False and deg_output is False:
wavelength_factor = wavelength / 360
else:
wavelength_factor = 1
output_array = input_array * pixel_type_factor * wavelength_factor
output_image = sitk.GetImageFromArray(output_array)
output_image = sitk.Cast(output_image, sitk.sitkFloat32)
meta.copy_relevant_metadata(output_image, itk_image)
return output_image
def apply_transform_fromfile(fixed_image: sitk.Image, moving_image: sitk.Image,
transform_path):
transform = sitk.ReadTransform(str(transform_path))
registered_image = sitk.Resample(moving_image, fixed_image, transform,
sitk.sitkLinear, 0.0,
moving_image.GetPixelID())
meta.copy_relevant_metadata(registered_image, moving_image)
return registered_image
def supervised_register_images(fixed_image: sitk.Image,
moving_image: sitk.Image,
initial_transform: sitk.Transform = None,
moving_path=None,
registration_parameters: dict = None):
"""Register two images
:param fixed_image: image that is being registered to
:param moving_image: image that is being transformed and registered
:param initial_transform: the type of registration/transform, e.g. affine or euler
:param registration_parameters: dictionary of registration key/value arguments
:return: Registered image, corresponding transform, metric, and stop
"""
# todo: Re-enable registering for RGB images
while True:
registration_method = define_registration_method(
registration_parameters)
fixed_final, moving_final, region_extracted = query_for_changes(
fixed_image, moving_image, initial_transform, registration_method,
moving_path)
reg_plot = RegistrationPlot(fixed_final,
moving_final,
transform=initial_transform)
(transform, metric,
stop) = register(fixed_final,
moving_final,
reg_plot,
registration_method=registration_method,
initial_transform=initial_transform)
if region_extracted:
itkplt.plot_overlay(fixed_image,
moving_image,
transform,
downsample=False)
if query_good_registration(transform, metric, stop):
break
# todo: change registration method query here
registered_image = sitk.Resample(moving_image, fixed_image, transform,
sitk.sitkLinear, 0.0,
moving_image.GetPixelID())
meta.copy_relevant_metadata(registered_image, moving_image)
plt.close('all')
return registered_image, transform, metric, stop
def extract_region(image: sitk.Image, size, origin, transform=None):
"""
Extract a region from a SimpleITK image
:param image: The SimpleITK image
:param size: The size of the region in physical space
:param origin: The origin of the region in physical space
:param transform: Image transform to apply before extracting the region
:return: A SimpleITK image that corresponds to the region
"""
if transform is not None:
translation = tran.get_translation(transform)
origin = origin + translation
size_array, index = get_region_size_origin_indices(size, origin,
image.GetSpacing())
region = sitk.Extract(image, size_array, index)
meta.copy_relevant_metadata(region, image)
return region
def bulk_threshold(input_dir,
output_dir,
output_suffix,
threshold=1,
skip_existing_images=False):
"""Apply intensity based thresholds to all images in folder"""
path_list = util.list_filetype_in_dir(input_dir, '.tif')
for i in range(len(path_list)):
new_path = blk.create_new_image_path(path_list[i], output_dir,
output_suffix)
if new_path.exists() and skip_existing_images:
continue
original = meta.setup_image(path_list[i])
new_image = apply_threshold(original,
os.path.basename(path_list[i]),
threshold=threshold)
meta.copy_relevant_metadata(new_image, original)
meta.write_image(new_image, new_path)
def bulk_convert_to_eightbit(input_dir, output_dir, output_suffix):
"""Convert all tif images in a directory to 8bit and save in new directory
Inputs:
input_dir -- Directory of images to convert
output_dir -- Directory to save converted images
output_suffix -- Text in output image name after the core/sample name
"""
path_list = util.list_filetype_in_dir(input_dir, '.tif')
for i in range(len(path_list)):
original = meta.setup_image(path_list[i])
new_image = convert_to_eightbit(original,
os.path.basename(path_list[i]))
new_path = blk.create_new_image_path(path_list[i], output_dir,
output_suffix)
meta.copy_relevant_metadata(new_image, original)
meta.write_image(new_image, new_path)