def preprocess(self, data_group):
input_data = data_group.preprocessed_case
if self.mask is not None:
mask_numpy = read_image_files(self.mask)[..., 0]
elif self.mask_preprocessor is not None:
mask_numpy = read_image_files(self.mask_preprocessor.mask_numpy)[..., 0]
else:
mask_numpy = None
if self.channels is not None:
return_data = np.copy(input_data).astype(float)
input_data = np.take(input_data, indices=self.channels, axis=-1)
if self.normalize_by_channel:
# Make this an optional parameter.
data_group.preprocessed_case = data_group.preprocessed_case.astype(float)
for channel in range(data_group.preprocessed_case.shape[-1]):
data_group.preprocessed_case[..., channel] = self.normalize(input_data[..., channel], mask_numpy)
else:
data_group.preprocessed_case = self.normalize(input_data, mask_numpy)
if self.channels is not None:
for channel_idx, channel in enumerate(self.channels):
return_data[..., channel] = data_group.preprocessed_case[..., channel_idx]
data_group.preprocessed_case = return_data
# TODO: Reduce redundancy in naming
self.output_data = data_group.preprocessed_case
def preprocess(self, data_group):
normalize_numpy = data_group.preprocessed_case
if self.mask is not None:
mask_numpy = read_image_files(self.mask)[..., 0]
elif self.mask_preprocessor is not None:
data_group_label = data_group.label
mask_numpy = read_image_files(
self.mask_preprocessor.data_dictionary[data_group.label][
self.mask_name])[..., 0]
else:
mask_numpy = None
if mask_numpy is not None:
vol_mean = np.mean(normalize_numpy[mask_numpy > 0])
vol_std = np.std(normalize_numpy[mask_numpy > 0])
normalize_numpy = (normalize_numpy - vol_mean) / vol_std
normalize_numpy[mask_numpy == 0] = 0
elif self.mask_zeros:
idx_nonzeros = np.nonzero(normalize_numpy)
vol_mean = np.mean(normalize_numpy[idx_nonzeros])
vol_std = np.mean(normalize_numpy[idx_nonzeros])
normalize_numpy[idx_nonzeros] = (normalize_numpy[idx_nonzeros] -
vol_mean) / vol_std
else:
vol_mean = np.mean(normalize_numpy)
vol_std = np.std(normalize_numpy)
normalize_numpy = (normalize_numpy - vol_mean) / vol_std
# TODO: Reduce redundancy in naming
self.output_data = normalize_numpy
data_group.preprocessed_case = normalize_numpy
def calc_volume(input_data, pixdim=None, affine=None, mask_value=0):
input_data, input_affine = read_image_files(input_data, return_affine=True)
pixdim = _get_pixdim(pixdim, affine, input_affine)
return pixdim[0] * pixdim[1] * pixdim[2] * calc_voxel_count(input_data, mask_value)
def execute(self, data_collection, return_array=False):
""" There is a lot of repeated code in the preprocessors. Think about preprocessor structures and work on this class.
"""
if self.verbose:
docker_print('Working on Preprocessor:', self.name)
for label, data_group in list(self.data_groups.items()):
self.generate_output_filenames(data_collection, data_group)
if type(data_group.preprocessed_case) is not list:
self.output_data = data_group.preprocessed_case
else:
for file_idx, output_filename in enumerate(self.output_filenames):
if os.path.isdir(data_group.preprocessed_case[file_idx]):
if self.overwrite or not os.path.exists(output_filename):
array_data, affine = read_image_files(data_group.preprocessed_case[file_idx], return_affine=True)
# TO-DO: Check if subsetting language behaviour below has edge cases.
save_data(array_data[..., 0], output_filename, reference_data=affine)
else:
self.output_filenames[file_idx] = data_group.preprocessed_case[file_idx]
data_group.preprocessed_case = self.output_filenames
self.output_data = data_group.preprocessed_case
if return_array:
self.convert_to_array_data(data_group)
def initialize(self, data_collection):
super(SkullStrip_Model, self).initialize(data_collection)
for label, data_group in data_collection.data_groups.iteritems():
reference_filename = data_group.data[data_collection.current_case][
self.reference_channel[0]]
self.mask_filename = self.generate_output_filename(
reference_filename, self.mask_string)
input_data = np.take(data_group.preprocessed_case,
self.reference_channel,
axis=-1)[np.newaxis, ...]
# Also Hacky
self.model.outputs[-1].model = self.model
self.model.outputs[-1].input_patch_shape = self.model.outputs[
-1].model.model.layers[0].input_shape
self.model.outputs[-1].process_case([input_data])
self.model.outputs[-1].postprocess()
save_numpy_2_nifti(
np.squeeze(self.model.outputs[-1].return_objects[-1]),
data_group.preprocessed_affine, self.mask_filename) # Hacky
self.mask_numpy = read_image_files(self.mask_filename,
return_affine=False)
def initialize(self, data_collection):
super(SkullStrip, self).initialize(data_collection)
for label, data_group in data_collection.data_groups.iteritems():
reference_filename = data_group.data[data_collection.current_case][
self.reference_channel]
self.mask_filename = self.generate_output_filename(
reference_filename, self.mask_string)
if type(data_group.preprocessed_case) is list:
input_file = data_group.preprocessed_case[
self.reference_channel]
else:
# What to do about affines here... Also, reroute this file to a temporary directory.
input_file = save_numpy_2_nifti(
data_group.preprocessed_case[..., self.reference_channel],
data_group.preprocessed_affine,
self.generate_output_filename(reference_filename))
specific_command = self.command + [
quotes(input_file),
quotes(self.mask_filename), '-f',
str(self.bet2_f), '-g',
str(self.bet2_g), '-m'
]
subprocess.call(' '.join(specific_command), shell=True)
os.rename(self.mask_filename + '_mask.nii.gz', self.mask_filename)
self.mask_numpy = read_image_files(self.mask_filename,
return_affine=False)
def convert_to_array_data(self, data_group):
data_group.preprocessed_case, affine = read_image_files(
self.output_data, return_affine=True)
if affine is not None:
data_group.preprocessed_affine = affine
def execute(self, data_collection):
if self.mask_numpy is None:
for label, data_group in list(data_collection.data_groups.items()):
input_data = np.take(data_group.preprocessed_case,
self.reference_channel,
axis=-1)[np.newaxis, ...]
# Hacky -- TODO: Revise.
self.model.outputs[-1].model = self.model
self.model.outputs[-1].input_patch_shape = self.model.outputs[
-1].model.model.layers[0].input_shape
self.model.outputs[-1].process_case(input_data)
self.model.outputs[-1].postprocess(input_data)
reference_filename = data_group.data[
data_collection.current_case][self.reference_channel[0]]
self.mask_filename = self.generate_output_filename(
reference_filename, self.mask_string)
save_numpy_2_nifti(
np.squeeze(self.model.outputs[-1].return_objects[-1]),
self.mask_filename,
data_group.preprocessed_affine) # Hacky
self.mask_numpy = read_image_files(self.mask_filename,
return_affine=False)
super(SkullStrip_Model, self).execute(data_collection)
def convert_to_array_data(self):
self.preprocessed_case, affine = read_image_files(
self.preprocessed_case, return_affine=True)
if affine is not None:
self.preprocessed_affine = affine
def get_data(self, index=None, return_affine=False):
""" Wonky behavior reading from hdf5 here.
"""
if self.source == 'hdf5':
preprocessed_case = self.data[index][:][np.newaxis][0]
# Storing affines needs work. How not to duplicate affines in case
# of augmentation, for example?
if self.data_affines is not None:
if self.data_affines.shape[0] == 0:
preprocessed_affine = None
else:
preprocessed_affine = self.data_affines[index]
else:
preprocessed_affine = None
else:
if type(self.preprocessed_case) is np.ndarray:
preprocessed_case, preprocessed_affine = self.preprocessed_case, self.preprocessed_affine
else:
preprocessed_case, preprocessed_affine = read_image_files(self.preprocessed_case, return_affine=True)
if return_affine:
return preprocessed_case, preprocessed_affine
else:
return preprocessed_case
return None
def calc_max_2D_diameter_ellipse(input_data,
pixdim=None,
affine=None,
mask_value=0,
axis=2,
calc_multiple=False):
input_data, input_affine = read_image_files(input_data, return_affine=True)
pixdim = _get_pixdim(pixdim, affine, input_affine)
input_data = input_data[..., -1]
connected_components = label(input_data, connectivity=2)
component_labels = np.unique(connected_components)
max_2ds = []
major_diameter = None
for label_idx in component_labels:
component = connected_components.astype(int)
component[connected_components != label_idx] = 0
major_diameter = None
for z_slice in xrange(component.shape[2]):
label_slice = component[..., z_slice]
if np.sum(label_slice) == 0:
continue
label_properties = regionprops(label_slice)
current_major = label_properties[0].major_axis_length
current_orientation = label_properties[0].orientation
x_dim = abs(np.cos(current_orientation) * current_major)
y_dim = abs(np.sin(current_orientation) * current_major)
current_major = ((x_dim * pixdim[0])**2 +
(y_dim * pixdim[1])**2)**.5
if major_diameter is None:
major_diameter = current_major
elif current_major > major_diameter:
major_diameter = current_major
if major_diameter is not None:
max_2ds += [major_diameter]
if calc_multiple:
return max_2ds
else:
return max(max_2ds)
def get_affine(self, index):
if self.source == 'directory':
if self.preprocessed_affine is None:
self.preprocessed_case, self.preprocessed_affine = read_image_files(self.preprocessed_case, return_affine=True)
return self.preprocessed_affine
# A little unsure of the practical implication of the storage code below.
elif self.source == 'storage':
return self.data[index][:][np.newaxis], self.data_affines[index]
return None
def preprocess(self, data_group):
if self.mask is not None:
mask_numpy = read_image_files(self.mask)[..., 0]
elif self.mask_preprocessor is not None:
mask_numpy = read_image_files(
self.mask_preprocessor.data_dictionary[data_group.label][
self.mask_name])[..., 0]
else:
mask_numpy = None
if self.normalize_by_channel:
for channel in xrange(data_group.preprocessed_case.shape[-1]):
data_group.preprocessed_case[..., channel] = self.normalize(
data_group.preprocessed_case[..., channel], mask_numpy)
else:
data_group.preprocessed_case = self.normalize(
data_group.preprocessed_case, mask_numpy)
# TODO: Reduce redundancy in naming
self.output_data = data_group.preprocessed_case
def calc_max_3D_diameter(input_data,
pixdim=None,
affine=None,
mask_value=0,
axis=2,
calc_multiple=False):
""" Combine repeated code with 2D max diameter?
"""
input_data, input_affine = read_image_files(input_data, return_affine=True)
pixdim = _get_pixdim(pixdim, affine, input_affine)
input_data = input_data[..., -1]
connected_components = label(input_data, connectivity=2)
component_labels = np.unique(connected_components)
max_3ds = []
major_diameter = None
for label_idx in component_labels:
component = connected_components.astype(int)
component[connected_components != label_idx] = 0
major_diameter = [None]
if np.sum(component) == 0:
continue
label_properties = regionprops(component)
current_major = label_properties[0].major_axis_length
current_orientation = label_properties[0].orientation
print current_orientation
if major_diameter is None:
major_diameter = current_major
elif current_major > major_diameter:
major_diameter = current_major
if major_diameter is not None:
max_3ds += [major_diameter * pixdim[0] * pixdim[1]]
if calc_multiple:
return max_3ds
else:
return max(max_3ds)
def calc_surface_area(input_data,
pixdim=None,
affine=None,
mask_value=0,
mode='edges'):
""" Reminder: Verify on real-world data.
Also, some of the binarization feels clumsy/ineffecient.
Also, this will over-estimate surface area, because
it is counting cubes instead of, say, triangular
surfaces
"""
input_data, input_affine = read_image_files(input_data, return_affine=True)
input_data = input_data[..., -1]
pixdim = _get_pixdim(pixdim, affine, input_affine)
if mode == 'mesh':
verts, faces = marching_cubes(input_data, 0, pixdim)
surface_area = mesh_surface_area(verts, faces)
elif mode == 'edges':
edges_kernel = np.zeros((3, 3, 3), dtype=float)
edges_kernel[1, 1, 0] = -1 * pixdim[0] * pixdim[1]
edges_kernel[0, 1, 1] = -1 * pixdim[1] * pixdim[2]
edges_kernel[1, 0, 1] = -1 * pixdim[0] * pixdim[2]
edges_kernel[1, 2, 1] = -1 * pixdim[0] * pixdim[2]
edges_kernel[2, 1, 1] = -1 * pixdim[1] * pixdim[2]
edges_kernel[1, 1, 2] = -1 * pixdim[0] * pixdim[1]
edges_kernel[1, 1,
1] = 1 * (2 * pixdim[0] * pixdim[1] + 2 * pixdim[0] *
pixdim[2] + 2 * pixdim[1] * pixdim[2])
label_numpy = np.copy(input_data)
label_numpy[label_numpy != mask_value] = 1
label_numpy[label_numpy == mask_value] = 0
edge_image = signal.convolve(label_numpy, edges_kernel, mode='same')
edge_image[edge_image < 0] = 0
surface_area = np.sum(edge_image)
else:
print 'Warning, mode parameter', mode, 'not available. Returning None.'
surface_area = None
return surface_area
def get_affine(self, index):
if self.source == 'directories':
if self.preprocessed_affine is None:
self.preprocessed_case, self.preprocessed_affine = read_image_files(
self.preprocessed_case, return_affine=True)
return self.preprocessed_affine
# A little unsure of the practical implication of the storage code below.
elif self.source == 'hdf5':
if self.data_affines.shape[0] == 0:
affine = None
else:
affine = self.data_affines[index]
return affine
return None
def load_case_data(self, case):
data_groups = self.get_data_groups()
# This is weird.
self.current_case = case
for data_group in data_groups:
if self.preprocessors != []:
data_group.preprocessed_case = copy.copy(
data_group.data[self.current_case])
else:
data_group.preprocessed_case = data_group.data[
self.current_case]
self.preprocess()
for data_group in data_groups:
if type(data_group.preprocessed_case) is np.ndarray:
data_group.preprocessed_case, data_group.preprocessed_affine = data_group.preprocessed_case, data_group.preprocessed_affine
else:
data_group.preprocessed_case, data_group.preprocessed_affine = read_image_files(
data_group.preprocessed_case, return_affine=True)
data_group.base_case, data_group.base_affine = data_group.get_data(
index=case, return_affine=True)
if self.preprocessors == []:
data_group.preprocessed_case, data_group.preprocessed_affine = data_group.base_case, data_group.base_affine
if data_group.source == 'hdf5':
data_group.base_casename = data_group.data_casenames[case][
0].decode("utf-8")
else:
data_group.base_case = data_group.base_case[np.newaxis, ...]
data_group.base_casename = case
for data_group in data_groups:
# Inconsistencies in batch size during preprocessing, TODO! Important.
data_group.preprocessed_case = data_group.preprocessed_case[
np.newaxis, ...]
if len(self.augmentations) != 0:
data_group.augmentation_cases[0] = data_group.preprocessed_case
def get_data(self, index, return_affine=False):
if self.source == 'directory':
self.preprocessed_case, affine = read_image_files(self.preprocessed_case, return_affine=True)
if affine is not None:
self.preprocessed_affine = affine
if return_affine:
return self.preprocessed_case, self.preprocessed_affine
else:
return self.preprocessed_case
elif self.source == 'storage':
if return_affine:
return self.data[index][:][np.newaxis], self.data_affines[index]
else:
return self.data[index][:][np.newaxis]
return None
def data_generator(self, data_group_labels, cases=None, yield_data=True):
# Referencing to data groups is a little wonky here, TODO: clean up
if data_group_labels is None:
data_group_labels = self.data_groups.keys()
data_groups = [self.data_groups[label] for label in data_group_labels]
for data_group in data_groups:
if len(self.augmentations) != 0:
data_group.augmentation_cases = [None] * (
1 + len(self.augmentations))
if cases is None:
cases = self.cases
for case_idx, case_name in enumerate(cases):
if self.verbose:
print 'Working on image.. ', case_idx, 'at', case_name
for data_group in data_groups:
# This is messy code. TODO: return to conditional below. Suspicious data has been laoded twice.
if case_name != data_group.base_casename:
data_group.base_case, data_group.base_affine = read_image_files(
data_group.data[data_group.cases.index(case_name)],
return_affine=True)
data_group.base_case = data_group.base_case[:][np.newaxis]
data_group.base_casename = case_name
if len(self.augmentations) != 0:
data_group.augmentation_cases[0] = data_group.base_case
recursive_augmentation_generator = self.recursive_augmentation(
data_groups, augmentation_num=0)
for i in xrange(self.multiplier):
generate_data = next(recursive_augmentation_generator)
if yield_data:
yield tuple([
data_group.augmentation_cases[-1]
for data_group in data_groups
])
else:
yield True
def get_shape(self):
# TODO: Add support for non-nifti files.
# Also this is not good. Perhaps specify shape in input?
if self.output_shape is None:
if self.data == {}:
print('No Data!')
return (0,)
elif self.base_shape is None:
if self.source == 'hdf5':
self.base_shape = self.data[0].shape
else:
self.base_shape = read_image_files(list(self.data.values())[0]).shape
self.output_shape = self.base_shape
else:
return None
return self.output_shape
def get_data(self, index=None, return_affine=False):
""" Wonky behavior reading from hdf5 here.
"""
if self.source == 'hdf5':
if return_affine:
return self.data[index][:][
np.newaxis], self.data_affines[index]
else:
return self.data[index][:][np.newaxis]
else:
self.preprocessed_case, affine = read_image_files(
self.preprocessed_case, return_affine=True)
if affine is not None:
self.preprocessed_affine = affine
if return_affine:
return self.preprocessed_case, self.preprocessed_affine
else:
return self.preprocessed_case
return None
def initialize(self, data_collection):
super(SkullStrip, self).initialize(data_collection)
for label, data_group in data_collection.data_groups.iteritems():
if type(data_group.preprocessed_case) is list:
input_file = data_group.preprocessed_case[
self.reference_channel]
else:
# What to do about affines here...
input_file = save_numpy_2_nifti(
data_group.preprocessed_case[..., self.reference_channel],
data_group.preprocessed_affine,
'DEEPNEURO_TEMP_FILE.nii.gz')
base_filename = data_group.data[data_collection.current_case][
self.reference_channel]
self.mask_filename = self.generate_output_filename(
base_filename, self.mask_string)
specific_command = self.command + [
input_file, self.mask_filename, '-f',
str(self.bet2_f), '-g',
str(self.bet2_g), '-m'
]
subprocess.call(' '.join(specific_command),
shell=True,
stdout=FNULL,
stderr=subprocess.STDOUT)
os.rename(self.mask_filename + '_mask.nii.gz', self.mask_filename)
self.mask_numpy = read_image_files(self.mask_filename,
return_affine=False)
self.data_groups[data_group_label].write_to_storage()
return
def add_channel(self,
case,
input_data,
data_group_labels=None,
channel_dim=-1):
""" This function and remove_channel are edge cases that should be dealt with outside of data_collection.
"""
# TODO: Add functionality for inserting channel at specific index, multiple channels
if isinstance(input_data, str):
input_data = read_image_files([input_data])
if data_group_labels is None:
data_groups = list(self.data_groups.values())
else:
data_groups = [
self.data_groups[label] for label in data_group_labels
]
for data_group in data_groups:
if case != self.current_case:
self.load_case_data(case)
data_group.preprocessed_case = np.concatenate(
(data_group.preprocessed_case, input_data[np.newaxis, ...]),
def create_mosaic(input_volume, output_filepath=None, label_volume=None, generate_outline=True, mask_value=0, step=1, dim=2, cols=8, label_buffer=5, rotate_90=3, flip=True):
"""This creates a mosaic of 2D images from a 3D Volume.
Parameters
----------
input_volume : TYPE
Any neuroimaging file with a filetype supported by qtim_tools, or existing numpy array.
output_filepath : None, optional
Where to save your output, in a filetype supported by matplotlib (e.g. .png). If
label_volume : None, optional
Whether to create your mosaic with an attached label filepath / numpy array. Will not perform volume transforms from header (yet)
generate_outline : bool, optional
If True, will generate outlines for label_volumes, instead of filled-in areas. Default is True.
mask_value : int, optional
Background value for label volumes. Default is 0.
step : int, optional
Will generate an image for every [step] slice. Default is 1.
dim : int, optional
Mosaic images will be sliced along this dimension. Default is 2, which often corresponds to axial.
cols : int, optional
How many columns in your output mosaic. Rows will be determined automatically. Default is 8.
label_buffer : int, optional
Images more than [label_buffer] slices away from a slice containing a label pixel will note be included. Default is 5.
rotate_90 : int, optional
If the output mosaic is incorrectly rotated, you may rotate clockwise [rotate_90] times. Default is 3.
flip : bool, optional
If the output is incorrectly flipped, you may set to True to flip the data. Default is True.
No Longer Returned
------------------
Returns
-------
output_array: N+1 or N-dimensional array
The generated mosaic array.
"""
image_numpy = read_image_files(input_volume)
if step is None:
step = 1
if label_volume is not None:
label_numpy = read_image_files(label_volume)
if generate_outline:
label_numpy = generate_label_outlines(label_numpy, dim, mask_value)
# This is fun in a wacky way, but could probably be done more concisely and effeciently.
mosaic_selections = []
for i in range(label_numpy.shape[dim]):
label_slice = np.squeeze(label_numpy[[slice(None) if k != dim else slice(i, i + 1) for k in range(3)]])
if np.sum(label_slice) != 0:
mosaic_selections += list(range(i - label_buffer, i + label_buffer))
mosaic_selections = np.unique(mosaic_selections)
mosaic_selections = mosaic_selections[mosaic_selections >= 0]
mosaic_selections = mosaic_selections[mosaic_selections <= image_numpy.shape[dim]]
mosaic_selections = mosaic_selections[::step]
color_range_image = [np.min(image_numpy), np.max(image_numpy)]
color_range_label = [np.min(label_numpy), np.max(label_numpy)]
# One day, specify rotations by affine matrix.
# Is test slice necessary? Operate directly on shape if possible.
test_slice = np.rot90(np.squeeze(image_numpy[[slice(None) if k != dim else slice(0, 1) for k in range(3)]]), rotate_90)
slice_width = test_slice.shape[1]
slice_height = test_slice.shape[0]
mosaic_image_numpy = np.zeros((int(slice_height * np.ceil(float(len(mosaic_selections)) / float(cols))), int(test_slice.shape[1] * cols)), dtype=float)
mosaic_label_numpy = np.zeros_like(mosaic_image_numpy)
row_index = 0
col_index = 0
for i in mosaic_selections:
image_slice = np.rot90(np.squeeze(image_numpy[[slice(None) if k != dim else slice(i, i + 1) for k in range(3)]]), rotate_90)
label_slice = np.rot90(np.squeeze(label_numpy[[slice(None) if k != dim else slice(i, i + 1) for k in range(3)]]), rotate_90)
# Again, specify from affine matrix if possible.
if flip:
image_slice = np.fliplr(image_slice)
label_slice = np.fliplr(label_slice)
if image_slice.size > 0:
mosaic_image_numpy[int(row_index):int(row_index + slice_height), int(col_index):int(col_index + slice_width)] = image_slice
mosaic_label_numpy[int(row_index):int(row_index + slice_height), int(col_index):int(col_index + slice_width)] = label_slice
if col_index == mosaic_image_numpy.shape[1] - slice_width:
col_index = 0
row_index += slice_height
else:
col_index += slice_width
mosaic_label_numpy = np.ma.masked_where(mosaic_label_numpy == 0, mosaic_label_numpy)
if output_filepath is not None:
plt.figure(figsize=(mosaic_image_numpy.shape[0] / 100, mosaic_image_numpy.shape[1] / 100), dpi=100, frameon=False)
plt.margins(0, 0)
plt.gca().set_axis_off()
plt.gca().xaxis.set_major_locator(plt.NullLocator())
plt.gca().yaxis.set_major_locator(plt.NullLocator())
plt.imshow(mosaic_image_numpy, 'gray', vmin=color_range_image[0], vmax=color_range_image[1], interpolation='none')
plt.imshow(mosaic_label_numpy, 'jet', vmin=color_range_label[0], vmax=color_range_label[1], interpolation='none')
plt.savefig(output_filepath, bbox_inches='tight', pad_inches=0.0, dpi=1000)
plt.clf()
plt.close()
return mosaic_image_numpy
else:
color_range_image = [np.min(image_numpy), np.max(image_numpy)]
test_slice = np.rot90(np.squeeze(image_numpy[[slice(None) if k != dim else slice(0, 1) for k in range(3)]]), rotate_90)
slice_width = test_slice.shape[1]
slice_height = test_slice.shape[0]
mosaic_selections = np.arange(image_numpy.shape[dim])[::step]
mosaic_image_numpy = np.zeros((int(slice_height * np.ceil(float(len(mosaic_selections)) / float(cols))), int(test_slice.shape[1] * cols)), dtype=float)
row_index = 0
col_index = 0
for i in mosaic_selections:
image_slice = np.squeeze(image_numpy[[slice(None) if k != dim else slice(i, i + 1) for k in range(3)]])
image_slice = np.rot90(image_slice, rotate_90)
if flip:
image_slice = np.fliplr(image_slice)
mosaic_image_numpy[int(row_index):int(row_index + slice_height), int(col_index):int(col_index + slice_width)] = image_slice
if col_index == mosaic_image_numpy.shape[1] - slice_width:
col_index = 0
row_index += slice_height
else:
col_index += slice_width
if output_filepath is not None:
plt.figure(figsize=(mosaic_image_numpy.shape[0] / 100, mosaic_image_numpy.shape[1] / 100), dpi=100, frameon=False)
plt.margins(0, 0)
plt.gca().set_axis_off()
plt.gca().xaxis.set_major_locator(plt.NullLocator())
plt.gca().yaxis.set_major_locator(plt.NullLocator())
plt.imshow(mosaic_image_numpy, 'gray', vmin=color_range_image[0], vmax=color_range_image[1], interpolation='none')
plt.savefig(output_filepath, bbox_inches='tight', pad_inches=0.0, dpi=500)
plt.clf()
plt.close()
return mosaic_image_numpy
def calc_voxel_count(input_data, mask_value=0):
input_data = read_image_files(input_data)
return input_data[input_data != mask_value].size
def check_data(output_data=None,
data_collection=None,
batch_size=4,
merge_batch=True,
show_output=True,
output_filepath=None,
viz_rows=None,
viz_mode_2d=None,
viz_mode_3d='2d_slice',
color_range=None,
output_groups=None,
combine_outputs=False,
rgb_output=True,
colorbar=True,
subplot_rows=None,
title=None,
subplot_titles=None,
output_directory=None,
case_name=None,
**kwargs):
if data_collection is not None:
if batch_size > data_collection.total_cases * data_collection.multiplier:
batch_size = data_collection.total_cases * data_collection.multiplier
generator = data_collection.data_generator(perpetual=True,
verbose=False,
batch_size=batch_size)
case_name = data_collection.current_case
output_data = next(generator)
if type(output_data) is not dict:
output_data = {'output_data': output_data}
# Very bad, reformat.
output_data = {
label: data
for label, data in list(output_data.items()) if '_affine' not in label
and '_augmentation_string' not in label and 'casename' not in label
}
for label, data in list(output_data.items()):
if type(data) is str:
output_data[label] = read_image_files(data)[np.newaxis, ...]
if color_range is None:
color_range = {
label: [np.min(data), np.max(data)]
for label, data in list(output_data.items())
}
if output_groups is not None:
output_data = {
label: data
for label, data in list(output_data.items())
if label in output_groups
}
if not show_output:
subplot_titles = None
output_images = OrderedDict()
if data_collection is None:
reference_key = list(output_data)[0]
batch_size = output_data[reference_key].shape[0]
if viz_rows is None:
viz_rows = int(np.ceil(np.sqrt(batch_size)))
else:
viz_rows = min(viz_rows, batch_size)
viz_columns = int(np.ceil(batch_size / float(viz_rows)))
for label, data in list(output_data.items()):
if '_affine' in label or '_augmentation_string' in label or 'casename' in label:
continue
if data.ndim == 5:
output_images, color_range = display_3d_data(
data,
color_range,
viz_mode_3d,
label,
output_images,
viz_rows,
viz_columns,
subplot_titles=subplot_titles,
**kwargs)
elif data.ndim == 4:
if data.shape[-1] == 2:
for i in range(data.shape[-1]):
if subplot_titles is None:
subplot_title = label + '_' + str(i)
else:
subplot_title = subplot_titles[label][i]
output_images[subplot_title] = merge_data(
data[..., i][..., np.newaxis], [viz_rows, viz_columns],
1)
color_range[subplot_title] = color_range[label]
if data.shape[-1] not in [1, 3]:
output_images[label + '_RGB'] = merge_data(
data[..., 0:3], [viz_rows, viz_columns], 3)
color_range[label + '_RGB'] = color_range[label]
for i in range(3, data.shape[-1]):
output_images[label + '_' + str(i)] = merge_data(
data[..., i][..., np.newaxis], [viz_rows, viz_columns],
1)
color_range[label + '_' + str(i)] = color_range[label]
else:
output_images[label] = merge_data(data,
[viz_rows, viz_columns],
data.shape[-1])
elif data.ndim == 3:
output_images[label] = merge_data(data, [viz_rows, viz_columns],
data.shape[-1])
# elif data.ndim == 2:
# output_images[label] = display_1d_data(data, [viz_rows, viz_columns])
if show_output:
plots = len(list(output_images.keys()))
if subplot_rows is None:
subplot_rows = int(np.ceil(np.sqrt(plots)))
plot_columns = int(np.ceil(plots / float(subplot_rows)))
fig, axarr = plt.subplots(plot_columns, subplot_rows)
# matplotlib is so annoying
if subplot_rows == 1 and plot_columns == 1:
axarr = np.array([axarr]).reshape(1, 1)
elif subplot_rows == 1 or plot_columns == 1:
axarr = axarr.reshape(plot_columns, subplot_rows)
for plot_idx, (label, data) in enumerate(output_images.items()):
image_row = plot_idx % plot_columns
image_column = plot_idx // plot_columns
if data.shape[-1] == 3:
# Weird matplotlib bug/feature:
if np.min(data) < 0:
data = (data - np.min(data)) / (np.max(data) -
np.min(data))
plt_image = axarr[image_row, image_column].imshow(
np.squeeze(data),
cmap=plt.get_cmap('hot'),
vmin=color_range[label][0],
vmax=color_range[label][1],
interpolation='none')
if colorbar:
fig.colorbar(plt_image, ax=axarr[image_row, image_column])
elif data.shape[-1] == 1:
plt_image = axarr[image_row, image_column].imshow(
np.squeeze(data),
cmap='gray',
vmin=color_range[label][0],
vmax=color_range[label][1],
interpolation='none')
if colorbar:
fig.colorbar(plt_image,
ax=axarr[image_row, image_column],
cmap='gray')
axarr[image_row, image_column].set_title(label)
for plot_idx in range(len(output_images), subplot_rows * plot_columns):
image_row = plot_idx % plot_columns
image_column = plot_idx // plot_columns
fig.delaxes(axarr[image_row, image_column])
if title is not None:
fig.suptitle(title, fontsize=28)
plt.show()
output_filepaths = {}
if (output_directory is not None or output_filepath is not None):
for label, data in list(output_images.items()):
output_images[label] = image_preprocess(data)
if output_filepath is not None:
output_filepaths[label] = save_data(
output_images[label],
replace_suffix(output_filepath, '', '_' + label))
continue
if output_directory is not None and case_name is not None:
output_filepaths[label] = save_data(
output_images[label],
os.path.join(
output_directory,
nifti_splitext(
replace_suffix(os.path.basename(case_name), '',
'_' + label))[0]) + '.png')
return output_filepaths, output_images