def test_region_based(self):
"""Executes the complete pipeline of the graph cut algorithm."""
# create the graph from the image
label_image = self.__label_image
graph = graph_from_labels(label_image,
self.__fg_marker,
self.__bg_marker,
boundary_term=self.__boundary_term)
# alter the graph, removing some edges that are undesired
nweights = graph.get_nweights()
for edge in self.__get_bad_edges():
if edge in nweights: del nweights[edge]
else: del nweights[(edge[1], edge[0])]
# create new graph from old graph to check the setting methods of the Graph object
graph_new = Graph()
graph_new.set_nodes(graph.get_node_count())
graph_new.set_source_nodes(graph.get_source_nodes())
graph_new.set_sink_nodes(graph.get_sink_nodes())
graph_new.set_nweights(nweights)
if graph_new.inconsistent():
self.fail('The newly generated graph is inconsistent. Reasons: {}'.
format('\n'.join(graph_new.inconsistent())))
# build graph cut graph from graph
gcgraph = GraphDouble(len(graph_new.get_nodes()),
len(graph_new.get_nweights()))
gcgraph.add_node(len(graph_new.get_nodes()))
for node, weight in graph_new.get_tweights().iteritems():
gcgraph.add_tweights(int(node - 1), weight[0], weight[1])
for edge, weight in graph_new.get_nweights().iteritems():
gcgraph.add_edge(int(edge[0] - 1), int(edge[1] - 1), weight[0],
weight[1])
# execute min-cut / executing BK_MFMC
try:
maxflow = gcgraph.maxflow()
except Exception as e:
self.fail('An error was thrown during the external executions: {}'.
format(e.message))
# apply results to the label image
label_image = filter.relabel_map(
label_image, gcgraph.what_segment, lambda fun, rid: 0
if gcgraph.termtype.SINK == fun(int(rid) - 1) else 1)
# check results for validity
self.assertEqual(
maxflow, self.__maxflow,
'The resulting maxflow {} differs from the expected one {}.'.
format(maxflow, self.__maxflow))
self.assertSequenceEqual(
label_image.tolist(), self.__result,
'The resulting cut is wrong. Expected\n {}\n got\n{}'.format(
scipy.asarray(self.__result, dtype=scipy.bool_), label_image))
def test_region_based(self):
"""Executes the complete pipeline of the graph cut algorithm."""
# create the graph from the image
label_image = self.__label_image
graph = graph_from_labels(label_image,
self.__fg_marker,
self.__bg_marker,
boundary_term=self.__boundary_term)
# alter the graph, removing some edges that are undesired
nweights = graph.get_nweights()
for edge in self.__get_bad_edges():
if edge in nweights: del nweights[edge]
else: del nweights[(edge[1], edge[0])]
# create new graph from old graph to check the setting methods of the Graph object
graph_new = Graph()
graph_new.set_nodes(graph.get_node_count())
graph_new.set_source_nodes(graph.get_source_nodes())
graph_new.set_sink_nodes(graph.get_sink_nodes())
graph_new.set_nweights(nweights)
if graph_new.inconsistent():
self.fail('The newly generated graph is inconsistent. Reasons: {}'.format('\n'.join(graph_new.inconsistent())))
# build graph cut graph from graph
gcgraph = GraphDouble(len(graph_new.get_nodes()), len(graph_new.get_nweights()))
gcgraph.add_node(len(graph_new.get_nodes()))
for node, weight in graph_new.get_tweights().iteritems():
gcgraph.add_tweights(int(node - 1), weight[0], weight[1])
for edge, weight in graph_new.get_nweights().iteritems():
gcgraph.add_edge(int(edge[0] - 1), int(edge[1] - 1), weight[0], weight[1])
# execute min-cut / executing BK_MFMC
try:
maxflow = gcgraph.maxflow()
except Exception as e:
self.fail('An error was thrown during the external executions: {}'.format(e.message))
# apply results to the label image
label_image = filter.relabel_map(label_image,
gcgraph.what_segment,
lambda fun, rid: 0 if gcgraph.termtype.SINK == fun(int(rid) - 1) else 1)
# check results for validity
self.assertEqual(maxflow, self.__maxflow, 'The resulting maxflow {} differs from the expected one {}.'.format(maxflow, self.__maxflow))
self.assertSequenceEqual(label_image.tolist(), self.__result, 'The resulting cut is wrong. Expected\n {}\n got\n{}'.format(scipy.asarray(self.__result, dtype=scipy.bool_), label_image))
def main():
# parse cmd arguments
parser = getParser()
parser.parse_args()
args = getArguments(parser)
# prepare logger
logger = Logger.getInstance()
if args.debug: logger.setLevel(logging.DEBUG)
elif args.verbose: logger.setLevel(logging.INFO)
# check if output image exists
if not args.force:
if os.path.exists(args.output):
logger.warning('The output image {} already exists. Exiting.'.format(args.output))
exit(-1)
# select boundary term
if args.boundary == 'stawiaski':
boundary_term = graphcut.energy_label.boundary_stawiaski
logger.info('Selected boundary term: stawiaski')
else:
boundary_term = graphcut.energy_label.boundary_difference_of_means
logger.info('Selected boundary term: difference of means')
# load input images
region_image_data, reference_header = load(args.region)
badditional_image_data, _ = load(args.badditional)
markers_image_data, _ = load(args.markers)
# split marker image into fg and bg images
fgmarkers_image_data, bgmarkers_image_data = split_marker(markers_image_data)
# check if all images dimensions are the same
if not (badditional_image_data.shape == region_image_data.shape == fgmarkers_image_data.shape == bgmarkers_image_data.shape):
logger.critical('Not all of the supplied images are of the same shape.')
raise ArgumentError('Not all of the supplied images are of the same shape.')
# recompute the label ids to start from id = 1
logger.info('Relabel input image...')
region_image_data = filter.relabel(region_image_data)
# generate graph
logger.info('Preparing graph...')
gcgraph = graphcut.graph_from_labels(region_image_data,
fgmarkers_image_data,
bgmarkers_image_data,
boundary_term = boundary_term,
boundary_term_args = (badditional_image_data)) # second is directedness of graph , 0)
logger.info('Removing images that are not longer required from memory...')
del fgmarkers_image_data
del bgmarkers_image_data
del badditional_image_data
# execute min-cut
logger.info('Executing min-cut...')
maxflow = gcgraph.maxflow()
logger.debug('Maxflow is {}'.format(maxflow))
# apply results to the region image
logger.info('Applying results...')
mapping = [0] # no regions with id 1 exists in mapping, entry used as padding
mapping.extend(map(lambda x: 0 if gcgraph.termtype.SINK == gcgraph.what_segment(int(x) - 1) else 1,
scipy.unique(region_image_data)))
region_image_data = filter.relabel_map(region_image_data, mapping)
# save resulting mask
save(region_image_data.astype(scipy.bool_), args.output, reference_header, args.force)
logger.info('Successfully terminated.')
def main():
# parse cmd arguments
parser = getParser()
parser.parse_args()
args = getArguments(parser)
# prepare logger
logger = Logger.getInstance()
if args.debug: logger.setLevel(logging.DEBUG)
elif args.verbose: logger.setLevel(logging.INFO)
# check if output image exists
if not args.force:
if os.path.exists(args.output):
logger.warning(
'The output image {} already exists. Exiting.'.format(
args.output))
exit(-1)
# load input images
region_image_data, reference_header = load(args.region)
markers_image_data, _ = load(args.markers)
gradient_image_data, _ = load(args.gradient)
# split marker image into fg and bg images
logger.info('Extracting foreground and background markers...')
fgmarkers_image_data, bgmarkers_image_data = split_marker(
markers_image_data)
# check if all images dimensions are the same shape
if not (gradient_image_data.shape == region_image_data.shape ==
fgmarkers_image_data.shape == bgmarkers_image_data.shape):
logger.critical(
'Not all of the supplied images are of the same shape.')
raise ArgumentError(
'Not all of the supplied images are of the same shape.')
# collect cut objects
cut_xy = __get_bg_bounding_pipe(bgmarkers_image_data)
# cut volumes
old_size = region_image_data.shape
gradient_image_data = gradient_image_data[cut_xy]
region_image_data = region_image_data[cut_xy]
fgmarkers_image_data = fgmarkers_image_data[cut_xy]
bgmarkers_image_data = bgmarkers_image_data[cut_xy]
# recompute the label ids to start from id = 1
logger.info('Relabel input image...')
region_image_data = filter.relabel(region_image_data)
# generate graph
logger.info('Preparing graph...')
gcgraph = graphcut.graph_from_labels(
region_image_data,
fgmarkers_image_data,
bgmarkers_image_data,
boundary_term=graphcut.energy_label.boundary_stawiaski,
boundary_term_args=(
gradient_image_data)) # second is directedness of graph , 0)
logger.info('Removing images that are not longer required from memory...')
del fgmarkers_image_data
del bgmarkers_image_data
del gradient_image_data
# execute min-cut
logger.info('Executing min-cut...')
maxflow = gcgraph.maxflow()
logger.debug('Maxflow is {}'.format(maxflow))
# apply results to the region image
logger.info('Applying results...')
mapping = [
0
] # no regions with id 1 exists in mapping, entry used as padding
mapping.extend(
map(
lambda x: 0 if gcgraph.termtype.SINK == gcgraph.what_segment(
int(x) - 1) else 1, scipy.unique(region_image_data)))
region_image_data = filter.relabel_map(region_image_data, mapping)
# generating final image by increasing the size again
output_image_data = scipy.zeros(old_size, dtype=scipy.bool_)
output_image_data[cut_xy] = region_image_data
# save resulting mask
save(output_image_data, args.output, reference_header, args.force)
logger.info('Successfully terminated.')
def main():
# parse cmd arguments
parser = getParser()
parser.parse_args()
args = getArguments(parser)
# prepare logger
logger = Logger.getInstance()
if args.debug: logger.setLevel(logging.DEBUG)
elif args.verbose: logger.setLevel(logging.INFO)
# check if output image exists
if not args.force:
if os.path.exists(args.output):
logger.warning('The output image {} already exists. Exiting.'.format(args.output))
exit(-1)
# select boundary term
if args.boundary == 'stawiaski':
boundary_term = graphcut.energy_label.boundary_stawiaski
logger.info('Selected boundary term: stawiaski')
else:
boundary_term = graphcut.energy_label.boundary_difference_of_means
logger.info('Selected boundary term: difference of means')
# select regional term
if args.regional == 'atlas':
regional_term = graphcut.energy_label.regional_atlas
else:
regional_term = None
# load input images
region_image_data, reference_header = load(args.region)
markers_image_data, _ = load(args.markers)
# loading and splitting the marker image
fgmarkers_image_data, bgmarkers_image_data = split_marker(markers_image_data)
badditional_image_data, _ = load(args.badditional)
if 'radditional' in args:
radditional_image_data, _ = load(args.radditional)
else:
radditional_image_data = False
# check if all images dimensions are the same
if not (badditional_image_data.shape == region_image_data.shape == fgmarkers_image_data.shape == bgmarkers_image_data.shape):
logger.critical('Not all of the supplied images are of the same shape.')
raise ArgumentError('Not all of the supplied images are of the same shape.')
if not bool == type(radditional_image_data):
if not (badditional_image_data.shape == radditional_image_data.shape):
logger.critical('Not all of the supplied images are of the same shape.')
raise ArgumentError('Not all of the supplied images are of the same shape.')
# recompute the label ids to start from id = 1
logger.info('Relabel input image...')
region_image_data = filter.relabel(region_image_data)
# generate graph
logger.info('Preparing graph...')
gcgraph = graphcut.graph_from_labels(region_image_data,
fgmarkers_image_data,
bgmarkers_image_data,
regional_term = regional_term,
boundary_term = boundary_term,
regional_term_args = (radditional_image_data, args.alpha),
boundary_term_args = (badditional_image_data)) # second (optional) parameter is directedness of graph , 0)
logger.info('Removing images that are not longer required from memory...')
del fgmarkers_image_data
del bgmarkers_image_data
del radditional_image_data
del badditional_image_data
# execute min-cut
logger.info('Executing min-cut...')
maxflow = gcgraph.maxflow()
logger.debug('Maxflow is {}'.format(maxflow))
# apply results to the region image
logger.info('Applying results...')
mapping = [0] # no regions with id 1 exists in mapping, entry used as padding
mapping.extend(map(lambda x: 0 if gcgraph.termtype.SINK == gcgraph.what_segment(int(x) - 1) else 1,
scipy.unique(region_image_data)))
region_image_data = filter.relabel_map(region_image_data, mapping)
# save resulting mask
save(region_image_data.astype(scipy.bool_), args.output, reference_header, args.force)
logger.info('Successfully terminated.')
def main():
# prepare logger
logger = Logger.getInstance()
logger.setLevel(logging.DEBUG)
# input image locations
#i = '/home/omaier/Experiments/Regionsegmentation/Evaluation_Viscous/00originalvolumes/o09.nii' # original image
g = '/home/omaier/Experiments/Regionsegmentation/Evaluation_Viscous/01gradient/o09_gradient.nii' # gradient magnitude image
l = '/home/omaier/Experiments/GraphCut/RegionalTerm/images/label_full.nii' # watershed label image
fg = '/home/omaier/Experiments/GraphCut/RegionalTerm/images/fg_markers.nii'
bg = '/home/omaier/Experiments/GraphCut/RegionalTerm/images/bg_markers.nii'
# output image locations
r = '/home/omaier/Experiments/GraphCut/BoundaryTerm/graphcut_full.nii' # liver mask
# load images
#i_i = load(i)
g_i = load(g)
l_i = load(l)
fg_i = load(fg)
bg_i = load(bg)
# extract and prepare image data
#i_d = scipy.squeeze(i_i.get_data())
g_d = scipy.squeeze(g_i.get_data())
l_d = scipy.squeeze(l_i.get_data())
fg_d = scipy.squeeze(fg_i.get_data())
bg_d = scipy.squeeze(bg_i.get_data())
# crop input images to achieve faster execution
#crop = [slice(50, -100),
# slice(50, -100),
# slice(50, -100)]
#g_d = g_d[crop]
#l_d = l_d[crop]
#fg_d = fg_d[crop]
#bg_d = bg_d[crop]
# recompute the label ids to start from id
logger.info('Relabel input image...')
l_d = filter.relabel(l_d)
# generate graph
logger.info('Preparing graph...')
gr = graphcut.graph_from_labels(l_d, fg_d, bg_d, boundary_term = graphcut.boundary_stawiaski, boundary_term_args = g_d)
#inconsistent = gr.inconsistent()
#if inconsistent:
# logger.error('The created graph contains inconsistencies: {}'.format('\n'.join(inconsistent)))
# build graph cut graph from graph
logger.info('Generating BK_MFMC C++ graph...')
gcgraph = graphcut.GraphDouble(len(gr.get_nodes()), len(gr.get_nweights()))
gcgraph.add_node(len(gr.get_nodes()))
for node, weight in gr.get_tweights().iteritems():
gcgraph.add_tweights(int(node - 1), weight[0], weight[1])
for edge, weight in gr.get_nweights().iteritems():
gcgraph.add_edge(int(edge[0] - 1), int(edge[1] - 1), weight[0], weight[1])
# execute min-cut
logger.info('Executing min-cut...')
maxflow = gcgraph.maxflow()
logger.debug('Maxflow is {}'.format(maxflow))
# collect
logger.info('Applying results...')
l_d = filter.relabel_map(l_d, gcgraph.what_segment, lambda fun, rid: 0 if gcgraph.termtype.SINK == fun(int(rid) - 1) else 1)
logger.info('Saving images resulting mask...')
# save resulting mask
l_d = l_d.astype(scipy.bool_)
save(image_like(l_d, fg_i), r)
logger.info('Done!')
def main():
# prepare logger
logger = Logger.getInstance()
logger.setLevel(logging.DEBUG)
# input image locations
#i = '/home/omaier/Experiments/Regionsegmentation/Evaluation_Viscous/00originalvolumes/o09.nii' # original image
g = '/home/omaier/Experiments/Regionsegmentation/Evaluation_Viscous/01gradient/o09_gradient.nii' # gradient magnitude image
l = '/home/omaier/Experiments/GraphCut/RegionalTerm/images/label_full.nii' # watershed label image
fg = '/home/omaier/Experiments/GraphCut/RegionalTerm/images/fg_markers.nii'
bg = '/home/omaier/Experiments/GraphCut/RegionalTerm/images/bg_markers.nii'
# output image locations
r = '/home/omaier/Experiments/GraphCut/BoundaryTerm/graphcut_full.nii' # liver mask
# load images
#i_i = load(i)
g_i = load(g)
l_i = load(l)
fg_i = load(fg)
bg_i = load(bg)
# extract and prepare image data
#i_d = scipy.squeeze(i_i.get_data())
g_d = scipy.squeeze(g_i.get_data())
l_d = scipy.squeeze(l_i.get_data())
fg_d = scipy.squeeze(fg_i.get_data())
bg_d = scipy.squeeze(bg_i.get_data())
# crop input images to achieve faster execution
#crop = [slice(50, -100),
# slice(50, -100),
# slice(50, -100)]
#g_d = g_d[crop]
#l_d = l_d[crop]
#fg_d = fg_d[crop]
#bg_d = bg_d[crop]
# recompute the label ids to start from id
logger.info('Relabel input image...')
l_d = filter.relabel(l_d)
# generate graph
logger.info('Preparing graph...')
gr = graphcut.graph_from_labels(l_d,
fg_d,
bg_d,
boundary_term=graphcut.boundary_stawiaski,
boundary_term_args=g_d)
#inconsistent = gr.inconsistent()
#if inconsistent:
# logger.error('The created graph contains inconsistencies: {}'.format('\n'.join(inconsistent)))
# build graph cut graph from graph
logger.info('Generating BK_MFMC C++ graph...')
gcgraph = graphcut.GraphDouble(len(gr.get_nodes()), len(gr.get_nweights()))
gcgraph.add_node(len(gr.get_nodes()))
for node, weight in gr.get_tweights().iteritems():
gcgraph.add_tweights(int(node - 1), weight[0], weight[1])
for edge, weight in gr.get_nweights().iteritems():
gcgraph.add_edge(int(edge[0] - 1), int(edge[1] - 1), weight[0],
weight[1])
# execute min-cut
logger.info('Executing min-cut...')
maxflow = gcgraph.maxflow()
logger.debug('Maxflow is {}'.format(maxflow))
# collect
logger.info('Applying results...')
l_d = filter.relabel_map(
l_d, gcgraph.what_segment, lambda fun, rid: 0
if gcgraph.termtype.SINK == fun(int(rid) - 1) else 1)
logger.info('Saving images resulting mask...')
# save resulting mask
l_d = l_d.astype(scipy.bool_)
save(image_like(l_d, fg_i), r)
logger.info('Done!')
def main():
# parse cmd arguments
parser = getParser()
parser.parse_args()
args = getArguments(parser)
# prepare logger
logger = Logger.getInstance()
if args.debug: logger.setLevel(logging.DEBUG)
elif args.verbose: logger.setLevel(logging.INFO)
# check if output image exists
if not args.force:
if os.path.exists(args.output):
logger.warning('The output image {} already exists. Exiting.'.format(args.output))
exit(-1)
# load input images
region_image_data, reference_header = load(args.region)
markers_image_data, _ = load(args.markers)
gradient_image_data, _ = load(args.gradient)
# split marker image into fg and bg images
logger.info('Extracting foreground and background markers...')
fgmarkers_image_data, bgmarkers_image_data = split_marker(markers_image_data)
# check if all images dimensions are the same shape
if not (gradient_image_data.shape == region_image_data.shape == fgmarkers_image_data.shape == bgmarkers_image_data.shape):
logger.critical('Not all of the supplied images are of the same shape.')
raise ArgumentError('Not all of the supplied images are of the same shape.')
# collect cut objects
cut_xy = __get_bg_bounding_pipe(bgmarkers_image_data)
# cut volumes
old_size = region_image_data.shape
gradient_image_data = gradient_image_data[cut_xy]
region_image_data = region_image_data[cut_xy]
fgmarkers_image_data = fgmarkers_image_data[cut_xy]
bgmarkers_image_data = bgmarkers_image_data[cut_xy]
# recompute the label ids to start from id = 1
logger.info('Relabel input image...')
region_image_data = filter.relabel(region_image_data)
# generate graph
logger.info('Preparing graph...')
gcgraph = graphcut.graph_from_labels(region_image_data,
fgmarkers_image_data,
bgmarkers_image_data,
boundary_term = graphcut.energy_label.boundary_stawiaski,
boundary_term_args = (gradient_image_data)) # second is directedness of graph , 0)
logger.info('Removing images that are not longer required from memory...')
del fgmarkers_image_data
del bgmarkers_image_data
del gradient_image_data
# execute min-cut
logger.info('Executing min-cut...')
maxflow = gcgraph.maxflow()
logger.debug('Maxflow is {}'.format(maxflow))
# apply results to the region image
logger.info('Applying results...')
mapping = [0] # no regions with id 1 exists in mapping, entry used as padding
mapping.extend(map(lambda x: 0 if gcgraph.termtype.SINK == gcgraph.what_segment(int(x) - 1) else 1,
scipy.unique(region_image_data)))
region_image_data = filter.relabel_map(region_image_data, mapping)
# generating final image by increasing the size again
output_image_data = scipy.zeros(old_size, dtype=scipy.bool_)
output_image_data[cut_xy] = region_image_data
# save resulting mask
save(output_image_data, args.output, reference_header, args.force)
logger.info('Successfully terminated.')