def get_subdirs(dirpath, wildcard='*', outputfile='experiment_data.yaml'):
dirlist = []
if os.path.exists(dirpath):
logger.info('dirpath = ' + dirpath)
# print completedirpath
else:
logger.error('Wrong path: ' + dirpath)
raise Exception('Wrong path : ' + dirpath)
dirpath = os.path.abspath(dirpath)
# print 'copmpletedirpath = ', completedirpath
# import pdb; pdb.set_trace()
dirlist = {
o: {
'abspath': os.path.abspath(os.path.join(dirpath, o))
}
for o in os.listdir(dirpath) if os.path.isdir(os.path.join(dirpath, o))
}
# import pdb; pdb.set_trace()
# print [o for o in os.listdir(dirpath) if
# os.path.isdir(os.path.abspath(o))]
# dirlist.append(infile)
# print "current file is: " + infile
misc.obj_to_file(dirlist, 'experiment_data.yaml', 'yaml')
return dirlist
def get_subdirs(dirpath, wildcard='*', outputfile='experiment_data.yaml'):
dirlist = []
if os.path.exists(dirpath):
logger.info('dirpath = ' + dirpath)
# print completedirpath
else:
logger.error('Wrong path: ' + dirpath)
raise Exception('Wrong path : ' + dirpath)
dirpath = os.path.abspath(dirpath)
# print 'copmpletedirpath = ', completedirpath
# import pdb; pdb.set_trace()
dirlist = {
o: {'abspath': os.path.abspath(os.path.join(dirpath, o))}
for o in os.listdir(dirpath) if os.path.isdir(
os.path.join(dirpath, o))
}
# import pdb; pdb.set_trace()
# print [o for o in os.listdir(dirpath) if
# os.path.isdir(os.path.abspath(o))]
# dirlist.append(infile)
# print "current file is: " + infile
misc.obj_to_file(dirlist, 'experiment_data.yaml', 'yaml')
return dirlist
def delete_config_records(filename, records_to_save=[]):
"""
All records of config file are deleted except records_to_save.
"""
if os.path.isfile(filename):
cfg = misc.obj_from_file(filename, filetype='yaml')
new_cfg = subdict(cfg, records_to_save)
print(cfg)
misc.obj_to_file(new_cfg, "test_" + filename, filetype='yaml')
def delete_config_records(filename, records_to_save=[]):
"""
All records of config file are deleted except records_to_save.
"""
if os.path.isfile(filename):
cfg = misc.obj_from_file(filename, filetype='yaml')
new_cfg = subdict(cfg, records_to_save)
print cfg
misc.obj_to_file(new_cfg, "test_" + filename , filetype='yaml')
def update_config_records(filename, new_cfg):
"""
All records of config file are updated exept records_to_save.
"""
if os.path.isfile(filename):
cfg = misc.obj_from_file(filename, filetype='yaml')
cfg.update(new_cfg)
print cfg
misc.obj_to_file(new_cfg, "test_" + filename , filetype='yaml')
def update_config_records(filename, new_cfg):
"""
All records of config file are updated exept records_to_save.
"""
if os.path.isfile(filename):
cfg = misc.obj_from_file(filename, filetype='yaml')
cfg.update(new_cfg)
print(cfg)
misc.obj_to_file(new_cfg, "test_" + filename, filetype='yaml')
def test_obj_to_and_from_file_pklz_with_auto(self):
testdata = np.random.random([4, 4, 3])
test_object = {'a': 1, 'data': testdata}
filename = 'test_obj_to_and_from_file_with_auto.pklz'
misc.obj_to_file(test_object, filename, 'auto')
saved_object = misc.obj_from_file(filename, 'auto')
self.assertTrue(saved_object['a'] == 1)
self.assertTrue(saved_object['data'][1, 1, 1] == testdata[1, 1, 1])
os.remove(filename)
def test_obj_to_and_from_file_pickle(self):
testdata = np.random.random([4, 4, 3])
test_object = {'a': 1, 'data': testdata}
filename = 'test_obj_to_and_from_file.pkl'
misc.obj_to_file(test_object, filename, 'pickle')
saved_object = misc.obj_from_file(filename, 'pickle')
self.assertTrue(saved_object['a'] == 1)
self.assertTrue(saved_object['data'][1, 1, 1] == testdata[1, 1, 1])
os.remove(filename)
def test_obj_to_and_from_file_yaml_with_ndarray_to_yaml(self):
testdata = np.random.random([4, 4, 3])
test_object = {'a': 1, 'data': testdata, "lst":[1, 2, 3]}
filename = 'test_obj_to_and_from_file.yaml'
misc.obj_to_file(test_object, filename, 'yaml', ndarray_to_list=True)
saved_object = misc.obj_from_file(filename, 'yaml')
self.assertTrue(saved_object['a'] == 1)
self.assertTrue(saved_object['data'][1][1][1] == testdata[1, 1, 1])
os.remove(filename)
def test_obj_to_and_from_file_yaml_with_ndarray_to_yaml(self):
testdata = np.random.random([4, 4, 3])
test_object = {'a': 1, 'data': testdata, "lst": [1, 2, 3]}
filename = 'test_obj_to_and_from_file.yaml'
misc.obj_to_file(test_object, filename, 'yaml', ndarray_to_list=True)
saved_object = misc.obj_from_file(filename, 'yaml')
self.assertTrue(saved_object['a'] == 1)
self.assertTrue(saved_object['data'][1][1][1] == testdata[1, 1, 1])
os.remove(filename)
def test_obj_to_and_from_file_with_directories(self):
import shutil
testdata = np.random.random([4, 4, 3])
test_object = {'a': 1, 'data': testdata}
dirname = '__test_write_and_read'
filename = '__test_write_and_read/test_obj_to_and_from_file.pkl'
misc.obj_to_file(test_object, filename, 'pickle')
saved_object = misc.obj_from_file(filename, 'pickle')
self.assertTrue(saved_object['a'] == 1)
self.assertTrue(saved_object['data'][1, 1, 1] == testdata[1, 1, 1])
shutil.rmtree(dirname)
def test_obj_to_and_from_file_with_directories(self):
import shutil
testdata = np.random.random([4, 4, 3])
test_object = {'a': 1, 'data': testdata}
dirname = '__test_write_and_read'
filename = '__test_write_and_read/test_obj_to_and_from_file.pkl'
misc.obj_to_file(test_object, filename, 'pickle')
saved_object = misc.obj_from_file(filename, 'pickle')
self.assertTrue(saved_object['a'] == 1)
self.assertTrue(saved_object['data'][1, 1, 1] == testdata[1, 1, 1])
shutil.rmtree(dirname)
def get_config(filename, default_cfg):
"""
Looks config file and update default_cfg values.
If file does not exist it is created.
"""
if os.path.isfile(filename):
cfg = misc.obj_from_file(filename, filetype='yaml')
default_cfg.update(cfg)
cfg_out = default_cfg
else:
misc.obj_to_file(default_cfg, filename, filetype='yaml')
cfg_out = default_cfg
# default config
return cfg_out
def get_config(filename, default_cfg):
"""
Looks config file and update default_cfg values.
If file does not exist it is created.
"""
if os.path.isfile(filename):
cfg = misc.obj_from_file(filename, filetype='yaml')
default_cfg.update(cfg)
cfg_out = default_cfg
else:
misc.obj_to_file(default_cfg, filename, filetype='yaml')
cfg_out = default_cfg
# default config
return cfg_out
def check_config_version_and_remove_old_records(filename, version,
records_to_save):
"""
Check if config file version is ok. If it is not all records except
records_to_save are deleted and config_version in file is set to version.
It is used to update user configuration.
"""
if os.path.isfile(filename):
cfg = misc.obj_from_file(filename, filetype='yaml')
if ('config_version' in cfg and (cfg['config_version'] == version)):
# everything is ok, no need to panic
return
else:
# older version of config file
cfg = misc.obj_from_file(filename, filetype='yaml')
misc.obj_to_file(cfg, filename + '.old', filetype='yaml')
print 'cfg ', cfg
new_cfg = subdict(cfg, records_to_save)
new_cfg['config_version'] = version
print 'ncfg ', new_cfg
misc.obj_to_file(new_cfg, filename, filetype='yaml')
def check_config_version_and_remove_old_records(filename, version,
records_to_save):
"""
Check if config file version is ok. If it is not all records except
records_to_save are deleted and config_version in file is set to version.
It is used to update user configuration.
"""
if os.path.isfile(filename):
cfg = misc.obj_from_file(filename, filetype='yaml')
if ('config_version' in cfg and (cfg['config_version'] == version)):
# everything is ok, no need to panic
return
else:
# older version of config file
cfg = misc.obj_from_file(filename, filetype='yaml')
misc.obj_to_file(cfg, filename + '.old', filetype='yaml')
print('cfg ', cfg)
new_cfg = subdict(cfg, records_to_save)
new_cfg['config_version'] = version
print('ncfg ', new_cfg)
misc.obj_to_file(new_cfg, filename, filetype='yaml')
def main():
#logger = logging.getLogger(__name__)
logger = logging.getLogger()
logger.setLevel(logging.WARNING)
ch = logging.StreamHandler()
logger.addHandler(ch)
#logger.debug('input params')
# input parser
parser = argparse.ArgumentParser(description=
'Segmentation of bones, lungs and heart.')
parser.add_argument('-i','--datadir',
default=None,
help='path to data dir')
parser.add_argument('-o','--output',
default=None,
help='output file')
parser.add_argument('-d', '--debug', action='store_true',
help='run in debug mode')
parser.add_argument('-ss', '--segspine', action='store_true',
help='run spine segmentaiton')
parser.add_argument('-sl', '--seglungs', action='store_true',
help='run lungs segmentation')
parser.add_argument('-sh', '--segheart', action='store_true',
help='run heart segmentation')
parser.add_argument('-sb', '--segbones', action='store_true',
help='run bones segmentation')
parser.add_argument('-exd', '--exampledata', action='store_true',
help='run unittest')
parser.add_argument('-so', '--show_output', action='store_true',
help='Show output data in viewer')
args = parser.parse_args()
if args.debug:
logger.setLevel(logging.DEBUG)
if args.exampledata:
args.dcmdir = '../sample_data/liver-orig001.raw'
# if dcmdir == None:
#else:
#dcm_read_from_dir('/home/mjirik/data/medical/data_orig/46328096/')
#data3d, metadata = dcmr.dcm_read_from_dir(args.dcmdir)
data3d , metadata = io3d.datareader.read(args.datadir)
sseg = SupportStructureSegmentation(data3d = data3d,
voxelsize_mm = metadata['voxelsize_mm'],
)
#sseg.orientation()
if args.segbones:
sseg.bone_segmentation()
if args.segspine:
sseg.spine_segmentation()
if args.seglungs or args.segheart:
sseg.lungs_segmentation()
if args.segheart:
sseg.heart_segmentation()
sseg.resize_back_to_orig()
#print ("Data size: " + str(data3d.nbytes) + ', shape: ' + str(data3d.shape) )
#igc = pycut.ImageGraphCut(data3d, zoom = 0.5)
#igc.interactivity()
#igc.make_gc()
#igc.show_segmentation()
# volume
#volume_mm3 = np.sum(oseg.segmentation > 0) * np.prod(oseg.voxelsize_mm)
#pyed = sed3.sed3(oseg.data3d, contour = oseg.segmentation)
#pyed.show()
if args.show_output:
sseg.visualization()
#savestring = raw_input ('Save output data? (y/n): ')
#sn = int(snstring)
if args.output is not None: # savestring in ['Y','y']:
import misc
data = sseg.export()
misc.obj_to_file(data, args.output, filetype = 'pickle')
def main():
#logger = logging.getLogger(__name__)
logger = logging.getLogger()
logger.setLevel(logging.WARNING)
ch = logging.StreamHandler()
logger.addHandler(ch)
#logger.debug('input params')
# input parser
parser = argparse.ArgumentParser(description=
'Segmentation of bones, lungs and heart.')
parser.add_argument('-i','--datadir',
default=None,
help='path to data dir')
parser.add_argument('-o','--output',
default=None,
help='output file')
parser.add_argument('-d', '--debug', action='store_true',
help='run in debug mode')
parser.add_argument('-ss', '--segspine', action='store_true',
help='run spine segmentaiton')
parser.add_argument('-sl', '--seglungs', action='store_true',
help='run lungs segmentation')
parser.add_argument('-sh', '--segheart', action='store_true',
help='run heart segmentation')
parser.add_argument('-sb', '--segbones', action='store_true',
help='run bones segmentation')
parser.add_argument('-exd', '--exampledata', action='store_true',
help='run unittest')
parser.add_argument('-so', '--show_output', action='store_true',
help='Show output data in viewer')
args = parser.parse_args()
if args.debug:
logger.setLevel(logging.DEBUG)
if args.exampledata:
args.dcmdir = '../sample_data/liver-orig001.raw'
# if dcmdir == None:
#else:
#dcm_read_from_dir('/home/mjirik/data/medical/data_orig/46328096/')
#data3d, metadata = dcmr.dcm_read_from_dir(args.dcmdir)
data3d , metadata = io3d.datareader.read(args.datadir, dataplus_format=False)
sseg = SupportStructureSegmentation(data3d = data3d,
voxelsize_mm = metadata['voxelsize_mm'],
)
#sseg.orientation()
if args.segbones:
sseg.bone_segmentation()
if args.segspine:
sseg.spine_segmentation()
if args.seglungs or args.segheart:
sseg.lungs_segmentation()
if args.segheart:
sseg.heart_segmentation()
sseg.resize_back_to_orig()
#print("Data size: " + str(data3d.nbytes) + ', shape: ' + str(data3d.shape) )
#igc = pycut.ImageGraphCut(data3d, zoom = 0.5)
#igc.interactivity()
#igc.make_gc()
#igc.show_segmentation()
# volume
#volume_mm3 = np.sum(oseg.segmentation > 0) * np.prod(oseg.voxelsize_mm)
#pyed = sed3.sed3(oseg.data3d, contour = oseg.segmentation)
#pyed.show()
if args.show_output:
sseg.visualization()
#savestring = raw_input ('Save output data? (y/n): ')
#sn = int(snstring)
if args.output is not None: # savestring in ['Y','y']:
import misc
data = sseg.export()
misc.obj_to_file(data, args.output, filetype = 'pickle')
def save_config(cfg, filename):
misc.obj_to_file(cfg, filename, filetype='yaml')
def save_config(cfg, filename):
misc.obj_to_file(cfg, filename, filetype='yaml')
