def remove_small_objects():
folder = '/media/julian/Daten/neuraldata/cremi_2016/'
file = 'cremi.splA.raw_neurons.crop.crop_10-200-200_110-712-712.disttransf.h5'
names = ('labels',)
keys = ('labels',)
ifp = ImageFileProcessing(
folder,
file, asdict=True,
image_names=names,
keys=keys)
ifp.startlogger(filename=None)
# Find all relevant labels
ifp.addfromfile('{}largeobjects.h5'.format(folder), image_ids=(0,))
for lbl in ifp.label_image_iterator(
'labels', 'largeobjects', accumulate=True, labellist=ifp.get_image('largeobjects')):
ifp.logging('Label {} done!', lbl)
ifp.getlabel(0, ids='largeobjects', targetids='background')
ifp.write(filename='largeobjectimage.h5')
ifp.logging('')
ifp.stoplogger()
def remove_small_objects():
folder = '/media/julian/Daten/neuraldata/cremi_2016/'
file = 'cremi.splA.raw_neurons.crop.crop_10-200-200_110-712-712.disttransf.h5'
names = ('labels', )
keys = ('labels', )
ifp = ImageFileProcessing(folder,
file,
asdict=True,
image_names=names,
keys=keys)
ifp.startlogger(filename=None)
# Find all relevant labels
ifp.addfromfile('{}largeobjects.h5'.format(folder), image_ids=(0, ))
for lbl in ifp.label_image_iterator(
'labels',
'largeobjects',
accumulate=True,
labellist=ifp.get_image('largeobjects')):
ifp.logging('Label {} done!', lbl)
ifp.getlabel(0, ids='largeobjects', targetids='background')
ifp.write(filename='largeobjectimage.h5')
ifp.logging('')
ifp.stoplogger()
__author__ = 'jhennies'
if __name__ == '__main__':
yamlfile = os.path.dirname(os.path.abspath(__file__)) + '/parameters.yml'
ifp = ImageFileProcessing(
yaml=yamlfile,
yamlspec={'image_path': 'intermedfolder', 'image_file': 'largeobjfile', 'image_names': 'largeobjname'},
asdict=True,
keys=('largeobj',)
)
params = ifp.get_params()
thisparams = params['localmax_on_disttransf']
ifp.addfromfile(params['intermedfolder']+params['largeobjmfile'], image_names=params['largeobjmnames'][0], ids='largeobjm')
ifp.startlogger(filename=ifp.get_params()['intermedfolder'] + 'locmax_on_disttransf.log', type='a')
# ifp.code2log(__file__)
ifp.code2log(inspect.stack()[0][1])
ifp.logging('')
ifp.logging('yamlfile = {}', yamlfile)
ifp.logging('ifp.get_data().keys() = {}', ifp.get_data().keys())
ifp.logging('ifp.shape() = {}', ifp.shape())
# Boundary distance transform
# a) Boundaries
ifp.logging('Finding boundaries ...')
ifp.pixels_at_boundary(
if __name__ == '__main__':
yamlfile = os.path.dirname(os.path.abspath(__file__)) + '/parameters.yml'
ifp = ImageFileProcessing(yaml=yamlfile,
yamlspec={
'image_path': 'intermedfolder',
'image_file': 'largeobjfile',
'image_names': 'largeobjname'
},
asdict=True,
keys=('largeobj', ))
params = ifp.get_params()
thisparams = params['localmax_on_disttransf']
ifp.addfromfile(params['intermedfolder'] + params['largeobjmfile'],
image_names=params['largeobjmnames'][0],
ids='largeobjm')
ifp.startlogger(filename=ifp.get_params()['intermedfolder'] +
'locmax_on_disttransf.log',
type='a')
# ifp.code2log(__file__)
ifp.code2log(inspect.stack()[0][1])
ifp.logging('')
ifp.logging('yamlfile = {}', yamlfile)
ifp.logging('ifp.get_data().keys() = {}', ifp.get_data().keys())
ifp.logging('ifp.shape() = {}', ifp.shape())
# Boundary distance transform
if __name__ == '__main__':
yamlfile = os.path.dirname(os.path.abspath(__file__)) + '/parameters.yml'
ifp = ImageFileProcessing(yaml=yamlfile,
yamlspec={
'image_path': 'intermedfolder',
'image_file': 'locmaxfile',
'image_names': ('locmaxnames', 0, 2)
},
asdict=True,
keys=('disttransf', 'locmax'))
params = ifp.get_params()
thisparams = params['paths_within_labels']
ifp.addfromfile(params['intermedfolder'] + params['largeobjfile'],
image_names=params['largeobjname'],
ids='largeobj')
ifp.startlogger(filename=params['intermedfolder'] +
'paths_within_labels.log',
type='a')
# ifp.code2log(__file__)
ifp.code2log(inspect.stack()[0][1])
ifp.logging('')
ifp.logging('yamlfile = {}', yamlfile)
ifp.logging('ifp.get_data().keys() = {}', ifp.get_data().keys())
ifp.logging('ifp.shape() = {}', ifp.shape())
ifp.logging('{}', ifp.amax())
yamlfile = os.path.dirname(
os.path.abspath(__file__)) + '/parameters.yml'
ifp = ImageFileProcessing(yaml=yamlfile,
yamlspec={
'image_path': 'intermedfolder',
'image_file': 'locmaxfile',
'image_names': ('locmaxnames', 1, 3)
},
asdict=True,
keys=('disttransf', 'locmax'))
params = ifp.get_params()
thisparams = params['paths_of_partners']
ifp.addfromfile(params['intermedfolder'] + params['largeobjmfile'],
image_names=params['largeobjmnames'],
ids=[
'largeobjm', 'mergeids_small', 'mergeids_random',
'mergeids_all'
])
ifp.addfromfile(params['intermedfolder'] + params['largeobjfile'],
image_names=params['largeobjname'],
ids='largeobj')
ifp.startlogger(filename=params['intermedfolder'] +
'paths_of_partners.log',
type='a')
# ifp.code2log(__file__)
ifp.code2log(inspect.stack()[0][1])
ifp.logging('')
ifp.logging('yamlfile = {}', yamlfile)
if __name__ == '__main__':
try:
yamlfile = os.path.dirname(os.path.abspath(__file__)) + '/parameters.yml'
ifp = ImageFileProcessing(
yaml=yamlfile,
yamlspec={'image_path': 'intermedfolder', 'image_file': 'locmaxfile', 'image_names': ('locmaxnames', 1, 3)},
asdict=True,
keys=('disttransf', 'locmax')
)
params = ifp.get_params()
thisparams = params['paths_of_partners']
ifp.addfromfile(params['intermedfolder']+params['largeobjmfile'], image_names=params['largeobjmnames'],
ids=['largeobjm', 'mergeids_small', 'mergeids_random', 'mergeids_all'])
ifp.addfromfile(params['intermedfolder']+params['largeobjfile'], image_names=params['largeobjname'], ids='largeobj')
ifp.startlogger(filename=params['intermedfolder'] + 'paths_of_partners.log', type='a')
# ifp.code2log(__file__)
ifp.code2log(inspect.stack()[0][1])
ifp.logging('')
ifp.logging('yamlfile = {}', yamlfile)
ifp.logging('ifp.get_data().keys() = {}', ifp.get_data().keys())
ifp.logging('ifp.shape() = {}', ifp.shape())
ifp.logging('ifp.amax() = {}', ifp.amax())
hfp = Hdf5Processing()
c = 0
return paths
if __name__ == '__main__':
yamlfile = os.path.dirname(os.path.abspath(__file__)) + '/parameters.yml'
ifp = ImageFileProcessing(
yaml=yamlfile,
yamlspec={'image_path': 'intermedfolder', 'image_file': 'locmaxfile', 'image_names': ('locmaxnames', 0, 2)},
asdict=True,
keys=('disttransf', 'locmax')
)
params = ifp.get_params()
thisparams = params['paths_within_labels']
ifp.addfromfile(params['intermedfolder']+params['largeobjfile'], image_names=params['largeobjname'], ids='largeobj')
ifp.startlogger(filename=params['intermedfolder'] + 'paths_within_labels.log', type='a')
# ifp.code2log(__file__)
ifp.code2log(inspect.stack()[0][1])
ifp.logging('')
ifp.logging('yamlfile = {}', yamlfile)
ifp.logging('ifp.get_data().keys() = {}', ifp.get_data().keys())
ifp.logging('ifp.shape() = {}', ifp.shape())
ifp.logging('{}', ifp.amax())
hfp = Hdf5Processing()
c = 0
for lblo in ifp.label_bounds_iterator('largeobj', 'curlabel', ids=('locmax', 'disttransf'), targetids=('curlocmax', 'curdisttransf'),
