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'),