def __resize_batch_helper(item,
inputfolder,
outputfolder,
order=1,
append_resolution_to_filename=True,
**kwargs_to_ignore):
inputfile, voxel_size = item
metadata = Metadata()
metadata.set_voxel_size(voxel_size)
stack = Stack(filename=inputfolder + inputfile)
zoom = np.array(stack.metadata['Voxel size arr']) / np.array(
metadata['Voxel size arr'])
stack.resize(zoom=zoom, order=order)
stack.metadata.set_voxel_size(metadata['Voxel size arr'])
path = os.path.dirname(inputfile)
strres = str(metadata['Voxel size']).replace(' ', ' ').replace(
' ', ' ').replace('[ ', '[').replace(' ', '_')
if path == '':
if append_resolution_to_filename:
outputname = outputfolder + inputfile[:
-4] + '_voxel_size_' + strres + '.tif'
else:
outputname = outputfolder + path + 'voxel_size_' + strres + '/' + inputfile.split(
'/')[-1]
else:
outputname = outputfolder + path + '_voxel_size_' + strres + '/' + inputfile.split(
'/')[-1]
stack.save(outputname)
stack.metadata.save(outputname[:-4] + '.csv')
def __compute_accuracy_measures_batch_helper(item, inputfolder, reffolder,
outputfolder, **kwargs_to_ignore):
if not reffolder.endswith('/'):
reffolder += '/'
parts = item.split('/')
name = parts[-1]
if len(parts) > 1:
base = parts[-2]
else:
base = ''
stack = Stack(filename=inputfolder + item)
if 'isPSF' not in stack.metadata.index or str(
stack.metadata['isPSF']) == 'False':
if os.path.exists(reffolder + item):
refstack = Stack(filename=reffolder + item)
elif os.path.exists(reffolder + name):
refstack = Stack(filename=reffolder + name)
elif os.path.exists(reffolder + base + '/' + name):
refstack = Stack(filename=reffolder + base + '/' + name)
elif os.path.exists(reffolder + name.split('_voxel_size')[0] + '.tif'):
refstack = Stack(filename=reffolder +
name.split('_voxel_size')[0] + '.tif')
else:
raise ValueError('No ground truth found for cell ' + item + '!')
input_voxel_size = stack.metadata['Voxel size arr']
zoom = np.array(stack.metadata['Voxel size arr']) / np.array(
refstack.metadata['Voxel size arr'])
stack.resize(zoom=zoom)
stats = stack.compute_accuracy_measures(refstack)
stack.metadata.set_voxel_size(input_voxel_size)
for c in stack.metadata.index:
try:
stats[c] = stack.metadata[c]
except ValueError:
stats[c] = str(stack.metadata[c])
stats['Name'] = item
filelib.make_folders([os.path.dirname(outputfolder + item)])
stats.to_csv(outputfolder + item[:-4] + '.csv', sep='\t')