def get_output_data(self, data_nr):
"""Returns the dataset that was produced by ilastik.
:param data_nr: number of dataset
:return: output dataset of ilastik
"""
return vigra.readHDF5(self._get_output_data_path(data_nr), const.default_export_key())
def get_output_data(self, data_nr):
"""Returns the dataset that was produced by ilastik.
:param data_nr: number of dataset
:return: output dataset of ilastik
"""
return vigra.readHDF5(self._get_output_data_path(data_nr),
const.default_export_key())
def merge_output_into_dataset(self, data_nr, n=0):
"""Merges the ilastik output in the dataset. The first n channels of the dataset are left unchanged.
It is assumed, that extend_data_tzyxc() has been called, so the channels are in the last dimension.
:param data_nr: number of dataset
:param n: number of channels that are left unchanged
"""
filepath = self.get_data_path(data_nr)
h5key = self.get_data_key(data_nr)
filepath_out = self._get_output_data_path(data_nr)
h5key_out = const.default_export_key()
merge_datasets(filepath, h5key, filepath_out, h5key_out, n=n, compression=self._compression)
def get_data_key(self, data_nr):
"""Returns the h5 key of the dataset.
:param data_nr: number of dataset
:return: key of the dataset inside its h5 file
:rtype: str
"""
if self.is_internal(data_nr):
dataset_id = self.get_dataset_id(data_nr)
data_key = const.localdataset(dataset_id)
else:
if self._datatype(data_nr) != "hdf5":
return const.default_export_key()
h5_key = const.filepath(data_nr)
data_path = vigra.readHDF5(self.project_filename, h5_key)
data_key = os.path.basename(data_path)
return data_key
def merge_output_into_dataset(self, data_nr, n=0):
"""Merges the ilastik output in the dataset. The first n channels of the dataset are left unchanged.
It is assumed, that extend_data_tzyxc() has been called, so the channels are in the last dimension.
:param data_nr: number of dataset
:param n: number of channels that are left unchanged
"""
filepath = self.get_data_path(data_nr)
h5key = self.get_data_key(data_nr)
filepath_out = self._get_output_data_path(data_nr)
h5key_out = const.default_export_key()
merge_datasets(filepath,
h5key,
filepath_out,
h5key_out,
n=n,
compression=self._compression)
def get_data_key(self, data_nr):
"""Returns the h5 key of the dataset.
:param data_nr: number of dataset
:return: key of the dataset inside its h5 file
:rtype: str
"""
if self.is_internal(data_nr):
dataset_id = self.get_dataset_id(data_nr)
data_key = const.localdataset(dataset_id)
else:
if self._datatype(data_nr) != "hdf5":
return const.default_export_key()
h5_key = const.filepath(data_nr)
data_path = vigra.readHDF5(self.project_filename, h5_key)
data_key = os.path.basename(data_path)
return data_key
