# Copyright 2019 Diamond Light Source Ltd.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
.. module:: morph_proc_line3D
:platform: Unix
:synopsis: a Larix module to remove inconsistent gaps in the resulted 3D binary mask by merging the boundaries
.. moduleauthor:: Daniil Kazantsev <scientificsoftware@diamond.ac.uk>
"""
from savu.plugins.plugin import Plugin
from savu.plugins.driver.multi_threaded_plugin import MultiThreadedPlugin
from savu.plugins.utils import register_plugin
import numpy as np
from larix.methods.segmentation import MORPH_PROC_LINE
[docs]@register_plugin
class MorphProcLine3d(Plugin, MultiThreadedPlugin):
def __init__(self):
super(MorphProcLine3d, self).__init__("MorphProcLine3d")
[docs] def setup(self):
in_dataset, out_dataset = self.get_datasets()
out_dataset[0].create_dataset(in_dataset[0], dtype=np.uint8)
in_pData, out_pData = self.get_plugin_datasets()
getall = ["VOLUME_XZ", "voxel_y"]
in_pData[0].plugin_data_setup('VOLUME_3D', 'single', getall=getall)
out_pData[0].plugin_data_setup('VOLUME_3D', 'single', getall=getall)
[docs] def pre_process(self):
# extract given parameters
self.primeclass = self.parameters['primeclass']
self.CorrectionWindow = self.parameters['correction_window']
self.iterationsNumb = self.parameters['iterations']
[docs] def process_frames(self, data):
# run the class merging module here:
inputdata = data[0].copy(order='C')
pars = {'maskdata' : np.uint8(inputdata),\
'primeClass': self.primeclass,\
'CorrectionWindow' : self.CorrectionWindow ,\
'iterationsNumb' : self.iterationsNumb}
mask_merged = MORPH_PROC_LINE(pars['maskdata'], pars['primeClass'],
pars['CorrectionWindow'], pars['iterationsNumb'])
return mask_merged
[docs] def nOutput_datasets(self):
return 1