savu.plugins.simulation.tomo_phantom_artifacts

Complexity

Total Complexity

13

Size/Duplication

Total Lines	94
Duplicated Lines	0 %

Importance

Changes

0

6 Methods

Rating	Name	Duplication	Size	Complexity
B	TomoPhantomArtifacts.process_frames()	0	40	8
A	TomoPhantomArtifacts.nOutput_datasets()	0	2	1
A	TomoPhantomArtifacts.get_max_frames()	0	2	1
A	TomoPhantomArtifacts.setup()	0	6	1
A	TomoPhantomArtifacts.nInput_datasets()	0	2	1
A	TomoPhantomArtifacts.__init__()	0	2	1

# Copyright 2014 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:: tomo_phantom_artifacts
   :platform: Unix
   :synopsis: Adding artifacts to the generated synthetic projection data using TomoPhantom

.. moduleauthor:: Daniil Kazantsev <scientificsoftware@diamond.ac.uk>
"""

import savu.plugins.utils as pu
from savu.plugins.plugin import Plugin
from savu.plugins.driver.cpu_plugin import CpuPlugin
from savu.plugins.utils import register_plugin

import tomophantom
from tomophantom.supp.artifacts import _Artifacts_
import os
import numpy as np

@register_plugin
class TomoPhantomArtifacts(Plugin, CpuPlugin):
    def __init__(self):
        super(TomoPhantomArtifacts, self).__init__('TomoPhantomArtifacts')

    def setup(self):
        in_dataset, out_dataset = self.get_datasets()
        out_dataset[0].create_dataset(in_dataset[0])
        in_pData, out_pData = self.get_plugin_datasets()
        in_pData[0].plugin_data_setup('SINOGRAM', self.get_max_frames())
        out_pData[0].plugin_data_setup('SINOGRAM', self.get_max_frames())

    def process_frames(self, data):
        sinogram = data[0]
        # apply a variety of artifacts to the generated data:
        _noise_={}
        if self.parameters['artifacts_noise_type'] is not None:
            _noise_ =  {'noise_type' : self.parameters['artifacts_noise_type'],
                        'noise_amplitude' : self.parameters['artifacts_noise_amplitude'],
                        'noise_seed' : 0,
                        'verbose' : False}
        # misalignment dictionary
        _sinoshifts_={}
        if self.parameters['artifacts_misalignment_maxamplitude'] is not None:
            _sinoshifts_ = {'sinoshifts_maxamplitude' : self.parameters['artifacts_misalignment_maxamplitude']}
        # adding zingers and stripes
        _zingers_={}
        if self.parameters['artifacts_zingers_percentage'] is not None:
            _zingers_ = {'zingers_percentage' : self.parameters['artifacts_zingers_percentage'],
                        'zingers_modulus' : self.parameters['artifacts_zingers_modulus']}
        _stripes_={}
        if self.parameters['artifacts_stripes_percentage'] is not None:
            _stripes_ = {'stripes_percentage' : self.parameters['artifacts_stripes_percentage'],
                        'stripes_maxthickness' : self.parameters['artifacts_stripes_maxthickness'],
                        'stripes_intensity' : self.parameters['artifacts_stripes_intensity'],
                        'stripes_type' : self.parameters['artifacts_stripes_type'],
                        'stripes_variability' : self.parameters['artifacts_stripes_variability']}
        # partial volume effect dictionary
        _pve_={}
        if self.parameters['artifacts_pve'] is not None:
            _pve_ = {'pve_strength' : self.parameters['artifacts_pve']}
        # fresnel propagator
        _fresnel_propagator_={}
        if self.parameters['artifacts_fresnel_distance'] is not None:
            _fresnel_propagator_ = {'fresnel_dist_observation' : self.parameters['artifacts_fresnel_distance'],
                        'fresnel_scale_factor' : self.parameters['artifacts_fresnel_scale_factor'],
                        'fresnel_wavelenght' : self.parameters['artifacts_fresnel_wavelenght']}
        if self.parameters['artifacts_misalignment_maxamplitude'] is not None:
            [sino_artifacts, shifts] = _Artifacts_(sinogram.copy(), **_noise_, **_zingers_, **_stripes_, **_sinoshifts_, **_pve_, **_fresnel_propagator_)
        else:
            sino_artifacts = _Artifacts_(sinogram.copy(), **_noise_, **_zingers_, **_stripes_, **_sinoshifts_, **_pve_, **_fresnel_propagator_)
        return sino_artifacts

The variable sino_artifacts does not seem to be defined for all execution paths.

    def get_max_frames(self):
        return 'single'

    def nInput_datasets(self):
        return 1

    def nOutput_datasets(self):
        return 1