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# Copyright 2014 Diamond Light Source Ltd. |
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# |
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# Licensed under the Apache License, Version 2.0 (the "License"); |
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# you may not use this file except in compliance with the License. |
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# You may obtain a copy of the License at |
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# |
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# http://www.apache.org/licenses/LICENSE-2.0 |
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# |
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# Unless required by applicable law or agreed to in writing, software |
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# distributed under the License is distributed on an "AS IS" BASIS, |
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. |
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# See the License for the specific language governing permissions and |
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# limitations under the License. |
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""" |
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.. module:: tomo_phantom_artifacts |
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:platform: Unix |
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:synopsis: Adding artifacts to the generated synthetic projection data using TomoPhantom |
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.. moduleauthor:: Daniil Kazantsev <[email protected]> |
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""" |
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import savu.plugins.utils as pu |
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from savu.plugins.plugin import Plugin |
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from savu.plugins.driver.cpu_plugin import CpuPlugin |
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from savu.plugins.utils import register_plugin |
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import tomophantom |
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from tomophantom.supp.artifacts import _Artifacts_ |
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import os |
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import numpy as np |
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@register_plugin |
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class TomoPhantomArtifacts(Plugin, CpuPlugin): |
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def __init__(self): |
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super(TomoPhantomArtifacts, self).__init__('TomoPhantomArtifacts') |
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def setup(self): |
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in_dataset, out_dataset = self.get_datasets() |
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out_dataset[0].create_dataset(in_dataset[0]) |
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in_pData, out_pData = self.get_plugin_datasets() |
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in_pData[0].plugin_data_setup('SINOGRAM', self.get_max_frames()) |
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out_pData[0].plugin_data_setup('SINOGRAM', self.get_max_frames()) |
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def process_frames(self, data): |
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sinogram = data[0] |
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# apply a variety of artifacts to the generated data: |
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_noise_={} |
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if self.parameters['artifacts_noise_type'] is not None: |
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_noise_ = {'noise_type' : self.parameters['artifacts_noise_type'], |
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'noise_amplitude' : self.parameters['artifacts_noise_amplitude'], |
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'noise_seed' : 0, |
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'verbose' : False} |
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# misalignment dictionary |
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_sinoshifts_={} |
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if self.parameters['artifacts_misalignment_maxamplitude'] is not None: |
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_sinoshifts_ = {'sinoshifts_maxamplitude' : self.parameters['artifacts_misalignment_maxamplitude']} |
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# adding zingers and stripes |
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_zingers_={} |
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if self.parameters['artifacts_zingers_percentage'] is not None: |
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_zingers_ = {'zingers_percentage' : self.parameters['artifacts_zingers_percentage'], |
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'zingers_modulus' : self.parameters['artifacts_zingers_modulus']} |
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_stripes_={} |
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if self.parameters['artifacts_stripes_percentage'] is not None: |
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_stripes_ = {'stripes_percentage' : self.parameters['artifacts_stripes_percentage'], |
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'stripes_maxthickness' : self.parameters['artifacts_stripes_maxthickness'], |
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'stripes_intensity' : self.parameters['artifacts_stripes_intensity'], |
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'stripes_type' : self.parameters['artifacts_stripes_type'], |
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'stripes_variability' : self.parameters['artifacts_stripes_variability']} |
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# partial volume effect dictionary |
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_pve_={} |
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if self.parameters['artifacts_pve'] is not None: |
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_pve_ = {'pve_strength' : self.parameters['artifacts_pve']} |
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# fresnel propagator |
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_fresnel_propagator_={} |
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if self.parameters['artifacts_fresnel_distance'] is not None: |
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_fresnel_propagator_ = {'fresnel_dist_observation' : self.parameters['artifacts_fresnel_distance'], |
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'fresnel_scale_factor' : self.parameters['artifacts_fresnel_scale_factor'], |
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'fresnel_wavelenght' : self.parameters['artifacts_fresnel_wavelenght']} |
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if self.parameters['artifacts_misalignment_maxamplitude'] is not None: |
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[sino_artifacts, shifts] = _Artifacts_(sinogram.copy(), **_noise_, **_zingers_, **_stripes_, **_sinoshifts_, **_pve_, **_fresnel_propagator_) |
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else: |
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sino_artifacts = _Artifacts_(sinogram.copy(), **_noise_, **_zingers_, **_stripes_, **_sinoshifts_, **_pve_, **_fresnel_propagator_) |
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return sino_artifacts |
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def get_max_frames(self): |
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return 'single' |
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def nInput_datasets(self): |
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return 1 |
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def nOutput_datasets(self): |
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return 1 |
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DiamondLightSource /
Savu
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