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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:: projection_2d_alignment |
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:platform: Unix |
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:synopsis: calculates horizontal-vertical shift vectors for fixing misaligned projection data |
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.. moduleauthor:: Daniil Kazantsev <[email protected]> |
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""" |
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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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from skimage.registration import phase_cross_correlation |
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import numpy as np |
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@register_plugin |
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class Projection2dAlignment(Plugin, CpuPlugin): |
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def __init__(self): |
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super(Projection2dAlignment, self).__init__('Projection2dAlignment') |
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def setup(self): |
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in_dataset, out_dataset = self.get_datasets() |
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in_pData, out_pData = self.get_plugin_datasets() |
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in_pData[0].plugin_data_setup('PROJECTION', self.get_max_frames()) |
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in_pData[1].plugin_data_setup('PROJECTION', self.get_max_frames()) |
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# create a metadata for storing shift vectors |
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slice_dirs = list(in_dataset[0].get_slice_dimensions()) |
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new_shape = (in_dataset[0].get_shape()[slice_dirs[0]], 2) |
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out_dataset[0].create_dataset(shape=new_shape, |
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axis_labels=['x.shifts', 'y.shifts'], |
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remove=True) |
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out_dataset[0].add_pattern("METADATA", core_dims=(1,), slice_dims=(0,)) |
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out_pData[0].plugin_data_setup('METADATA', self.get_max_frames()) |
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def process_frames(self, data): |
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projection = data[0] # extract a projection |
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projection_align = data[1] # extract a projection for alignment |
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# perform alignment |
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shift, error, diffphase = phase_cross_correlation( |
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projection, projection_align, upsample_factor=self.parameters['upsample_factor']) |
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return shift |
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def post_process(self): |
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out_data = self.get_out_datasets()[0] |
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shift_vector = out_data.data[:, :] # get a shift vector |
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shift_vector[:, [0, 1]] = shift_vector[:, [1, 0]] # swap axis in shift vector |
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# get previous projection shifts first from experimental metadata |
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shift_vector_prev = self.exp.meta_data.dict['projection_shifts'] |
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shift_vector_prev += shift_vector |
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self.exp.meta_data.set('projection_shifts', shift_vector_prev.copy()) |
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in_meta_data = self.get_in_meta_data()[0] |
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in_meta_data.set('projection_shifts', shift_vector_prev.copy()) |
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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 2 |
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def nOutput_datasets(self): |
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return 1 |
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DiamondLightSource /
Savu
