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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:: phase_unwrapping |
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:platform: Unix |
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:synopsis: A plugin for unwrapping phase-retrieved images. |
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.. moduleauthor:: Nghia Vo <[email protected]> |
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""" |
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from savu.plugins.utils import register_plugin |
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from savu.plugins.driver.cpu_plugin import CpuPlugin |
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from savu.plugins.plugin import Plugin |
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import numpy as np |
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import pyfftw.interfaces.scipy_fftpack as fft |
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@register_plugin |
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class PhaseUnwrapping(Plugin, CpuPlugin): |
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def __init__(self): |
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super(PhaseUnwrapping, self).__init__("PhaseUnwrapping") |
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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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View Code Duplication |
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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self.pattern = self.parameters['pattern'] |
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if self.pattern == "PROJECTION": |
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in_pData[0].plugin_data_setup(self.pattern, 'single') |
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out_pData[0].plugin_data_setup(self.pattern, 'single') |
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else: |
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in_pData[0].plugin_data_setup('SINOGRAM', 'single') |
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out_pData[0].plugin_data_setup('SINOGRAM', 'single') |
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def wrap_to_pi(self, mat): |
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return (mat + np.pi) % (2 * np.pi) - np.pi |
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def make_window(self, height, width): |
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wid_cen = width // 2 |
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hei_cen = height // 2 |
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ulist = (1.0 * np.arange(0, width) - wid_cen) / wid_cen |
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vlist = (1.0 * np.arange(0, height) - hei_cen) / hei_cen |
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u, v = np.meshgrid(ulist, vlist) |
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window = u ** 2 + v ** 2 |
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window1 = np.copy(window) |
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window1[hei_cen, wid_cen] = 1.0 |
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return window, window1 |
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def forward_operator(self, mat, window): |
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mat_res = fft.ifft2(fft.ifftshift(fft.fftshift( |
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fft.fft2(mat)) * window)) |
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return mat_res |
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def backward_operator(self, mat, window1): |
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mat_res = fft.ifft2(fft.ifftshift(fft.fftshift( |
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fft.fft2(mat)) / window1)) |
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return mat_res |
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def double_image(self, mat): |
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mat1 = np.hstack((mat, np.fliplr(mat))) |
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mat2 = np.vstack((np.flipud(mat1), mat1)) |
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return mat2 |
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def phase_unwrap_based_fft(self, mat, window, window1): |
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height, width = mat.shape |
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mat2 = self.double_image(mat) |
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mat_unwrap = np.real( |
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self.backward_operator(np.imag(self.forward_operator( |
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np.exp(mat2 * 1j), window) * np.exp(-1j * mat2)), window1)) |
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mat_unwrap = mat_unwrap[height:, 0:width] |
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return mat_unwrap |
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def phase_unwrap_iterative(self, mat_wrap, window, window1, n_iter): |
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mat_unwrap = self.phase_unwrap_based_fft(mat_wrap, window, window1) |
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for i in range(n_iter): |
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mat_wrap1 = self.wrap_to_pi(mat_unwrap) |
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mat_diff = mat_wrap - mat_wrap1 |
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nmean = np.mean(mat_diff) |
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mat_diff = self.wrap_to_pi(mat_diff - nmean) |
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phase_diff = self.phase_unwrap_based_fft(mat_diff, window, |
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window1) |
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mat_unwrap = mat_unwrap + phase_diff |
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return mat_unwrap |
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def pre_process(self): |
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inData = self.get_in_datasets()[0] |
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self.data_size = inData.get_shape() |
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(self.depth, self.height, self.width) = self.data_size[:3] |
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if self.pattern == "PROJECTION": |
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self.window, self.window1 = self.make_window(2 * self.height, |
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2 * self.width) |
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else: |
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self.window, self.window1 = self.make_window(2 * self.depth, |
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2 * self.width) |
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self.n_iter = self.parameters['n_iterations'] |
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def process_frames(self, data): |
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mat_unwrap = self.phase_unwrap_iterative(data[0], self.window, |
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self.window1, self.n_iter) |
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return mat_unwrap |
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DiamondLightSource /
Savu
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