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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:: dials_find_spots |
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:platform: Unix |
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:synopsis: A plugin to integrate azimuthally "symmetric" signals i.e. SAXS,\ |
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WAXS or XRD.Requires a calibration file |
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.. moduleauthor:: Aaron D. Parsons <[email protected]> |
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""" |
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import logging |
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import numpy as np |
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from savu.plugins.filters.base_filter import BaseFilter |
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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 scipy.ndimage import gaussian_filter |
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from dials.array_family import flex |
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from dials.algorithms.image.threshold import DispersionThreshold |
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#@register_plugin |
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class DialsFindSpots(BaseFilter, CpuPlugin): |
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""" |
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finding the single crystal peaks with dials |
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:param spotsize: approximate maximum spot size. Default: 45. |
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""" |
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def __init__(self): |
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logging.debug("Starting DialsFindSpots") |
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super(DialsFindSpots, |
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self).__init__("DialsFindSpots") |
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def process_frames(self, data): |
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data = data[0] |
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lp = gaussian_filter(data, 100) |
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hp = data - lp # poormans background subtraction |
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hp -= np.min(hp) |
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sh = hp.shape |
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hp = hp.astype('uint32') |
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hp = flex.int(hp) |
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mask = flex.bool(np.ones_like(hp).astype('bool')) |
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result1 = flex.bool(np.zeros_like(hp).astype('bool')) |
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spots = np.zeros_like(hp).astype('bool') |
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for i in range(3, self.parameters['spotsize'], 5): |
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algorithm = DispersionThreshold(sh, (i, i), 1, 1, 0, -1) |
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#print type(hp), type(mask), type(result1) |
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thing = algorithm(hp, mask, result1) |
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spots = spots + result1.as_numpy_array() |
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return [data, spots*data] |
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def setup(self): |
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in_datasets, out_datasets = self.get_datasets() |
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in_pData, out_pData = self.get_plugin_datasets() |
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diffractions = in_datasets[0] |
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powder = out_datasets[0] |
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single_crystal = out_datasets[1] |
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powder.create_dataset(diffractions) |
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single_crystal.create_dataset(diffractions) |
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in_pData, out_pData = self.get_plugin_datasets() |
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in_pData[0].plugin_data_setup('DIFFRACTION', self.get_max_frames()) |
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out_pData[0].plugin_data_setup('DIFFRACTION', self.get_max_frames()) |
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out_pData[1].plugin_data_setup('DIFFRACTION', self.get_max_frames()) |
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def get_max_frames(self): |
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return 'single' |
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def nOutput_datasets(self): |
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return 2 |
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DiamondLightSource /
Savu
