cohere-beamlines 4.2.1__tar.gz

cohere_beamlines-4.2.1/LICENSE

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+Copyright © 2019, UChicago Argonne, LLC
+All Rights Reserved
+ Software Name: CDI Reconstruction (cohere)
+By: Argonne National Laboratory
+OPEN SOURCE LICENSE
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+
+******************************************************************************************************
+DISCLAIMER
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+***************************************************************************************************

cohere_beamlines-4.2.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: cohere_beamlines
+Version: 4.2.1
+Summary: cohere beamline support
+Author-email: Barbara Frosik <bfrosik@anl.gov>, Ross Harder <rharder@anl.gov>
+License: Copyright © 2019, UChicago Argonne, LLC
+        All Rights Reserved
+         Software Name: CDI Reconstruction (cohere)
+        By: Argonne National Laboratory
+        OPEN SOURCE LICENSE
+        
+        Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+        2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+        3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+        
+        
+        ******************************************************************************************************
+        DISCLAIMER
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        ***************************************************************************************************
+        
+Project-URL: Homepage, https://github.com/AdvancedPhotonSource/cohere_beamlines
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pyqt5
+Requires-Dist: scikit-image
+Requires-Dist: xrayutilities
+Dynamic: license-file
+
+# cohere_beamlines
+
+This repository keeps correction fiels for supported beamlines.
+It is updated with a new event, such as new darkfield or whitefield file.

cohere_beamlines-4.2.1/README.md

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+# cohere_beamlines
+
+This repository keeps correction fiels for supported beamlines.
+It is updated with a new event, such as new darkfield or whitefield file.

cohere_beamlines-4.2.1/pyproject.toml

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+[build-system]
+requires = ["setuptools >= 77.0.3"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "cohere_beamlines"
+version = "4.2.1"
+authors = [
+  { name="Barbara Frosik", email="bfrosik@anl.gov" },
+  { name="Ross Harder", email="rharder@anl.gov" }
+]
+description = "cohere beamline support"
+readme = "README.md"
+requires-python = ">=3.11"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+]
+license = { file = "LICENSE" }
+
+dependencies = [
+                'pyqt5',
+                'scikit-image',
+                'xrayutilities',
+                ]
+
+[project.urls]
+Homepage = "https://github.com/AdvancedPhotonSource/cohere_beamlines"

cohere_beamlines-4.2.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

cohere_beamlines-4.2.1/src/cohere_beamlines/Petra3_P10/RSM_post_processing.py

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+#!/usr/local/bin/python2.7.3 -tttt
+"""
+Functions to cut and plot the result RSM.
+Created on Thu Apr 27 13:50:07 2023
+
+@author: renzhe
+@email: renzhe@ihep.ac.cn
+"""
+
+import numpy as np
+import matplotlib.pyplot as plt
+from scipy.ndimage import measurements
+import os
+
+
+def check_cut_box_size(bs, peak_pos, data_shape):
+    """
+    Check the box size possible for the symmetrical cut around the given peak position in the data.
+
+    Parameters
+    ----------
+    bs : list
+        The Half width of the boxsize in [Z, Y, X] order.
+    peak_pos : list
+        The peak position in the dataset.
+    data_shape : Unions(list|tuple)
+        The shape of the data to be cutted.
+
+    Returns
+    -------
+    bs : list
+        The suggested box size according to the shape of the data.
+
+    """
+    bs[0] = int(np.amin([bs[0], peak_pos[0] * 0.95, 0.95 * (data_shape[0] - peak_pos[0])]))
+    bs[1] = int(np.amin([bs[1], peak_pos[1] * 0.95, 0.95 * (data_shape[1] - peak_pos[1])]))
+    bs[2] = int(np.amin([bs[2], peak_pos[2] * 0.95, 0.95 * (data_shape[2] - peak_pos[2])]))
+    return bs
+
+
+def Cut_central(dataset, bs, cut_mode='maximum integration', peak_pos=None):
+    """
+    Cut the three dimensional dataset symmetrically with the box size given.
+
+    Parameters
+    ----------
+    dataset : ndarray
+        The three dimensional dataset to be cutted.
+    bs : list
+        The half width of the box size.
+    cut_mode : str, optional
+        The mode for choosing the center position for the cutting.
+        The cut mode can be 'maximum integration', 'maximum intensity', 'weight center' and 'given'.
+        'maximum integration': The dataset is cutted around the maximum integrated intensity in each dimension.
+        'maximum intensity': The dataset is cutted around the maximum intensity.
+        'weight center': The dataset is cutted around weight center in the box.
+        'given': The dataset is cutted around the given peak position.
+        The default is 'maximum integration'.
+    peak_pos : list, optional
+        The position for given peak position. The default is None.
+
+    Returns
+    -------
+    intcut : ndarray
+        The symmetrically cutted intensity.
+    peak_pos : list
+        The position of the peak position.
+    bs : list
+        The used box size for symmetrically cutting the dataset.
+
+    """
+    # Cutting the three dimensional data with the center of mass in the center of the intensity distribution
+    if cut_mode == 'maximum integration':
+        peak_pos = np.array([np.argmax(np.sum(dataset, axis=(1, 2))), np.argmax(np.sum(dataset, axis=(0, 2))), np.argmax(np.sum(dataset, axis=(0, 1)))], dtype=int)
+        print('finding the centeral position for the cutting')
+        bs = check_cut_box_size(bs, peak_pos, dataset.shape)
+        intcut = np.array(dataset[(peak_pos[0] - bs[0]):(peak_pos[0] + bs[0]), (peak_pos[1] - bs[1]):(peak_pos[1] + bs[1]), (peak_pos[2] - bs[2]):(peak_pos[2] + bs[2])])
+    elif cut_mode == 'maximum intensity':
+        peak_pos = np.unravel_index(np.argmax(dataset), dataset.shape)
+        bs = check_cut_box_size(bs, peak_pos, dataset.shape)
+        intcut = np.array(dataset[(peak_pos[0] - bs[0]):(peak_pos[0] + bs[0]), (peak_pos[1] - bs[1]):(peak_pos[1] + bs[1]), (peak_pos[2] - bs[2]):(peak_pos[2] + bs[2])])
+    elif cut_mode == 'weight center':
+        peak_pos = np.array(np.around(measurements.center_of_mass(dataset)), dtype=int)
+        bs = check_cut_box_size(bs, peak_pos, dataset.shape)
+        intcut = np.array(dataset[(peak_pos[0] - bs[0]):(peak_pos[0] + bs[0]), (peak_pos[1] - bs[1]):(peak_pos[1] + bs[1]), (peak_pos[2] - bs[2]):(peak_pos[2] + bs[2])])
+        print('cut according to the weight center')
+        i = 0
+        torlerence = 0.5
+        while not np.allclose(measurements.center_of_mass(intcut), np.array(bs, dtype=float) - 0.5, atol=torlerence):
+            peak_pos = np.array(peak_pos + np.around(measurements.center_of_mass(intcut) - np.array(bs, dtype=float) + 0.5), dtype=int)
+            bs = check_cut_box_size(bs, peak_pos, dataset.shape)
+            intcut = np.array(dataset[(peak_pos[0] - bs[0]):(peak_pos[0] + bs[0]), (peak_pos[1] - bs[1]):(peak_pos[1] + bs[1]), (peak_pos[2] - bs[2]):(peak_pos[2] + bs[2])])
+            i += 1
+            if i == 5:
+                print("Loosen the constrain for the weight center cutting")
+                torlerence = 1
+            elif i > 8:
+                print("could not find the weight center for the cutting")
+                break
+    elif cut_mode == 'given':
+        if peak_pos is None:
+            print('Could not find the given position for the cutting, please check it again!')
+            peak_pos = np.array((dataset.shape) / 2, dtype=int)
+        else:
+            peak_pos = np.array(peak_pos, dtype=int)
+        bs = check_cut_box_size(bs, peak_pos, dataset.shape)
+        intcut = np.array(dataset[(peak_pos[0] - bs[0]):(peak_pos[0] + bs[0]), (peak_pos[1] - bs[1]):(peak_pos[1] + bs[1]), (peak_pos[2] - bs[2]):(peak_pos[2] + bs[2])])
+    return intcut, peak_pos, bs
+
+
+def plot_with_units(RSM_int, q_origin, unit, pathsavetmp, qmax=np.array([]), display_range=None):
+    """
+    Plot and save the diffraction pattern with correct units.
+
+    Parameters
+    ----------
+    RSM_int : ndarray
+        The diffraction pattern to be plotted.
+    q_origin : list
+        The minimum origin of the diffraction pattern.
+    unit : float
+        The unit of the diffraction pattern.
+    pathsavetmp : str
+        The template for saving the diffraction pattern.
+        The parameter should be the complete path with %s in the filename for the position indicating different cut directions.
+    qmax : list, optional
+        If given, the cutted diffraction pattern will be displayed around the given position.
+        Else the integrated diffraction intensity will be plotted.
+        The default is np.array([]).
+    display_range : list, optional
+        The half width of the display range in [qz, qy, qx] order. The default is None.
+
+    Returns
+    -------
+    None.
+
+    """
+    dz, dy, dx = RSM_int.shape
+    qz = np.arange(dz) * unit + q_origin[0]
+    qy = np.arange(dy) * unit + q_origin[1]
+    qx = np.arange(dx) * unit + q_origin[2]
+    # save the qx qy qz cut of the 3D intensity
+    print('Saving the qx qy qz cuts......')
+    plt.figure(figsize=(12, 12))
+    pathsaveimg = pathsavetmp % ('qz')
+    if len(qmax) == 0:
+        plt.contourf(qx, qy, np.log10(np.sum(RSM_int, axis=0) + 1.0), 150, cmap='jet')
+    else:
+        plt.contourf(qx, qy, np.log10(RSM_int[qmax[0], :, :] + 1.0), 150, cmap='jet')
+    plt.xlabel(r'Q$_x$ ($1/\AA$)', fontsize=20, fontstyle='italic', fontfamily='Arial', fontweight='bold')
+    plt.ylabel(r'Q$_y$ ($1/\AA$)', fontsize=20, fontstyle='italic', fontfamily='Arial', fontweight='bold')
+    plt.axis('scaled')
+    plt.tick_params(axis='both', labelsize=20)
+    if (display_range is not None) and (len(qmax) != 0):
+        plt.xlim(qmax[2] * unit + q_origin[2] - display_range[2], qmax[2] * unit + q_origin[2] + display_range[2])
+        plt.ylim(qmax[1] * unit + q_origin[1] - display_range[1], qmax[1] * unit + q_origin[1] + display_range[1])
+    plt.savefig(pathsaveimg)
+    plt.show()
+    # plt.close()
+
+    plt.figure(figsize=(12, 12))
+    pathsaveimg = pathsavetmp % ('qy')
+    if len(qmax) == 0:
+        plt.contourf(qx, qz, np.log10(np.sum(RSM_int, axis=1) + 1.0), 150, cmap='jet')
+    else:
+        plt.contourf(qx, qz, np.log10(RSM_int[:, qmax[1], :] + 1.0), 150, cmap='jet')
+    plt.xlabel(r'Q$_x$ ($1/\AA$)', fontsize=20, fontstyle='italic', fontfamily='Arial', fontweight='bold')
+    plt.ylabel(r'Q$_z$ ($1/\AA$)', fontsize=20, fontstyle='italic', fontfamily='Arial', fontweight='bold')
+    plt.axis('scaled')
+    plt.tick_params(axis='both', labelsize=20)
+    if (display_range is not None) and (len(qmax) != 0):
+        plt.xlim(qmax[2] * unit + q_origin[2] - display_range[2], qmax[2] * unit + q_origin[2] + display_range[2])
+        plt.ylim(qmax[0] * unit + q_origin[0] - display_range[0], qmax[0] * unit + q_origin[0] + display_range[0])
+    plt.savefig(pathsaveimg)
+    plt.show()
+    # plt.close()
+
+    plt.figure(figsize=(12, 12))
+    pathsaveimg = pathsavetmp % ('qx')
+    if len(qmax) == 0:
+        plt.contourf(qy, qz, np.log10(np.sum(RSM_int, axis=2) + 1.0), 150, cmap='jet')
+    else:
+        plt.contourf(qy, qz, np.log10(RSM_int[:, :, qmax[2]] + 1.0), 150, cmap='jet')
+    plt.xlabel(r'Q$_y$ ($1/\AA$)', fontsize=20, fontstyle='italic', fontfamily='Arial', fontweight='bold')
+    plt.ylabel(r'Q$_z$ ($1/\AA$)', fontsize=20, fontstyle='italic', fontfamily='Arial', fontweight='bold')
+    plt.axis('scaled')
+    plt.tick_params(axis='both', labelsize=20)
+    if (display_range is not None) and (len(qmax) != 0):
+        plt.xlim(qmax[1] * unit + q_origin[1] - display_range[1], qmax[1] * unit + q_origin[1] + display_range[1])
+        plt.ylim(qmax[0] * unit + q_origin[0] - display_range[0], qmax[0] * unit + q_origin[0] + display_range[0])
+    plt.savefig(pathsaveimg)
+    plt.show()
+    # plt.close()
+    return
+
+
+def plot_without_units(RSM_int, mask, pathsavetmp):
+    """
+    Plot and save the diffraction pattern without units.
+
+    Parameters
+    ----------
+    RSM_int : ndarray
+        The diffraction pattern to be plotted.
+    mask : ndarray
+        The mask to be used. The masked pixels will be displayed by the red colors in the result plot.
+    pathsavetmp : str
+        The template for saving the diffraction pattern.
+        The parameter should be the complete path with %s in the filename for the position indicating different cut directions.
+
+    Returns
+    -------
+    None.
+
+    """
+    mask = np.ma.masked_where(mask == 0, mask)
+    dz, dy, dx = RSM_int.shape
+    # save the qx qy qz cut of the 3D intensity
+    print('Saving the qx qy qz cuts......')
+    plt.figure(figsize=(12, 12))
+    pathsaveimg = pathsavetmp % 'qz'
+    plt.imshow(np.log10(RSM_int[int(dz / 2), :, :] + 1.0), cmap='Blues')
+    if mask.ndim != 1:
+        plt.imshow(mask[int(dz / 2), :, :], cmap='Reds', alpha=0.5, vmin=0, vmax=1)
+    plt.xlabel(r'Q$_x$ (pixel)', fontsize=24)
+    plt.ylabel(r'Q$_y$ (pixel)', fontsize=24)
+    plt.axis('scaled')
+    plt.tick_params(axis='both', labelsize=24)
+    plt.savefig(pathsaveimg)
+    plt.show()
+    plt.close()
+
+    plt.figure(figsize=(12, 12))
+    pathsaveimg = pathsavetmp % 'qy'
+    plt.imshow(np.log10(RSM_int[:, int(dy / 2), :] + 1.0), cmap='Blues')
+    if mask.ndim != 1:
+        plt.imshow(mask[:, int(dy / 2), :], cmap='Reds', alpha=0.5, vmin=0, vmax=1)
+    plt.xlabel(r'Q$_x$ (pixel)', fontsize=24)
+    plt.ylabel(r'Q$_z$ (pixel)', fontsize=24)
+    plt.axis('scaled')
+    plt.tick_params(axis='both', labelsize=24)
+    plt.savefig(pathsaveimg)
+    plt.show()
+    plt.close()
+
+    plt.figure(figsize=(12, 12))
+    pathsaveimg = pathsavetmp % 'qx'
+    plt.imshow(np.log10(RSM_int[:, :, int(dx / 2)] + 1.0), cmap='Blues')
+    if mask.ndim != 1:
+        plt.imshow(mask[:, :, int(dx / 2)], cmap='Reds', alpha=0.5, vmin=0, vmax=1)
+    plt.xlabel(r'Q$_y$ (pixel)', fontsize=24)
+    plt.ylabel(r'Q$_z$ (pixel)', fontsize=24)
+    plt.axis('scaled')
+    plt.tick_params(axis='both', labelsize=24)
+    plt.savefig(pathsaveimg)
+    plt.show()
+    plt.close()
+    return
+
+
+def RSM2vti(pathsave, RSM_dataset, filename, RSM_unit, origin=(0, 0, 0)):
+    """
+    Save the reciprocal space map to vti format for reading with paraview.
+
+    Parameters
+    ----------
+    pathsave : str
+        The folder path to save the RSM.
+    RSM_dataset : ndarray
+        The RSM to be saved.
+    filename : str
+        The filename for the saving.
+    RSM_unit : float
+        The unit of the RSM.
+    origin : list, optional
+        The origin of the RSM. The default is (0, 0, 0).
+
+    Returns
+    -------
+    None.
+
+    """
+    import vtk
+    from vtk.util.numpy_support import numpy_to_vtk
+
+    pathsave = os.path.join(pathsave, filename)
+    imdata = vtk.vtkImageData()
+    imdata.SetOrigin(origin[0], origin[1], origin[2])
+    imdata.SetSpacing(RSM_unit, RSM_unit, RSM_unit)
+    imdata.SetDimensions(RSM_dataset.shape)
+
+    RSM_vtk = numpy_to_vtk(np.ravel(np.transpose(np.log10(RSM_dataset + 1.0))), deep=True, array_type=vtk.VTK_DOUBLE)
+
+    imdata.GetPointData().SetScalars(RSM_vtk)
+    writer = vtk.vtkXMLImageDataWriter()
+    writer.SetFileName(pathsave)
+    writer.SetInputData(imdata)
+
+    writer.Write()
+    return