xrayscatteringtools 0.0.1__tar.gz

xrayscatteringtools-0.0.1/.gitattributes

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xrayscatteringtools-0.0.1/.gitignore

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xrayscatteringtools-0.0.1/LICENSE

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+MIT License
+
+Copyright (c) 2025 David Romano
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

xrayscatteringtools-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: xrayscatteringtools
+Version: 0.0.1
+Summary: A library for gas phase analysis at the CXI endstation
+Project-URL: Homepage, https://github.com/Weber-Group/xrayscatteringtools
+Project-URL: Issues, https://github.com/Weber-Group/xrayscatteringtools/issues
+Author-email: David Romano <david_j_romano@brown.edu>
+License-Expression: MIT
+License-File: LICENSE
+Requires-Python: >=3.9
+Requires-Dist: h5py
+Requires-Dist: ipython
+Requires-Dist: matplotlib
+Requires-Dist: numpy<2
+Requires-Dist: pathlib
+Requires-Dist: pyyaml
+Requires-Dist: requests
+Requires-Dist: scipy>=1.11
+Requires-Dist: tqdm
+Requires-Dist: xraylib
+Provides-Extra: dev
+Requires-Dist: black>=24.0; extra == 'dev'
+Requires-Dist: mypy>=1.9; extra == 'dev'
+Requires-Dist: pytest>=8.0; extra == 'dev'
+Requires-Dist: ruff>=0.3; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# xrayscatteringtools
+
+## A python library for the analysis of data from the CXI endstation at the LCLS. 
+
+### List of all methods:
+All methods have full docstrings in the NumPy docstring standard.
+Proper namespaces have yet to be defined. Some of these functions can remain internal, and the more useful ones can be defined at the surface level.
+* calib
+  * geometry_calibration
+    - run_geometry_calibration()
+    - model()
+    - thompson_correction()
+    - geometry_correction()
+  * scattering_corrections
+    - correction_factor()
+    - Si_correction()
+    - KaptonHN_correction()
+    - Al_correction()
+    - Be_correction()
+    - cell_correction()
+    - Si_attenuation_length()
+    - Al_attenuation_length()
+    - Be_attenuation_length()
+    - KaptonHN_attenuation_length()
+    - J4M_efficiency()
+* theory
+  * iam
+    - iam_elastic_pattern()
+    - iam_inelastic_pattern()
+    - iam_total_pattern()
+    - iam_compton_spectrum()
+  * patterns
+    - sf6()
+* io
+  - combineRuns()
+  - get_tree()
+  - is_leaf()
+  - get_leaves()
+  - runNumToString()
+  - read_xyz()
+* plotting
+  - plot_jungfrau()
+  - compute_pixel_edges()
+* utils
+  - enable_underscore_cleanup()
+  - azimuthalBinning()
+  - keV2Angstroms()
+  - Angstroms2keV()
+  - q2theta()
+  - theta2q()
+  - element_symbol_to_number()
+  - element_number_to_symbol()

xrayscatteringtools-0.0.1/README.md

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+# xrayscatteringtools
+
+## A python library for the analysis of data from the CXI endstation at the LCLS. 
+
+### List of all methods:
+All methods have full docstrings in the NumPy docstring standard.
+Proper namespaces have yet to be defined. Some of these functions can remain internal, and the more useful ones can be defined at the surface level.
+* calib
+  * geometry_calibration
+    - run_geometry_calibration()
+    - model()
+    - thompson_correction()
+    - geometry_correction()
+  * scattering_corrections
+    - correction_factor()
+    - Si_correction()
+    - KaptonHN_correction()
+    - Al_correction()
+    - Be_correction()
+    - cell_correction()
+    - Si_attenuation_length()
+    - Al_attenuation_length()
+    - Be_attenuation_length()
+    - KaptonHN_attenuation_length()
+    - J4M_efficiency()
+* theory
+  * iam
+    - iam_elastic_pattern()
+    - iam_inelastic_pattern()
+    - iam_total_pattern()
+    - iam_compton_spectrum()
+  * patterns
+    - sf6()
+* io
+  - combineRuns()
+  - get_tree()
+  - is_leaf()
+  - get_leaves()
+  - runNumToString()
+  - read_xyz()
+* plotting
+  - plot_jungfrau()
+  - compute_pixel_edges()
+* utils
+  - enable_underscore_cleanup()
+  - azimuthalBinning()
+  - keV2Angstroms()
+  - Angstroms2keV()
+  - q2theta()
+  - theta2q()
+  - element_symbol_to_number()
+  - element_number_to_symbol()

xrayscatteringtools-0.0.1/pyproject.toml

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+[build-system]
+requires = ["hatchling >= 1.26"]
+build-backend = "hatchling.build"
+
+[project]
+name = "xrayscatteringtools"
+version = "0.0.1"
+description = "A library for gas phase analysis at the CXI endstation"
+authors = [
+    { name = "David Romano", email = "david_j_romano@brown.edu" }
+]
+readme = "README.md"
+license = "MIT"
+license-files = ["LICEN[CS]E*"]
+requires-python = ">=3.9"
+dependencies = [
+    "numpy<2",
+    "scipy>=1.11",
+    "pathlib",
+    "IPython",
+    "matplotlib",
+    "tqdm",
+    "h5py",
+    "requests",
+    "xraylib",
+    "pyyaml"
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=8.0",
+    "black>=24.0",
+    "mypy>=1.9",
+    "ruff>=0.3"
+]
+
+[project.urls]
+Homepage = "https://github.com/Weber-Group/xrayscatteringtools"
+Issues = "https://github.com/Weber-Group/xrayscatteringtools/issues"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-ra -q"
+
+[tool.black]
+line-length = 88
+target-version = ["py310"]
+
+[tool.ruff]
+line-length = 88
+select = ["E", "F", "W"]
+ignore = ["E501"]
+
+[tool.mypy]
+python_version = "3.10"
+strict = true

xrayscatteringtools-0.0.1/src/xrayscatteringtools/__init__.py

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+from .io import *
+from .plotting import *
+from .utils import *

xrayscatteringtools-0.0.1/src/xrayscatteringtools/calib/geometry_calibration.py

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+import numpy as np
+from scipy.interpolate import InterpolatedUnivariateSpline
+from scipy.optimize import curve_fit
+from xrayscatteringtools.utils import theta2q
+from xrayscatteringtools.calib.scattering_corrections import correction_factor
+
+def run_geometry_calibration(
+        raw_image,
+        x,
+        y,
+        mask,
+        theory_q,
+        theory_Iq,
+        photon_energy_keV,
+        initial_guess={'amplitude' : 1,'x0': 0, 'y0': 0, 'z0': 90000},
+        polarization = 0,
+        mask_center=True,
+        mask_center_size=7500,
+        bounds = ([0, -10_000, -10_000, 30_000], [np.inf, 10_000, 10_000, 150_000])
+        ):
+    """
+    Perform geometry calibration on a raw detector image using a theoretical scattering pattern.
+
+    This function fits the detector geometry parameters (x0, y0, z0) by comparing the
+    measured image to a theoretical scattering pattern and applying corrections for
+    polarization (Thompson), geometry, and angle-of-scattering effects.
+
+    Parameters
+    ----------
+    raw_image : ndarray
+        Array of measured intensities from the detector.
+    x : ndarray
+        Array of x-coordinates for each pixel.
+    y : ndarray
+        Array of y-coordinates for each pixel.
+    mask : ndarray of bool
+        Boolean mask array indicating which pixels to include in the fit.
+    theory_q : ndarray
+        1D array of scattering vector magnitudes corresponding to the theoretical pattern.
+    theory_Iq : ndarray
+        1D array of theoretical scattering intensities at each q.
+    photon_energy_keV : float
+        Photon energy of the X-ray in keV.
+    initial_guess : dict, optional
+        Initial guess for fit parameters:
+        - 'amplitude' : float, scaling of the intensity
+        - 'x0', 'y0', 'z0' : float, initial guesses for detector geometry
+        Default: {'amplitude': 1, 'x0': 0, 'y0': 0, 'z0': 90000}.
+    polarization : float, optional
+        Polarization direction (-pi/2 to pi/2). Default is 0 (horizontally polarized).
+    mask_center : bool, optional
+        If True, exclude pixels near the center from the fit. Default is True.
+    mask_center_size : float, optional
+        Radius (in pixels) of the excluded central region. Default is 7500.
+    fit_bounds : tuple of array_like, optional
+        Lower and upper bounds for the fit parameters. Default is 
+        ([0, -10000, -10000, 30000, -π/2], [inf, 10000, 10000, 150000, π/2]).
+
+    Returns
+    -------
+    fit : ndarray
+        3D array representing the fitted detector image (reshaped to match input dimensions).
+    popt : ndarray
+        Optimized fit parameters: [amplitude, x0, y0, z0]. In units of microns.
+    pcov : ndarray
+        Covariance matrix of the optimized parameters.
+
+    Notes
+    -----
+    The returned z0 distance must be converted to millimeters when editing the producer. It should not be in microns.
+    The fitting applies:
+    - `thompson_correction` for polarization effects,
+    - `geometry_correction` for geometric distortions,
+    - `correction_factor` for angle-of-scattering corrections (Lingyu Ma et al 2024 J. Phys. B: At. Mol. Opt. Phys. 57 205602).
+
+    Examples
+    --------
+    >>> fit, popt, pcov = run_geometry_calibration(raw_image, x, y, mask, theory_q, theory_Iq, 12.7)
+    """
+    # Step one: generate an interpolation for the theory pattern.
+    theory_interpolation = InterpolatedUnivariateSpline(theory_q, theory_Iq, ext=3) # Extrapolation 3. Returns Boundary value if outside of range.
+
+    # Step two: Define initial guess, bounds, and fitting function using a wrapper
+    p0 = [initial_guess['amplitude'], initial_guess['x0'], initial_guess['y0'], initial_guess['z0']]
+    def fitting_function(xy, amplitude, x0, y0, z0):
+        return model(xy, amplitude, x0, y0, z0, polarization, photon_energy_keV, theory_interpolation)
+
+    # Step three: Masking and formatting variables
+    center_mask = np.ones_like(raw_image, dtype=bool)
+    if mask_center:
+        center_mask[np.sqrt(x**2 + y**2) < mask_center_size] = False
+        
+    masked_data = np.ravel(raw_image[mask & center_mask])
+    x_masked = np.ravel(x[mask & center_mask])
+    y_masked = np.ravel(y[mask & center_mask])
+    xy_masked = [x_masked, y_masked]
+
+    # Step four: fitting the data
+    popt, pcov = curve_fit(fitting_function, xy_masked, masked_data, p0=p0, bounds=bounds)
+    fit = fitting_function([np.ravel(x), np.ravel(y)], *popt).reshape(raw_image.shape)
+    return fit, popt, pcov
+
+def model(xy, amplitude, x0, y0, z0, phi0, photon_energy_keV, theory_interpolation):
+    """
+    Calculate the theoretical detector image for given geometry parameters.
+
+    Parameters
+    ----------
+    xy : list of ndarray
+        [x, y] 2D arrays of pixel coordinates.
+    amplitude : float
+        Scaling factor for intensity.
+    x0, y0, z0 : float
+        Detector geometry parameters (pixel offsets and distance).
+    phi0 : float
+        Azimuthal rotation angle in radians.
+    photon_energy_keV : float
+        Photon energy in keV.
+    theory_interpolation : callable
+        Interpolated function for theoretical scattering intensities versus q.
+
+    Returns
+    -------
+    fit : ndarray
+        Flattened array of predicted intensities for each pixel.
+
+    """
+    # Pull out the x and y arrays from the input
+    x = xy[0]
+    y = xy[1]
+    # Center the arrays around x0 and y0
+    centered_x = x - x0
+    centered_y = y - y0
+    # Calculate the r array
+    r_matrix = np.sqrt(centered_x**2 + centered_y**2)
+    theta_matrix = np.arctan(r_matrix/z0)
+    q_matrix = theta2q(theta_matrix, photon_energy_keV)
+
+    # Calculate corrections
+    corrections = np.ones_like(q_matrix)
+    corrections *= thompson_correction(centered_x, centered_y, z0, phi0) # Polarization
+    corrections *= geometry_correction(centered_x, centered_y, z0) # Geometry
+    corrections *= correction_factor(q_matrix, photon_energy_keV) # Angle-Of-Scattering, Lingyu Ma et al 2024 J. Phys. B: At. Mol. Opt. Phys. 57 205602
+    fit = amplitude * theory_interpolation(q_matrix) * corrections
+    return fit
+
+def thompson_correction(x, y, z0, phi0):
+    """
+    Calculate the Thompson polarization correction for each pixel.
+
+    Parameters
+    ----------
+    x, y : ndarray
+        Pixel coordinates relative to detector origin.
+    z0 : float
+        Detector distance along beam axis.
+    phi0 : float
+        Azimuthal rotation angle in radians.
+
+    Returns
+    -------
+    correction : ndarray
+        Thompson correction factor for each pixel.
+
+    Notes
+    -----
+    See Lingyu Ma et al 2024 J. Phys. B: At. Mol. Opt. Phys. 57 205602
+
+    """
+    # Calculate the Thompson scattering correction factor
+    r_matrix = np.sqrt(x**2 + y**2)
+    theta = np.arctan(r_matrix/z0)
+    phi = np.arctan2(y, x) + phi0
+    correction = np.sin(phi)**2+np.cos(theta)**2*np.cos(phi)**2
+    return correction
+
+def geometry_correction(x, y, z0):
+    """
+    Compute geometric correction factor (cos^3(theta)) for a detector.
+
+    Parameters
+    ----------
+    x, y : ndarray
+        Pixel coordinates relative to detector origin.
+    z0 : float
+        Detector distance along beam axis.
+
+    Returns
+    -------
+    correction : ndarray
+        Geometric correction factor for each pixel.
+
+    Notes
+    -----
+    The geometry correction comes from the inverse square law and the effective area of the pixel.
+    The inverse square law accounts for cos^2(theta), and the effective area is another cos(theta).
+    See Lingyu Ma et al 2024 J. Phys. B: At. Mol. Opt. Phys. 57 205602
+
+
+    """
+    r_matrix = np.sqrt(x**2 + y**2)
+    theta = np.arctan(r_matrix / z0)
+    correction = np.cos(theta) ** 3
+    return correction