ewoksid31 0.1.0__tar.gz

ewoksid31-0.1.0/LICENSE.md

@@ -0,0 +1,20 @@
+# MIT License
+
+**Copyright (c) 2023 European Synchrotron Radiation Facility**
+
+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.

ewoksid31-0.1.0/PKG-INFO

@@ -0,0 +1,29 @@
+Metadata-Version: 2.1
+Name: ewoksid31
+Version: 0.1.0
+Summary: Data processing workflows for ID31
+Home-page: https://gitlab.esrf.fr/workflow/ewoksid31/
+Author: ESRF
+Author-email: wout.de_nolf@esrf.fr
+License: MIT
+Project-URL: Source, https://gitlab.esrf.fr/workflow/ewoksid31/
+Project-URL: Documentation, https://ewoksid31.readthedocs.io/
+Project-URL: Tracker, https://gitlab.esrf.fr/workflow/ewoksid31/issues/
+Keywords: ewoks
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+Provides-Extra: test
+Provides-Extra: dev
+Provides-Extra: doc
+License-File: LICENSE.md
+
+# ewoksid31
+
+Data processing workflows for ID31
+
+## Documentation
+
+https://ewoksid31.readthedocs.io/

ewoksid31-0.1.0/README.md

@@ -0,0 +1,7 @@
+# ewoksid31
+
+Data processing workflows for ID31
+
+## Documentation
+
+https://ewoksid31.readthedocs.io/

ewoksid31-0.1.0/pyproject.toml

@@ -0,0 +1,6 @@
+[build-system]
+requires = [
+    "setuptools>=46.4<63",
+    "wheel",
+]
+build-backend = "setuptools.build_meta"

ewoksid31-0.1.0/setup.cfg

@@ -0,0 +1,68 @@
+[metadata]
+name = ewoksid31
+version = attr: ewoksid31.__version__
+author = ESRF
+author_email = wout.de_nolf@esrf.fr
+description = Data processing workflows for ID31
+long_description = file: README.md
+long_description_content_type = text/markdown
+license = MIT
+url = https://gitlab.esrf.fr/workflow/ewoksid31/
+project_urls = 
+	Source = https://gitlab.esrf.fr/workflow/ewoksid31/
+	Documentation = https://ewoksid31.readthedocs.io/
+	Tracker = https://gitlab.esrf.fr/workflow/ewoksid31/issues/
+classifiers = 
+	Intended Audience :: Science/Research
+	License :: OSI Approved :: MIT License
+	Programming Language :: Python :: 3
+keywords = 
+	ewoks
+
+[options]
+package_dir = 
+	=src
+packages = find:
+python_requires = >=3.7
+install_requires = 
+	ewokscore
+	scipy
+	numpy
+
+[options.packages.find]
+where = src
+
+[options.extras_require]
+test = 
+	pytest >=7
+dev = 
+	%(test)s
+	black >=22
+	flake8 >=4
+doc = 
+	%(test)s
+	sphinx >=4.5
+	sphinx-autodoc-typehints >=1.16
+
+[options.entry_points]
+ewoks.tasks.class = 
+	ewoksid31.tasks.*=ewoksid31
+
+[options.package_data]
+* = *.mat
+
+[flake8]
+ignore = E501, E203, W503
+max-line-length = 88
+exclude = 
+	.eggs
+
+[coverage:run]
+omit = 
+	setup.py
+	*/tests/*
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

ewoksid31-0.1.0/setup.py

@@ -0,0 +1,4 @@
+import setuptools
+
+if __name__ == "__main__":
+    setuptools.setup()

ewoksid31-0.1.0/src/ewoksid31/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.1.0"

ewoksid31-0.1.0/src/ewoksid31/tasks/flatfield.py

@@ -0,0 +1,64 @@
+import numpy
+from scipy.io import loadmat
+from ewokscore import Task
+
+
+class FlatFieldFromEnergy(
+    Task,
+    input_names=["newflat", "oldflat", "energy"],
+    output_names=["flatfield"],
+):
+    """Interpolate an energy-stack of flat-field images.
+
+    The resulting flat-field image can be used as follows
+    to correct diffraction patterns for flat field:
+
+    .. code::
+
+        Icor = I / flatfield
+    """
+
+    def run(self):
+        energy = self.inputs.energy
+        new_flat = _interpolated_flatfield(self.inputs.newflat, "E", "F", energy)
+        old_flat = _interpolated_flatfield(self.inputs.oldflat, "Eold", "Fold", energy)
+        flatfield = old_flat / new_flat
+        flatfield[~numpy.isfinite(flatfield)] = 1
+        self.outputs.flatfield = flatfield
+
+
+def _interpolated_flatfield(
+    matlab_filename: str, energy_key: str, flatfield_key: str, energy: float
+) -> numpy.ndarray:
+    """
+    :param matlab_filename: matlab file from ID31 that contains an energy-stack of images
+    :param energy_key:
+    :param flatfield_key:
+    :param energy:
+    :return: interpolated image (nrow, ncol)
+    """
+    m = loadmat(matlab_filename)
+    flatfields = m[flatfield_key]
+    energies = numpy.squeeze(m[energy_key]).astype(float)
+    return _interpolate_flatfields(energies, flatfields, energy)
+
+
+def _interpolate_flatfields(
+    energies: numpy.ndarray, flatfields: numpy.ndarray, energy: float
+) -> numpy.ndarray:
+    """
+    :param energies: array of energies (nenergies,)
+    :param flatfields: stack of images (nrow, ncol, nenergies)
+    :param energy:
+    :return: interpolated image (nrow, ncol)
+    """
+    j = numpy.argsort(abs(energies - energy))[0:2]
+    j.sort()
+    j_before, j_after = j
+    e_before = energies[j_before]
+    e_after = energies[j_after]
+    w_before = (e_after - energy) / (e_after - e_before)
+    w_after = (energy - e_before) / (e_after - e_before)
+    f_before = flatfields[..., j_before]
+    f_after = flatfields[..., j_after]
+    return w_before * f_before + w_after * f_after

ewoksid31-0.1.0/src/ewoksid31/tests/resources/__init__.py

@@ -0,0 +1,7 @@
+import os
+
+ROOT_DIR = os.path.abspath(os.path.dirname(__file__))
+
+
+def resource_filename(*args) -> str:
+    return os.path.join(ROOT_DIR, *args)

ewoksid31-0.1.0/src/ewoksid31/tests/test_flatfield.py

@@ -0,0 +1,16 @@
+import numpy
+from .resources import resource_filename
+from ..tasks.flatfield import FlatFieldFromEnergy
+
+
+def test_flatfield():
+    inputs = {
+        "newflat": resource_filename("flats.mat"),
+        "oldflat": resource_filename("flats_old.mat"),
+        "energy": 90.0,
+    }
+    task = FlatFieldFromEnergy(inputs=inputs)
+    task.execute()
+    # Flat-field correction:
+    #  Icor = I * 0.8115191925457376 = I / flatfield
+    numpy.testing.assert_allclose(1 / task.outputs.flatfield[0, 0], 0.8115191925457376)

ewoksid31-0.1.0/src/ewoksid31.egg-info/PKG-INFO

@@ -0,0 +1,29 @@
+Metadata-Version: 2.1
+Name: ewoksid31
+Version: 0.1.0
+Summary: Data processing workflows for ID31
+Home-page: https://gitlab.esrf.fr/workflow/ewoksid31/
+Author: ESRF
+Author-email: wout.de_nolf@esrf.fr
+License: MIT
+Project-URL: Source, https://gitlab.esrf.fr/workflow/ewoksid31/
+Project-URL: Documentation, https://ewoksid31.readthedocs.io/
+Project-URL: Tracker, https://gitlab.esrf.fr/workflow/ewoksid31/issues/
+Keywords: ewoks
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+Provides-Extra: test
+Provides-Extra: dev
+Provides-Extra: doc
+License-File: LICENSE.md
+
+# ewoksid31
+
+Data processing workflows for ID31
+
+## Documentation
+
+https://ewoksid31.readthedocs.io/

ewoksid31-0.1.0/src/ewoksid31.egg-info/SOURCES.txt

@@ -0,0 +1,19 @@
+LICENSE.md
+README.md
+pyproject.toml
+setup.cfg
+setup.py
+src/ewoksid31/__init__.py
+src/ewoksid31.egg-info/PKG-INFO
+src/ewoksid31.egg-info/SOURCES.txt
+src/ewoksid31.egg-info/dependency_links.txt
+src/ewoksid31.egg-info/entry_points.txt
+src/ewoksid31.egg-info/requires.txt
+src/ewoksid31.egg-info/top_level.txt
+src/ewoksid31/tasks/__init__.py
+src/ewoksid31/tasks/flatfield.py
+src/ewoksid31/tests/__init__.py
+src/ewoksid31/tests/test_flatfield.py
+src/ewoksid31/tests/resources/__init__.py
+src/ewoksid31/tests/resources/flats.mat
+src/ewoksid31/tests/resources/flats_old.mat

ewoksid31-0.1.0/src/ewoksid31.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

ewoksid31-0.1.0/src/ewoksid31.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[ewoks.tasks.class]
+ewoksid31.tasks.* = ewoksid31

ewoksid31-0.1.0/src/ewoksid31.egg-info/requires.txt

@@ -0,0 +1,16 @@
+ewokscore
+scipy
+numpy
+
+[dev]
+pytest>=7
+black>=22
+flake8>=4
+
+[doc]
+pytest>=7
+sphinx>=4.5
+sphinx-autodoc-typehints>=1.16
+
+[test]
+pytest>=7

ewoksid31-0.1.0/src/ewoksid31.egg-info/top_level.txt

@@ -0,0 +1 @@
+ewoksid31