Merge remote-tracking branch 'upstream/main' into 2024.01

doc/source/changelog.rst

@@ -1,5 +1,5 @@
 :Author: Jérôme Kieffer
-:Date: 15/01/2024
+:Date: 10/01/2024
 :Keywords: changelog
 
 Change-log of versions

doc/source/man/pyFAI-benchmark.rst

@@ -44,6 +44,9 @@ Usage
 **-d**, **--debug**
    switch to verbose/debug mode
 
+**--no-proc**
+   do not benchmark using the central processor
+
 **-c**, **--cpu**
    perform benchmark using OpenCL on the CPU
 
@@ -58,8 +61,7 @@ Usage
    limited memory)
 
 **-n** NUMBER, **--number** NUMBER
-   Runtime for each test, in seconds, by
+   Perform the test for this amount of time, by default 10s/measurment
-   default 10
 
 **-2d**, **--2dimention**
    Benchmark also algorithm for 2D-regrouping
@@ -71,7 +73,25 @@ Usage
    Perfrom memory profiling (Linux only)
 
 **-r** REPEAT, **--repeat** REPEAT
-   Repeat each benchmark x times to take the best, by default only run once
+   Repeat each measurement x times to take the best
+
+**-ps** PIXELSPLIT [PIXELSPLIT ...], **--pixelsplit** PIXELSPLIT [PIXELSPLIT ...]
+   Benchmark using specific pixel splitting protocols: no, bbox, pseudo,
+   full, all
+
+**-algo** ALGORITHM [ALGORITHM ...], **--algorithm** ALGORITHM [ALGORITHM ...]
+   Benchmark using specific algorithms: histogram, CSR, CSC, all
+
+**-i** IMPLEMENTATION [IMPLEMENTATION ...], **--implementation** IMPLEMENTATION [IMPLEMENTATION ...]
+   Benchmark using specific algorithm implementations: python, cython,
+   opencl, all
+
+**-f** FUNCTION, **--function** FUNCTION
+   Benchmark legacy (legacy), engine function (ng), or both (all)
+
+**--all**
+   Benchmark using all available methods and devices
+
 
 Results
 -------

pyproject.toml

@@ -99,4 +99,4 @@ pyFAI-integrate = 'pyFAI.app.integrate:main'
 
 [tool.cibuildwheel]
 # Skip 32-bit builds and PyPy
-skip = ["*-win32", "*-manylinux_i686", "pp*"]
+skip = ["*-win32", "*-manylinux_i686", "pp*", "*musllinux*"]

src/pyFAI/azimuthalIntegrator.py

@@ -30,7 +30,7 @@ __author__ = "Jérôme Kieffer"
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "21/11/2023"
+__date__ = "11/01/2024"
 __status__ = "stable"
 __docformat__ = 'restructuredtext'
 
@@ -47,7 +47,7 @@ from . import units
 from .utils import EPS32, deg2rad, crc32
 from .utils.decorators import deprecated, deprecated_warning
 from .containers import Integrate1dResult, Integrate2dResult, SeparateResult, ErrorModel
-from .io import DefaultAiWriter
+from .io import DefaultAiWriter, save_integrate_result
 from .io.ponifile import PoniFile
 error = None
 from .method_registry import IntegrationMethod
@@ -1099,8 +1099,7 @@ class AzimuthalIntegrator(Geometry):
         result._set_metadata(metadata)
 
         if filename is not None:
-            writer = DefaultAiWriter(filename, self)
+            save_integrate_result(filename, result)
-            writer.write(result)
 
         return result
 
@@ -1600,9 +1599,7 @@ class AzimuthalIntegrator(Geometry):
         result._set_has_solidangle_correction(correctSolidAngle)
 
         if filename is not None:
-            writer = DefaultAiWriter(filename, self)
+            save_integrate_result(filename, result)
-            writer.write(result)
-
         return result
 
     _integrate1d_ng = integrate1d_ng
@@ -2102,8 +2099,7 @@ class AzimuthalIntegrator(Geometry):
         result._set_metadata(metadata)
 
         if filename is not None:
-            writer = DefaultAiWriter(filename, self)
+            save_integrate_result(filename, result)
-            writer.write(result)
 
         return result
 
@@ -2617,8 +2613,7 @@ class AzimuthalIntegrator(Geometry):
             result._set_std(sem)
 
         if filename is not None:
-            writer = DefaultAiWriter(filename, self)
+            save_integrate_result(filename, result)
-            writer.write(result)
 
         return result
 

src/pyFAI/io/__init__.py

@@ -42,7 +42,7 @@ __author__ = "Jerome Kieffer"
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "25/09/2023"
+__date__ = "11/01/2024"
 __status__ = "production"
 __docformat__ = 'restructuredtext'
 
@@ -999,6 +999,9 @@ def save_integrate_result(filename, result, title="title", sample="sample", inst
     """
     if filename.endswith(".nxs"):
         raise RuntimeError("Implement Nexus writer")
+    elif filename.endswith(".xrdml"):
+        from .xrdml import save_xrdml
+        save_xrdml(filename, result)
     else:
-            writer = DefaultAiWriter(filename, result.poni)
+        writer = DefaultAiWriter(filename, result.poni)
-            writer.write(result)
+        writer.write(result)

src/pyFAI/io/meson.build

@@ -6,7 +6,8 @@ py.install_sources(
     'nexus.py',
     'ponifile.py',
     'sparse_frame.py',
-    'spots.py'],
+    'spots.py',
+    'xrdml.py'],
   pure: false,   # Will be installed next to binaries
   subdir: 'pyFAI/io'  # Folder relative to site-packages to install to
 )

src/pyFAI/io/xrdml.py

@@ -0,0 +1,121 @@
+# coding: utf-8
+#
+#    Project: Azimuthal integration
+#             https://github.com/silx-kit/pyFAI
+#
+#    Copyright (C) 2024-2024 European Synchrotron Radiation Facility, Grenoble, France
+#
+#    Principal author:       Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
+#
+# 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.
+
+"""Module for exporting XRDML powder diffraction files
+Inspiration from
+"""
+
+__author__ = "Jérôme Kieffer"
+__license__ = "MIT"
+__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
+__date__ = "11/01/2024"
+__docformat__ = 'restructuredtext'
+
+import os
+from xml.etree import  ElementTree as et
+from .nexus import get_isotime
+from .. import version as pyFAI_version
+
+def save_xrdml(filename, result):
+    """
+
+    https://www.researchgate.net/profile/Mohamed-Ali-392/post/XRD_Refinement_for_TiO2_Anatase_using_MAUD/attachment/60fa1d85647f3906fc8af2f3/AS%3A1048546157539329%401627004293526/download/sample.xrdml
+    """
+    now = get_isotime()
+    dirname = os.path.dirname(os.path.abspath(filename))
+    if not os.path.isdir(dirname):
+        os.makedirs(dirname, exist_ok=True)
+
+    xrdml = et.Element("xrdMeasurements", {"xmlns":"http://www.xrdml.com/XRDMeasurement/1.0",
+                                           "xmlns:xsi":"http://www.w3.org/2001/XMLSchema-instance",
+                                           "xsi:schemaLocation": "http://www.xrdml.com/XRDMeasurement/1.3 http://www.xrdml.com/XRDMeasurement/1.3/XRDMeasurement.xsd",
+                                           "status": "Completed"})
+    sample = et.Element("sample", type="To be analyzed")
+    xid = et.Element("id")
+    xid.text = "000000-0000"
+    sample.append(xid)
+    name = et.Element("name")
+    name.text = "sample"
+    sample.append(name)
+    xrdml.append(sample)
+    measurement = et.Element("xrdMeasurement", {"measurementType":"Scan", "status":"Completed"})
+    wavelength = result.poni.wavelength
+    if wavelength:
+        txtwavelength = str(wavelength*1e10)
+        usedWavelength = et.Element("usedWavelength", intended="K-Alpha")
+        k_alpha1 = et.Element("kAlpha1", unit="Angstrom")
+        k_alpha1.text = txtwavelength
+        usedWavelength.append(k_alpha1)
+        k_alpha2 = et.Element("kAlpha2", unit="Angstrom")
+        k_alpha2.text = txtwavelength
+        usedWavelength.append(k_alpha2)
+        k_beta = et.Element("kBeta", unit="Angstrom")
+        k_beta.text = txtwavelength
+        usedWavelength.append(k_beta)
+        ratio = et.Element("ratioKAlpha2KAlpha1")
+        ratio.text = "0"
+        usedWavelength.append(ratio)
+        measurement.append(usedWavelength)
+    scan = et.Element("scan", {"appendNumber":"0",
+                               "mode":"Pre-set time",
+                               "measurementType": "Area measurement",
+                               "scanAxis":"Gonio",
+                               "status":"Completed"})
+    header = et.Element("header")
+    for stamp in ("startTimeStamp", "endTimeStamp"):
+        estamp = et.Element(stamp)
+        estamp.text = now
+        header.append(estamp)
+    author = et.Element("author")
+    name = et.Element("name")
+    name.text = "pyFAI"
+    author.append(name)
+    header.append(author)
+    source = et.Element("source")
+    sw = et.Element("applicationSoftware", version=pyFAI_version)
+    sw.text='pyFAI'
+    source.append(sw)
+    header.append(source)
+    scan.append(header)
+    datapoints = et.Element("dataPoints")
+    positions = et.Element("positions", axis=result.unit.short_name, unit=result.unit.unit_symbol)
+    for pos, idx in {"startPosition": 0, "endPosition":-1}.items():
+        position = et.Element(pos)
+        position.text = str(result.radial[idx])
+        positions.append(position)
+    datapoints.append(positions)
+    ct = et.Element("commonCountingTime", unit="seconds")
+    ct.text = "1.00"
+    datapoints.append(ct)
+    intensities = et.Element("intensities", unit="counts")
+    intensities.text = " ".join(str(i) for i in result.intensity)
+    datapoints.append(intensities)
+    scan.append(datapoints)
+    measurement.append(scan)
+    xrdml.append(measurement)
+    with open(filename, "wb") as w:
+        w.write(et.tostring(xrdml))

src/pyFAI/test/test_io.py

@@ -32,7 +32,7 @@ __author__ = "Jérôme Kieffer"
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "09/01/2024"
+__date__ = "10/01/2024"
 
 import unittest
 import os
@@ -296,6 +296,38 @@ class TestSpotWriter(unittest.TestCase):
         self.assertGreater(size.st_size, sum(i.size for i in self.spots), "file is large enough")
 
 
+class TestXrdmlWriter(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls)->None:
+        super(TestXrdmlWriter, cls).setUpClass()
+        cls.img = fabio.open(UtilsTest.getimage("Pilatus1M.edf"))
+        cls.ai = pyFAI.load(UtilsTest.getimage("Pilatus1M.poni"))
+        cls.result = cls.ai.integrate1d(cls.img.data, 200, method=("no", "histogram", "cython"), unit="2th_deg")
+    @classmethod
+    def tearDownClass(cls)->None:
+        super(TestXrdmlWriter, cls).tearDownClass()
+        cls.ai = cls.img = cls.result=None
+
+    def test_xrdml(self):
+        from ..io.xrdml import save_xrdml
+        fd, tmpfile = UtilsTest.tempfile(".xrdml")
+        os.close(fd)
+        save_xrdml(tmpfile, self.result)
+        self.assertGreater(os.path.getsize(tmpfile), 3000)
+
+    def test_integration(self):
+        fd, tmpfile = UtilsTest.tempfile(".xrdml")
+        os.close(fd)
+        self.ai.integrate1d(self.img.data, 200, method=("no", "histogram", "cython"), unit="2th_deg",
+                            filename=tmpfile)
+        self.assertGreater(os.path.getsize(tmpfile), 3000)
+        from xml.etree import ElementTree as et
+        with open(tmpfile, "rb") as f:
+            xml = et.fromstring(f.read())
+
+
+
 def suite():
     testsuite = unittest.TestSuite()
     loader = unittest.defaultTestLoader.loadTestsFromTestCase
@@ -304,6 +336,7 @@ def suite():
     testsuite.addTest(loader(TestHDF5Writer))
     testsuite.addTest(loader(TestFabIOWriter))
     testsuite.addTest(loader(TestSpotWriter))
+    testsuite.addTest(loader(TestXrdmlWriter))
     testsuite.addTest(loader(TestPoniFile))
     return testsuite