Script 'mail_helper' called by obssrc
Hello community,
here is the log from the commit of package python-fabio for openSUSE:Factory
checked in at 2024-07-11 20:33:07
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-fabio (Old)
and /work/SRC/openSUSE:Factory/.python-fabio.new.17339 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-fabio"
Thu Jul 11 20:33:07 2024 rev:7 rq:1186778 version:2024.4
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-fabio/python-fabio.changes
2024-03-06 23:04:42.781707693 +0100
+++ /work/SRC/openSUSE:Factory/.python-fabio.new.17339/python-fabio.changes
2024-07-11 20:33:47.542208236 +0200
@@ -1,0 +2,9 @@
+Thu Jul 4 07:20:42 UTC 2024 - Steve Kowalik <steven.kowa...@suse.com>
+
+- Update to 2024.4:
+ * Support for new style GE-files (contribution from Patrick Avery)
+ * Support sparse frames without background (for XPCS)
+ * Support for Numpy v2.0
+ * Support Python 3.7-3.12
+
+-------------------------------------------------------------------
Old:
----
fabio-2023.10.tar.gz
New:
----
fabio-2024.4.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-fabio.spec ++++++
--- /var/tmp/diff_new_pack.9k83R9/_old 2024-07-11 20:33:48.730251190 +0200
+++ /var/tmp/diff_new_pack.9k83R9/_new 2024-07-11 20:33:48.738251480 +0200
@@ -16,9 +16,9 @@
#
-%define pyversion 2023.10.0
+%define pyversion 2024.4.0
Name: python-fabio
-Version: 2023.10
+Version: 2024.4
Release: 0
Summary: Image IO for images produced by 2D X-ray detectors
License: BSD-3-Clause AND GPL-2.0-or-later AND LGPL-3.0-or-later AND MIT
@@ -59,13 +59,11 @@
find src -name '*.py' -and ! -path src/fabio/_version.py -exec sed -i
'1{/^#!/d}' '{}' ';' -exec chmod -x '{}' ';'
%build
-%{python_expand # _version.py is called during meson build
-sed -i '1{s|^#!.*$|#!%{__$python}|}' src/fabio/_version.py
-%{$python_pyproject_wheel}
-}
+%pyproject_wheel
%install
%pyproject_install
+%python_expand sed -i '1{s|^#!.*$|#!%{__$python}|}'
%{buildroot}%{$python_sitearch}/fabio/version.py
%python_clone -a %{buildroot}%{_bindir}/densify_Bragg
%python_clone -a %{buildroot}%{_bindir}/fabio-convert
%python_clone -a %{buildroot}%{_bindir}/fabio_viewer
++++++ fabio-2023.10.tar.gz -> fabio-2024.4.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/.github/workflows/python-package.yml
new/fabio-2024.4/.github/workflows/python-package.yml
--- old/fabio-2023.10/.github/workflows/python-package.yml 2023-10-26
10:30:27.000000000 +0200
+++ new/fabio-2024.4/.github/workflows/python-package.yml 2024-04-11
16:35:31.000000000 +0200
@@ -15,7 +15,7 @@
runs-on: ubuntu-latest
strategy:
matrix:
- python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+ python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
steps:
- uses: actions/checkout@v2
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/.github/workflows/release.yml
new/fabio-2024.4/.github/workflows/release.yml
--- old/fabio-2023.10/.github/workflows/release.yml 1970-01-01
01:00:00.000000000 +0100
+++ new/fabio-2024.4/.github/workflows/release.yml 2024-04-11
16:35:31.000000000 +0200
@@ -0,0 +1,147 @@
+name: Build and deploy
+
+on:
+ workflow_dispatch:
+ release:
+ types:
+ - published
+
+jobs:
+ build_sdist:
+ name: Build source distribution
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v4
+ - uses: actions/setup-python@v5
+ with:
+ python-version: "3.12"
+ cache: "pip"
+ - name: Install dependencies
+ run: |
+ python -m pip install --upgrade pip
+ pip install build twine
+ - name: Build sdist
+ run: python -m build --sdist
+ - name: Check the package
+ run: python -m twine check dist/*
+ - uses: actions/upload-artifact@v4
+ with:
+ name: cibw-sdist
+ path: dist/*.tar.gz
+
+ test_sdist:
+ needs: [build_sdist]
+ name: Test source distribution
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v4
+ - uses: actions/setup-python@v5
+ with:
+ python-version: "3.12"
+ cache: "pip"
+ - uses: actions/download-artifact@v4
+ with:
+ name: cibw-sdist
+ path: dist
+ - name: Install from sdist
+ run: pip install "$(ls dist/fabio-*.tar.gz)"
+ - name: Run tests
+ run: python -c "import fabio.test, sys;
sys.exit(fabio.test.run_tests())"
+
+ build_doc:
+ name: Build documentation
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v4
+ - uses: actions/setup-python@v5
+ with:
+ python-version: "3.12"
+ cache: "pip"
+ - name: Install pandoc&graphviz
+ run: sudo apt-get install pandoc graphviz
+ - name: Install fabio
+ run: pip install .
+ - name: Install documentation dependencies
+ run: pip install -r requirements.txt
+ - name: Build doc
+ env:
+ READTHEDOCS: "True" # To skip checking that fabio is installed
locally
+ run: |
+ export FABIO_VERSION="$(python -c 'import fabio;
print(fabio.strictversion)')"
+ sphinx-build doc/source/ "fabio-${FABIO_VERSION}_documentation/"
+ zip -r "fabio-${FABIO_VERSION}_documentation.zip"
"fabio-${FABIO_VERSION}_documentation/"
+ - uses: actions/upload-artifact@v4
+ with:
+ name: documentation
+ path: fabio-*_documentation.zip
+
+ build_wheels:
+ name: Build wheels on ${{ matrix.os }}-${{ matrix.cibw_archs }}
+ runs-on: ${{ matrix.os }}
+ strategy:
+ # Ensure that a wheel builder finishes even if another fails
+ fail-fast: false
+ matrix:
+ include:
+ - os: ubuntu-20.04
+ cibw_archs: "auto64"
+ - os: ubuntu-20.04
+ cibw_archs: "aarch64"
+ - os: ubuntu-20.04
+ cibw_archs: "ppc64le"
+ - os: windows-2019
+ cibw_archs: "auto64"
+ - os: macos-11
+ cibw_archs: "x86_64"
+ macos_target: "10.9"
+ - os: macos-14
+ cibw_archs: "arm64"
+ macos_target: "11.0"
+
+ steps:
+ - uses: actions/checkout@v4
+ - uses: docker/setup-qemu-action@v3
+ if: runner.os == 'Linux'
+ with:
+ platforms: all
+ - uses: pypa/cibuildwheel@v2.16.5
+ env:
+ # Use silx wheelhouse: needed for ppc64le
+ CIBW_ENVIRONMENT_LINUX:
"PIP_FIND_LINKS=https://www.silx.org/pub/wheelhouse/
PIP_TRUSTED_HOST=www.silx.org"
+
+ CIBW_BUILD: cp37-* cp38-* cp39-* cp310-* cp311-* cp312-*
+ # Do not build for pypy and muslinux
+ CIBW_SKIP: pp* *-musllinux_*
+ CIBW_ARCHS: ${{ matrix.cibw_archs }}
+
+ MACOSX_DEPLOYMENT_TARGET: "${{ matrix.macos_target }}"
+
+ # Install test dependencies
+ CIBW_TEST_COMMAND: python -c "import fabio.test, sys;
sys.exit(fabio.test.run_tests())"
+ # Skip tests for emulated architectures
+ # and Python3.8 on macos/arm64
(https://github.com/pypa/cibuildwheel/pull/1169)
+ CIBW_TEST_SKIP: "*-*linux_{aarch64,ppc64le,s390x} cp38-macosx_arm64"
+
+ - uses: actions/upload-artifact@v4
+ with:
+ name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+ path: ./wheelhouse/*.whl
+
+ pypi-publish:
+ needs: [build_doc, build_sdist, build_wheels, test_sdist]
+ name: Upload release to PyPI
+ runs-on: ubuntu-latest
+ environment:
+ name: pypi
+ permissions:
+ id-token: write
+ if: github.event_name == 'release' && github.event.action == 'published'
+ # or, alternatively, upload to PyPI on every tag starting with 'v' (remove
on: release above to use this)
+ # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+ steps:
+ - uses: actions/download-artifact@v4
+ with:
+ pattern: cibw-*
+ path: dist
+ merge-multiple: true
+ - uses: pypa/gh-action-pypi-publish@release/v1
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/bootstrap.py
new/fabio-2024.4/bootstrap.py
--- old/fabio-2023.10/bootstrap.py 2023-10-26 10:30:27.000000000 +0200
+++ new/fabio-2024.4/bootstrap.py 2024-04-11 16:35:31.000000000 +0200
@@ -10,7 +10,7 @@
__authors__ = ["Frédéric-Emmanuel Picca", "Jérôme Kieffer"]
__contact__ = "jerome.kief...@esrf.eu"
__license__ = "MIT"
-__date__ = "03/03/2023"
+__date__ = "11/04/2024"
import sys
import os
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/build-deb.sh
new/fabio-2024.4/build-deb.sh
--- old/fabio-2023.10/build-deb.sh 2023-10-26 10:30:27.000000000 +0200
+++ new/fabio-2024.4/build-deb.sh 2024-04-11 16:35:31.000000000 +0200
@@ -29,9 +29,9 @@
project=fabio
source_project=fabio
-version=$(PYTHONPATH=src/fabio python3 -c"import _version;
print(_version.version)")
-strictversion=$(PYTHONPATH=src/fabio python3 -c"import _version;
print(_version.strictversion)")
-debianversion=$(PYTHONPATH=src/fabio python3 -c"import _version;
print(_version.debianversion)")
+version=$(PYTHONPATH=src/fabio python3 -c"import version;
print(version.version)")
+strictversion=$(PYTHONPATH=src/fabio python3 -c"import version;
print(version.strictversion)")
+debianversion=$(PYTHONPATH=src/fabio python3 -c"import version;
print(version.debianversion)")
deb_name=$(echo "$source_project" | tr '[:upper:]' '[:lower:]')
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/doc/source/Changelog.rst
new/fabio-2024.4/doc/source/Changelog.rst
--- old/fabio-2023.10/doc/source/Changelog.rst 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/doc/source/Changelog.rst 2024-04-11 16:35:31.000000000
+0200
@@ -1,6 +1,15 @@
Changelog
=========
+FabIO-2024.4.0:
+................
+- Support for new style GE-files (contribution from Patrick Avery)
+- Support sparse frames without background
+- Fix documentation (Thanks Wout)
+- Automatize the release (Thanks Thomas)
+- Support for Numpy v2.0
+- Support Python 3.7-3.12
+
FabIO-2023.10.0:
................
- New tutorial on the ccreation of multiframe Tiff
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/doc/source/conf.py
new/fabio-2024.4/doc/source/conf.py
--- old/fabio-2023.10/doc/source/conf.py 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/doc/source/conf.py 2024-04-11 16:35:31.000000000 +0200
@@ -13,10 +13,7 @@
import sys
import os
-import glob
-import subprocess
-on_rtd = os.environ.get('READTHEDOCS') == 'True'
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -26,7 +23,7 @@
import fabio
project_dir = os.path.abspath(os.path.join(__file__, "..", "..", ".."))
build_dir = os.path.abspath(fabio.__file__)
- if on_rtd:
+ if os.environ.get('READTHEDOCS') == 'True':
print("On Read The Docs")
print("build_dir", build_dir)
print("project_dir", project_dir)
@@ -55,19 +52,11 @@
extensions = ['sphinx.ext.autodoc',
'sphinx.ext.mathjax',
+ 'sphinx_rtd_theme',
'sphinxcontrib.programoutput',
- "nbsphinx"
+ 'nbsphinx'
]
-# Set the theme to sphinx_rtd_theme when *not* building on Read The Docs.
-# The theme is set to default otherwise as Read The Docs uses its own theme
anyway.
-if not on_rtd:
- try:
- import sphinx_rtd_theme
- extensions.append('sphinx_rtd_theme')
- except:
- print("sphinx_rtd_theme is not available")
-
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
@@ -81,7 +70,7 @@
master_doc = 'index'
# General information about the project.
-from fabio._version import strictversion, version, __date__ as fabio_date
+from fabio.version import strictversion, __date__ as fabio_date
year = fabio_date.split("/")[-1]
copyright = u'2006-%s, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret,
Brian Pauw and Jerome Kieffer' % (year)
@@ -136,7 +125,7 @@
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
-html_theme = 'default' if on_rtd else 'sphinx_rtd_theme'
+html_theme = 'sphinx_rtd_theme'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/doc/source/coverage.rst
new/fabio-2024.4/doc/source/coverage.rst
--- old/fabio-2023.10/doc/source/coverage.rst 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/doc/source/coverage.rst 2024-04-11 16:35:31.000000000
+0200
@@ -1,18 +1,17 @@
Test coverage report for fabio
==============================
-Measured on *fabio* version 2023.10.0, 25/10/2023
+Measured on *fabio* version 2024.4.0, 11/04/2024
.. csv-table:: Test suite coverage
:header: "Name", "Stmts", "Exec", "Cover"
:widths: 35, 8, 8, 8
- "GEimage.py", "106", "80", "75.5 %"
+ "GEimage.py", "116", "90", "77.6 %"
"HiPiCimage.py", "61", "54", "88.5 %"
"OXDimage.py", "352", "325", "92.3 %"
- "TiffIO.py", "781", "648", "83.0 %"
- "__init__.py", "35", "29", "82.9 %"
- "_version.py", "40", "39", "97.5 %"
+ "TiffIO.py", "781", "643", "82.3 %"
+ "__init__.py", "34", "28", "82.4 %"
"adscimage.py", "4", "4", "100.0 %"
"binaryimage.py", "60", "44", "73.3 %"
"bruker100image.py", "286", "243", "85.0 %"
@@ -25,14 +24,14 @@
"eigerimage.py", "194", "139", "71.6 %"
"esperantoimage.py", "158", "137", "86.7 %"
"fabioformats.py", "90", "65", "72.2 %"
- "fabioimage.py", "467", "386", "82.7 %"
- "fabioutils.py", "392", "316", "80.6 %"
+ "fabioimage.py", "468", "387", "82.7 %"
+ "fabioutils.py", "392", "312", "79.6 %"
"file_series.py", "370", "280", "75.7 %"
"fit2dimage.py", "91", "76", "83.5 %"
"fit2dmaskimage.py", "79", "75", "94.9 %"
"fit2dspreadsheetimage.py", "47", "40", "85.1 %"
"hdf5image.py", "98", "67", "68.4 %"
- "jpeg2kimage.py", "82", "56", "68.3 %"
+ "jpeg2kimage.py", "82", "74", "90.2 %"
"jpegimage.py", "47", "45", "95.7 %"
"kcdimage.py", "107", "76", "71.0 %"
"limaimage.py", "180", "151", "83.9 %"
@@ -42,14 +41,15 @@
"mrcimage.py", "85", "65", "76.5 %"
"nexus.py", "233", "130", "55.8 %"
"numpyimage.py", "77", "53", "68.8 %"
- "openimage.py", "122", "105", "86.1 %"
+ "openimage.py", "130", "112", "86.2 %"
"pilatusimage.py", "43", "38", "88.4 %"
"pixiimage.py", "107", "91", "85.0 %"
"pnmimage.py", "137", "86", "62.8 %"
"raxisimage.py", "103", "91", "88.3 %"
- "sparseimage.py", "135", "93", "68.9 %"
+ "sparseimage.py", "146", "97", "66.4 %"
"speimage.py", "162", "157", "96.9 %"
"tifimage.py", "128", "121", "94.5 %"
+ "version.py", "40", "35", "87.5 %"
"xcaliburimage.py", "586", "462", "78.8 %"
"xsdimage.py", "94", "70", "74.5 %"
"app/__init__.py", "0", "0", "0.0 %"
@@ -58,10 +58,12 @@
"compression/agi_bitfield.py", "171", "148", "86.5 %"
"compression/compression.py", "245", "188", "76.7 %"
"ext/__init__.py", "0", "0", "0.0 %"
- "utils/ExternalResources.py", "180", "133", "73.9 %"
+ "test/__init__.py", "22", "15", "68.2 %"
+ "test/codecs/__init__.py", "87", "81", "93.1 %"
+ "utils/ExternalResources.py", "181", "134", "74.0 %"
"utils/__init__.py", "0", "0", "0.0 %"
- "utils/cli.py", "60", "52", "86.7 %"
+ "utils/cli.py", "60", "48", "80.0 %"
"utils/deprecation.py", "67", "63", "94.0 %"
"utils/pilutils.py", "49", "39", "79.6 %"
- "fabio total", "9609", "7542", "78.5 %"
+ "fabio total", "9748", "7661", "78.6 %"
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/meson.build
new/fabio-2024.4/meson.build
--- old/fabio-2023.10/meson.build 2023-10-26 10:30:27.000000000 +0200
+++ new/fabio-2024.4/meson.build 2024-04-11 16:35:31.000000000 +0200
@@ -2,7 +2,7 @@
'c', 'cython',
license: 'MIT',
meson_version: '>= 0.60',
- version: run_command('src/fabio/_version.py',
+ version: run_command(['version.py', '--wheel'],
check:true).stdout().strip(),
)
@@ -13,6 +13,7 @@
endif
cc = meson.get_compiler('c')
+cy = meson.get_compiler('cython')
m_dep = cc.find_library('m', required : false)
if m_dep.found()
add_project_link_arguments('-lm', language : 'c')
@@ -23,4 +24,11 @@
py = py_mod.find_installation()
py_dep = py.dependency()
+py.install_sources([
+ 'version.py',
+],
+ pure: false, # Will be installed next to binaries
+ subdir: 'fabio' # Folder relative to site-packages to install to
+)
+
subdir('src/fabio')
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/package/debian12/control
new/fabio-2024.4/package/debian12/control
--- old/fabio-2023.10/package/debian12/control 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/package/debian12/control 2024-04-11 16:35:31.000000000
+0200
@@ -7,6 +7,9 @@
Build-Depends: cython3,
debhelper,
dh-python,
+ devscripts,
+ python3-tomli,
+ python3-mesonpy,
python3-all-dev,
python3-pil,
python3-lxml,
@@ -18,10 +21,7 @@
python3-sphinxcontrib.programoutput,
python3-sphinx-rtd-theme,
python3-h5py,
- python3-tomli,
- python3-mesonpy,
help2man,
- devscripts,
python3-pyqt5,
python3-matplotlib,
bitshuffle,
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/package/debian12/rules
new/fabio-2024.4/package/debian12/rules
--- old/fabio-2023.10/package/debian12/rules 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/package/debian12/rules 2024-04-11 16:35:31.000000000
+0200
@@ -38,3 +38,7 @@
python3 build-doc.py
dh_installdocs "build/sphinx" -p fabio-doc
dh_installdocs
+
+override_dh_sphinxdoc:
+ dh_sphinxdoc -X searchtools.js
+
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/pyproject.toml
new/fabio-2024.4/pyproject.toml
--- old/fabio-2023.10/pyproject.toml 2023-10-26 10:30:27.000000000 +0200
+++ new/fabio-2024.4/pyproject.toml 2024-04-11 16:35:31.000000000 +0200
@@ -54,15 +54,13 @@
"meson; platform_system!='Windows'",
'ninja',
'wheel',
- 'numpy',
- 'Cython>=0.25',
- 'numpy',
+ 'Cython>=0.29',
'pyproject-metadata>=0.5.0',
'tomli>=1.0.0'
]
[project.urls]
-homepage = 'http://silx.org'
+homepage = 'http://www.silx.org'
documentation = 'http://www.silx.org/doc/fabio/latest/'
source = 'https://github.com/silx-kit/fabio'
download = 'https://github.com/silx-kit/fabio/releases'
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/requirements.txt
new/fabio-2024.4/requirements.txt
--- old/fabio-2023.10/requirements.txt 2023-10-26 10:30:27.000000000 +0200
+++ new/fabio-2024.4/requirements.txt 2024-04-11 16:35:31.000000000 +0200
@@ -11,3 +11,4 @@
sphinx
sphinxcontrib-programoutput
sphinx-rtd-theme
+nbsphinx
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/src/fabio/GEimage.py
new/fabio-2024.4/src/fabio/GEimage.py
--- old/fabio-2023.10/src/fabio/GEimage.py 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/src/fabio/GEimage.py 2024-04-11 16:35:31.000000000
+0200
@@ -41,8 +41,12 @@
import io
import numpy
import struct
+from .edfimage import EdfImage
from .fabioimage import FabioImage
from .fabioutils import next_filename, previous_filename
+from .openimage import MAGIC_NUMBERS
+
+EDF_MAGIC_NUMBERS = [(x, y) for x, y in MAGIC_NUMBERS if y == 'edf']
GE_HEADER_INFO = [
# Name, length in bytes, format for struct (None means string)
@@ -265,6 +269,20 @@
raise IOError("GE file size is incorrect")
nframes = file_size // bytes_per_frames
self.header['NumberOfFrames'] = nframes
+ elif any(self.header["ImageFormat"].startswith(x) for x, _ in
EDF_MAGIC_NUMBERS):
+ # At APS, they started saving some GE headers with an EDF format
in ~2022
+
+ # Use the same metadata as the blank header...
+ self.header.update(self.BLANKED_HEADER_METADATA)
+
+ # Read the EDF header
+ cur = infile.tell()
+ infile.seek(0)
+ header = EdfImage._read_header_block(infile, 1)
+ infile.seek(cur, io.SEEK_SET)
+
+ # Extract any needed info from the EDF header
+ self.header['NumberOfFrames'] = int(header[0]["Num_Images"])
def read(self, fname, frame=None):
"""Read header into self.header and the data into self.data."""
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/src/fabio/OXDimage.py
new/fabio-2024.4/src/fabio/OXDimage.py
--- old/fabio-2023.10/src/fabio/OXDimage.py 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/src/fabio/OXDimage.py 2024-04-11 16:35:31.000000000
+0200
@@ -482,7 +482,7 @@
dim2 = self._shape[0]
while pos_inp < stream_size and pos_out < array_size:
if pos_out % dim2 == 0:
- last = 0
+ last = numpy.int64(0)
else:
last = current
value = raw[pos_inp]
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/src/fabio/__init__.py
new/fabio-2024.4/src/fabio/__init__.py
--- old/fabio-2023.10/src/fabio/__init__.py 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/src/fabio/__init__.py 2024-04-11 16:35:31.000000000
+0200
@@ -28,7 +28,7 @@
__contact__ = "jerome.kief...@esrf.eu"
__license__ = "GPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "21/06/2023"
+__date__ = "15/03/2024"
__status__ = "stable"
import sys
@@ -39,8 +39,7 @@
logging.basicConfig()
import os
-from ._version import __date__ as date # noqa
-from ._version import version, version_info, hexversion, strictversion # noqa
+from .version import __date__ as date, version, version_info, hexversion,
strictversion # noqa
from . import fabioformats as _fabioformats
# provide a global fabio API
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/src/fabio/_version.py
new/fabio-2024.4/src/fabio/_version.py
--- old/fabio-2023.10/src/fabio/_version.py 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/src/fabio/_version.py 1970-01-01 01:00:00.000000000
+0100
@@ -1,124 +0,0 @@
-#!/usr/bin/env python3
-# coding: utf-8
-#
-# Project: X-ray image reader
-# https://github.com/silx-kit/fabio
-#
-# Copyright (C) 2015-20230 European Synchrotron Radiation Facility,
Grenoble, France
-#
-# Principal author: Jérôme Kieffer (jerome.kief...@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.
-
-"""Unique place where the version number is defined.
-
-Module for version handling:
-
-provides:
-* version = "1.2.3" or "1.2.3-beta4"
-* version_info = named tuple (1,2,3,"beta",4)
-* hexversion: 0x010203B4
-* strictversion = "1.2.3b4
-* debianversion = "1.2.3~beta4"
-* calc_hexversion: the function to transform a version_tuple into an integer
-
-This is called hexversion since it only really looks meaningful when viewed as
the
-result of passing it to the built-in hex() function.
-The version_info value may be used for a more human-friendly encoding of the
same information.
-
-The hexversion is a 32-bit number with the following layout:
-Bits (big endian order) Meaning
-1-8 PY_MAJOR_VERSION (the 2 in 2.1.0a3)
-9-16 PY_MINOR_VERSION (the 1 in 2.1.0a3)
-17-24 PY_MICRO_VERSION (the 0 in 2.1.0a3)
-25-28 PY_RELEASE_LEVEL (0xA for alpha, 0xB for beta, 0xC for release
candidate and 0xF for final)
-29-32 PY_RELEASE_SERIAL (the 3 in 2.1.0a3, zero for final releases)
-
-Thus 2.1.0a3 is hexversion 0x020100a3.
-
-"""
-
-__author__ = "Jérôme Kieffer"
-__contact__ = "jerome.kief...@esrf.eu"
-__license__ = "MIT"
-__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "07/08/2023"
-__status__ = "production"
-__docformat__ = 'restructuredtext'
-__all__ = ["date", "version_info", "strictversion", "hexversion",
"debianversion",
- "calc_hexversion"]
-
-RELEASE_LEVEL_VALUE = {"dev": 0,
- "alpha": 10,
- "beta": 11,
- "candidate": 12,
- "final": 15}
-
-PRERELEASE_NORMALIZED_NAME = {"dev": "a",
- "alpha": "a",
- "beta": "b",
- "candidate": "rc"}
-
-MAJOR = 2023
-MINOR = 10
-MICRO = 0
-RELEV = "final" # <16
-SERIAL = 0 # <16
-date = __date__
-
-from collections import namedtuple
-_version_info = namedtuple("version_info", ["major", "minor", "micro",
"releaselevel", "serial"])
-
-version_info = _version_info(MAJOR, MINOR, MICRO, RELEV, SERIAL)
-
-strictversion = version = debianversion = "%d.%d.%d" % version_info[:3]
-if version_info.releaselevel != "final":
- _prerelease = PRERELEASE_NORMALIZED_NAME[version_info[3]]
- version += "%s%s" % (_prerelease, version_info[-1])
- debianversion += "~adev%i" % version_info[-1] if RELEV == "dev" else
"~%s%i" % (_prerelease, version_info[-1])
- strictversion += _prerelease + str(version_info[-1])
-
-
-def calc_hexversion(major=0, minor=0, micro=0, releaselevel="dev", serial=0):
- """Calculate the hexadecimal version number from the tuple version_info:
-
- :param major: integer
- :param minor: integer
- :param micro: integer
- :param relev: integer or string
- :param serial: integer
- :return: integer always increasing with revision numbers
- """
- try:
- releaselevel = int(releaselevel)
- except ValueError:
- releaselevel = RELEASE_LEVEL_VALUE.get(releaselevel, 0)
-
- hex_version = int(serial)
- hex_version |= releaselevel * 1 << 4
- hex_version |= int(micro) * 1 << 8
- hex_version |= int(minor) * 1 << 16
- hex_version |= int(major) * 1 << 24
- return hex_version
-
-
-hexversion = calc_hexversion(*version_info)
-
-if __name__ == "__main__":
- print(version)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/src/fabio/app/eiger2crysalis.py
new/fabio-2024.4/src/fabio/app/eiger2crysalis.py
--- old/fabio-2023.10/src/fabio/app/eiger2crysalis.py 2023-10-26
10:30:27.000000000 +0200
+++ new/fabio-2024.4/src/fabio/app/eiger2crysalis.py 2024-04-11
16:35:31.000000000 +0200
@@ -38,7 +38,7 @@
__author__ = "Jerome Kieffer"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__licence__ = "MIT"
-__date__ = "23/02/2023"
+__date__ = "15/03/2024"
__status__ = "production"
FOOTER = """To import your files as a project:
@@ -401,7 +401,7 @@
":param full: complete/slow mask analysis"
if self.progress:
self.progress.update(self.progress.max_value - 1, "Generate mask")
- dummy_value = numpy.cast[self.mask.dtype](-1)
+ dummy_value = numpy.asarray(-numpy.ones(1), dtype=self.mask.dtype)[-1]
#-1 in the given datatype
mask = (self.mask==dummy_value).astype(numpy.int8)
esperantoimage.EsperantoImage.DUMMY = 1
new_mask =
self.geometry_transform(esperantoimage.EsperantoImage(data=mask).data)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/src/fabio/cbfimage.py
new/fabio-2024.4/src/fabio/cbfimage.py
--- old/fabio-2023.10/src/fabio/cbfimage.py 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/src/fabio/cbfimage.py 2024-04-11 16:35:31.000000000
+0200
@@ -245,7 +245,7 @@
return binary_data
if ("Content-MD5" in self.header) and check_MD5:
- ref = numpy.string_(self.header["Content-MD5"])
+ ref = numpy.bytes_(self.header["Content-MD5"])
obt = md5sum(binary_data)
if ref != obt:
logger.error("Checksum of binary data mismatch: expected
%s, got %s" % (ref, obt))
@@ -294,14 +294,14 @@
b"Content-Type: application/octet-stream;",
b' conversions="x-CBF_BYTE_OFFSET"',
b'Content-Transfer-Encoding: BINARY',
- numpy.string_("X-Binary-Size: %d" %
(len(binary_blob))),
+ numpy.bytes_("X-Binary-Size: %d" % (len(binary_blob))),
b"X-Binary-ID: 1",
- numpy.string_('X-Binary-Element-Type: "%s"' % (dtype)),
+ numpy.bytes_('X-Binary-Element-Type: "%s"' % (dtype)),
b"X-Binary-Element-Byte-Order: LITTLE_ENDIAN",
b"Content-MD5: " + md5sum(binary_blob),
- numpy.string_("X-Binary-Number-of-Elements: %d" %
(dim1 * dim2)),
- numpy.string_("X-Binary-Size-Fastest-Dimension: %d" %
dim1),
- numpy.string_("X-Binary-Size-Second-Dimension: %d" %
dim2),
+ numpy.bytes_("X-Binary-Number-of-Elements: %d" % (dim1
* dim2)),
+ numpy.bytes_("X-Binary-Size-Fastest-Dimension: %d" %
dim1),
+ numpy.bytes_("X-Binary-Size-Second-Dimension: %d" %
dim2),
b"X-Binary-Size-Padding: 1",
b"",
self.STARTER + binary_blob,
@@ -354,22 +354,22 @@
keys are always unicode (str in python3)
values are bytes
"""
- EOL = [numpy.string_(i) for i in ("\r", "\n", "\r\n", "\n\r")]
- BLANK = [numpy.string_(i) for i in (" ", "\t")] + EOL
- SINGLE_QUOTE = numpy.string_("'")
- DOUBLE_QUOTE = numpy.string_('"')
- SEMICOLUMN = numpy.string_(';')
- DOT = numpy.string_('.')
+ EOL = [numpy.bytes_(i) for i in ("\r", "\n", "\r\n", "\n\r")]
+ BLANK = [numpy.bytes_(i) for i in (" ", "\t")] + EOL
+ SINGLE_QUOTE = numpy.bytes_("'")
+ DOUBLE_QUOTE = numpy.bytes_('"')
+ SEMICOLUMN = numpy.bytes_(';')
+ DOT = numpy.bytes_('.')
START_COMMENT = (SINGLE_QUOTE, DOUBLE_QUOTE)
- BINARY_MARKER = numpy.string_("--CIF-BINARY-FORMAT-SECTION--")
- HASH = numpy.string_("#")
- LOOP = numpy.string_("loop_")
+ BINARY_MARKER = numpy.bytes_("--CIF-BINARY-FORMAT-SECTION--")
+ HASH = numpy.bytes_("#")
+ LOOP = numpy.bytes_("loop_")
UNDERSCORE = ord("_")
- QUESTIONMARK = numpy.string_("?")
- STOP = numpy.string_("stop_")
- GLOBAL = numpy.string_("global_")
- DATA = numpy.string_("data_")
- SAVE = numpy.string_("save_")
+ QUESTIONMARK = numpy.bytes_("?")
+ STOP = numpy.bytes_("stop_")
+ GLOBAL = numpy.bytes_("global_")
+ DATA = numpy.bytes_("data_")
+ SAVE = numpy.bytes_("save_")
def __init__(self, _strFilename=None):
"""
@@ -416,7 +416,7 @@
else:
raise RuntimeError("CIF.loadCIF: what is %s type %s" %
(_strFilename, type(_strFilename)))
if _bKeepComment:
- self._parseCIF(numpy.string_(infile.read()))
+ self._parseCIF(numpy.bytes_(infile.read()))
else:
self._parseCIF(CIF._readCIF(infile))
if own_fd:
@@ -454,13 +454,13 @@
if "read" not in dir(instream):
raise RuntimeError("CIF._readCIF(instream): I expected instream to
be an opened file,\
here I got %s type %s" % (instream, type(instream)))
- out_bytes = numpy.string_("")
+ out_bytes = numpy.bytes_("")
for sLine in instream:
- nline = numpy.string_(sLine)
+ nline = numpy.bytes_(sLine)
pos = nline.find(cls.HASH)
if pos >= 0:
if cls.isAscii(nline):
- out_bytes += nline[:pos] + numpy.string_(os.linesep)
+ out_bytes += nline[:pos] + numpy.bytes_(os.linesep)
if pos > 80:
logger.warning("This line is too long and could cause
problems in PreQuest: %s", sLine)
else:
@@ -535,7 +535,7 @@
idx += 1 + bytes_text[idx + 1:].find(cls.SINGLE_QUOTE)
if idx >= len(bytes_text) - 1:
fields.append(bytes_text[1:-1].strip())
- bytes_text = numpy.string_("")
+ bytes_text = numpy.bytes_("")
finished = True
break
@@ -552,7 +552,7 @@
idx += 1 + bytes_text[idx + 1:].find(cls.DOUBLE_QUOTE)
if idx >= len(bytes_text) - 1:
fields.append(bytes_text[1:-1].strip())
- bytes_text = numpy.string_("")
+ bytes_text = numpy.bytes_("")
finished = True
break
@@ -594,7 +594,7 @@
bytes_text = bytes_text[end_binary:].strip()
else:
fields.append(bytes_text)
- bytes_text = numpy.string_("")
+ bytes_text = numpy.bytes_("")
break
return fields
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/src/fabio/eigerimage.py
new/fabio-2024.4/src/fabio/eigerimage.py
--- old/fabio-2023.10/src/fabio/eigerimage.py 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/src/fabio/eigerimage.py 2024-04-11 16:35:31.000000000
+0200
@@ -2,7 +2,7 @@
#
# Project: FabIO X-ray image reader
#
-# Copyright (C) 2010-2016 European Synchrotron Radiation Facility
+# Copyright (C) 2010-2024 European Synchrotron Radiation Facility
# Grenoble, France
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -45,7 +45,7 @@
__contact__ = "jerome.kief...@esrf.fr"
__license__ = "MIT"
__copyright__ = "ESRF"
-__date__ = "05/07/2022"
+__date__ = "15/03/2024"
import logging
logger = logging.getLogger(__name__)
@@ -184,7 +184,7 @@
for i, ds in enumerate(self.dataset):
if ds is None:
# we are in a trouble
- data = numpy.atleast_2d(numpy.NaN)
+ data = numpy.atleast_2d(numpy.nan)
elif isinstance(ds, h5py.Dataset):
data = numpy.atleat_2d(ds[()])
else:
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/src/fabio/ext/dense.pyx
new/fabio-2024.4/src/fabio/ext/dense.pyx
--- old/fabio-2023.10/src/fabio/ext/dense.pyx 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/src/fabio/ext/dense.pyx 2024-04-11 16:35:31.000000000
+0200
@@ -8,7 +8,7 @@
# Project: Fable Input/Output
# https://github.com/silx-kit/fabio
#
-# Copyright (C) 2020-2023 European Synchrotron Radiation Facility,
Grenoble, France
+# Copyright (C) 2020-2024 European Synchrotron Radiation Facility,
Grenoble, France
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
@@ -31,7 +31,7 @@
"""Densification of sparse frame format
"""
__author__ = "Jérôme Kieffer"
-__date__ = "20/10/2023"
+__date__ = "19/03/2024"
__contact__ = "jerome.kief...@esrf.fr"
__license__ = "MIT"
@@ -249,12 +249,15 @@
cdef:
Py_ssize_t i, j, size, pos, size_over, width, height
double value, fres, fpos, idelta, start, std
- bint integral, noisy, do_normalization=False
+ bint integral, noisy, do_normalization=False, do_background=True
any_t[:, ::1] dense
float[:,::1] c_normalization
MT mt
- size = radius.shape[0]
- assert background.shape[0] == size
+ if radius is None:
+ do_background = False
+ else:
+ size = radius.shape[0]
+ assert background.shape[0] == size
size_over = index.shape[0]
assert intensity.shape[0] == size_over
integral = numpy.issubdtype(dtype, numpy.integer)
@@ -277,36 +280,37 @@
mt = MT(seed)
with nogil:
- start = radius[0]
- idelta = <double>(size - 1)/(radius[size-1] - start)
-
- #Linear interpolation
- for i in range(height):
- for j in range(width):
- fpos = (mask[i,j] - start)*idelta
- if (fpos<0) or (fpos>=size) or (not isfinite(fpos)):
- dense[i,j] = dummy
- else:
- pos = <uint32_t> fpos
- if pos+1 == size:
- value = background[pos]
- fres = 0.0
+ if do_background:
+ start = radius[0]
+ idelta = <double>(size - 1)/(radius[size-1] - start)
+
+ #Linear interpolation
+ for i in range(height):
+ for j in range(width):
+ fpos = (mask[i,j] - start)*idelta
+ if (fpos<0) or (fpos>=size) or (not isfinite(fpos)):
+ dense[i,j] = dummy
else:
- fres = fpos - pos
- value = (1.0 - fres)*background[pos] +
fres*background[pos+1]
- if noisy:
+ pos = <uint32_t> fpos
if pos+1 == size:
- std = background_std[pos]
+ value = background[pos]
fres = 0.0
else:
- std = (1.0 - fres)*background_std[pos] +
fres*background_std[pos+1]
- value = max(0.0, mt._normal_m(value, std))
- if do_normalization:
- value *= c_normalization[i, j]
- if integral:
- dense[i,j] = <any_t>(value + 0.5) #this is rounding
- else:
- dense[i,j] = <any_t>(value)
+ fres = fpos - pos
+ value = (1.0 - fres)*background[pos] +
fres*background[pos+1]
+ if noisy:
+ if pos+1 == size:
+ std = background_std[pos]
+ fres = 0.0
+ else:
+ std = (1.0 - fres)*background_std[pos] +
fres*background_std[pos+1]
+ value = max(0.0, mt._normal_m(value, std))
+ if do_normalization:
+ value *= c_normalization[i, j]
+ if integral:
+ dense[i,j] = <any_t>(value + 0.5) #this is
rounding
+ else:
+ dense[i,j] = <any_t>(value)
# Assignment of outliers
for i in range(size_over):
j = index[i]
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/src/fabio/fabioimage.py
new/fabio-2024.4/src/fabio/fabioimage.py
--- old/fabio-2023.10/src/fabio/fabioimage.py 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/src/fabio/fabioimage.py 2024-04-11 16:35:31.000000000
+0200
@@ -816,6 +816,7 @@
fobj.seek(0)
elif self._need_a_seek_to_read and mode[0] == "r":
fo = python_uncompress(fname, mode)
+ print(fname, mode, fo)
fobj = fabioutils.BytesIO(fo.read(), fname, mode)
else:
fobj = python_uncompress(fname, mode)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/src/fabio/meson.build
new/fabio-2024.4/src/fabio/meson.build
--- old/fabio-2023.10/src/fabio/meson.build 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/src/fabio/meson.build 2024-04-11 16:35:31.000000000
+0200
@@ -6,7 +6,6 @@
subdir('utils')
py.install_sources([
- '_version.py',
'adscimage.py',
'binaryimage.py',
'bruker100image.py',
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/src/fabio/nexus.py
new/fabio-2024.4/src/fabio/nexus.py
--- old/fabio-2023.10/src/fabio/nexus.py 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/src/fabio/nexus.py 2024-04-11 16:35:31.000000000 +0200
@@ -29,11 +29,11 @@
"""
-__author__ = "Jerome Kieffer"
+__author__ = "Jérôme Kieffer"
__contact__ = "jerome.kief...@esrf.eu"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "28/04/2021"
+__date__ = "15/03/2024"
__status__ = "production"
__docformat__ = 'restructuredtext'
@@ -44,7 +44,7 @@
import time
import numpy
from .fabioutils import exists
-from ._version import version
+from .version import version
logger = logging.getLogger(__name__)
try:
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/src/fabio/openimage.py
new/fabio-2024.4/src/fabio/openimage.py
--- old/fabio-2023.10/src/fabio/openimage.py 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/src/fabio/openimage.py 2024-04-11 16:35:31.000000000
+0200
@@ -42,7 +42,9 @@
import os.path
import logging
+import re
from . import fabioutils
+from .compression import ExternalCompressors
from .fabioutils import FilenameObject, BytesIO
from .fabioimage import FabioImage
@@ -149,6 +151,18 @@
return "marccd"
else:
return "tif"
+
+ if format_type == "edf" and isinstance(filename, str):
+ # Might be GE with an EDF header. Check the extension.
+ extension = filename.split(".")[-1]
+ # If it is a compression extension, check the next one up.
+ if f'.{extension}' in ExternalCompressors.COMMANDS:
+ extension = filename.split(".")[-2]
+
+ # If the extension is `ge` plus a number, assume it is GE
+ if re.search(r'^ge\d*$', extension):
+ return "GE"
+
return format_type
raise Exception("Could not interpret magic string")
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/src/fabio/sparseimage.py
new/fabio-2024.4/src/fabio/sparseimage.py
--- old/fabio-2023.10/src/fabio/sparseimage.py 2023-10-26 10:30:27.000000000
+0200
+++ new/fabio-2024.4/src/fabio/sparseimage.py 2024-04-11 16:35:31.000000000
+0200
@@ -3,7 +3,7 @@
# Project: X-ray image reader
# https://github.com/silx-kit/fabio
#
-# Copyright 2020-2021(C) European Synchrotron Radiation Facility, Grenoble,
France
+# Copyright 2020-2024(C) European Synchrotron Radiation Facility, Grenoble,
France
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
@@ -37,7 +37,7 @@
__contact__ = "jerome.kief...@esrf.fr"
__license__ = "MIT"
__copyright__ = "2020 ESRF"
-__date__ = "09/02/2023"
+__date__ = "19/03/2024"
import logging
logger = logging.getLogger(__name__)
@@ -82,7 +82,11 @@
:param seed: numerical seed for random number generator
:return dense array
"""
- dense = numpy.interp(mask, radius, background)
+ dtype = intensity.dtype
+ if radius is None or background is None:
+ dense = numpy.zeros(radius.shape, dtype=dtype)
+ else:
+ dense = numpy.interp(mask, radius, background)
if background_std is not None:
if seed is not None:
numpy.random.seed(seed)
@@ -93,7 +97,7 @@
flat = dense.ravel()
flat[index] = intensity
- dtype = intensity.dtype
+
if numpy.issubdtype(dtype, numpy.integer):
# Foolded by banker's rounding !!!!
dense +=0.5
@@ -173,9 +177,13 @@
raise NotGoodReader("HDF5 file does not contain any default
NXdata.")
nx_data = entry[default_data]
self.mask = nx_data["mask"][()]
- self.radius = nx_data["radius"][()]
- self.background_avg = nx_data["background_avg"][()]
- self.background_std = nx_data["background_std"][()]
+ try:
+ self.radius = nx_data["radius"][()]
+ self.background_avg = nx_data["background_avg"][()]
+ self.background_std = nx_data["background_std"][()]
+ except KeyError:
+ logger.info("No background information found")
+ self.radius = self.background_avg = self.background_std = None
self.frame_ptr = nx_data["frame_ptr"][()]
self.index = nx_data["index"][()]
self.intensity = nx_data["intensity"][()]
@@ -183,7 +191,7 @@
self.dummy = self.intensity.dtype.type(nx_data["dummy"][()])
except KeyError:
if self.intensity.dtype.char in numpy.typecodes['AllFloat']:
- self.dummy = numpy.NaN
+ self.dummy = numpy.nan
else:
self.dummy = 0
@@ -205,19 +213,29 @@
logger.warning("Not data have been read from disk")
return
start, stop = self.frame_ptr[index:index + 2]
- if cython_densify is not None:
- return cython_densify.densify(self.mask,
- self.radius,
- self.index[start:stop],
- self.intensity[start:stop],
- self.dummy,
- self.intensity.dtype,
- self.background_avg[index],
- self.background_std[index] * self.noisy if
self.noisy else None,
- self.normalization)
+ if self.radius is None:
+ if cython_densify is None: # Numpy implementation
+ dense = densify(self.mask,
+ None,
+ self.index[start:stop],
+ self.intensity[start:stop],
+ self.dummy,
+ None,
+ None,
+ self.normalization)
+ else: # Cython
+ dense = cython_densify.densify(self.mask,
+ None,
+ self.index[start:stop],
+ self.intensity[start:stop],
+ self.dummy,
+ self.intensity.dtype,
+ None,
+ None,
+ self.normalization)
else:
- # Fall-back on numpy code.
- return densify(self.mask,
+ if cython_densify is None: # Numpy
+ dense = densify(self.mask,
self.radius,
self.index[start:stop],
self.intensity[start:stop],
@@ -225,7 +243,18 @@
self.background_avg[index],
self.background_std[index] * self.noisy if
self.noisy else None,
self.normalization)
-
+ else:
+ dense = cython_densify.densify(self.mask,
+ self.radius,
+ self.index[start:stop],
+ self.intensity[start:stop],
+ self.dummy,
+ self.intensity.dtype,
+ self.background_avg[index],
+ self.background_std[index] *
self.noisy if self.noisy else None,
+ self.normalization)
+ return dense
+
def getframe(self, num):
""" returns the frame numbered 'num' in the stack if applicable"""
if self.nframes > 1:
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore'
old/fabio-2023.10/src/fabio/test/codecs/test_esperantoimage.py
new/fabio-2024.4/src/fabio/test/codecs/test_esperantoimage.py
--- old/fabio-2023.10/src/fabio/test/codecs/test_esperantoimage.py
2023-10-26 10:30:27.000000000 +0200
+++ new/fabio-2024.4/src/fabio/test/codecs/test_esperantoimage.py
2024-04-11 16:35:31.000000000 +0200
@@ -134,7 +134,7 @@
def test_values(self):
esp = fabio.open(UtilsTest.getimage("reference.esperanto.bz2")[:-4])
npy = fabio.open(UtilsTest.getimage("reference.npy.bz2")[:-4])
- self.assertEqual(numpy.alltrue(esp.data == npy.data), True, "Images
are the same")
+ self.assertTrue(numpy.array_equal(esp.data, npy.data), "Images are the
same")
def suite():
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/src/fabio/test/codecs/test_geimage.py
new/fabio-2024.4/src/fabio/test/codecs/test_geimage.py
--- old/fabio-2023.10/src/fabio/test/codecs/test_geimage.py 2023-10-26
10:30:27.000000000 +0200
+++ new/fabio-2024.4/src/fabio/test/codecs/test_geimage.py 2024-04-11
16:35:31.000000000 +0200
@@ -53,6 +53,7 @@
("GE_aSI_detector_image_1529", (2048, 2048), (1515, 16353, 1833.0311,
56.9124)),
("GE_image_1frame_intact_header.ge", (2048, 2048), (1515, 16353,
2209.1113, 437.6377)),
("GE_image_1frame_blanked_header.ge", (2048, 2048), (1300, 16349,
1886.41111, 117.0603)),
+ ("dark_before_000428.edf.ge5", (2048, 2048), (1300, 16349, 1833.87892,
84.5265)),
]
def setUp(self):
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/src/fabio/utils/ExternalResources.py
new/fabio-2024.4/src/fabio/utils/ExternalResources.py
--- old/fabio-2023.10/src/fabio/utils/ExternalResources.py 2023-10-26
10:30:27.000000000 +0200
+++ new/fabio-2024.4/src/fabio/utils/ExternalResources.py 2024-04-11
16:35:31.000000000 +0200
@@ -289,7 +289,8 @@
if not gz_file_exists:
try:
- gzip.open(fullimagename_gz, "wb").write(decompressed)
+ with gzip.open(fullimagename_gz, "wb") as g:
+ g.write(decompressed)
except IOError:
raise IOError("unable to write gzipped \
data to disk at %s" % self.data_home)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/src/fabio/utils/deprecation.py
new/fabio-2024.4/src/fabio/utils/deprecation.py
--- old/fabio-2023.10/src/fabio/utils/deprecation.py 2023-10-26
10:30:27.000000000 +0200
+++ new/fabio-2024.4/src/fabio/utils/deprecation.py 2024-04-11
16:35:31.000000000 +0200
@@ -1,7 +1,7 @@
# coding: utf-8
# /*##########################################################################
#
-# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+# Copyright (c) 2016-2024 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
@@ -24,15 +24,16 @@
# ###########################################################################*/
"""Bunch of useful decorators"""
-__authors__ = ["Jerome Kieffer", "H. Payno", "P. Knobel"]
+__authors__ = ["Jérôme Kieffer", "H. Payno", "P. Knobel"]
__license__ = "MIT"
-__date__ = "18/12/2020"
+__date__ = "15/03/2024"
import logging
import functools
import traceback
import re
-from .. import _version
+
+from ..version import calc_hexversion, hexversion as ref_hexversion
depreclog = logging.getLogger("fabio.DEPRECATION")
@@ -54,7 +55,7 @@
releaselevel = result[3]
if releaselevel is None:
releaselevel = 0
- return _version.calc_hexversion(major, minor, micro, releaselevel,
serial=0)
+ return calc_hexversion(major, minor, micro, releaselevel, serial=0)
def deprecated(func=None, reason=None, replacement=None, since_version=None,
@@ -154,7 +155,7 @@
deprecated_since = hexversion
else:
deprecated_since = _CACHE_VERSIONS[deprecated_since]
- log_as_debug = _version.hexversion < deprecated_since
+ log_as_debug = ref_hexversion < deprecated_since
else:
log_as_debug = False
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-2023.10/version.py new/fabio-2024.4/version.py
--- old/fabio-2023.10/version.py 1970-01-01 01:00:00.000000000 +0100
+++ new/fabio-2024.4/version.py 2024-04-11 16:35:31.000000000 +0200
@@ -0,0 +1,124 @@
+#!/usr/bin/env python3
+# coding: utf-8
+#
+# Project: X-ray image reader
+# https://github.com/silx-kit/fabio
+#
+# Copyright (C) 2015-2024 European Synchrotron Radiation Facility,
Grenoble, France
+#
+# Principal author: Jérôme Kieffer (jerome.kief...@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.
+
+"""Unique place where the version number is defined.
+
+Module for version handling:
+
+provides:
+* version = "1.2.3" or "1.2.3-beta4"
+* version_info = named tuple (1,2,3,"beta",4)
+* hexversion: 0x010203B4
+* strictversion = "1.2.3b4
+* debianversion = "1.2.3~beta4"
+* calc_hexversion: the function to transform a version_tuple into an integer
+
+This is called hexversion since it only really looks meaningful when viewed as
the
+result of passing it to the built-in hex() function.
+The version_info value may be used for a more human-friendly encoding of the
same information.
+
+The hexversion is a 32-bit number with the following layout:
+Bits (big endian order) Meaning
+1-8 PY_MAJOR_VERSION (the 2 in 2.1.0a3)
+9-16 PY_MINOR_VERSION (the 1 in 2.1.0a3)
+17-24 PY_MICRO_VERSION (the 0 in 2.1.0a3)
+25-28 PY_RELEASE_LEVEL (0xA for alpha, 0xB for beta, 0xC for release
candidate and 0xF for final)
+29-32 PY_RELEASE_SERIAL (the 3 in 2.1.0a3, zero for final releases)
+
+Thus 2.1.0a3 is hexversion 0x020100a3.
+
+"""
+
+__author__ = "Jérôme Kieffer"
+__contact__ = "jerome.kief...@esrf.eu"
+__license__ = "MIT"
+__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
+__date__ = "11/04/2024"
+__status__ = "production"
+__docformat__ = 'restructuredtext'
+__all__ = ["date", "version_info", "strictversion", "hexversion",
"debianversion",
+ "calc_hexversion"]
+
+RELEASE_LEVEL_VALUE = {"dev": 0,
+ "alpha": 10,
+ "beta": 11,
+ "candidate": 12,
+ "final": 15}
+
+PRERELEASE_NORMALIZED_NAME = {"dev": "a",
+ "alpha": "a",
+ "beta": "b",
+ "candidate": "rc"}
+
+MAJOR = 2024
+MINOR = 4
+MICRO = 0
+RELEV = "final" # <16
+SERIAL = 0 # <16
+date = __date__
+
+from collections import namedtuple
+_version_info = namedtuple("version_info", ["major", "minor", "micro",
"releaselevel", "serial"])
+
+version_info = _version_info(MAJOR, MINOR, MICRO, RELEV, SERIAL)
+
+strictversion = version = debianversion = "%d.%d.%d" % version_info[:3]
+if version_info.releaselevel != "final":
+ _prerelease = PRERELEASE_NORMALIZED_NAME[version_info[3]]
+ version += "%s%s" % (_prerelease, version_info[-1])
+ debianversion += "~adev%i" % version_info[-1] if RELEV == "dev" else
"~%s%i" % (_prerelease, version_info[-1])
+ strictversion += _prerelease + str(version_info[-1])
+
+
+def calc_hexversion(major=0, minor=0, micro=0, releaselevel="dev", serial=0):
+ """Calculate the hexadecimal version number from the tuple version_info:
+
+ :param major: integer
+ :param minor: integer
+ :param micro: integer
+ :param relev: integer or string
+ :param serial: integer
+ :return: integer always increasing with revision numbers
+ """
+ try:
+ releaselevel = int(releaselevel)
+ except ValueError:
+ releaselevel = RELEASE_LEVEL_VALUE.get(releaselevel, 0)
+
+ hex_version = int(serial)
+ hex_version |= releaselevel * 1 << 4
+ hex_version |= int(micro) * 1 << 8
+ hex_version |= int(minor) * 1 << 16
+ hex_version |= int(major) * 1 << 24
+ return hex_version
+
+
+hexversion = calc_hexversion(*version_info)
+
+if __name__ == "__main__":
+ print(version)
