Hello community, here is the log from the commit of package python-roifile for openSUSE:Factory checked in at 2020-11-29 12:30:09 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/python-roifile (Old) and /work/SRC/openSUSE:Factory/.python-roifile.new.5913 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "python-roifile" Sun Nov 29 12:30:09 2020 rev:2 rq:851333 version:2020.8.13 Changes: -------- --- /work/SRC/openSUSE:Factory/python-roifile/python-roifile.changes 2020-08-14 13:11:02.893249493 +0200 +++ /work/SRC/openSUSE:Factory/.python-roifile.new.5913/python-roifile.changes 2020-11-29 12:30:19.326117107 +0100 @@ -1,0 +2,12 @@ +Thu Nov 26 07:20:28 UTC 2020 - andy great <andythe_great@pm.me> + +- Update to version 2020.8.13. + * Support writing to ZIP file. + * Support os.PathLike file names. + +------------------------------------------------------------------- +Sat Aug 1 16:24:41 UTC 2020 - andy great <andythe_great@pm.me> + +- Update spec file to use python alternative. + +------------------------------------------------------------------- Old: ---- roifile-2020.5.28.tar.gz New: ---- roifile-2020.8.13.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ python-roifile.spec ++++++ --- /var/tmp/diff_new_pack.THNLMu/_old 2020-11-29 12:30:19.914117702 +0100 +++ /var/tmp/diff_new_pack.THNLMu/_new 2020-11-29 12:30:19.918117705 +0100 @@ -20,7 +20,7 @@ %define packagename roifile %{?!python_module:%define python_module() python-%{**} python3-%{**}} Name: python-roifile -Version: 2020.5.28 +Version: 2020.8.13 Release: 0 Summary: Read and write ImageJ ROI format License: BSD-3-Clause @@ -32,11 +32,13 @@ BuildRequires: python-rpm-macros BuildRequires: %{python_module Cython} BuildRequires: %{python_module numpy >= 1.15.1} -BuildRequires: %{python_module matplotlib >= 3.1} -BuildRequires: %{python_module tifffile} +BuildRequires: %{python_module matplotlib >= 3.2} +BuildRequires: %{python_module tifffile >= 2020.8.13} Requires: python-numpy >= 1.15.1 -Requires: python-matplotlib >= 3.1 -Requires: python-tifffile +Requires: python-matplotlib >= 3.2 +Requires: python-tifffile >= 2020.8.13 +Requires(post): update-alternatives +Requires(postun): update-alternatives BuildArch: noarch %python_subpackages @@ -56,7 +58,17 @@ %install %python_install +%python_clone -a %{buildroot}%{_bindir}/%{packagename} + + %python_expand %fdupes %{buildroot}%{$python_sitelib} +%prepare_alternative %{packagename} + +%post +%python_install_alternative %{packagename} + +%postun +%python_uninstall_alternative %{packagename} %check # Test not given @@ -64,7 +76,7 @@ %files %{python_files} %doc README.rst %license LICENSE -%{_bindir}/%{packagename} +%python_alternative %{_bindir}/%{packagename} %{python_sitelib}/*egg-info/ %{python_sitelib}/%{packagename}/ ++++++ roifile-2020.5.28.tar.gz -> roifile-2020.8.13.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/roifile-2020.5.28/README.rst new/roifile-2020.8.13/README.rst --- old/roifile-2020.5.28/README.rst 2020-05-28 17:10:13.000000000 +0200 +++ new/roifile-2020.8.13/README.rst 2020-08-14 05:40:40.000000000 +0200 @@ -15,21 +15,23 @@ :License: BSD 3-Clause -:Version: 2020.5.28 +:Version: 2020.8.13 Requirements ------------ -* `CPython >= 3.6 <https://www.python.org>`_ +* `CPython >= 3.7 <https://www.python.org>`_ * `Numpy 1.15.1 <https://www.numpy.org>`_ -* `Tifffile 2020.5.25 <https://pypi.org/project/tifffile/>`_ (optional) -* `Matplotlib 3.1 <https://pypi.org/project/matplotlib/>`_ (optional) +* `Tifffile 2020.8.13 <https://pypi.org/project/tifffile/>`_ (optional) +* `Matplotlib 3.2 <https://pypi.org/project/matplotlib/>`_ (optional) Revisions --------- +2020.8.13 + Support writing to ZIP file. + Support os.PathLike file names. 2020.5.28 Fix int32 to hex color conversion. Fix coordinates of closing path. -2020.5.2 Fix reading TIFF files with no overlays. 2020.5.1 Split positions from counters. @@ -39,6 +41,9 @@ Notes ----- +The ImageJ ROI format cannot store integer coordinate values outside the +range of -32768 to 32767 (16-bit signed). + Other Python packages handling ImageJ ROIs: * `ijpython_roi <https://github.com/dwaithe/ijpython_roi>`_ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/roifile-2020.5.28/roifile/roifile.py new/roifile-2020.8.13/roifile/roifile.py --- old/roifile-2020.5.28/roifile/roifile.py 2020-05-28 17:10:13.000000000 +0200 +++ new/roifile-2020.8.13/roifile/roifile.py 2020-08-14 05:40:40.000000000 +0200 @@ -45,21 +45,23 @@ :License: BSD 3-Clause -:Version: 2020.5.28 +:Version: 2020.8.13 Requirements ------------ -* `CPython >= 3.6 <https://www.python.org>`_ +* `CPython >= 3.7 <https://www.python.org>`_ * `Numpy 1.15.1 <https://www.numpy.org>`_ -* `Tifffile 2020.5.25 <https://pypi.org/project/tifffile/>`_ (optional) -* `Matplotlib 3.1 <https://pypi.org/project/matplotlib/>`_ (optional) +* `Tifffile 2020.8.13 <https://pypi.org/project/tifffile/>`_ (optional) +* `Matplotlib 3.2 <https://pypi.org/project/matplotlib/>`_ (optional) Revisions --------- +2020.8.13 + Support writing to ZIP file. + Support os.PathLike file names. 2020.5.28 Fix int32 to hex color conversion. Fix coordinates of closing path. -2020.5.2 Fix reading TIFF files with no overlays. 2020.5.1 Split positions from counters. @@ -69,6 +71,9 @@ Notes ----- +The ImageJ ROI format cannot store integer coordinate values outside the +range of -32768 to 32767 (16-bit signed). + Other Python packages handling ImageJ ROIs: * `ijpython_roi <https://github.com/dwaithe/ijpython_roi>`_ @@ -109,10 +114,11 @@ """ -__version__ = '2020.5.28' +__version__ = '2020.8.13' __all__ = ('ImagejRoi', 'ROI_TYPE', 'ROI_SUBTYPE', 'ROI_OPTIONS') +import os import sys import enum import struct @@ -276,6 +282,7 @@ For ZIP or TIFF files, return a list of ImagejRoi. """ + filename = os.fspath(filename) if filename[-4:].lower() == '.tif': import tifffile with tifffile.TiffFile(filename) as tif: @@ -400,7 +407,7 @@ dtype=self.byteorder + 'u4', buffer=data, offset=counters_offset - ) + ) self.counters = (counters & 0xFF).astype('u1') self.counter_positions = counters >> 8 @@ -433,7 +440,7 @@ buffer=data, offset=64, order='F' - ).copy() + ).copy() if self.subpixelresolution: self.subpixel_coordinates = numpy.ndarray( @@ -442,7 +449,7 @@ buffer=data, offset=64 + self.n_coordinates * 4, order='F' - ).copy() + ).copy() elif self.composite and self.roitype == ROI_TYPE.RECT: self.multi_coordinates = numpy.ndarray( @@ -450,17 +457,34 @@ dtype=self.byteorder + 'f4', buffer=data, offset=64 - ).copy() + ).copy() elif self.roitype not in (ROI_TYPE.RECT, ROI_TYPE.LINE, ROI_TYPE.OVAL): log_warning(f'cannot handle ImagejRoi type {self.roitype!r}') return self - def tofile(self, filename): - """Write ImagejRoi to a new ROI file.""" - with open(filename, 'wb') as fh: - fh.write(self.tobytes()) + def tofile(self, filename, name=None, mode=None): + """Write ImagejRoi to a ROI or ZIP file. + + Existing ZIP files are opened for append. + + """ + filename = os.fspath(filename) + if filename[-4:].lower() == '.zip': + import zipfile + if name is None: + name = self.name if self.name else self.autoname + if name[-4:].lower() != '.roi': + name += '.roi' + if mode is None: + mode = 'a' if os.path.exists(filename) else 'w' + with zipfile.ZipFile(filename, mode) as zf: + with zf.open(name, 'w') as fh: + fh.write(self.tobytes()) + else: + with open(filename, 'wb') as fh: + fh.write(self.tobytes()) def tobytes(self): """Return ImagejRoi as bytes.""" @@ -700,15 +724,17 @@ [self.left, self.bottom], [self.right, self.bottom], [self.right, self.top], - [self.left, self.top]], 'f4') + [self.left, self.top]], + 'f4' + ) else: coords = numpy.empty((0, 2), dtype=self.byteorder + 'i4') return [coords] if multi else coords - def hexcolor(self, b): + def hexcolor(self, b, default=None): """Return color (bytes) as hex triplet or None if black.""" if b == ROI_COLOR_NONE: - return None + return default if self.byteorder == '>': return f'#{b[1]:02x}{b[2]:02x}{b[3]:02x}' return f'#{b[3]:02x}{b[2]:02x}{b[1]:02x}' @@ -777,6 +803,17 @@ )) @property + def autoname(self): + """Return name generated from positions.""" + y = (self.bottom - self.top) // 2 + x = (self.right - self.left) // 2 + name = f'{y:05}-{x:05}' + if self.counter_positions is not None: + tzc = int(self.counter_positions.max()) + name = f'{tzc:05}-' + name + return name + + @property def utf16(self): """Return UTF-16 codec depending on byteorder.""" return 'utf-16' + ('be' if self.byteorder == '>' else 'le') @@ -814,6 +851,7 @@ def test_imagejroi(): """Test roifile.ImagejRoi class.""" + # test ROIs from a ZIP file rois = ImagejRoi.fromfile('tests/ijzip.zip') assert len(rois) == 7 for roi in rois: @@ -821,6 +859,16 @@ roi.coordinates() roi.__str__() + # re-write ROIs to a ZIP file + try: + os.remove('_test.zip') + except OSError: + pass + for roi in rois: + roi.tofile('_test.zip') + assert ImagejRoi.fromfile('_test.zip')[-1] == rois[-1] + + # verify box_combined roi = ImagejRoi.fromfile('tests/box_combined.roi') assert roi.tobytes() == ImagejRoi.frombytes(roi.tobytes()).tobytes() assert roi.name == '0464-0752' @@ -834,6 +882,7 @@ assert roi.multi_coordinates[0] == 0.0 roi.__str__() + # read a ROI from a TIFF file for roi in ImagejRoi.fromfile('tests/IJMetadata.tif'): assert roi == ImagejRoi.frombytes(roi.tobytes()) roi.coordinates() @@ -850,7 +899,6 @@ ``python -m roifile file_or_directory`` """ - import os from glob import glob if argv is None: diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/roifile-2020.5.28/setup.py new/roifile-2020.8.13/setup.py --- old/roifile-2020.5.28/setup.py 2020-05-28 17:10:13.000000000 +0200 +++ new/roifile-2020.8.13/setup.py 2020-08-14 05:40:40.000000000 +0200 @@ -39,8 +39,13 @@ long_description=readme, author='Christoph Gohlke', author_email='cgohlke@uci.edu', - url='https://www.lfd.uci.edu/~gohlke/', license='BSD', + url='https://www.lfd.uci.edu/~gohlke/', + project_urls={ + 'Bug Tracker': 'https://github.com/cgohlke/roifile/issues', + 'Source Code': 'https://github.com/cgohlke/roifile', + # 'Documentation': 'https://', + }, packages=['roifile'], entry_points={ 'console_scripts': ['roifile = roifile.roifile:main']}, @@ -49,7 +54,7 @@ extras_require={ 'all': [ 'matplotlib>=3.1', - 'tifffile>=2020.5.25', + 'tifffile>=2020.6.3', ] }, platforms=['any'], @@ -60,7 +65,6 @@ 'Intended Audience :: Developers', 'Operating System :: OS Independent', 'Programming Language :: Python :: 3 :: Only', - 'Programming Language :: Python :: 3.6', 'Programming Language :: Python :: 3.7', 'Programming Language :: Python :: 3.8', 'Programming Language :: Python :: 3.9',