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_gr...@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_gr...@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='cgoh...@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',
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