debian/0000755000000000000000000000000012243723642007173 5ustar debian/rules0000755000000000000000000000117312100264722010244 0ustar #!/usr/bin/make -f # As per code source need to handle big endian with: DEB_HOST_ARCH_ENDIAN:=$(shell dpkg-architecture -qDEB_HOST_ARCH_ENDIAN) ifeq ($(DEB_HOST_ARCH_ENDIAN),big) export CFLAGS=-DMSB=0 endif %: dh $@ --with python2 override_dh_auto_clean: dh_auto_clean override_dh_install: dh_numpy install -D -m0755 $(CURDIR)/debian/tifffile.sh $(CURDIR)/debian/python-tifffile/usr/bin/tifffile override_dh_installman: dh_installman debian/tifffile.1 debian/tifffile.1: debian/tifffile.1.in help2man --include=debian/tifffile.1.in --output=debian/tifffile.1 --no-info tifffile get-orig-source: ./debian/get-orig-source debian/watch0000644000000000000000000000041012243723220010207 0ustar version=3 opts=uversionmangle=s/(\d)[_\.\-\+]?((RC|rc|pre|dev|beta|alpha|b|a)\d*)$/$1~$2/,\ dversionmangle=s/\+(debian|dfsg|ds|deb)\d*$//;s/^(\d{4})(\d\d)(\d\d)$/$1.$2.$3/ \ https://github.com/malaterre/tifffile/tags .*/(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz)) debian/changelog0000644000000000000000000000515612243723220011044 0ustar tifffile (20131103-1) unstable; urgency=low * New upstream * Add support for MicroManager files * Fix tifffile when no option is passed. Closes: #730166 -- Mathieu Malaterre Thu, 21 Nov 2013 18:05:24 +0100 tifffile (20130502-1) unstable; urgency=low * New upstream * Upload to sid -- Mathieu Malaterre Tue, 21 May 2013 11:01:48 +0200 tifffile (20130118-1) experimental; urgency=low * New upstream * Rename package to follow python policy * Add Conflicts/Replaces with tifffile * Use compat 9 to get harderning flag * Really fix compilation on big endian machine -- Mathieu Malaterre Thu, 24 Jan 2013 18:00:44 +0100 tifffile (20121214-1) experimental; urgency=low * New upstream * Fix compilation on big endian machine (arm & mips) * Use CFLAGS/LDFLAGS for hardening goal -- Mathieu Malaterre Sun, 13 Jan 2013 17:23:57 +0100 tifffile (20121018-1) experimental; urgency=low * New upstream - Handle unpacking of RGB data - Fix issue with numpy/Python 3.x * Move mathplotlib to Recommends since not required * Make sure to use numpy >= 1.6.2 -- Mathieu Malaterre Thu, 08 Nov 2012 15:11:47 +0100 tifffile (20120421-1) unstable; urgency=low * New upstream * Remove DMUA flag * Change to my @d.o alias -- Mathieu Malaterre Sun, 22 Apr 2012 10:03:28 +0200 tifffile (20120308-1) unstable; urgency=low * New upstream - Add support for StructuredAnnotations in OME/TIFF. -- Mathieu Malaterre Wed, 21 Mar 2012 22:03:57 +0100 tifffile (20120223-1) unstable; urgency=low * New upstream - Handle LSM510 bug * Fix d/rules to handle big-endian machine. * d/rules: add missing call to dh_numpy. * Bump Std-Vers to 3.9.3, no changes needed -- Mathieu Malaterre Mon, 05 Mar 2012 10:41:19 +0100 tifffile (20120101-1) unstable; urgency=low * New upstream * Better support for writing out BigTIFF -- Mathieu Malaterre Mon, 16 Jan 2012 12:08:32 +0100 tifffile (20111215-2) unstable; urgency=low * New upstream. Remove deprecated options -- Mathieu Malaterre Mon, 19 Dec 2011 12:07:48 +0100 tifffile (20111126-1) unstable; urgency=low * New upstream. Better support for BigTIFF -- Mathieu Malaterre Fri, 02 Dec 2011 09:40:39 +0100 tifffile (20111112-1) unstable; urgency=low * Initial Debian Upload (Closes: #648767) -- Mathieu Malaterre Sun, 13 Nov 2011 19:41:37 +0100 debian/tifffile.1.in0000644000000000000000000000165311744737520011464 0ustar [NAME] tifffile \- Read image and meta-data from TIFF, STK, LSM, OME-TIFF, and FluoView files. [SYNOPSIS] .B tifffile .RI [ options ] " files" ... [DESCRIPTION] Only a subset of the TIFF specification is supported, mainly uncompressed and losslessly compressed 1-32 bit integer as well as 32 and 64-bit float images, which are commonly used in scientific imaging. TIFF, the Tagged Image File Format, is under the control of Adobe Systems. STK and LSM are TIFF with custom extensions used by MetaMorph respectively Carl Zeiss MicroImaging. Currently only primary info records are read for STK, FluoView, and NIH image formats. [AUTHOR] Christoph Gohlke for the Debian GNU/Linux system, but may be used by others. [SEE ALSO] .BR tiffdump (1), .BR tiffinfo (1). debian/control0000644000000000000000000000330712243723220010571 0ustar Source: tifffile Priority: optional Section: python Maintainer: Debian Med Packaging Team Uploaders: Mathieu Malaterre Build-Depends: debhelper (>= 9), python-all-dev (>= 2.6.6-3~), python-numpy (>= 1:1.7.1) X-Python-Version: >= 2.6 Standards-Version: 3.9.4 Homepage: http://www.lfd.uci.edu/~gohlke/ Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/tifffile/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/tifffile/trunk/ Package: python-tifffile Architecture: any Depends: ${python:Depends}, ${misc:Depends}, ${shlibs:Depends}, python-importlib Recommends: python-matplotlib (>= 1.3) Provides: ${python:Provides} Replaces: tifffile Conflicts: tifffile Description: Read and write image data from and to TIFF files Image and meta-data can be read from TIFF, BigTIFF, OME-TIFF, STK, LSM, NIH, ImageJ, MicroManager, FluoView, SEQ and GEL files. . Only a subset of the TIFF specification is supported, mainly uncompressed and losslessly compressed 2**(0 to 6) bit integer, 16, 32 and 64-bit float, grayscale and RGB(A) images, which are commonly used in bio-scientific imaging. Specifically, reading JPEG/CCITT compressed image data or EXIF/IPTC/GPS/XMP meta-data is not implemented. Only primary info records are read for STK, FluoView, MicroManager, and NIH image formats. . TIFF, the Tagged Image File Format, is under the control of Adobe Systems. BigTIFF allows for files greater than 4 GB. STK, LSM, FluoView, SEQ, GEL, and OME-TIFF, are custom extensions defined by MetaMorph, Carl Zeiss MicroImaging, Olympus, Media Cybernetics, Molecular Dynamics, and the Open Microscopy Environment consortium respectively. debian/get-orig-source0000755000000000000000000000223512077014100012121 0ustar #!/bin/sh set -e PACKAGE=tifffile VERSION=${VERSION:-$2} TARFILE=${TARFILE:-$3} if [ -z ${VERSION}]; then VERSION=`dpkg-parsechangelog | sed -n -e 's/^Version: \(.*\)-[^-]*$/\1/p'` fi REVISION=`echo $VERSION | sed -e 's/^.*svn//g'` if [ -z ${TARFILE}]; then TARFILE=${PACKAGE}_${VERSION}.orig.tar.gz fi FOLDER=${PACKAGE}-${VERSION} mkdir ${FOLDER} cd ${FOLDER} # http://bugs.debian.org/692752 #wget -c http://www.lfd.uci.edu/~gohlke/code/tifffile.py.html curl -s -o tifffile.py.html "http://www.lfd.uci.edu/~gohlke/code/tifffile.py.html" #wget -c http://www.lfd.uci.edu/~gohlke/code/tifffile.c.html curl -s -o tifffile.c.html "http://www.lfd.uci.edu/~gohlke/code/tifffile.c.html" # do not keep .py extension as we install it into usr/bin links -dump tifffile.py.html > tifffile.py sed -i -e 's/^ //g' tifffile.py links -dump tifffile.c.html > tifffile.c sed -i -e 's/^ //g' tifffile.c rm *.html # compute version: PYVERSION=`grep "^:Version:" tifffile.py | cut -d' ' -f2 | sed -e 's/\.//g'` if [ "$PYVERSION" != "$VERSION" ]; then echo "$PYVERSION and $VERSION are not compatible" exit 1 fi cd .. GZIP="--best --no-name" tar czf ${TARFILE} ${FOLDER} rm -rf ${FOLDER} debian/tifffile.sh0000755000000000000000000000015412077015203011312 0ustar #!/usr/bin/env python import sys import tifffile if __name__ == "__main__": sys.exit(tifffile.main()) debian/copyright0000644000000000000000000000346411735345422011136 0ustar Format: http://dep.debian.net/deps/dep5/ Upstream-Name: tifffile Source: http://www.lfd.uci.edu/~gohlke/ Files: * Copyright: © 2008-2011, Christoph Gohlke, © 2008-2011, The Regents of the University of California Produced by the Laboratory for Fluorescence Dynamics. License: BSD Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holders nor the names of any contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: debian/* Copyright: © 2011 Mathieu Malaterre License: BSD Same as above debian/source/0000755000000000000000000000000012243723504010470 5ustar debian/source/format0000644000000000000000000000001411660007572011700 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000212100264722010360 0ustar 9 debian/tifffile.10000644000000000000000000000350212243723220011035 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3. .TH TIFFFILE "1" "November 2013" "tifffile 2013.11.03" "User Commands" .SH NAME tifffile \- Read image and meta-data from TIFF, STK, LSM, OME-TIFF, and FluoView files. .SH SYNOPSIS .B tifffile .RI [ options ] " files" ... .SH DESCRIPTION Only a subset of the TIFF specification is supported, mainly uncompressed and losslessly compressed 1-32 bit integer as well as 32 and 64-bit float images, which are commonly used in scientific imaging. TIFF, the Tagged Image File Format, is under the control of Adobe Systems. STK and LSM are TIFF with custom extensions used by MetaMorph respectively Carl Zeiss MicroImaging. Currently only primary info records are read for STK, FluoView, and NIH image formats. .PP Read and write image data from and to TIFF files. .SH OPTIONS .TP \fB\-\-version\fR show program's version number and exit .TP \fB\-h\fR, \fB\-\-help\fR show this help message and exit .TP \fB\-p\fR PAGE, \fB\-\-page\fR=\fIPAGE\fR display single page .TP \fB\-s\fR SERIES, \fB\-\-series\fR=\fISERIES\fR display series of pages of same shape .TP \fB\-\-nomultifile\fR don't read OME series from multiple files .TP \fB\-\-noplot\fR don't display images .TP \fB\-\-interpol\fR=\fIINTERPOL\fR image interpolation method .TP \fB\-\-dpi\fR=\fIDPI\fR set plot resolution .TP \fB\-\-debug\fR raise exception on failures .TP \fB\-\-test\fR try read all images in path .TP \fB\-\-doctest\fR runs the internal tests .HP \fB\-v\fR, \fB\-\-verbose\fR .HP \fB\-q\fR, \fB\-\-quiet\fR .SH AUTHOR Christoph Gohlke for the Debian GNU/Linux system, but may be used by others. .SH "SEE ALSO" .BR tiffdump (1), .BR tiffinfo (1). debian/patches/0000755000000000000000000000000012243723504010617 5ustar debian/patches/setuppy.patch0000644000000000000000000000163612243723220013352 0ustar Index: tifffile-20130118/setup.py =================================================================== --- /dev/null 1970-01-01 00:00:00.000000000 +0000 +++ tifffile-20130118/setup.py 2013-01-20 16:54:05.050851246 +0100 @@ -0,0 +1,23 @@ +"""A Python script to build the _tifffile extension module. + +Usage:: ``python setup.py build_ext --inplace`` + +""" + +from distutils.core import setup, Extension +import numpy + +setup(name='_tifffile', + version="2013.11.03", + description="Reads image and meta-data from many bio-scientific formats such as plain TIFF, BigTIFF, OME-TIFF, STK, LSM, NIH, ImageJ, GEL, and FluoView files", + keywords="tiff,stk,lsm", + author="Christoph Gohlke", + url="http://www.lfd.uci.edu/~gohlke/", + license="BSD", + py_modules=['tifffile'], + ext_modules=[ + Extension( + '_tifffile', ['tifffile.c'], + include_dirs=[numpy.get_include()] + )], +) debian/patches/series0000644000000000000000000000003612243723220012026 0ustar setuppy.patch bug730166.patch debian/patches/bug730166.patch0000644000000000000000000000143612243723220013103 0ustar Description: AttributeError: 'NoneType' object has no attribute 'group' Author: Philipp Kern Bug-Debian: http://bugs.debian.org/730166 Forwarded: http://bugs.debian.org/730166#19 Reviewed-By: Mathieu Malaterre --- tifffile-20131103.orig/tifffile.py +++ tifffile-20131103/tifffile.py @@ -3124,7 +3124,7 @@ def main(argv=None): search_doc = lambda r, d: re.search(r, __doc__).group(1) if __doc__ else d parser = optparse.OptionParser( usage="usage: %prog [options] path", - description=search_doc("\n\n([^|]*?)\n\n", ''), + description=search_doc("^([^\n]+)", ""), version="%%prog %s" % search_doc(":Version: (.*)", "Unknown")) opt = parser.add_option opt('-p', '--page', dest='page', type='int', default=-1,