carandraug

Function help text in scripts and command line

octave
I guess I'm one of the few [[citation needed]] that writes Octave programs instead of only things meant to run from the Octave console. You end up with a few hundred lines of Octave and tens of functions in a single file. For debugging you just source the whole thing. I always thought that Octave's help function only handled functions in their own m files, the help text being the first or second block of comments that does not start with Author or Copyright. Read more...

My Free software activities in May 2017

free software
Octave Bugs and patches: Fixed (bug #47115) where label2rgb in the Image package would not work with labelled images of type uint32 and uint64. Reason was that behind the scenes ind2rgb from the Octave core was being used, and Octave imitates Matlab in that labelled images can only be up to uint16. That sounds like a silly limitation so I dropped it from core in ind2rgb and ind2gray. However, there's other places where that limitation is in place and needs to be lifted such as cmunique, cmpermute, and the display functions. Read more...

My Free software activities in April 2017

free software
Octave Still reviewing the pending bugs and patches for the Image package: fixed graythresh Otsu method when images have all the same value (bug #45333) by Avinoam Kalma. new function imsharpen by Avinoam Kalma. fixed normxcorr2 returning 0 for regions where image has all the same value (bug #50122) by Hartmut Gimpel. fixed computation of ellipse properties (bug #49613) by Avinoam Kalma. imreconstruct should clip marker values higher than mask instead of throwing an error (bug #48794) Somehow got myself responsible for more things. Read more...

My Free software activities in March 2017

free software
This month I finished my PhD thesis Octave Attended OctConf 2017 at CERN where I presented how I use Octave at work for microscope image analysis. The slides are online although to be honest, I prefer to keep the slides with only a few images and talk through them wile waving my arms. I am unsure how useful they are outside the context of me talking. Also at OctConf 2017, I gave two workshops: one on preparing Octave packages, and another on Autotools. Read more...

My Free software activities in February 2017

free software
Perl New release of Pod::Weaver::Section::GenerateSection to make it work in Windows and newer perl versions. New release of Pod::Weaver::Section::Legal::Complicated with a user testsuite. Until now it was an author only test because I'm afraid of changes in Dist::Zilla and Pod::Weaver but I think it's more important to have the tests available to cpantesters. New release of Dist::Zilla::PluginBundle::BioPerl which drops deprecated plugins, adds a minimal testsuite, fixes an indexing problem in CPAN, and broken links for the bugtrackers. Read more...

My Free software activities in January 2017

free software
Octave After more than 5 years as leader of the Octave Forge project, I have stepped down. That role is now handled by a team of three Octave Forge developers Julien Bect, Olaf Till, and Oliver Heimlich. Perl I made a new release of Pod::Weaver::Section::GenerateSection a Pod::Weaver plugin that allows to add sections to a module distribution from the weaver configuration. I only meant to fix two typos (caught by lintian) and ended up spending almost two days writing its test suite. Read more...

Shutdown system at a specific time

sysadmin
I need to shutdown a server at a specific hour a few days from now. The command `shutdown <https://linux.die.net/man/8/shutdown>`_ allows to specify the hour but not the day so that can't be used. It also allows to specify a number of minutes from "now" which implies computing that value. So the following can be used: sudo shutdown -h +$(($(($(date -d 'yyyy-mm-dd hh:mm:ss' +"%s") - $(date +"%s"))) / 60)) I guess there is also the `at <https://linux. Read more...

Install Bioformats in Debian and Ubuntu

bioformats sysadmin
Bioformats is not packaged in Debian and therefore, not in Ubuntu either. To install it in a way that will make it play best with the rest of the system, following the expected standards, use the following (adjusting the download URL for the bioformats version you want): sudo mkdir /usr/local/share/java/ sudo wget http://downloads.openmicroscopy.org/bio-formats/5.1.3/artifacts/bioformats_package.jar \ -O /usr/local/share/java/bioformats_package-5.1.3.jar sudo ln -s bioformats_package-5.1.3.jar \ /usr/local/share/java/bioformats_package.jar This mimics how java packages are installed by Debian. Read more...

Snapshot release of image package 2.1.1

developer image-package image-processing octave octave-forge
The image package has accumulated a lot of changes since its last release and I'm hoping to make a new release soon (to match the release of Octave 3.8.0). I have prepared a snapshot tarball (version 2.1.1) with the current development status which can be installed easily with pkg. Would be great if users of the image package could give it a try and report any problems that the many changes may have caused. Read more...

GSoC 2013: imerode and imdilate (update #6)

developer gsoc-2013 image-processing octave
Since I deviated so much from the original project while fixing the image IO functions in Octave core I decided to only focus on optimizing the imerode and imdilate in the final phase of GSoC. The reason is that these are at the core of many functions in the image package. On the original project it was planned to do all the work by expanding the __spatial_filtering__ function and that's where I previously started. Read more...
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