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Benjamin Rosemann<p>Ein lang ersehnter Wunsch von mir: Eigene <a href="https://mastodon.social/tags/Clustering" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Clustering</span></a> Methoden in <a href="https://mastodon.social/tags/OpenRefine" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenRefine</span></a> benutzen.</p><p>Verfügbar seit Version 3.9.0 und funktioniert seit 3.9.3 auch mit <a href="https://mastodon.social/tags/Jython" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Jython</span></a> und <a href="https://mastodon.social/tags/Clojure" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Clojure</span></a>.</p><p>Hier eine Anleitung zur Benutzung im <a href="https://mastodon.social/tags/FDMLab" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FDMLab</span></a> Blog.</p><p><a href="https://fdmlab.landesarchiv-bw.de/workshop/openrefine-fortgeschrittene/19-erweitertes-clustering/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">fdmlab.landesarchiv-bw.de/work</span><span class="invisible">shop/openrefine-fortgeschrittene/19-erweitertes-clustering/</span></a></p><p><a href="https://mastodon.social/tags/LandesarchivBW" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>LandesarchivBW</span></a></p>
Albert Cardona<p>True as always that the way to make software run faster is to make it do less operations. After all, CPUs can only execute a fixed number of operations per unit of time.</p><p>Here, I tweaked code for serial section registration that drops execution time from 27 seconds to 100 milliseconds: a 270x speed up.</p><p>All it had to do is to search for matching SIFT features in one image only within a predetermined radius centered on one SIFT feature in another image. Extremely effective for when e.g., the maximum translation is known.</p><p>The matching code using a KDTree:<br><a href="https://github.com/acardona/scripts/blob/master/java/asm/my/PointMatchesFast.java#L56" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/acardona/scripts/bl</span><span class="invisible">ob/master/java/asm/my/PointMatchesFast.java#L56</span></a></p><p>The test script:<br><a href="https://github.com/acardona/scripts/blob/dev/python/imagej/FIBSEM/tests/test_matchNearbyFeatures.py" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/acardona/scripts/bl</span><span class="invisible">ob/dev/python/imagej/FIBSEM/tests/test_matchNearbyFeatures.py</span></a></p><p><a href="https://mathstodon.xyz/tags/FijiSc" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FijiSc</span></a> <a href="https://mathstodon.xyz/tags/java" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>java</span></a> <a href="https://mathstodon.xyz/tags/jython" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>jython</span></a> <a href="https://mathstodon.xyz/tags/volumeEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>volumeEM</span></a> <a href="https://mathstodon.xyz/tags/vEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>vEM</span></a></p>
Joxean Koret (@matalaz)<p>Some questions regarding Ghidra:</p><p>* NetworkX libraries don't support Jython, right?<br>* Which Python 3.X bridge is the most used for Ghidra? Is it Ghidrathon? Or perhaps ghidra-bridge?<br>* Do you happen to know if there are differences big enough to worry about supporting Ghidrathon or Ghidra Bridge?</p><p><a href="https://mastodon.social/tags/Ghidra" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Ghidra</span></a> <a href="https://mastodon.social/tags/NetworkX" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>NetworkX</span></a> <a href="https://mastodon.social/tags/Jython" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Jython</span></a> <a href="https://mastodon.social/tags/Ghidrathon" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Ghidrathon</span></a> <a href="https://mastodon.social/tags/GhidraBridge" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>GhidraBridge</span></a><br><a href="https://mastodon.social/tags/Python3" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Python3</span></a> <a href="https://mastodon.social/tags/Python2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Python2</span></a></p>
Albert Cardona<p><span class="h-card" translate="no"><a href="https://aus.social/@geordie" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>geordie</span></a></span> </p><p>Here is an old-school image processing tutorial for <a href="https://mathstodon.xyz/tags/FijiSc" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FijiSc</span></a> in <a href="https://mathstodon.xyz/tags/jython" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>jython</span></a> 2.7 (python for java):</p><p><a href="https://syn.mrc-lmb.cam.ac.uk/acardona/fiji-tutorial/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">syn.mrc-lmb.cam.ac.uk/acardona</span><span class="invisible">/fiji-tutorial/</span></a></p><p>Enjoy!</p>
Tamir Bahar<p>The many wonders of supporting a Python2.7 project in 2023...</p><p>Thank, Jython!</p><p><a href="https://mastodon.social/tags/python" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>python</span></a> <a href="https://mastodon.social/tags/jython" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>jython</span></a> <a href="https://mastodon.social/tags/ghidra" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ghidra</span></a></p>
Albert Cardona<p>The underlying source code is here, if you want to try registering pairs of images with a non-linear transformation such as a thin-plate spline, on the basis of blockmatching features:</p><p><a href="https://github.com/acardona/scripts/blob/master/python/imagej/examples/blockmatching_elastic_registration_X-ray.py" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/acardona/scripts/bl</span><span class="invisible">ob/master/python/imagej/examples/blockmatching_elastic_registration_X-ray.py</span></a></p><p><a href="https://mathstodon.xyz/tags/FijiSc" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FijiSc</span></a> <a href="https://mathstodon.xyz/tags/jython" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>jython</span></a> <a href="https://mathstodon.xyz/tags/ImageProcessing" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ImageProcessing</span></a> <a href="https://mathstodon.xyz/tags/java" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>java</span></a></p>
Albert Cardona<p>Every time I need to run an image processing task, the open source software <a href="https://mathstodon.xyz/tags/FijiSc" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FijiSc</span></a> delivers. </p><p>The javadocs are up to date <a href="https://javadoc.scijava.org/" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="">javadoc.scijava.org/</span><span class="invisible"></span></a> , the libraries just work – particularly <a href="https://mathstodon.xyz/tags/ImgLib2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ImgLib2</span></a> <a href="https://imagej.net/libs/imglib2/" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="">imagej.net/libs/imglib2/</span><span class="invisible"></span></a></p><p>And the examples of my own tutorial <a href="https://syn.mrc-lmb.cam.ac.uk/acardona/fiji-tutorial/" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">syn.mrc-lmb.cam.ac.uk/acardona</span><span class="invisible">/fiji-tutorial/</span></a> written in python 2.7 for the <a href="https://mathstodon.xyz/tags/JVM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>JVM</span></a> (<a href="https://mathstodon.xyz/tags/jython" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>jython</span></a>), despite some being a decade old, they all just work. Grateful every day for the outstanding backwards compatibility plus the new plugins and libraries that continue to grow <a href="https://fiji.sc" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="">fiji.sc</span><span class="invisible"></span></a></p><p>Many thanks to the many, many developers and maintainers, particularly Curtis Rueden, who is presently cutting out a new release: 2.11.0 <a href="https://forum.image.sc/t/plugin-maintainers-can-you-test-fiji-2-11-0/78852/18" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">forum.image.sc/t/plugin-mainta</span><span class="invisible">iners-can-you-test-fiji-2-11-0/78852/18</span></a></p><p><a href="https://mathstodon.xyz/tags/ImageProcessing" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ImageProcessing</span></a></p>
Brian Schlining :verified:<p><span class="h-card"><a href="https://mastodon.social/@lodurel" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>lodurel</span></a></span> </p><p>Rough timeline of my programming language use:</p><p>1. <a href="https://hachyderm.io/tags/Basic" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Basic</span></a> - 1978<br>2. <a href="https://hachyderm.io/tags/Matlab" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Matlab</span></a> - 1995-present<br>3. <a href="https://hachyderm.io/tags/Java" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Java</span></a> - 1997-present<br>4. <a href="https://hachyderm.io/tags/C" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>C</span></a> - 1999-2016<br>5. <a href="https://hachyderm.io/tags/Python" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Python</span></a> - 2002-present<br>6. <a href="https://hachyderm.io/tags/Jython" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Jython</span></a> - 2002-2003<br>7. <a href="https://hachyderm.io/tags/Groovy" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Groovy</span></a> - 2003-2010<br>8. <a href="https://hachyderm.io/tags/Objective" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Objective</span></a>-C - 2003-2006<br>9. <a href="https://hachyderm.io/tags/Scala" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Scala</span></a> - 2010-present<br>10. <a href="https://hachyderm.io/tags/JavaScript" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>JavaScript</span></a> - 2020-present<br>11. <a href="https://hachyderm.io/tags/TypeScript" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>TypeScript</span></a> - 2021-present</p>
Albert Cardona<p><span class="h-card"><a href="https://mastodon.social/@hynek" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>hynek</span></a></span> Same here—my best online posts are notes to future self, for e.g., image processing code snippets I don’t want to relearn. Here, some in <a href="https://mathstodon.xyz/tags/jython" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>jython</span></a> driving <a href="https://mathstodon.xyz/tags/FijiSc" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FijiSc</span></a>’s <a href="https://mathstodon.xyz/tags/java" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>java</span></a> libraries to register images, transform N-dimensional images, visualise them in 2d/3d/4d, make GUIs, and more: <a href="https://syn.mrc-lmb.cam.ac.uk/acardona/fiji-tutorial" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">syn.mrc-lmb.cam.ac.uk/acardona</span><span class="invisible">/fiji-tutorial</span></a> I hear many found these useful.</p>
Albert Cardona<p>For an introduction to <a href="https://qoto.org/tags/FijiSc" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FijiSc</span></a> from the comfort of <a href="https://qoto.org/tags/python" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>python</span></a> (or rather, <a href="https://qoto.org/tags/jython" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>jython</span></a> 2.7), see my online tutorial, walking you through image processing concepts with working code that you can copy-paste into the Script Editor, which has code autocompletion to facilitate class and method discovery across the many libraries: <a href="https://syn.mrc-lmb.cam.ac.uk/acardona/fiji-tutorial/" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">syn.mrc-lmb.cam.ac.uk/acardona</span><span class="invisible">/fiji-tutorial/</span></a></p>