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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/fast">Debian Med / fast</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/fast/commit/29f27eaea2d36fa566ffae6af5467d1277f500bc">29f27eae</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-01T17:42:28Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Write a description for the libfast-examples
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fast/commit/dc55d957e7eca0d1dcfd70777476d16f6e050666">dc55d957</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-01T17:43:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install libfast-examples description file
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/fast/commit/269aa9135b62ca4dacfe92ac24bbd507b6212407">269aa913</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-01T20:07:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Directory creation is redundant now so remove this
</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#402fe5e14f733ce6db50eed62c945aaf5e3dd504">
debian/libfast-examples.install
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<li class="file-stats">
<a href="#1b89a5b5bbc7c98270d1aa13a2ab3282a3afa103">
<span class="new-file">
+
debian/missing-sources/using_libfast-examples
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</li>
<li class="file-stats">
<a href="#e4a9b5062289a8068346ba4ead097cfb8e7131c2">
debian/patches/modify_libs_and_output.patch
</a>
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<h4>Changes:</h4>
<li id="402fe5e14f733ce6db50eed62c945aaf5e3dd504">
<a href="https://salsa.debian.org/med-team/fast/compare/1babb75b56b002c2e3d428cc56b940b71788e8ad...269aa9135b62ca4dacfe92ac24bbd507b6212407#402fe5e14f733ce6db50eed62c945aaf5e3dd504"><strong>debian/libfast-examples.install</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,3 +22,4 @@ debian/tmp/usr/fast/bin/NonLocalMeans2D usr/lib/fast</td>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC22" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">fast</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">seededRegionGrowingSegmentation</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">fast</span></span>
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">fast</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">streamImagesFromDisk</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">fast</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">fast</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">testFAST</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">fast</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">missing</span><span class="o" style="font-weight: 600;">-</span><span class="nx">sources</span><span class="o" style="font-weight: 600;">/</span><span class="nx">using_libfast</span><span class="o" style="font-weight: 600;">-</span><span class="nx">examples</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">libfast</span><span class="o" style="font-weight: 600;">-</span><span class="nx">examples</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span></pre>
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<li id="1b89a5b5bbc7c98270d1aa13a2ab3282a3afa103">
<a href="https://salsa.debian.org/med-team/fast/compare/1babb75b56b002c2e3d428cc56b940b71788e8ad...269aa9135b62ca4dacfe92ac24bbd507b6212407#1b89a5b5bbc7c98270d1aa13a2ab3282a3afa103"><strong>debian/missing-sources/using_libfast-examples</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Synopsis</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">----------</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">The libfast-examples package encompasses a variety of binaries for the "fast" package. These binaries </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">are located at /usr/lib/fast and can be selectively executed alongside either the libfast-data package or </span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">any external data. These binaries can be used for experimentation, testing the framework or even </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">used for computation.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Usage</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">----------</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">The example binaries can either use and compute your data or data from the libfast-data package. If </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">using libfast-data, download this package and extract the compressed file (FAST_Test_Data.xz) situated in </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">/usr/lib/fast. Most of the binaries will then automatically look in the newly extracted ../data </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">directory when run.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">In some cases, the path to a specific data needs to be stated. For instance, the "liverVesselSegmentation" </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">binary requires a path to the CT file as an argument.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Information about these binaries, and their source origins, can be read at https://github.com/smistad/FAST/wiki/Examples</span></pre>
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<li id="e4a9b5062289a8068346ba4ead097cfb8e7131c2">
<a href="https://salsa.debian.org/med-team/fast/compare/1babb75b56b002c2e3d428cc56b940b71788e8ad...269aa9135b62ca4dacfe92ac24bbd507b6212407#e4a9b5062289a8068346ba4ead097cfb8e7131c2"><strong>debian/patches/modify_libs_and_output.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,8 +5,8 @@ Author: Shayan Doust <hello@shayandoust.me></td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">Index: fast/CMakeLists.txt</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fast.orig/CMakeLists.txt 2019-0<span class="idiff left right">8-31 12:13:11.067543072</span> +0100</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fast/CMakeLists.txt 2019-0<span class="idiff left right">8-31 12:13:59.735356876</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fast.orig/CMakeLists.txt 2019-0<span class="idiff left right">9-01 19:24:24.824877063</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fast/CMakeLists.txt 2019-0<span class="idiff left right">9-01 19:24:49.669024504</span> +0100</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="p">@@ -34,7 +34,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> option(FAST_MODULE_WholeSlideImaging "Build whole slide imaging module" OFF)</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> option(FAST_MODULE_Clarius "Build clarius ultrasound module" OFF)</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,14 +56,12 @@ Index: fast/CMakeLists.txt</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> ## Build test executable</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> if(FAST_BUILD_TESTS)</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> add_executable(testFAST ${FAST_TEST_SOURCE_FILES} source/FAST/Algorithms/CoherentPointDrift/Rigid.cpp source/FAST/Algorithms/CoherentPointDrift/Rigid.hpp source/FAST/Algorithms/CoherentPointDrift/Affine.cpp source/FAST/Algorithms/CoherentPointDrift/Affine.hpp)</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="p">@@ -242,6 +263,10 @@</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"> # dlls automatically to the bin folder. </span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="p">@@ -243,5 +264,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> include(cmake/FASTCustomCommands.cmake)</span>
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62
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> endif(NOT FAST_BUILD_QT5 AND WIN32)</span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+execute_process(COMMAND mkdir -p usr/share/fast/assets)</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+execute_process(COMMAND cp -r ../doc/images usr/share/fast/assets)</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
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65
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+install(TARGETS FAST-STATIC DESTINATION .)</span></span>
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66
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+install(TARGETS FAST DESTINATION .)</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="idiff left right"> </span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;"><span class="idiff left right">+</span></span></span>
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68
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"> include(cmake/ModulePython.cmake)</span>
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69
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> include(cmake/InstallFAST.cmake)</span></pre>
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