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lipase
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18 Commits

Author SHA1 Message Date
Guillaume Raffy e397e3aa0f added a preprocess sequence plugin 
This was requested by Claire Bourlieu to ease the preprocessing.  This preprocessing could easily be done manuelly with Fiji but a bit tedious...
 2020-11-04 19:37:14 +01:00
Guillaume Raffy ad18e2e451 more work on graffy/lipase#3 : added a plugin to detect globules based on circular symmetry. 
-  the detection is not great at the moment (15 globules detected amongst the 50), because:
  1. the parameters are probably not optimal
  2. the mask used is incomplete
  3. some particules are very difficult to detect anyway
- added documentation
- still need some more work:
  1  output the radius of detected particles
  2. analyse why detection is not optimal
  3. handle weights w_r and w_a
  4. filter out radial profiles that are not expected
  5. improve the computation of the peakness s_p

v1.02
 2020-04-17 19:30:48 +02:00
Guillaume Raffy d382139a0d fixed bug introduced today that caused the package file to not contain jars/Lib/fr.univ-rennes1.ipr.lipase.lib.jar 2020-04-10 17:21:12 +02:00
Guillaume Raffy 595fc09571 moved the build files outside the repository 
In order to prevent pollution of repository with temporary files, the build files can now be where the user wants via BUILD_ROOT_PATH makefile variable.
 2020-04-10 15:14:33 +02:00
Guillaume Raffy 13eb92c76e allows the user to choose the location of the tests output data 
This prevents pollution of git repository with temporary files and is done via a makefile variable TESTS_OUTPUT_DATA_PATH.
 2020-04-10 13:26:05 +02:00
Guillaume Raffy e8b1e331fe added a function that creates an image containing a circle 
this function will be used for to complete #3
 2020-04-02 15:52:43 +02:00
Guillaume Raffy e3ab3b6140 v1.01 : added the "Ipr/Lipase/Compute Globules Area" plugin 
fixes #2
 2020-03-27 16:49:21 +01:00
Guillaume Raffy 57c594cf4d added documentation 2020-03-18 16:26:32 +01:00
Guillaume Raffy 68e2c82eae improved documentation: 
- fixed markdown issues
- added minutes for today's meeting
- now make clean also cleans the documentation temporary files
 2020-02-14 18:27:30 +01:00
Guillaume Raffy f96b4a8ff6 fixed bug that caused make install to not updating the package when plugiins change 2019-10-08 17:52:30 +02:00
Guillaume Raffy 1919e67e8c fixed bug that caused make install to fail on an existing install 2019-10-08 16:41:30 +02:00
Guillaume Raffy 38b5d2c6fb fixed bug in makefile that caused the lipase package to have absolute paths instead of relative paths 2019-10-07 12:05:25 +02:00
Guillaume Raffy 8c3a5b0d72 lipase is now released as a package on an owncloud directory 
This will ease the deployment to users.
 2019-10-04 18:48:35 +02:00
Guillaume Raffy 1c44113747 added missing install of ij opencv plugin 2019-10-04 12:11:15 +02:00
Guillaume Raffy ad07463c64 fixes to continuous integration 
1. I forgot to specify fiji and raw data locations in jenkinsfile
2. the absence of fiji wasn't detected by the test
 2019-10-04 11:47:34 +02:00
Guillaume Raffy 34fc0aca26 Replaced bash scripts with makefile. 
The resulting system is clearer and more generic (easier to change location of fiji or root images, as it is now located in one single place :  the makefile). Some actions such as the installation of fiji are left as scripts outside the makefile.
 2019-10-04 11:36:53 +02:00
Guillaume Raffy 5166363522 added basic jenkins file to automate the build of hello 2019-03-07 10:56:01 +01:00
Guillaume Raffy 6e903069ec added dummy program to test jenkins 2019-03-07 10:32:23 +01:00