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15 Commits

Author SHA1 Message Date
Guillaume Raffy 1ae9821a6e renamed preprocessing.py as telemos.py because it contains functions that have been translated from matlab telemos toolbox 2020-02-14 11:32:46 +01:00
Guillaume Raffy df1a9b869f refactoring: renamed width() into get_width() to avoid confusion with properties 2020-02-13 14:34:32 +01:00
Guillaume Raffy 777db445be compute_traps_mask now returns a traps mask, as expected 
- to do this I had to split test_template_matcher into 2 unit tests (one of them being  a unit test just for template matching)
 2020-02-06 15:30:36 +01:00
Guillaume Raffy cc6d89ed7c reverted unwanted change in last commit 2020-01-30 16:45:28 +01:00
Guillaume Raffy 1702d97965 now a clean trap image is computed as the median value of all traps 2020-01-30 16:44:11 +01:00
Guillaume Raffy dcf5d61f3d refactored traps detector into 3 different classes and cleaned up 2020-01-29 18:19:01 +01:00
Guillaume Raffy 224234c3e7 added code to detect the traps 
This processing will be needed to compute the traps mask
This code needs to be cleaned
 2020-01-29 12:11:43 +01:00
Guillaume Raffy f7ad17f9e8 added a function to remove lighting non uniformity 2019-10-08 16:40:39 +02:00
Guillaume Raffy fe389f7897 Fixed bug : now test0001.bash fails if the python script fails. 
This allows to now detect if the test succeeds or not. Also turned test_preprocessing into a proper unit test. This test is now much cleaner, as preprocessing.py does no longer require ij related code.
 2019-10-01 12:25:15 +02:00
Guillaume Raffy d9b8605dc2 fixed bug in plugins parameter passing that prevented test0001 to work 2019-09-30 16:18:32 +02:00
Guillaume Raffy 228ae4ab54 fixed errors detected by pylint 2019-09-18 12:34:52 +02:00
Guillaume Raffy 7994afd01a started the abstraction of the image processing engine so that the lipase image processing can be executed without imagej if it's deemed to slow in the end. 2019-09-16 15:53:27 +02:00
Guillaume Raffy e8523efd18 added nearly all of estimate_white's post processing (particles removal) 
As a result, the implementation of estimate_white is getting closer to completion. However, the performance of fiji's gray morphology is very poor, which makes it practically unusable with the default settings provided in the original code (estimateWhiteFluoImageTelemos)

Bug 2623 - Faire un traitement automatique pour les images du projet lipase
 2019-09-13 15:15:01 +02:00
Guillaume Raffy d50cd1825e fixed bug that caused test0001 to fail finding lipase module 2019-07-17 19:11:14 +02:00
Guillaume Raffy 04e46b27dd started to translate matlab telemosToolbox's preprocessing functions into jython so that they can benefit from fiji framework 
- started to write estimate_white, with its unit test
- refactor: split lipase.py into modules
- cleanup : removed unused files and unused jenkins steps
- improved jenkinsfile

Bug 2623 - Faire un traitement automatique pour les images du projet lipase
 2019-07-17 16:56:05 +02:00