76094378b9
reenabled tests that were accidentally disabled
2020-03-12 17:09:03 +01:00
ded2856619
added a debugging mechansism so that debug images can now be turned on or off
2020-02-14 18:28:34 +01:00
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
df1a9b869f
refactoring: renamed width() into get_width() to avoid confusion with properties
2020-02-13 14:34:32 +01:00
777db445be
compute_traps_mask now returns a traps mask, as expected
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- 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
cc6d89ed7c
reverted unwanted change in last commit
2020-01-30 16:45:28 +01:00
1702d97965
now a clean trap image is computed as the median value of all traps
2020-01-30 16:44:11 +01:00
dcf5d61f3d
refactored traps detector into 3 different classes and cleaned up
2020-01-29 18:19:01 +01:00
224234c3e7
added code to detect the traps
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This processing will be needed to compute the traps mask
This code needs to be cleaned
2020-01-29 12:11:43 +01:00
f7ad17f9e8
added a function to remove lighting non uniformity
2019-10-08 16:40:39 +02:00
61f6d9aeba
cleanup ununsed files and comments
2019-10-04 12:27:25 +02:00
Guillaume Raffy
fe389f7897
Fixed bug : now test0001.bash fails if the python script fails.
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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
b7b1f81fa7
improved source code layout
2019-09-16 11:54:13 +02:00
Guillaume Raffy
669d5822d1
made test001.bash usable on my workstation in addition to jenkin server
2019-09-13 15:16:12 +02:00
Guillaume Raffy
e8523efd18
added nearly all of estimate_white's post processing (particles removal)
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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
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- 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
Guillaume Raffy
Guillaume Raffy