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11 Commits

Author SHA1 Message Date
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
Guillaume Raffy 76607c19fc refactor : moved catalog code in a separate module 2019-07-16 14:00:24 +02:00
Guillaume Raffy 57b3f2e074 now the code shows more clearly what it intends to do : attempts to find the white reference. 2019-07-16 11:48:39 +02:00
Guillaume Raffy 22d272733b added method to compute the median image of a sequence, in order to estimate the background 
also refactored to ease reading

note: these changes were done by me on 18/06/2019 and are still work in progress...
 2019-07-16 11:11:13 +02:00
Guillaume Raffy 874755ad2f added the computation of the measure of correlation between a fluo image and a white, with the goal of finding the white image amongst the different depths that match the best a given fluo image 2019-04-26 10:59:46 +02:00
Guillaume Raffy cf68f8900c managed to compute the image mean value 2019-04-24 12:32:16 +02:00
Guillaume Raffy 14d3535388 put all ijopencv test code into a separate file 
As a result, lipase code is no longer using ijopencv.
ijopencv, based on javacpp provides poor compatibility with
opencv's cpython bindings, not to mention it's much less
convenient. Therefore, I'm not sure that I'll use ijopencv at all...
 2019-04-12 12:53:17 +02:00
Guillaume Raffy 361fb552e7 made lots of tests to attempt to use opencv's calcHist function 
Due to the lack of documentation, I had to do a lot of tests to find out
how to use opencv in jython, as the interface is not the same as in
python...
In the end, I managed to work out a set of arguments that deosn't cause
an exception.
 2019-04-11 20:23:20 +02:00
Guillaume Raffy 44512ba4eb Reorganised directories to ease identification of sequences. 
The sequence id now cantain the id of the image capture campaign
 2019-04-01 12:26:37 +02:00
Guillaume Raffy 72011d47a4 now the hyperstack contains all the channels and enhances their contrast 2019-03-29 11:57:52 +01:00
Guillaume Raffy 7d116b4dca started the development of imagej scripts to process the images captures on soleil platform 
At this stage, the script is able to load and duisplay a sequence as an 
imageJ hyperstack
 2019-03-29 11:07:31 +01:00