Guillaume Raffy
74d7f9e603
finished abstracting image processing engine
...
all imagej related code has now been moved to ijimageengine.py
2019-09-16 16:31:33 +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
6ef25bd5e0
improved function name
2019-09-16 11:40:26 +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)
...
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
40d1fdd34b
improved speed and reliablility of jenkins build by replacing the download of the fiji package with the use of a predownloaded version.
2019-07-17 19:29:26 +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
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
21c0fd56ad
added modifications made on 09/04/2019
2019-07-16 11:12:39 +02:00
Guillaume Raffy
22d272733b
added method to compute the median image of a sequence, in order to estimate the background
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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
1c4e9f2597
fixed pep8
2019-04-12 16:28:40 +02:00
Guillaume Raffy
dcfa11694c
added documentation to wrap up ijopencv tests
2019-04-12 16:28:08 +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
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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
de1e837d60
added image proc test in continuous integration
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this test (which runes fiji image processing) will help detect
regressions.
2019-04-08 19:18:45 +02:00
Guillaume Raffy
44512ba4eb
Reorganised directories to ease identification of sequences.
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The sequence id now cantain the id of the image capture campaign
2019-04-01 12:26:37 +02:00
Guillaume Raffy
69abd7e660
made a proper documentation
2019-03-29 15:58:18 +01:00
Guillaume Raffy
f438c6f9a6
added documentation
2019-03-29 15:13:54 +01:00
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
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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
Guillaume Raffy
87923e96d9
now that we have the physix agent, we use it to build lipase, as it's more appropriate.
2019-03-21 15:44:17 +01:00
Guillaume Raffy
430e7b0c2f
as master agent fails (missing g++ compiler), made lipase buid use msspec_agent_amd64 as before
2019-03-20 15:54:49 +01:00
Guillaume Raffy
6e6ea63658
configured the jenkins file to use the agent 'master' to see if it works
2019-03-20 15:33:43 +01:00
Guillaume Raffy
5030dbc37d
and now in english
2019-03-07 14:54:41 +01:00
Guillaume Raffy
57596ffb24
and now in german! ach!
2019-03-07 14:32:11 +01:00
Guillaume Raffy
52e041f0b5
french translation
2019-03-07 11:46:05 +01:00
Guillaume Raffy
01fee2f3b2
fixed bug in shell commands
2019-03-07 11:43:41 +01:00
Guillaume Raffy
cdc261f701
fixed comments
2019-03-07 11:33:59 +01:00
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
Guillaume Raffy
64e55b0945
Initial commit
2019-03-07 10:22:51 +01:00
Guillaume Raffy