838b84512a
added the notes I took in meetings since the beginning of the project
2020-02-14 11:30:31 +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
9ce4823e7a
improved trap binarizer : it now uses a manual threshold value to allow the user to adjust it.
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As a result, both sides of the trap are now detected
2020-02-05 12:45:16 +01:00
b4458c0697
added the processing that computes the traps mask from the clean trap image
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Bug 2804 - Faire un traitement qui détecte les pièges
2020-02-04 18:00:54 +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
a64eed47da
removed unused code
2020-01-29 12:13:16 +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
6e165b8fc6
removed unnecessary comments
2019-10-09 17:43:03 +02:00
7973cfc3ec
The Estimate White plugin now takes the selected stack as input instead of asking the user the sequence
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This makes Estimate White plugin's UI more in line with imagej's plugin conventions.
2019-10-09 17:42:32 +02:00
44dacc1a97
The user can now display just a specific channel of a sequence
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This will be useful to allow the user to perform some processings on the currently opened stack instead of choosing the stack from a list each time an image processing is launched : this will ease adjustment of image processing parameters.
2019-10-09 14:36:09 +02:00
738a3a8c25
the user can now choose parameters when performing white estimate
2019-10-08 17:54:00 +02:00
f96b4a8ff6
fixed bug that caused make install to not updating the package when plugiins change
2019-10-08 17:52:30 +02:00
1919e67e8c
fixed bug that caused make install to fail on an existing install
2019-10-08 16:41:30 +02:00
f7ad17f9e8
added a function to remove lighting non uniformity
2019-10-08 16:40:39 +02:00
0b4bb9b608
removed unused imports
2019-10-08 16:38:50 +02:00
a021464642
now that lipase is realeased as a package, I updated the user documentation accordingly
2019-10-07 12:25:01 +02:00
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
8c3a5b0d72
lipase is now released as a package on an owncloud directory
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This will ease the deployment to users.
2019-10-04 18:48:35 +02:00
61f6d9aeba
cleanup ununsed files and comments
2019-10-04 12:27:25 +02:00
1c44113747
added missing install of ij opencv plugin
2019-10-04 12:11:15 +02:00
ad07463c64
fixes to continuous integration
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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
34fc0aca26
Replaced bash scripts with makefile.
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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
78c8749aba
now jenkins build is no longer affected by a previous broken build
2019-10-01 12:45:22 +02:00
Guillaume Raffy
41c9263f81
fixed bug that caused test0001.bash to fail
2019-10-01 12:37:57 +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
696d02757a
fixed bug in jenkins file (fiji location)
2019-09-30 16:04:30 +02:00
Guillaume Raffy
3f534229fd
added install of ij-opencv-plugins in fiji, as lipase uses them
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the test of lipase can't currently succeed (it actually fails but the error is not currently detected) because lipase requires opencv.
2019-09-30 15:39:38 +02:00
Guillaume Raffy
e8f23bb445
added a plugin that allows the user to display his chosen sequence in imagej
2019-09-27 14:20:00 +02:00
Guillaume Raffy
d71793ad9c
Added the ability of the user to choose the channel for which he wants to compute the white estimate.
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As a result the Estimate White plugin is now usable.
2019-09-26 15:11:59 +02:00
Guillaume Raffy
e6217b38a3
Added 2 menu plugins that allow the user to interactively use lipase
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The 2 available plugins are:
- Define Raw Images Root: this plugin allows the user to tell lipase where the raw images are stored
- Estimate White: this plugin allows the user to trigger the computation of a white image estimate for the given sequence and the given channel (the sequence id an the channel ids are currently hardcoded but it is of course planned to make it user selectable)
These changes involved quite a lot of work:
- added the support of a lipase user settings file to store user dependent things such as the location of the lipase raw images (to allow the user to use lipase plugins without having to specify the raw images locations again an again)
- investigations on how to make different lipase plugins use a common lipase library: the library is packagesd into a jar file placed in Fiji/jars/lib, while the plugins (menu items) are placed into Fiji/plugins directory
- investigations on fiji script parameters (for plugins input output)
2019-09-26 10:25:02 +02:00
Guillaume Raffy
228ae4ab54
fixed errors detected by pylint
2019-09-18 12:34:52 +02:00
Guillaume Raffy
d973c0e1cd
now the _remove_particles method is complete
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added an average filter so that it is now equivalent to the matlab code it's based on.
2019-09-18 12:06:18 +02:00
Guillaume Raffy
1fd2fc4281
Now the grayscale morphology in estimate_white is performed in a reasonable time.
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The performance improvement is obtained by using opencv's gray morphology operators instad of imagej's
2019-09-18 10:23:21 +02:00
Guillaume Raffy
74d7f9e603
finished abstracting image processing engine
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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)
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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
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
Guillaume Raffy