0d19ff936b
forgot to add this in my last 2 commits
2020-04-01 12:01:38 +02:00
ab30dc2d86
- fixed bug (introduced in my last commit) that broke release_lipase_package.bash
2020-04-01 12:00:57 +02:00
87e70aba22
- added user documentation for lipase imagej plugins
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- the lipase manual pdf document is now released
2020-03-31 18:57:36 +02:00
e3ab3b6140
v1.01 : added the "Ipr/Lipase/Compute Globules Area" plugin
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fixes #2
2020-03-27 16:49:21 +01:00
97af360b7b
made pylint check imports now that my vscode project is properly configured
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nb: my vscode project is at the moment outside git repos, so the fix to the vscode project is not visible in git. But fwiw, I declared PYTHONPATH variable in a .env file at the root of the workspace.
2020-03-27 12:34:08 +01:00
693b8de376
attempt to make file paths also work in windows
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fixes #1
2020-03-24 19:41:06 +01:00
7103ea2a97
added friday's meeting notes
2020-03-24 14:49:19 +01:00
22c112a18d
now the globules area estimator's results are stored as hdf5 files
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- saving results as hdf5 allows easy usage or exploration of results using hdfview or hdfcompass, or by any that supports hdf5 files.
- I had to add support for hdf5 file export, which was more complicate than using h5py library (which is not available in fiji's jython). So instead of using h5py, I wrote a generic hdf5 data structure (not restricted to jython), that can be saved using the jython jhdf5 library.
2020-03-20 14:36:21 +01:00
f4aa0423ac
added doc generation in jenkins continuous integration
2020-03-18 16:42:14 +01:00
8f6d1188e5
added a a method that estimates the global area of globules over time
2020-03-18 16:33:14 +01:00
57c594cf4d
added documentation
2020-03-18 16:26:32 +01:00
3c8f14f34b
fixed bug that caused the plugin Estimate_White to be broken since 14/02/2020
2020-03-12 17:37:27 +01:00
76094378b9
reenabled tests that were accidentally disabled
2020-03-12 17:09:03 +01:00
ac93fb411f
now the catalog automatically searches the sequences in the source inmage directory provided by the user
2020-03-11 16:14:22 +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
68e2c82eae
improved documentation:
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- fixed markdown issues
- added minutes for today's meeting
- now make clean also cleans the documentation temporary files
2020-02-14 18:27:30 +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
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
Guillaume Raffy