8f6d1188e5
added a a method that estimates the global area of globules over time
2020-03-18 16:33:14 +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
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
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
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
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
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
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
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
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
Guillaume Raffy