bfca19e039
more work related to graffy/lipase#3 : for each pixel, the profile of variance along the circle is now computed. This image basically measures the non-roundedness for each pixel.
2020-04-08 13:38:16 +02:00
5a144f1907
added test test_stack_mean which was used to find bug in IJHyperstack.get_image
2020-04-08 12:47:09 +02:00
c42972736f
fixed bug that caused IJHyperstack.getimage to be able to modify the hyperstack instance
2020-04-08 12:43:10 +02:00
608fefce0a
more work towards graffy/lipase#3 : replaced circle kernels with circle arc kernels, as circle arcs are needed to compute the variance of the image along the circles. Note that at the moment the code doesn't yet compute the variance.
...
This commit is not intended to change the radial profile image.
2020-04-07 14:15:54 +02:00
f0a624fc2b
more work related to graffy/lipase#3
...
- the user can now use radial profile image processing through a new plugin (Radial Profile)
- improved the computation of the radial profile : the profile is now normalised (no longer bigger weights for big circles)
2020-04-06 18:49:29 +02:00
4daf2bfe91
now there is an image processing to compute the radial profile (needed for graffy/lipase#3 ).
2020-04-06 16:35:28 +02:00
e8b1e331fe
added a function that creates an image containing a circle
...
this function will be used for to complete #3
2020-04-02 15:52:43 +02:00
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
...
- 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
...
fixes #2
2020-03-27 16:49:21 +01:00
97af360b7b
made pylint check imports now that my vscode project is properly configured
...
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
...
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
...
- 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:
...
- 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
...
- 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.
...
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
...
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
...
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
...
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
...
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
...
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
...
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.
...
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
Guillaume Raffy