Guillaume Raffy
f686d89204
imagej's headless regression no longer causes tests to fail (as these failures only happen in headless mode, see issue #6 )
...
also added a logging mechanism to reduce stdout pollution (printing to stdout doesn't play nicely with python's unittest mechanism)
2022-01-25 07:44:23 +01:00
Guillaume Raffy
4dba5a99af
now Compute_Globules_Area displays the images of detected particles
...
- this allows the user to check if the image processing settings are correct
- fixes #5
2021-11-22 14:20:58 +01:00
Guillaume Raffy
71b1ed5b8b
added image processing listener utilities
...
copied from https://subversion.ipr.univ-rennes1.fr/repos/main/projects/libraries/python but they will need admting though
2021-11-19 18:04:30 +01:00
110aa17dbb
attempted to fix a bug in mkdir_p that fails on jenkins
2020-11-24 14:26:44 +01:00
ae6de7ffef
preprocess_sequence plugin : added the ablilty to smooth the dark image to avoid infinite pixel values in the result
...
infinite pixel values happen when a pixel in the dark image has the same value as its counterpart in the white image (in a dark area, this can happen)
2020-11-24 13:57:45 +01:00
e397e3aa0f
added a preprocess sequence plugin
...
This was requested by Claire Bourlieu to ease the preprocessing. This preprocessing could easily be done manuelly with Fiji but a bit tedious...
2020-11-04 19:37:14 +01:00
7b108fde5b
notes taken at the meeting of 10/07/2020
2020-11-03 15:58:51 +01:00
4e79d33d53
added comments
2020-07-08 15:41:17 +02:00
357f5fd03b
changed location of lipase release
2020-07-08 14:31:15 +02:00
594b99884b
added notes taken at this morning's meeting
2020-07-07 15:36:19 +02:00
4836bc5f7a
fixed bug introduced in my last commit : the number of frames of a sequence was alwys 0 when no frame was missing
2020-06-23 16:18:35 +02:00
52dbaeeb4f
handle the case where the recording has been cancelled by the user and therefore the actual number of frames is lower than initially planned
2020-06-23 15:57:21 +02:00
25d0aaf0fb
fixed stupid error in Makefile relative location
2020-04-17 20:06:56 +02:00
30a491f7d6
fixed bug that caused the release mechanism to fail when the build directory contains old packages
2020-04-17 19:54:58 +02:00
ad18e2e451
more work on graffy/lipase#3 : added a plugin to detect globules based on circular symmetry.
...
- the detection is not great at the moment (15 globules detected amongst the 50), because:
1. the parameters are probably not optimal
2. the mask used is incomplete
3. some particules are very difficult to detect anyway
- added documentation
- still need some more work:
1 output the radius of detected particles
2. analyse why detection is not optimal
3. handle weights w_r and w_a
4. filter out radial profiles that are not expected
5. improve the computation of the peakness s_p
v1.02
2020-04-17 19:30:48 +02:00
97dc74f08c
configured sphinx to generate decent api documentation
...
This was primarily done to detect bad restructuredtext syntax in python code.
This allowed me to detect and fix quite a few errors. In order to fix the orrors in the output document, I also added quite a lot of docstrings, as sphinx autodoc ignores classes and functions that don't have docstrings.
This was my first experience with sphinx but I'm not quite happy with it, as it requires too much verbose and time consuming helps and hinting to produce something decent. Moreobver, it suffers from a lack of examples for non basic usage, such as :
- how to expose to the user the __item__ methods
- how to document multiple return values
- etc.
2020-04-14 18:58:03 +02:00
463cd9d0d9
added sphinx settings in order to use sphinx to check the syntax of arguments
...
I'm not planning at the moment to use sphinx to generate the user documentation, as latex seems richer....
2020-04-14 10:40:50 +02:00
5216c828fd
fixed bug that cause release_lipase_package.bash to not handle the case when the package is not in the current directory
2020-04-10 18:02:30 +02:00
2891b02d4e
and another attempt...
2020-04-10 17:53:01 +02:00
85def10051
another attempt...
2020-04-10 17:50:45 +02:00
543da2e735
still fixing relasing of packages...
2020-04-10 17:38:54 +02:00
b9f18bfb46
fix to package release (hopefully) that I broke in revent commits
2020-04-10 17:34:13 +02:00
d382139a0d
fixed bug introduced today that caused the package file to not contain jars/Lib/fr.univ-rennes1.ipr.lipase.lib.jar
2020-04-10 17:21:12 +02:00
81c0e91897
hope that the syntax for BUILD_ROOT_PATH is right this time
2020-04-10 16:41:37 +02:00
c24cb10899
fix (hopefully) jenkins syntax with BUILD_ROOT_PATH
2020-04-10 15:24:40 +02:00
595fc09571
moved the build files outside the repository
...
In order to prevent pollution of repository with temporary files, the build files can now be where the user wants via BUILD_ROOT_PATH makefile variable.
2020-04-10 15:14:33 +02:00
13eb92c76e
allows the user to choose the location of the tests output data
...
This prevents pollution of git repository with temporary files and is done via a makefile variable TESTS_OUTPUT_DATA_PATH.
2020-04-10 13:26:05 +02:00
2505d69692
forgot to commit this file in my last commit!
2020-04-08 14:29:21 +02:00
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
Guillaume Raffy
Guillaume Raffy