graffy
/
lipase
1
0
Fork 0
Code Issues 2 Pull Requests Releases Wiki Activity

Commit Graph

  • e9e0ac3a6c now jenkins sends an e-mail to guillaume raffy when the validation fails master Guillaume Raffy 2022-03-16 10:48:54 +0100
  • 50c145e491 added find_dark2 (improved find_dark method) Guillaume Raffy 2022-03-10 19:50:52 +0100
  • d6046e1b8a cleaned up and fixed notebook as it wasn't actually working from fresh Guillaume Raffy 2022-03-10 18:34:26 +0100
  • e487d92307 investigated a method to estimate the dark for images that have been captured with missing reference dark images. Guillaume Raffy 2022-03-10 12:09:15 +0100
  • fcd9dde587 added a figure to show another sequence type (globules without trap) Guillaume Raffy 2022-03-08 18:32:20 +0100
  • af6fdffdd3 added notes taken about last meeting Guillaume Raffy 2022-02-23 10:51:04 +0100
  • 4932427663 display sequence will now allow the loading of sequences with missing frames Guillaume Raffy 2022-01-26 22:25:42 +0100
  • 2acff0f175 display sequence now presents the list of sequences in a sorted way Guillaume Raffy 2022-01-26 18:47:33 +0100
  • 6882b4af35 display sequence now gives a title to the images it opens. Guillaume Raffy 2022-01-26 18:11:17 +0100
  • d5f948d304 the channel chooser of `Display Sequence` plugin is now properly populated at startup Guillaume Raffy 2022-01-25 17:11:27 +0100
  • 5b107236c9 Handle the case where the user selects a Pos<n> directory as raw image root Guillaume Raffy 2022-01-25 16:16:31 +0100
  • ebcfb1747f raw images root path now supports directory paths that contain non ascii characters Guillaume Raffy 2022-01-25 15:40:53 +0100
  • 442645d710 prevented the console window to appear and diaply messages that are irrelevant to users. Guillaume Raffy 2022-01-25 14:53:37 +0100
  • dbc22ea3b1 Display Sequence now displays an informative messagebox inseatd of crashing when the list of sequence is empty Guillaume Raffy 2022-01-25 12:33:09 +0100
  • 74d78d21e2 added notes taken in past 2 meetings related to lipase Guillaume Raffy 2022-01-25 07:45:38 +0100
  • f686d89204 imagej's headless regression no longer causes tests to fail (as these failures only happen in headless mode, see issue #6) Guillaume Raffy 2022-01-25 07:44:23 +0100
  • 4dba5a99af now Compute_Globules_Area displays the images of detected particles Guillaume Raffy 2021-11-22 14:20:58 +0100
  • 71b1ed5b8b added image processing listener utilities Guillaume Raffy 2021-11-19 18:04:30 +0100
  • 110aa17dbb attempted to fix a bug in mkdir_p that fails on jenkins Guillaume Raffy 2020-11-24 14:26:44 +0100
  • ae6de7ffef preprocess_sequence plugin : added the ablilty to smooth the dark image to avoid infinite pixel values in the result Guillaume Raffy 2020-11-24 13:57:45 +0100
  • e397e3aa0f added a preprocess sequence plugin Guillaume Raffy 2020-11-04 19:37:14 +0100
  • 7b108fde5b notes taken at the meeting of 10/07/2020 Guillaume Raffy 2020-11-03 15:58:51 +0100
  • 4e79d33d53 added comments Guillaume Raffy 2020-07-08 15:41:17 +0200
  • 357f5fd03b changed location of lipase release Guillaume Raffy 2020-07-08 14:31:15 +0200
  • 594b99884b added notes taken at this morning's meeting Guillaume Raffy 2020-07-07 15:36:19 +0200
  • 4836bc5f7a fixed bug introduced in my last commit : the number of frames of a sequence was alwys 0 when no frame was missing Guillaume Raffy 2020-06-23 16:18:35 +0200
  • 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 Guillaume Raffy 2020-06-23 15:57:21 +0200
  • 25d0aaf0fb fixed stupid error in Makefile relative location Guillaume Raffy 2020-04-17 20:06:56 +0200
  • 30a491f7d6 fixed bug that caused the release mechanism to fail when the build directory contains old packages Guillaume Raffy 2020-04-17 19:54:58 +0200
  • 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 Guillaume Raffy 2020-04-17 19:30:48 +0200
  • 97dc74f08c configured sphinx to generate decent api documentation Guillaume Raffy 2020-04-14 18:58:03 +0200
  • 463cd9d0d9 added sphinx settings in order to use sphinx to check the syntax of arguments Guillaume Raffy 2020-04-14 10:40:50 +0200
  • 5216c828fd fixed bug that cause release_lipase_package.bash to not handle the case when the package is not in the current directory Guillaume Raffy 2020-04-10 18:02:30 +0200
  • 2891b02d4e and another attempt... Guillaume Raffy 2020-04-10 17:53:01 +0200
  • 85def10051 another attempt... Guillaume Raffy 2020-04-10 17:50:45 +0200
  • 543da2e735 still fixing relasing of packages... Guillaume Raffy 2020-04-10 17:38:54 +0200
  • b9f18bfb46 fix to package release (hopefully) that I broke in revent commits Guillaume Raffy 2020-04-10 17:34:13 +0200
  • d382139a0d fixed bug introduced today that caused the package file to not contain jars/Lib/fr.univ-rennes1.ipr.lipase.lib.jar Guillaume Raffy 2020-04-10 17:21:12 +0200
  • 81c0e91897 hope that the syntax for BUILD_ROOT_PATH is right this time Guillaume Raffy 2020-04-10 16:41:37 +0200
  • c24cb10899 fix (hopefully) jenkins syntax with BUILD_ROOT_PATH Guillaume Raffy 2020-04-10 15:24:40 +0200
  • 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. Guillaume Raffy 2020-04-10 15:14:33 +0200
  • 13eb92c76e allows the user to choose the location of the tests output data Guillaume Raffy 2020-04-10 13:26:05 +0200
  • 2505d69692 forgot to commit this file in my last commit! Guillaume Raffy 2020-04-08 14:29:21 +0200
  • 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. Guillaume Raffy 2020-04-08 13:38:16 +0200
  • 5a144f1907 added test test_stack_mean which was used to find bug in IJHyperstack.get_image Guillaume Raffy 2020-04-08 12:47:09 +0200
  • c42972736f fixed bug that caused IJHyperstack.getimage to be able to modify the hyperstack instance Guillaume Raffy 2020-04-08 12:43:10 +0200
  • 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. Guillaume Raffy 2020-04-07 14:15:54 +0200
  • 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) Guillaume Raffy 2020-04-06 18:49:29 +0200
  • 4daf2bfe91 now there is an image processing to compute the radial profile (needed for graffy/lipase#3). Guillaume Raffy 2020-04-06 16:35:28 +0200
  • e8b1e331fe added a function that creates an image containing a circle Guillaume Raffy 2020-04-02 15:52:43 +0200
  • 0d19ff936b forgot to add this in my last 2 commits Guillaume Raffy 2020-04-01 12:01:38 +0200
  • ab30dc2d86 - fixed bug (introduced in my last commit) that broke release_lipase_package.bash Guillaume Raffy 2020-04-01 12:00:57 +0200
  • 87e70aba22 - added user documentation for lipase imagej plugins - the lipase manual pdf document is now released Guillaume Raffy 2020-03-31 18:57:36 +0200
  • e3ab3b6140 v1.01 : added the "Ipr/Lipase/Compute Globules Area" plugin Guillaume Raffy 2020-03-27 16:49:21 +0100
  • 97af360b7b made pylint check imports now that my vscode project is properly configured Guillaume Raffy 2020-03-27 12:34:08 +0100
  • 693b8de376 attempt to make file paths also work in windows v1.00 Guillaume Raffy 2020-03-24 19:41:06 +0100
  • 7103ea2a97 added friday's meeting notes Guillaume Raffy 2020-03-24 14:49:19 +0100
  • 22c112a18d now the globules area estimator's results are stored as hdf5 files Guillaume Raffy 2020-03-20 14:36:21 +0100
  • f4aa0423ac added doc generation in jenkins continuous integration Guillaume Raffy 2020-03-18 16:42:14 +0100
  • 8f6d1188e5 added a a method that estimates the global area of globules over time Guillaume Raffy 2020-03-18 16:33:14 +0100
  • 57c594cf4d added documentation Guillaume Raffy 2020-03-18 16:26:32 +0100
  • 3c8f14f34b fixed bug that caused the plugin Estimate_White to be broken since 14/02/2020 Guillaume Raffy 2020-03-12 17:37:27 +0100
  • 76094378b9 reenabled tests that were accidentally disabled Guillaume Raffy 2020-03-12 17:09:03 +0100
  • ac93fb411f now the catalog automatically searches the sequences in the source inmage directory provided by the user Guillaume Raffy 2020-03-11 16:14:22 +0100
  • ded2856619 added a debugging mechansism so that debug images can now be turned on or off Guillaume Raffy 2020-02-14 18:28:34 +0100
  • 68e2c82eae improved documentation: - fixed markdown issues - added minutes for today's meeting - now make clean also cleans the documentation temporary files Guillaume Raffy 2020-02-14 18:27:30 +0100
  • 1ae9821a6e renamed preprocessing.py as telemos.py because it contains functions that have been translated from matlab telemos toolbox Guillaume Raffy 2020-02-14 11:32:46 +0100
  • 838b84512a added the notes I took in meetings since the beginning of the project Guillaume Raffy 2020-02-14 11:30:31 +0100
  • df1a9b869f refactoring: renamed width() into get_width() to avoid confusion with properties Guillaume Raffy 2020-02-13 14:34:32 +0100
  • 777db445be compute_traps_mask now returns a traps mask, as expected Guillaume Raffy 2020-02-06 15:30:36 +0100
  • 9ce4823e7a improved trap binarizer : it now uses a manual threshold value to allow the user to adjust it. Guillaume Raffy 2020-02-05 12:45:16 +0100
  • b4458c0697 added the processing that computes the traps mask from the clean trap image Guillaume Raffy 2020-02-04 18:00:54 +0100
  • cc6d89ed7c reverted unwanted change in last commit Guillaume Raffy 2020-01-30 16:45:28 +0100
  • 1702d97965 now a clean trap image is computed as the median value of all traps Guillaume Raffy 2020-01-30 16:44:11 +0100
  • dcf5d61f3d refactored traps detector into 3 different classes and cleaned up Guillaume Raffy 2020-01-29 18:19:01 +0100
  • a64eed47da removed unused code Guillaume Raffy 2020-01-29 12:13:16 +0100
  • 224234c3e7 added code to detect the traps Guillaume Raffy 2020-01-29 12:11:43 +0100
  • 6e165b8fc6 removed unnecessary comments Guillaume Raffy 2019-10-09 17:43:03 +0200
  • 7973cfc3ec The Estimate White plugin now takes the selected stack as input instead of asking the user the sequence Guillaume Raffy 2019-10-09 17:42:32 +0200
  • 44dacc1a97 The user can now display just a specific channel of a sequence Guillaume Raffy 2019-10-09 14:36:09 +0200
  • 738a3a8c25 the user can now choose parameters when performing white estimate Guillaume Raffy 2019-10-08 17:54:00 +0200
  • f96b4a8ff6 fixed bug that caused make install to not updating the package when plugiins change Guillaume Raffy 2019-10-08 17:52:30 +0200
  • 1919e67e8c fixed bug that caused make install to fail on an existing install Guillaume Raffy 2019-10-08 16:41:30 +0200
  • f7ad17f9e8 added a function to remove lighting non uniformity Guillaume Raffy 2019-10-08 16:40:39 +0200
  • 0b4bb9b608 removed unused imports Guillaume Raffy 2019-10-08 16:38:50 +0200
  • a021464642 now that lipase is realeased as a package, I updated the user documentation accordingly Guillaume Raffy 2019-10-07 12:25:01 +0200
  • 38b5d2c6fb fixed bug in makefile that caused the lipase package to have absolute paths instead of relative paths Guillaume Raffy 2019-10-07 12:05:25 +0200
  • 8c3a5b0d72 lipase is now released as a package on an owncloud directory Guillaume Raffy 2019-10-04 18:48:35 +0200
  • 61f6d9aeba cleanup ununsed files and comments Guillaume Raffy 2019-10-04 12:27:25 +0200
  • 1c44113747 added missing install of ij opencv plugin Guillaume Raffy 2019-10-04 12:11:15 +0200
  • ad07463c64 fixes to continuous integration Guillaume Raffy 2019-10-04 11:47:34 +0200
  • 34fc0aca26 Replaced bash scripts with makefile. Guillaume Raffy 2019-10-04 11:36:53 +0200
  • 78c8749aba now jenkins build is no longer affected by a previous broken build Guillaume Raffy 2019-10-01 12:45:22 +0200
  • 41c9263f81 fixed bug that caused test0001.bash to fail Guillaume Raffy 2019-10-01 12:37:57 +0200
  • fe389f7897 Fixed bug : now test0001.bash fails if the python script fails. Guillaume Raffy 2019-10-01 12:25:15 +0200
  • d9b8605dc2 fixed bug in plugins parameter passing that prevented test0001 to work Guillaume Raffy 2019-09-30 16:18:32 +0200
  • 696d02757a fixed bug in jenkins file (fiji location) Guillaume Raffy 2019-09-30 16:04:30 +0200
  • 3f534229fd added install of ij-opencv-plugins in fiji, as lipase uses them Guillaume Raffy 2019-09-30 15:39:38 +0200
  • e8f23bb445 added a plugin that allows the user to display his chosen sequence in imagej Guillaume Raffy 2019-09-27 14:20:00 +0200
  • d71793ad9c Added the ability of the user to choose the channel for which he wants to compute the white estimate. Guillaume Raffy 2019-09-26 15:11:59 +0200