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Projet lipase porté par vvie
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Guillaume Raffy 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
doc configured sphinx to generate decent api documentation 2020-04-14 18:58:03 +02:00
scripts 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
src configured sphinx to generate decent api documentation 2020-04-14 18:58:03 +02:00
tests allows the user to choose the location of the tests output data 2020-04-10 13:26:05 +02:00
.gitignore started to translate matlab telemosToolbox's preprocessing functions into jython so that they can benefit from fiji framework 2019-07-17 16:56:05 +02:00
Jenkinsfile and another attempt... 2020-04-10 17:53:01 +02:00
LICENSE Initial commit 2019-03-07 10:22:51 +01:00
Makefile 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
README.md forgot to add this in my last 2 commits 2020-04-01 12:01:38 +02:00

README.md

lipase

An image processing software suite for the project lipase (Véronique Vié, Institut de Physique de Rennes)

This software suite is developed as a python script for fiji (an image processing package based on imageJ).

What it does

As the development is at its early stages, it does not much at the moment:

  • loads a sequence of images into fiji in the form of an hyperstack (5d images : width, height, depth, channels, time)

How to install

  1. make sure that fiji is installed on your computer. If not, get it from https://fiji.sc/
  2. make sure that fiji has the IJ-OpenCV-plugins
    • in Fiji, select the Help->Update... menu item
    • in the Manage update sites window, tick the IJ-OpenCV-plugins (URL = http://sites.imagej.net/IJ-OpenCV/) if it's not ticked.
    • click the close button of the Manage update sites window
    • click Apply changes button in the ImageJ Updater window
    • wait until the plugins are installed and quit Fiji
  3. Install lipase
    • lipase is released as a package named lipase-<lipase-version>.zip. This package can be built from sources using the make package command, provided you have all the build tools on your machine (make, javac, zip).
    • simply unzip the package lipase-<lipase-version>.zip in Fiji root directory
  4. launch fiji and check that you have lipase tools in the menu Plugins/Ipr/Lipase

How to use

see lipase-manual.pdf (this document can be built from sources using the make doc command, provided you have all the build tools on your machine (make, pdflatex, imagemagick)

Notes

http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:microscope_image_correlation_spectroscopy:start