Image j split #22
Closed
Image j split #22
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Sometimes, you only want to use parts of Fiji as a library, not start the interactive ImageJ. To do this, start 'Miji(false)'. By default, ImageJ will still be started (e.g. 'Miji' does the same as 'Miji(true)'). Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
While at it, almost rewrite the thing to avoid unnecessary cd'ing. Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
Unfortunately, a restart is required if Java3D was not installed, but it is as convenient now as we could make it, at least. Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
This file only contains comments, as it is meant to be published using Matlab's publish() function. Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
Signed-off-by: Stephan Preibisch <stephan.preibisch@gmx.de>
We also have to ensure that the bin folder in the MATLAB jre path is writable, otherwise it will confuse the user. Reported by Peter Beemiller Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
Now that Johannes fixed the surface plot mode of the 3D viewer, we can put this demo back. It is a demo explainging how to get the MATLAB logo rendered in 3D in Fiji 3D viewer. Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Apparently, the light was bluish, dunno whether we can do that, too :O) Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
... also if the user asked the main window to be hidden... Noticed and reported by Walter de Back. Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
In Miji.m, there it a call to fiji.User_Plugins.installScripts(); Unfortunately, this causes a nasty bug with MATLAB: calling this static method modifies the static MATLAB java path, which is normally forbidden. The consequences of that are nasty: adding a class to the dynamic class path can be refused, because it would be falsy recorded in the static path. On top of that, the static path is fsck in a weird way, with file separator from Unix, causing a mess on Windows platform. So we give it up as now. Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
In the same vein as the previous commit... Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Interoperability for the win. Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
…rrayImg Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
The Miji.m script adds Fiji.app/jars and Fiji.app/plugins to the MATLAB classpath by explicitly iterating over *.jar in these directories. Thus it was not recursing to subdirectories - notably /jars/bio-formats. The script will now recurse through subdirectories to find jars. Adapted from: http://stackoverflow.com/questions/2652630/ how-to-get-all-files-under-a-specific-directory-in-matlab
Instead of manually adding filesep let's let MATLAB decide how to make a full file path.
This proposed change removes a bug I described on imagej-dev . Any other use of javaaddpath, say to develop one's other software, loses the instance of MIJ. This is because javaaddpath automatically calls clear java. By returning the MIJ instance as a workspace object, the MIJ instance will not be cleared. The only change for the user is to call: MIJ = Miji; instead of just Miji; Signed-off by: Mark Hiner
This changes all relevant scripts from javax.vecmath to org.scijava.vecmath, since we now ship vecmath as a standard dependency!
Java 3D 1.6 now ships with Fiji. It does not need to be (and cannot be!) installed separately.
…pt spam of printing every artifact added to the classpath to the console. Related commit: imagej/imagej-matlab@2633d12 - Remove `cd ..` to stay in the same directory while loading Miji - Only turn warnings off for: `MATLAB:javaclasspath:jarAlreadySpecified`
ImageJ.m src\scripts\update
|
Sorry, I just realized that this PR is a duplicate. |
Merged
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This is a proposal.
Sometime you may want to access ImageJ Java classes from MATLAB without launching ImageJ GUI. This is particularly important if you want to execute ImageJ command from within MATLAB
parforloop (parallel computing).Apparently, this has been achieved by using the legacy
Miji(false). This is mainly becauseImageJ(false)(headless mode) never works.However,
ImageJ.mis actually made of two parts: one to add ImageJ 's jJava class paths to MATLAB, and the other to launch ImageJ GUI.My suggestion here is to split
ImageJ.minto two, so that one can add Java class paths without ImageJ GUI usingImageJ_javaaddpath.m.Alternatively, instead of splitting
ImageJ.minto two, if we can say the outcome ofImageJ_javaaddpath.m. i.e. having access to ImageJ Java classes, can be considered as headless mode, a simple change like below toImageJ.mmay be useful.Apart from being able to access Java API, what else do you need for a headless ImageJ instance?
It's OK to give up this PR if people don't like the idea. Just a try.
Best,
Kouichi