I'm running SITK on ipython trying to get a handle on how it works and as part of it i'm trying to open an image by:
sitk.show(image)
But when imageJ opens I get this error: File is not in a supported format, a reader plugin is not available, or it was not found:
/tmp/TempFile-142820.nii
I did a quick search and it looks like I need to add the HandleExtraFileTypes plugin, I've looked at Problems with an ImageJ plugin and http://imagej.net/plugins/file-handler.html but I can't figure out how to implement this plugin into imageJ. I can't seem to find a "plugins" folder for imageJ. I'm running all of this on a mac by the way.
Any help would be much appreciated.
After downloading the plugin file, in ImageJ plugin menu, pick install, select the file/folder you downloaded and ImageJ will install it (ImageJ finds the plugin folder for you here). Restart ImageJ and the plugin should work.
Related
I have downloaded imageJ source and imported into Eclipse. At the moment, I'm working on a plugin for imageJ and I can run imageJ with my plugin from eclipse and debug if I want. My problem is that I wish to init imageJ from eclipse but with the bioformats reader plugin loaded so I could open .lif files. How can I introduce this plugin into the imageJ source code? I have tried to add dependecies to the .jar file of bioformats in my project but it doesn't work.
Do not copy around source files, nor JAR files. You should manage your project dependencies using Maven or similar 21st century build tool (Gradle is also effective). Add a dependency on net.imagej:ij and ome:formats-gpl and maybe other Bio-Formats artifacts, as you need.
See also:
The Development page of the ImageJ wiki.
The minimal-ij1-plugin example
Just for who ever is looking at the same problem:
Download all the source code: https://github.com/openmicroscopy/bioformats
Copy the folder: bioformats-develop\components\bio-formats-plugins\src to your project.
Copy loci.plugins.LociImporter.java to ij.plugin.
Delete loci.plugins.LociImporter.java
Modify ij.plugin.LociImporter.java and add the line of arg:
public void run(String arg) {
DebugTools.enableLogging("INFO");
arg = "location=[Local machine] windowless=false "; //<-This one
[...]
}
Modify loci.plugins.in.Importer.java:
//import loci.plugins.LociImporter;//substitute this import per
import ij.plugin.LociImporter;//this one
Modify ij.Menus.java:
[...]
Menu importMenu = getMenu("File>Import", true);
addPlugInItem(importMenu, "Bio-Formats", "ij.plugin.LociImporter",0,false); //<-Add this line
[...]
Add bioformats.jar as an external lib to the project.
Run the project. Now you can open .lif from file->import->Bio-Formats. With this modification you won't be able to do drag and drop but you will be able to use this plugin just opening files with this menu. As this is only using the "import" this is only useful for opening. If you want something about saving, you should call loci.plugins.LociExporter("") in the same way I did for the import. (actually with my modification we are calling ij.plugin.LociImporter("location=[Local machine] windowless=false ")
I am trying to learn about native Android, using NDK.
I find some sample projects in NDK folder and on the Internet. After much configuration, they are runnable.
But, my problem is: when I open a .c or .h file in JNI folder with Eclipse (just want to see what it is), Eclipse shows many error in this file. For example, it don't know what is JNIEnv, jobject, jstring.
I haven't made any change in the project, just opening it. Errors mean I can't rerun it again except if I delete it from the workspace then reimport it.
Eclipse does not work well with C/C++ files. At least, for me it did not.
After some search, I have managed to configure Code::Blocks to support NDK, please see this answer to the question:
Need a simple Linux C++ IDE (Android NDK) .
I am trying to create a plugin that will automatically generate an external tool when eclipse opens. I have looked into some options and it seems the best way to get it done is by loading a .launch file, with the information to create the external tool, into eclipse when the plugin is run. Up to now I have not been able to find a way to do this, does anyone know how it could be accomplished?
You can use DebugUITools to launch your .launch file. More information you can find in this eclipse article.
For almost every library I've come to see a link of the JAVADOCS jar to be downloaded, plain and simple. Why There is no jar for SWT ? and if there is why it's not on their website ..
Please note that I know there is a version in Eclipse help, and there is an online version, which I can't link to cause It doesn't validate cause it's in php ! no Index.html found
Though that's not what I'm looking for I tried it, I'm using SWT.jar and I want to attach the javadocs jar to it so when CTRL+Space and highlight a method I just see the docs right away beside etc you know..
Anyway Because I think SWT is so great I feel like there is a simple way to do that and I just can't see it maybe. if there is nothing I think I should file a feature request or somethin' to them.
Ok I kinda knew this question was not going to get much interest, so I gave it another try and I came back cause I don't want anyone to waste 1 hour of trying to figure out something like that..
Download the swt zip
Go to eclipse and load existing project
you'll find src.zip in that project
unzip src.zip and copy the folder "org" org\eclipse\swt..
paste that folder in src (inside the project)
select org folder in eclipse then go to project >> generate javadocs
If you're in windows you probably going to press on (Configure) to pick up the Javadoc.exe file it's in the C:\programFiles\java\jdk-xyz\bin\
choose where you want to drop the doc files, next then finish
ok, just go to the files and zip it, P.S zip the files don't zip the folder which contains the files cause when you load the docs as archive and validate it won't see the index.html
if you want to know how to load the archive, google it's in (in project properties>> java buildpath >> libraries tab >> swt jar >> add jar >> add your SWT.jar then expand and edit the javadoc location..
That was Robo detailed I know, I just don't want someone to read this and still can't do it
The suggested way to develop SWT apps is by following the instructions at Developing SWT applications using Eclipse. Each download page of eclipse includes an SWT section with SWT source complete zips.
The second way as mentioned is to look in your eclipse/plugins directory and use the 2 arch compatible jars provided there:
org.eclipse.swt.gtk.linux.x86_64_3.7.0.v3735b.jar
org.eclipse.swt.gtk.linux.x86_64.source_3.7.0.v3735b.jar
The source jar can be attached so as to provide javadoc. The javadoc (for most of the API shipped with eclipse) is stored in the eclipse/plugins/org.eclipse.platform.doc.isv_3.7.0.v20110602-0800.jar jar. If you unzip that, it should be in reference/api
I know that Eclipse is setting up a maven repository, although a quick scan for org.eclipse.swt only found 3.6.2 binaries and source. See http://maven.eclipse.org. They're still in they trail phase.
I've followed this tutorial:
Eclipse Plugin
This tutorial explain why create a HTML Editor.
I need a Text editor,just for auto-highlight some words, anyway I thought this tuto should be a good one to start with.
The thing is that I created the Plugin project and the only thing that I changed it was the extension "pat" instead "html, htm", just that. After that I created a .pat file, but eclipse doesn't open it with my plugin, and my text editor is not in the editor's list.
Any suggestion??
Let me know if you need more information.
My guess is that you have just created the plugin, but aren't running it in your current Eclipse instance. That can be verified by opening the view "Plugin registry". That will show a list of all plugins, see if the plugin you have created is in that list.
If you click on the run button in Eclipse you will open a run configuration dialog. In one of the tabs, you get to choose what plugins should be available. Make sure your plug-in is selected. This will start up a new Eclipse instance that will run your plugin.
To make your plugin be a part of your ordinary Eclipse installation, you will need to export it to a jar and copy that jar to the dropins catalog.