From e4b4eeda5bc1a21452e3f39132955c2b96f95281 Mon Sep 17 00:00:00 2001 From: Stefan Helfrich Date: Fri, 5 Jul 2019 08:24:51 +0200 Subject: [PATCH] README: fix some typos and add links --- README.md | 39 ++++++++++++++++++++------------------- 1 file changed, 20 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index 11fedb1..097cfd3 100644 --- a/README.md +++ b/README.md @@ -38,11 +38,13 @@ parameters can also be bound to table columns. Thus advanced workflows with different prametrizations for each image become available for high-throughput or batch processing. -We currently support a basic set of input and output parameters (for images:`Img` and `ImgPlus`) that can be -extended by core or third party developers as needed. These parameters get +We currently support a basic set of input and output parameters (for images: +[`Img`](https://javadoc.scijava.org/ImgLib2/net/imglib2/img/Img.html) and +[`ImgPlus`](https://javadoc.scijava.org/ImageJ/net/imagej/ImgPlus.html)) that can +be extended by core or third party developers as needed. These parameters get converted with adapters that translate the table centric data model of KNIME to ImageJ2 and vice versa. However, not all plugins can be executed with KNIME, -apart from suitable parameter annotations and adapters it is very important, +apart from suitable parameter annotations and adapters it is very important that a plugin supports headless execution such that it fits the "configure once execute often" paradigm of KNIME: @@ -53,41 +55,40 @@ public class ExampleCommand implements Command { } ``` -The ImageJ2 plugin comes with some pre installed example plugins , like edge -detection or the ImageJ2 shadow plugins, that demonstrate the neat integration -of KNIME and ImageJ2. Additionally an ImageJ2 version of Tubeness 1.2 +The ImageJ2 plugin comes with some pre-installed examples, like edge detection +or the ImageJ2 shadow plugins, that demonstrate the neat integration +of KNIME and ImageJ2. Additionally, an ImageJ2 version of Tubeness 1.2 (http://www.longair.net/edinburgh/imagej/tubeness/) has been included as a demonstration of a more advanced plugin (use grayscale images to test it). Most importantly, ImageJ2 plugins can easily be added to KNIME via KNIME update sites or with the local installations of the plugins (mainly intended for development purposes). To test the local installation mode go to the Image Processing Preference Page (File -> Preferences -> KNIME -> Image Processing Plugin) and -select ImageJ2 Plugin Installation, then choose an ImageJ2 plugin jar-file (with -sezpoz annotations), install it and restart KNIME. The plugins become available -in the local node repository according to the menu annotations of the plugin. +select ImageJ2 Plugin Installation, then choose an ImageJ2 plugin jar-file, install +it and restart KNIME. The plugins become availablevin the local node repository +according to the menu annotations of the plugin. The KNIME integration of ImageJ2 is currently a beta release but with the ongoing development of ImageJ2 we hope to improve the integration between both tools. However, the current version already allows to write algorithms, that run -in KNIME and ImageJ2 at the same time, without requiring a deeper knowledge of -the KNIME API. +in KNIME as well as ImageJ2, without requiring a deeper knowledge of the KNIME API. Development ------------- ### Add your own ImageJ2 plugins to KNIME -1. Setup your eclipse for KNIP development as described in +1. Set your Eclipse up for KNIP development as described in the [knip-sdk-setup](https://github.com/knime-ip/knip-sdk-setup) repository. The ``knip-sdk-nightly-full`` contains everything you'll need to start developing right away. -2. Clone this repository and import the ``org.knime.knip.imagej2.buddydemo`` project it into your workspace. +2. Clone this repository and import the ``org.knime.knip.imagej2.buddydemo`` project into your workspace. -3. From within eclipse, copy the ``org.knime.knip.imagej2.buddydemo`` project - and rename it so that it is applicable to you, e.g: ``com.example.knime.imagej2plugins``. +3. From within Eclipse, copy the ``org.knime.knip.imagej2.buddydemo`` project + and rename it to your needs, e.g: ``com.example.knime.imagej2plugins``. 3. Adjust the builder settings: - - rightclick on the project and select _Properties_ -> _Builders_, then - doubleclick on __EclipseHelper__. In the menu that opens you need to adjust + - right click on the project and select _Properties_ -> _Builders_, then + double click on __EclipseHelper__. In the menu that opens you need to adjust the code in the _Arguments_ section. Change the line: ``` -classpath "${project_classpath:org.knime.knip.imagej2.buddydemo}" @@ -96,8 +97,8 @@ Development ``` -classpath "${project_classpath:com.example.knime.imagej2plugins}" ``` - To test If everything worked out, navigate to the project directory using - your operating systems file browser, and check if the file + To test if everything worked out, navigate to the project directory using + your operating system's file browser, and check if the file ``bin/META-INF/json/plugins/json/org.scijava.plugin.Plugin`` was created. If the file was not created this could be due to a failing builder because of the system java version. See [Common Pitfalls](#common-pitfalls)