Skip to content

Commit

Permalink
README: fix some typos and add links
Browse files Browse the repository at this point in the history
  • Loading branch information
stelfrich committed Jul 5, 2019
1 parent fe521ec commit e4b4eed
Showing 1 changed file with 20 additions and 19 deletions.
39 changes: 20 additions & 19 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -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:

Expand All @@ -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 "${project_classpath:org.knime.knip.imagej2.buddydemo}"
Expand All @@ -96,8 +97,8 @@ Development
```
-classpath "${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)
Expand Down

0 comments on commit e4b4eed

Please sign in to comment.