The Script Interpreter is a Read–eval–print loop allowing scripting from the command line.
Getting Started
Start it via Plugins › Scripting › Script Interpreter or by typing ⇧ Shift + [.
Usage Examples
The examples below are written in “C-like” syntax. They should work as-is e.g. in Groovy, Jython, and JavaScript, but will need adjustment for languages like Clojure whose syntax diverges more from C.
| Operation | Code |
|---|---|
| Get the active dataset | image = imageDisplay.getActiveDataset() |
| Run an op | blurred = op.run("filter.gauss", image, 5) |
| Quick display (no metadata!) | ui.show("Blurred", blurred) |
| Wrap image to dataset | ds = dataset.create(blurred) |
| Get dataset dimensionality | ds.numDimensions() |
| Get length of dim #d | ds.dimension(d) |
| Get dim #d axis type | ds.axis(d).type() |
| Override dim #d axis type | ds.axis(d).setType(Axes.CHANNEL) |
| Blend channels when displaying | ds.setCompositeChannelCount(3) |
| Wrap dataset to data view | dv = imageDisplay.createDataView(ds); dv.rebuild() |
| Set color table for channel #0 | dv.setColorTable(ColorTables.MAGENTA, 0) |
| Set color table for channel #1 | dv.setColorTable(ColorTables.GREEN, 1) |
| Set color table for channel #2 | dv.setColorTable(ColorTables.BLUE, 2) |
| Wrap data view to display | disp = display.createDisplay("Blurred", dv) |
| Get a display by title | disp = display.getDisplay("Blurred") |
Get DataView from display |
dv = disp[0] |
Get dataset from DataView |
ds = dv.getData() |
You can import Axes from net.imagej.axis, and ColorTables from net.imagej.display.
See the ImageJ2 Tutorials for more recipes.
Inspecting API of an Object
The script interpreter does not yet have tab completion. :-( But you can using the following (Python) function to list the methods of an object:
def methods(obj, prefix=""):
return "\n".join(row["name"] + "(" + row["arguments"] + ") -> " + row["returns"] for row in notebook.methods(obj, prefix))
E.g.:
>>> methods(imageDisplay, "getActive")
getActiveDataset(<none>) -> net.imagej.Dataset
getActiveDataset(net.imagej.display.ImageDisplay) -> net.imagej.Dataset
getActiveDatasetView(<none>) -> net.imagej.display.DatasetView
getActiveDatasetView(net.imagej.display.ImageDisplay) -> net.imagej.display.DatasetView
getActiveImageDisplay(<none>) -> net.imagej.display.ImageDisplay
getActivePosition(<none>) -> net.imagej.Position
getActivePosition(net.imagej.display.ImageDisplay) -> net.imagej.Position
Issues
The Script Interpreter is still somewhat immature. Currently, Groovy works fine, but there some issues with other scripting languages.
