Dear all,
*** TL;DR:
How do I proceed to get multiple input Datasets as ImageJ2 parameters
from open images in Fiji?
***
I was recently exploring ImageJ2 scripting in Fiji and found the
OpsThresholdIJ1Analyze template [1] in the script editor very helpful.
When trying to get more than one @net.imagej.Dataset input parameter
however, I noticed some inconsistencies.
Let me try to illustrate with the two following scripts:
# @DisplayService display
# @OpService ops
# @net.imagej.Dataset inputData1
from net.imglib2.meta import ImgPlus
display.createDisplay("my1", ImgPlus(inputData1))
The above script re-displays the current image as expected (I tried with
the Blobs sample image open, which will be re-displayed with a
non-inverted LUT.)
When I ask for two input datasets (right after a fresh start of Fiji
with only the Blobs sample image open):
# @DisplayService display
# @OpService ops
# @net.imagej.Dataset inputData1
# @net.imagej.Dataset inputData2
from net.imglib2.meta import ImgPlus
display.createDisplay("my1", ImgPlus(inputData1))
display.createDisplay("my2", ImgPlus(inputData2))
an error message is displayed: "A Dataset is required but none exist."
The same error message is displayed when I open a second image in Fiji
before running the script.
Now, when I run script #2 after script #1 was run at least once, I get a
dialog with two choices "InputData1" and "InputData2", both choice
fields containing "blobs.gif" and a number of "Untitled" entries (where
can this title be set, by the way?).
I guess that a choice is only displayed if there are ImageJ2 datasets
(i.e. wrapped ImagePlus) already available. The single input case seems
to be special-cased as it auto-wraps the currently open image.
So how do I proceed to get more than one input in ImageJ2 scripting from
open (ImageJ1-)images?
Thanks for your advice,
Regards,
Jan
[1]:
https://github.com/imagej/imagej-legacy/blob/master/src/main/resources/script_templates/Python/OpsThresholdIJ1Analyze.py
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