[ImageJ-devel] ImageJ2 scripting

[Jan Eglinger]

Dear Mark and Curtis,

thank you very much for the quick replies and helpful pointers!

Jan


On 27.04.2015 20:42, Curtis Rueden wrote:
> Hi Jan,
>
> Here is another version of the script, which avoids wrapping each
> Dataset in another ImgPlus (which the framework would then wrap into yet
> another Dataset....):
>
>     # @DisplayService display
>     # @OpService ops
>     # @net.imagej.Dataset inputData1
>     # @net.imagej.Dataset inputData2
>
>     inputData1.setName("my1")
>     inputData2.setName("my2")
>     display.createDisplay(inputData1)
>     display.createDisplay(inputData2)
>
> But note that you also don't need to explicitly call createDisplay. Any
> output parameters of your script will automatically have displays
> created for them. E.g.:
>
>     # @OUTPUT net.imagej.Dataset outputData
>
> Will be shown at the conclusion of the script.
>
> Apologies for the appalling lack of documentation -- it would be great
> to flesh out the wiki docs about all this.
>
> HTH,
> Curtis
>
> On Mon, Apr 27, 2015 at 1:23 PM, Mark Hiner <hiner at wisc.edu
> <mailto:hiner at wisc.edu>> wrote:
>
>     Hi Jan,
>
>     >an error message is displayed: "A Dataset is required but none exist."
>
>     This was due to limitations with the input preprocessor presenting
>     the list of datasets. Since ImagePluses aren't explicitly tracked by
>     the IJ2 framework, having an ImagePlus recognized as a Dataset
>     requires some extra layers. We had covered the single input case
>     (which is why your first script worked) but not the general
>     multi-input case. There is an issue tracking the multi-input
>     <https://github.com/imagej/imagej-legacy/issues/106> case, which I
>     resolved today. So this should work as intended in our next release
>     - and thank you for the motivation to wrap this up!
>
>     You can also manually enable ImagePlus <> Dataset synchronization to
>     ensure ImagePluses always have a corresponding Dataset:
>     http://imagej.net/Compatibility#Translation_of_data_structures
>
>     >(where can this title be set, by the way?)
>
>     For the multiple choice input selection, the labels are based on the
>     name of the input type. Since the input type is Dataset, the Dataset
>     name is used (which delegates to the wrapped ImgPlus). In your code
>     you are applying labels to the Display, but not the underlying
>     dataset - if you name the ImgPlus, or explicitly create a Dataset
>     and set its name, that name will propagate up to the input chooser
>     (and the Display). As a side note, you should use the
>     net.imagej.ImgPlus instead of the net.imglib2.meta.
>
>     An updated script would be:
>
>
>         # @DisplayService display
>         # @OpService ops
>         # @net.imagej.Dataset inputData1
>         # @net.imagej.Dataset inputData2
>
>         from net.imagej import ImgPlus
>
>         display.createDisplay(ImgPlus(inputData1, "my1"))
>         display.createDisplay(ImgPlus(inputData2, "my2"))
>
>     Hope that helps. Let me know if you have any other questions.
>
>     Best,
>     Mark
>
>     On Mon, Apr 27, 2015 at 8:58 AM, Jan Eglinger
>     <jan.eglinger at gmail.com <mailto:jan.eglinger at gmail.com>> wrote:
>
>         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
>