Re: Calling Pairwise Stitch plugin from a script

Posted by Fred Damen on Jun 11, 2020; 1:10am
URL: http://imagej.273.s1.nabble.com/Calling-Pairwise-Stitch-plugin-from-a-script-tp5023466p5023488.html

Greetings Alex,

I do not seem to have this plugin, although, how I would proceed to
resolve your issue is...

Plugins>Utilities>Find Command...
Allows you to find what ImageJ thinks the command string is.

Generally I cheat and turn on recording
Plugins>Macros>Record...
and run the command that I intend to put in my java plugin.  There is a
selection for the language on the top of the recording window, albeit no
Python.

The Java code that will process your IJ.run or IJ.runPlugIn is available
online, I usually google 'imagej java classname' (in this case IJ for
classname) and the documentation and color coded source code is generally
found.  From a cursory look it seems as though your trying to use:

/** Runs the specified plugin using the specified image. */
public static Object runPlugIn(ImagePlus imp, String className, String arg)

so I assume that something like
IJ.runPlugIn(imp3, 'plugin.Stitching_Pairwise', arguments);
is what you are looking for.

I suspect that you should be able to call the Stitching_Pairwise.run or
its other methods directly, n.b., google imagej java Stitching_Pairwise.

Enjoy,

Fred


On Wed, June 10, 2020 1:42 pm, Alex wrote:

>
>
> Fred, 
> Thanks ... 
>
>>From what I can tell the IJ.run takes a string that is a command
>> (https://imagej.nih.gov/ij/developer/api/ij/IJ.html#run-ij.ImagePlus-java.lang.String-java.lang.String-),
>> where IJ.runPlugIn takes a string that is a className
>> (https://imagej.nih.gov/ij/developer/api/ij/IJ.html#runPlugIn-ij.ImagePlus-java.lang.String-java.lang.String-.  
> I'll give the string formatting a try per your suggestion.  What name do
> you suggest using other than the title for the imp objects?
> Alex
>
>
>
>
>     On Wednesday, June 10, 2020, 11:30:29 AM PDT, Fred Damen
> <[hidden email]> wrote:
>
>  Greetings,
>
> I do not use Python but...
>
> You refer to the name of the plugin slightly differently in each case, the
> name needs to pass a comparison to be considered found.
>
> String in the argument parameter need to be enclosed in [], especially if
> they include spaces.
>
> I suspect that the image titles are not the variable names. Usually some
> form of the file name.
>
> Fred
>
>
>
> On Wed, June 10, 2020 1:05 pm, Alex wrote:
>>  I'm getting closer but still not there yet ... 
>> In the FIJI script editor I can do 
>>
>> from ij import IJ
>>
>> import ij.plugin
>>
>> imp1 = IJ.openImage('/path/to/composite0.tif')
>>
>> imp2 = IJ.openImage('/path/to/composite1.tif')
>>
>> imp3 = IJ.createImage("Stitched","RGB",1,1,1)
>>
>> IJ.run(imp3, "Pairwise stitching", "first_image=" + imp1.getTitle() + "
>> second_image=" + imp2.getTitle() + " fusion_method=[Linear Blending]
>> fused_image=result.tif check_peaks=20 ignore display_fusion
>> compute_overlap subpixel_accuracy x=-1056.3646 y=-5.4877
>> registration_channel_image_1=[Only channel 1]
>> registration_channel_image_2=[Only channel 1]")
>>
>> That works.  However, in my IDE IJ.run returns
>>
>> Unrecognized command: "Pairwise stitching"
>>
>> So I'm trying 
>> from ij import IJ
>> import ij.plugin
>>
>> imp1 =
>> IJ.openImage('/Users/alex/Desktop/test_files/D12/merged/composite0.tif')
>>
>>
>> imp2 =
>> IJ.openImage('/Users/alex/Desktop/test_files/D12/merged/composite1.tif')
>>
>>
>> imp3 = IJ.createImage("Stitched","RGB",1,1,1)
>> IJ.runPlugIn('plugin.Stitching_Pairwise', imp3.getTitle(),
>>              'first_image=' + imp1.getTitle() +
>>              ' second_image=' + imp2.getTitle() +
>>              ' fusion_method=[Linear Blending]' +
>>              ' fused_image=result.tif' +
>>              ' check_peaks=20' +
>>              ' ignore display_fusion' +
>>              ' compute_overlap' +
>>              ' subpixel_accuracy' +
>>              ' x=-1056.3646 y=-5.4877' +
>>              ' registration_channel_image_1=[Only channel 1]' +
>>              ' registration_channel_image_2=[Only channel 1]')
>>
>> This seems to execute but the result is not in imp3.
>> Any thoughts would be greatly appreciated.
>>
>>
>>
>>
>>
>>
>>
>>    On Wednesday, June 10, 2020, 01:04:28 AM PDT, Alex
>> <[hidden email]> wrote:
>>
>>  I'm trying to figure out the syntax for calling the Pairwise Stitch
>> plugin from a Python Script.
>> I can get the plugin to react but I can't figure out the syntax for the
>> input arguments.  I tired the macro recorder but its hints don't seem
>> to
>> be helpful.
>> I've tried: 
>> imp1 = IJ.openImage('/path/to/image1.tif')
>> imp2 =
>> IJ.openImage('/path/to/image2.tif')IJ.runPlugIn('plugin.Stitching_Pairwise',
>> 'imp1', 'imp2')
>> That doesn't complain about argument 1 not being a string or less than 2
>> images being open, but I can't figure out how to pass the additional
>> input
>> arguments to setup the plugin, or how to return the result.
>> Any help would be greatly appreciated.
>> ThanksAlex
>>
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