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Calling Pairwise Stitch plugin from a script

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Alex-2

Calling Pairwise Stitch plugin from a script

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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Alex-2

Re: Calling Pairwise Stitch plugin from a script

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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Fred Damen

Re: Calling Pairwise Stitch plugin from a script

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 ...Â
> In the FIJI script editor I can doÂ
>
> 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.Â However, in my IDE IJ.run returns
>
> Unrecognized command: "Pairwise stitching"
>
> So I'm tryingÂ
> 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.Â I tired the macro recorder but its hints don't seem to
> be helpful.
> I've tried:Â
> 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
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Alex-2

Re: Calling Pairwise Stitch plugin from a script

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:

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Fred Damen

Re: Calling Pairwise Stitch plugin from a script

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,Â
> Thanks ...Â
>
>>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-.Â Â
> I'll give the string formatting a try per your suggestion.Â 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:
>>Â I'm getting closer but still not there yet ...ÃÂ
>> In the FIJI script editor I can doÃÂ
>>
>> 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.ÃÂ However, in my IDE IJ.run returns
>>
>> Unrecognized command: "Pairwise stitching"
>>
>> So I'm tryingÃÂ
>> 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(),
>>Â Â Â Â Â Â Â 'first_image=' + imp1.getTitle() +
>>Â Â Â Â Â Â Â ' second_image=' + imp2.getTitle() +
>>Â Â Â Â Â Â Â ' fusion_method=[Linear Blending]' +
>>Â Â Â Â Â Â Â ' fused_image=result.tif' +
>>Â Â Â Â Â Â Â ' check_peaks=20' +
>>Â Â Â Â Â Â Â ' ignore display_fusion' +
>>Â Â Â Â Â Â Â ' compute_overlap' +
>>Â Â Â Â Â Â Â ' subpixel_accuracy' +
>>Â Â Â Â Â Â Â ' x=-1056.3646 y=-5.4877' +
>>Â Â Â Â Â Â Â ' registration_channel_image_1=[Only channel 1]' +
>>Â Â Â Â Â Â Â ' registration_channel_image_2=[Only channel 1]')
>>
>> This seems to execute but the result is not in imp3.
>> Any thoughts would be greatly appreciated.
>>
>>
>>
>>
>>
>>
>>
>>Â Â On Wednesday, June 10, 2020, 01:04:28 AM PDT, Alex
>> <[hidden email]> wrote:
>>
>>Â 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.ÃÂ I tired the macro recorder but its hints don't seem
>> to
>> be helpful.
>> I've tried:ÃÂ
>> 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
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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