Posted by
Alex-2 on
Jun 10, 2020; 6:05pm
URL: http://imagej.273.s1.nabble.com/Calling-Pairwise-Stitch-plugin-from-a-script-tp5023466p5023473.html
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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