how to set calibration in API

Posted by Aryeh Weiss on May 09, 2017; 1:23pm
URL: http://imagej.273.s1.nabble.com/how-to-set-calibration-in-API-tp5018687.html

I wrote a python script to import my AFM image files, and it works
great. These are small text images, with some metadata prepended, so I
used this example as a starting point:

http://imagej.net/Jython_Scripting_Examples#Creating_an_image_from_a_text_file

However, one of the things that I want to do is to set the spatial
calibration of the imported image.
Right now I am doing it this way:
IJ.run(imp, "Properties...", "channels=1 slices=1 frames=1 unit=micron
pixel_width="+str(xCal)+" pixel_height="+str(yCal)+" voxel_depth=1.0000")

where xCal and yCal are previously found from the metadata.

There must be a way to do it without this call to IJ.run

I thought to use the Calibration class:
https://imagej.nih.gov/ij/developer/api/ij/measure/Calibration.html

and this let me set the units, but I did not see a method here to change
the value of the calibration.

ImagePlus has setProperty(java.lang.String key, java.lang.Object value)

but for this I need to know the name of the key (which I suppose I can
get from the popup window of the Properties... command).

So my questions are:

1. What is the correct way to do this?

2. If setProperty() is the way to go, where in the API can I find a list
of the predefined properties?

Thank is advance.

--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]


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