Annotations in DigitalMicrograph via Python

Question

Has anyone had success getting line (or any other) annotations to show using Python in DM? My code is:

img = DM.CreateImage(...)
img_disp = img.CreateImageDisplay(1)
img_disp.AddNewComponent(2, 512, 0, 512, 1000)
img.ShowImage()
del imgk

Theoretically, this should draw a horizontal line annotation, but I'm not seeing anything in my images even though I can find a child component of type 'line annotation' in the image display component. There is also the function NewLineAnnotation() in Python but I can't find a function like ComponentAddChildAtEnd() that exists in the DM scripting language.

BmyGuest · Accepted Answer · 2020-04-17 13:08:17Z

0

The problem you have is, thatShowImage() creates a new display which is not the same as your img_disp.

You have two ways of resolving this:

Either You create an imageDocument and then add the created imageDisplay to it.
Or you use the ShowImage first and then get the imageDisplay.

I would recommend the 2nd solution unless for some reason you do not want to display the image in a first place. So the code would be:

# This is a PYTHON script to be run in DigitalMicrograph
import numpy as np
img = DM.CreateImage( np.arange(120000).reshape(300, 400).copy() )
img.ShowImage()
img.GetImageDisplay(0).AddNewComponent(2, 150, 100, 150, 300)
del img

The equivalent DM-script would be:

// This is a DM-script to be run in DigitalMicrograph
image img := IntegerImage("Test",4,0,400,300) = irow
img.ShowImage()
img.ImageGetImageDisplay(0).ComponentAddNewComponent(2,150,100,150,300)

edited Apr 17, 2020 at 13:08

answered Apr 17, 2020 at 13:02

BmyGuest

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2 Comments

Luke Over a year ago

Thanks, I used the 2nd solution and it now works! Do you know a directer way to change the properties of the new annotation than using GetNthChildOfType by any chance since defining a new line annotation and then adding it to the image display doesn't seem to work in python.

BmyGuest Over a year ago

@Luke, no I don't. It seems the missing ComponentAddChild... commands in Python seem to be an oversight and should possibly just be added in one of the next releases, provided somebody files a feature-request/issue-report with the Gatan issue reporting site. Personally, I use the scripting differently. I prefer doing DM-scripts and only calling out to Python for the extended functionality where needed instead of doing all in a Python script. When really needed, I rather do a short "hybrid" script. But that's personal preference.

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