Python script to load any format supported by hyperspy directly into GMS 3.4+

gms_load_hyperspy.py

'''
Python script to load any format supported by hyperspy directly into GMS
Must be copied and pasted into Gatan DigitalMicrograph (aka Gatan Microscopy Suite) version 3.4+
Call by `load_img(filepath)` at the bottom of the script. Can not be called outside of GMS.
Does not automatically convert the data type to EELS or EDS
Written by Thomas Aarholt, see https://gist.github.com/thomasaarholt/fccf06d56ff84cf76345b44dae30871e for newer versions
Feedback and forks are very welcome.
MUST: First import of hyperspy (or scipy) must NOT be run with "Execute on background thread" checked. One
can then swap to background thread and rerun.
v. 0.3: Added delete statements to ensure python objects don't stay in memory.
v. 0.4: Added explanation for when GMS python freezes due to a numpy/GMS bug.
v. 0.5: Fix bug in offset of axes manager in DM
v. 0.6: Fix wrong order of axes calibrations
v. 0.7: Add automatic recognition of EDS and EELS spectra and support for undefined units
v. 0.71: Added warning that it must be run on main thread
v. 0.72: Only transpose data if loading EELS or EDS data (TODO: Cover all *spectrum*-images
v. 0.73: Explicitly request c-ordered copy - Thanks Bernhard!
'''

import DigitalMicrograph as DM
import hyperspy.api as hs
from pathlib import Path
import traits

def load_img(path):
    s = hs.load(path)
    if type(s) is list:
        for si in s:
            process_signal(si, path=path)
    else:
        process_signal(s, path=path)
    del s

def process_signal(s, path=""):
    #
    # DM indexes oppositely to numpy, must transpose 
    # Use hyperspy transpose to avoid having to fiddle with swapping axes
    try:
        sigtype = s.metadata.Signal.signal_type
        if "EDS" in sigtype or "EELS" in sigtype:
            axes = s.axes_manager._axes
            s = s.T
        else:
            axes = s.axes_manager._axes
    except:
        pass
    
    # Create and calibrate DM file
    img = DM.CreateImage(s.data.copy(order='C')) # (copy to avoid array being a view)
    img.SetName(s.metadata.General.title)
    
    # If EDS or EELS, add metadata before showing so that it is recognised as that type
    try:
        sigtype = s.metadata.Signal.signal_type
        if "EDS" in sigtype:
            imgTG = img.GetTagGroup()
            imgTG.SetTagAsString( "Meta Data:Signal","X-ray")
        elif "EELS" in sigtype:
            imgTG = img.GetTagGroup()
            imgTG.SetTagAsString( "Meta Data:Signal","EELS")
    except:
        pass

    for ax in axes:
        offset = ax.offset
        scale = ax.scale
        unit = ax.units
        # blank units are a special trait that GMS can't handle 
        if type(unit) is traits.trait_base._Undefined:
            unit = ""
        index = ax.index_in_axes_manager
        img.SetDimensionCalibration(index, offset, scale, unit, 0)
    img.ShowImage()

    del s
    del img

# In windows we can put the letter r in front of strings to be able to
# use backslash \ in addresses
load_img(r"C:\Users\thomasaar\OneDrive - Universitetet i Oslo\Collaboration\Oslo\Cecilie Data\2\EELS Spectrum Image.dm4") # Replace filename here