Pyprismatic function that saves to the hyperspy format

prism.py

def prism(file, path=None, focus=0, FP=20, alpha=20.0e-3):
    import gc
    gc.collect()
    import os
    import pyprismatic as pr
    file = os.path.abspath(file)
    
    save_path = path
    path, filename = os.path.split(file)
    name, _ = os.path.splitext(filename)
    name += '_FP{0}'.format(FP)
    #name = name + '_focus_' + str(focus)
    if save_path == None:
        save_path = path
    output = os.path.join(save_path, name + '.mrc')

    probestep = 0.1 # Å
    potential_spacing = 0.05 # Å

    include_thermal_effects = bool(FP)

    meta = pr.Metadata(
        filenameAtoms=file, 
        E0=300e3,
        potBound = 2.0,
        probeSemiangle=alpha,
        alphaBeamMax = alpha+4e-3,
        interpolationFactorX=4, 
        interpolationFactorY=4, 
        filenameOutput=output,
        probeStepX = probestep,
        probeStepY = probestep,
        realspacePixelSizeX = potential_spacing,
        realspacePixelSizeY = potential_spacing,
        detectorAngleStep = 0.001,
        sliceThickness = 1.625,
        scanWindowXMin = 0.38,
        scanWindowXMax = 0.58,
        scanWindowYMin = 0.39,
        scanWindowYMax = 0.61,
        #scanWindowXMin = 0.14,
        #scanWindowXMax = 0.855,
        #scanWindowYMin = 0.1666,
        #scanWindowYMax = 0.8333,
        numFP = FP,
        probeDefocus = focus,
        numGPUs=1,
        numThreads=10,
        includeThermalEffects=include_thermal_effects,
        tileX=1,
        tileY=1,
    )

    from time import time
    t1 = time()
    meta.go()
    t2 = time()
    print('It took',(t2 - t1)/60, 'min')

    import hyperspy.api as hs
    s = hs.signals.Signal2D(pr.fileio.readMRC(output)).as_signal2D((0,2))
    s.metadata.add_node('Simulation')
    s.metadata.Simulation.Software = 'Prismatic'
    for field in meta.fields:
        s.metadata.Simulation[field] = getattr(meta, field)

    metadata = s.metadata.Simulation
    s.axes_manager[0].name = 'Acceptance Angle'
    s.axes_manager[0].scale = metadata.detectorAngleStep*1000
    s.axes_manager[0].units = 'mrad'
    s.axes_manager[1].name = 'x'
    s.axes_manager[2].name = 'y'
    s.axes_manager[1].units = s.axes_manager[2].units = 'Å'
    s.axes_manager[1].scale = metadata.probeStepX
    s.axes_manager[2].scale = metadata.probeStepY

    s.save(os.path.join(save_path, name + '.hspy'), overwrite=True)
    print('Saved in ' + os.path.join(save_path, name + '.hspy'))
    return s