Process images¶

Functions to process image files.

`clean_threshold`(images, threshold)	Cleans image stack using a fixed threshold value.
`load_images`(scans, cat, detector_key[, ...])	Load scans with 2D images.
`get_curvature`(image[, binx, biny, ...])	Get the curvature of an image.
`get_spectrum`(image, curvature[, biny])	Extract the spectrum of a single image.
`get_spectra`(images, curvature[, biny])	Extract several spectrum.

polartools.process_images.clean_threshold(images, threshold)[source]¶

Cleans image stack using a fixed threshold value.

Sets all value above the threshold to nan.

Parameters:

imagesstack of images: Images to be cleaned.
thresholdfloat, integer: Value of the threshold to be applied.

Returns:

clean_imagesstack of images: Clean images.

polartools.process_images.get_curvature(image, binx=10, biny=1, constant_offset=None, plot=False)[source]¶

Get the curvature of an image.

A second order polynomial is fit to the cross correlation of each slice using the pyrixs algorithm. See pyrixs for more details. Ideally used with an image with large intensity and a single peak.

Parameters:

imagenumpy.array or dask.array: Image to be used.
binxinteger, optional: Bin size in the horizontal direction in pixels. Defaults to 10.
binyinteger, optional: Bin size in the vertical direction in pixels. Defaults to 1.
constant_offsetinteger: Offset for the curvature. This is only relevant for the plot, does not affect the use of the curvature to extract the spectra. Defaults to None, which triggers an automatic offset calculation.
plotboolean: Flag to plot image and curvature.

Returns:

curvaturelist: List of polynomial coefficients [c0, c1, c2] where: y = c0 + c1.x + c2.x^2.

See also

pyrixs.extract()

polartools.process_images.load_images(scans, cat, detector_key, cleanup=None, normalize=None, positioner=None)[source]¶

Load scans with 2D images.

Note that this function forces explicity outputs:

If multiple scans are passed, it will return the average of the scans.
If positioner = None, it will average all images. The resulting image will have shape = (pixels_horizontal, pixels_vertical).
If positioner not None, it will not average all images. The resulting image will have shape = (positioner_size, pixels_horizontal, pixels_vertical).

Parameters:

scansiterable

List of scan_id or uids.

catdatabroker catalog

Catalog.

detector_keystring

Name of item that holds the images

cleanupdictionary, optional

Clean up functions and arguments. Available functions:

{‘threshold’: threshold_value}

For custom functions, use:

{‘function’: (myfunc, (arg1, arg2, …))} where myfunc is a function with call: myfunc(images, arg1, arg2, …) These function can be stacked. For example, the call: {‘threshold’: 100, ‘threshold’: 10, ‘function’: (myfunc, (arg1, arg2))} will run the threshold function twice with 100 and 10 as argument, then myfunc with (arg1, arg2).

normalizestring, optional

Name of detector that will be used to normalize data. Default is None.

positionerstring, optional

Name of positioner to be read. Defaults to None.

Returns:

imagesdask array: Processed images.
positioner_valuesnumpy ndarray, optional: Values of the positioner. It is only returned if positioner is not None.

polartools.process_images.process_rxes(scans, cat, detector_key, curvature, cleanup=None, normalize=None, positioner=None, biny=1)[source]¶

Wrapper with typical RXES data processing.

Parameters:

scansiterable

List of scan_id or uids.

catdatabroker catalog

Catalog.

detector_keystring

Name of item that holds the images

curvatureiterable

List of polynomial coefficients [c0, c1, c2] where: y = c0 + c1.x + c2.x^2.

cleanupdictionary, optional

Clean up functions and arguments. Available functions:

{‘threshold’: threshold_value}

For custom functions, use:

{‘function’: (myfunc, (arg1, arg2, …))} where myfunc is a function with call: myfunc(images, arg1, arg2, …) These function can be stacked. For example, the call: {‘threshold’: 100, ‘threshold’: 10, ‘function’: (myfunc, (arg1, arg2))} will run the threshold function twice with 100 and 10 as argument, then myfunc with (arg1, arg2).

normalizestring, optional

Name of detector that will be used to normalize data. Default is None.

positionerstring, optional

Name of positioner to be read. Defaults to None.

binyinteger, optional

Bin size in the vertical direction in pixels. Defaults to 1.

Returns:

spectrum or spectraarray: Processed spectrum (if positioner is None) or spectra (if positioner is not None).
positioner_valuesnumpy ndarray, optional: Values of the positioner. It is only returned if positioner is not None.

polartools.process_images.process_rxes_mcd(scans, cat, detector_key, curvature, cleanup=None, normalize=None, positioner=None, biny=1)[source]¶

Wrapper with typical RXES-MCD data processing.

Parameters:

scansiterable: List of scan_id or uids.
catdatabroker catalog: Catalog.
detector_keystring: Name of item that holds the images
curvatureiterable: List of polynomial coefficients [c0, c1, c2] where: y = c0 + c1.x + c2.x^2.
cleanupdictionary, optional: Clean up functions and arguments. Available functions: - {‘threshold’: threshold_value} For custom functions, use: - {‘function’: (myfunc, (arg1, arg2, …))} where myfunc is a function with call: myfunc(images, arg1, arg2, …) These function can be stacked. For example, the call: {‘threshold’: 100, ‘threshold’: 10, ‘function’: (myfunc, (arg1, arg2))} will run the threshold function twice with 100 and 10 as argument, then myfunc with (arg1, arg2).
normalizestring, optional: Name of detector that will be used to normalize data. Default is None.
positionerstring, optional: Name of positioner to be read. Defaults to None.
binyinteger, optional: Bin size in the vertical direction in pixels. Defaults to 1.
Returns
——-
rxesarray: Processed x-ray emission spectrum(if positioner is None) or spectra (if positioner is not None).
mcdarray: Processed x-ray emission dichroism spectrum (if positioner is None) or spectra (if positioner is not None).
positioner_valuesnumpy ndarray, optional: Values of the positioner. It is only returned if positioner is not None.