paws.core.operations.IO.CALIBRATION package

Submodules

paws.core.operations.IO.CALIBRATION.Fit2DToPONI module

class paws.core.operations.IO.CALIBRATION.Fit2DToPONI.Fit2DToPONI

Bases: paws.core.operations.Operation.Operation

Produce PONI calibration parameters from a Fit2D calibration result.

Reads in Fit2D calibration result from a text file, converts it to a dict of PyFAI PONI parameters.

WARNING: Some developers have claimed that the Fit2D software itself computes tilted geometries incorrectly. If using actual Fit2D output with tilts, it is suggested that a new calibration be attempted, with a different package (something other than Fit2D). Use tilts from Fit2D output at your own risk.

Format of text file for Fit2D parameters is expected to be: directDist=____ # sample-detector centerX=____ # beam center on detector, in pixels centerY=____ # beam center on detector, in pixels pixelX=____ # pixel width, microns pixelY=____ # pixel height, microns tilt=____ # degrees tiltPlanRotation=____ # degrees splineFile=____ # optional detector distortion correction file

run()

Operation.run() should use the Operation.inputs and set values for all of the items in Operation.outputs.

paws.core.operations.IO.CALIBRATION.NikaToPONI module

class paws.core.operations.IO.CALIBRATION.NikaToPONI.NikaToPONI

Bases: paws.core.operations.Operation.Operation

Converts Nika calibration output (saved in a text file) to a dict of PyFAI PONI parameters, by first converting from Nika to Fit2D, then using a pyFAI.AzimuthalIntegrator to convert from Fit2D to PONI format.

WARNING: the map from Nika’s horizontal and vertical tilts to Fit2D’s tilt and tiltPlanRotation has not yet been verified by the developers. Use this operation with nonzero tilts at your own risk.

Input a text file expressing results of Nika automated calibration. Output a dict of pyFAI PONI calibration parameters. Format of text file for Nika output is expected to be: sample_to_CCD_mm=____ pixel_size_x_mm=____ pixel_size_y_mm=____ beam_center_x_pix=____ beam_center_y_pix=____ horizontal_tilt_deg=____ vertical_tilt_deg=____ wavelength_A=____

run()

Operation.run() should use the Operation.inputs and set values for all of the items in Operation.outputs.

paws.core.operations.IO.CALIBRATION.ReadPONI module

class paws.core.operations.IO.CALIBRATION.ReadPONI.ReadPONI

Bases: paws.core.operations.Operation.Operation

Read in a dict of PyFAI PONI parameters. Input path to a .poni file representing a calibrated measurement geometry.

run()

Operation.run() should use the Operation.inputs and set values for all of the items in Operation.outputs.

paws.core.operations.IO.CALIBRATION.WXDToPONI module

class paws.core.operations.IO.CALIBRATION.WXDToPONI.WXDToPONI

Bases: paws.core.operations.Operation.Operation

Convert WXDIFF .calib output to a dict of PyFAI PONI parameters, by first converting from WXDIFF to Fit2D, then using a pyFAI.AzimuthalIntegrator to convert from Fit2D to PONI format.

The conversion from WXDiff parameters to Fit2D parameters was originally contributed to paws by Fang Ren.

Input .calib file from WXDIFF automated calibration, input pixel size and polarization factor, output dict of pyFAI PONI calibration parameters.

run()

Operation.run() should use the Operation.inputs and set values for all of the items in Operation.outputs.

Module contents

The INPUT.CALIBRATION category has operations for reading in calibration parameters and converting them between different formats. Some of the common formats are described here. Over time, these descriptions should improve. Contact the paws developers to contribute information or report inconsistencies.

PONI (PyFAI) FORMAT

PONI: point of normal incidence. This is the format used internally by the PyFAI (Python Fast Azimuthal Integration) package. PONI format projects the point-shaped sample orthogonally onto projector plane, and gives the coordinates of that projection as the PONI, such that the sample to PONI distance is the shortest distance from sample to detector plane. coordinate axes: x1 vertical, x2 and x3 horizontal, x3 along beam. detector axes: with zero rotations, d1 vertical, d2 horizontal, d3 along beam. axes defined on C format, first dimension is vertical, second dimension is horizontal. the first dimension (vertical) is fast, the second dimension (horizontal) is slow.

PONI dict keys and definitions: - ‘dist’: distance in meters from sample to PONI on detector plane - ‘poni1’: vertical coordinate of PONI on detector axes, in meters - ‘poni2’: horizontal coordinate of PONI on detector axes, in meters - ‘rot1’: rotation of detector body about x1, applied first, radians - ‘rot2’: rotation of detector body about x2, applied second, radians - ‘rot3’: rotation of detector body about beam axis x3, applied third, radians - ‘pixel1’: pixel dimension along d1 (vertical), meters - ‘pixel2’: pixel dimension along d2 (horizontal), meters - ‘wavelength’: wavelength in meters - ‘fpolz’: polarization factor- not actually a PONI parameter, but it’s ok to put it here - ‘detector’: optional pyFAI detector object - ‘splineFile’ optional spline file describing detector distortion

NIKA FORMAT

The calibration performed by the Nika software package uses a calibrant image, the rectangular pixel dimensions (in mm), and the wavelength (in Angstrom), to solve the sample to CCD distance in mm, the position at which the beam axis intersects the detector plane in pixels, and the horizontal and vertical tilts of the detector in degrees.

Nika does not generate a file to save calibration parameters, so they have to be recorded by hand in a file. Paws Operations should be written to read them from a file in the following format (one parameter=value per line, no spaces): - sample_to_CCD_mm=____ - pixel_size_x_mm=____ - pixel_size_y_mm=____ - beam_center_x_pix=____ - beam_center_y_pix=____ - horizontal_tilt_deg=____ - vertical_tilt_deg=____ - wavelength_A=____

FIT2D FORMAT

Detector plane origin is the bottom left corner of the detector.

Fit2D dict keys and definitions: - ‘directDist’: direct distance to detector plane along beam axis, in mm - ‘centerX’: horizontal position on the detector plane where the beam intersects, in px - ‘centerY’: vertical position on the detector plan where the beam intersects, in px - ‘pixelX’: horizontal size of pixel, in um - ‘pixelY’: vertical size of pixel, in um - ‘tilt’: detector tilt in degrees (TODO:clarify) - ‘tiltPlanRotation’: detector rotation in degrees = 360 minus WXDIFF alpha (TODO:clarify) - ‘splineFile’ optional spline file describing detector distortion

WXDIFF FORMAT

Similar to Fit2D format, but knowledge about WXDIFF is hard to come by. I hope it can be cleanly documented here over time. Detector plane origin is the bottom left corner of the detector.

.calib file lines (and notes): - imagetype=uncorrected-q TODO: describe - dtype=uint16 img data type = unsigned 16-bit integers - horsize=___ horizontal extent of image, in pixels - versize=___ vertical extent of image, in pixels - region_ulc_x=___ TODO: describe - region_ulc_y=___ TODO: describe - bcenter_x=___ horizontal coordinate where the beam axis intersects the detector plane - bcenter_y=___ vertical coordinate where the beam axis intersects the detector plane - detect_dist=___ direct distance from the sample to the detector plane intersection, along the beam axis, in pixels - detect_tilt_alpha=___ rotation of detector tilt axis plane in radians = 360 minus Fit2D tiltPlanRotation - detect_tilt_delta=___ detector tilt in radians (TODO:clarify) - wavelenght=___ the typo ‘wavelenght’ is built into wxdiff, and it is reported in angstroms - Qconv_const=___ TODO: describe