Grating

extra.applications.Grating1DCalibration

Grating1DCalibration(offset: Optional[int] = None, min_pixel: int = 0, max_pixel: int = 1280, sigma: float = 2.0)

Bases: SerializableMixin

Calibrate a 1D grating spectrometer.

Parameters:

Name	Type	Description	Default
offset	Optional[int]	Offset of the first pulse.	None
sigma	float	Smoothing factor to apply to data to reduce noise in pixels.	2.0

Example:

bkg_run = open_run(proposal=900485, run=590)
calib_run = open_run(proposal=900485, run=611)
scan = Scan(calib_run["SA3_XTD10_MONO/MDL/PHOTON_ENERGY", "actualEnergy"])
grating_signal = calib_run["SQS_EXP_GH2-2/CORR/RECEIVER:daqOutput", "data.adc"]
pulses = XrayPulses(calib_run)
grating_calib = Grating1DCalibration()
grating_calib.setup(grating_signal, scan, pulses)

# apply it in new data
new_run = open_run(...)
grating_calib.apply(new_run)

to_file

to_file(filename: str)

Dump all data needed for applying the calibration into an h5 file.

Parameters:

Name	Type	Description	Default
filename	str	The output file name.	required

from_file classmethod

from_file(filename: str)

Load setup saved with save previously.

setup

setup(grating_signal: KeyData, scan: Scan, pulses: XrayPulses, grating_mask: Optional[KeyData] = None)

Setup calibration.

Parameters:

Name	Type	Description	Default
grating_signal	KeyData	Where to read the grating data from. Example: signal_run["SQS_EXP_GH2-2/CORR/RECEIVER:daqOutput", "data.adc"]	required
scan	Scan	Scan object identfying where to read the undulator energy from. Example: Scan(run["SA3_XTD10_MONO/MDL/PHOTON_ENERGY", "actualEnergy"])	required
pulses	XrayPulses	Object with bunch pattern table. Example: XrayPulses(run)	required
grating_mask	Optional[KeyData]	Grating mask from the calibration system. Example: signal_run["SQS_EXP_GH2-2/CORR/RECEIVER:daqOutput", "data.mask"]	None

guess_offset

guess_offset()

Guess offset.

get_pulse_period

get_pulse_period(pulses: XrayPulses)

Estimate difference between samples in neighbour pulses.

Parameters:

Name	Type	Description	Default
pulses	XrayPulses	XrayPulses element for the run.	required

Returns: Sample difference between neighbour pulses.

apply_mask

apply_mask(arr)

Interpolate nans.

load_data

load_data()

Load calibration data.

mask_calibration_point

mask_calibration_point(energy: float, mask: bool = False, tol: float = 1.0)

If mask is False, the point at a given energy is ignored when performing the fit. A call to fit must be redone after this.

Parameters:

Name	Type	Description	Default
energy	float	Energy value, in the same units as provided in scan.	required
mask	bool	If True, keep the point. If False, remove it.	False
tol	float	Tolerance for energy matching.	1.0

fit

fit()

Fit line.

plot

plot()

Plot fit.

apply

apply(run: DataCollection, load_all: bool = True) -> xr.Dataset

Apply calibration to a new analysis run. It is assumed it contains the same settings.

Parameters:

Name	Type	Description	Default
run	DataCollection	Input run.	required
load_all	bool	If True, load all data in memory at once. This is faster, but uses more memory. Disable if not enough memory is available.	True

extra.applications.Grating2DCalibration

Grating2DCalibration(angle: float = 0.0)

Bases: SerializableMixin

Calibrate a 2D grating spectrometer.

Parameters:

Name	Type	Description	Default
angle	float	The rotation angle in degrees if the camera is not aligned.	0.0

to_file

to_file(filename: str)

Dump all data needed for applying the calibration into an h5 file.

Parameters:

Name	Type	Description	Default
filename	str	The output file name.	required

from_file classmethod

from_file(filename: str)

Load setup saved with save previously.

setup

setup(grating_signal: KeyData, scan: Scan, grating_bkg: Optional[KeyData] = None, grating_motor: Optional[KeyData] = None)

Setup calibration.

Parameters:

Name	Type	Description	Default
grating_signal	KeyData	Where to read the grating data from. Example: signal_run["SQS_DIAG3_BIU/CAM/CAM_6:daqOutput, "data.image.pixels"]	required
scan	Scan	Scan object identfying where to read the undulator energy from. Example: Scan(run["SA3_XTD10_MONO/MDL/PHOTON_ENERGY", "actualEnergy"])	required
grating_bkg	Optional[KeyData]	Where to read the grating background data from. Example: bkg_run["SQS_DIAG3_BIU/CAM/CAM_6:daqOutput, "data.image.pixels"]	None
grating_motor	Optional[KeyData]	KeyData corresponding to the motor position. Example: signal_run['SQS_DIAG3_SCAM/MOTOR/ST_AXIS_X', 'encoderPosition.value']	None

get_background_template

get_background_template()

Get the background template.

estimate_crop_roi

estimate_crop_roi(nrows: int, ncols: int)

Calculate rectangle to be selected to crop the image and avoid edge effects.

Parameters:

Name	Type	Description	Default
nrows	int	Number of pixel rows.	required
ncols	int	Number of pixel columns.	required

load_data

load_data()

Load calibration data.

crop

crop(data: ndarray) -> np.ndarray

Crop picture after rotation to avoid edges.

Parameters:

Name	Type	Description	Default
data	ndarray	The input data.	required

Returns: Cropped data.

fit

fit()

Fit line.

plot

plot()

Plot fit.

apply

apply(run: DataCollection, load_all: bool = True) -> xr.Dataset

Apply calibration to a new analysis run. It is assumed it contains the same settings.

Parameters:

Name	Type	Description	Default
run	DataCollection	Input run.	required
load_all	bool	If True, load all data in memory at once. This is faster, but uses more memory. Disable if not enugh memory is available.	True