calibrate

Every OpenHSI camera is unique and requires calibration before use. This module provides the abstractions to create the calibration data which are then used in operation.

Calibration Routines

Tip

This module can be imported using from openhsi.calibrate import *

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sum_gaussians

 sum_gaussians (x:<built-infunctionarray>, *args)

Compute the summed Gaussians given the array indicies x and mushed arguments of amplitude, peak position, peak width, constant

	Type	Details
x	array	indicies
args
Returns	array	summed Gaussian curves array

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SettingsBuilderMixin

 SettingsBuilderMixin ()

Initialize self. See help(type(self)) for accurate signature.

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create_settings_builder

 create_settings_builder (clsname:str, cam_class:type)

Create a SettingsBuilder class called clsname based on your chosen cam_class.

	Type	Details
clsname	str
cam_class	type	Camera Class
Returns	type	“SettingsBuilder Class”

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SettingsBuilderMetaclass

 SettingsBuilderMetaclass (clsname:str, cam_class, attrs)

type(object_or_name, bases, dict) type(object) -> the object’s type type(name, bases, dict) -> a new type

Using the SettingsBuilderMixin

There are a few ways to create a SettingsBuilder class that words for your custom camera. (They involve Python metaclasses and mixins)

For example, you can then create a SettingsBuilder class that works for your custom camera by doing one of the following.

Note

Below we use the ‘SimulatedCamera’ class. When calibrating a real camera you would replace SimulatedCamera with your camera class.

# using helper function
SettingsBuilder = create_settings_builder("SettingsBuilder",SimulatedCamera)

# using Metaclasses
SettingsBuilder = SettingsBuilderMetaclass("SettingsBuilder",SimulatedCamera,{})

# initialising
sb = SettingsBuilder(json_path="../assets/cam_settings.json", 
                     pkl_path="../assets/cam_calibration.pkl")

Allocated 69.93 MB of RAM. There was 4892.03 MB available.

# pure mixin
class CalibrateOpenHSI(SettingsBuilderMixin, SimulatedCamera):
    pass

sb = CalibrateOpenHSI(mode="flat",json_path="../assets/cam_settings.json", pkl_path="../assets/cam_calibration.pkl")

Allocated 69.93 MB of RAM. There was 4690.48 MB available.

Find illuminated sensor area

We assume the x axis (or detector columns) are used for the spectral channels, the rows correspond to the cross-track dimension and are limited by the optics (slit). The useable area is cropped out (windowing can also be used to reduce data intake).

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SettingsBuilderMixin.retake_flat_field

 SettingsBuilderMixin.retake_flat_field (show:bool=True)

Take and store an image of with the OpenHSI slit illuminated but a uniform light source.

	Type	Default	Details
show	bool	True	flag to show taken image
Returns	Image

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SettingsBuilderMixin.update_row_minmax

 SettingsBuilderMixin.update_row_minmax (edgezone:int=4, show:bool=True)

Find edges of slit in flat field images and determine region to crop.

	Type	Default	Details
edgezone	int	4	number of pixel buffer to add to crop region
show	bool	True	flag to show plot of slice and edges identified
Returns	Curve

hvimg=sb.retake_flat_field(show=True)
hvimg.opts(width=400,height=400)
print(sb.calibration["flat_field_pic"].max())
hvimg

255

sb.update_row_minmax()

Locs row_min: 7 and row_max: 912

sb.update_resolution()

Smile Correction

The emissions lines, which should be straight vertical, appear slightly curved. This is smile error (error in the spectral dimension).

sb.mode_change("HgAr")

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SettingsBuilderMixin.retake_emission_lines

 SettingsBuilderMixin.retake_emission_lines (show:bool=True,
                                             nframes:int=10)

Take and store an image with camera illuminated with a calibration source.

	Type	Default	Details
show	bool	True	flag to show
nframes	int	10	number of frames to average for image
Returns	Image

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SettingsBuilderMixin.retake_HgAr

 SettingsBuilderMixin.retake_HgAr (show:bool=True, nframes:int=10)

Take and store an image with OpenHSI camera illuminated with a HgAr calibration source.

	Type	Default	Details
show	bool	True	flag to show
nframes	int	10	number of frames to average for image
Returns	Image

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SettingsBuilderMixin.update_smile_shifts

 SettingsBuilderMixin.update_smile_shifts (show=True)

Determine Smile and shifts to correct from spectral lines image.

	Type	Default	Details
show	bool	True	flag to show plot of smile shifts for each cross track pixel.
Returns	Curve

hvimg=sb.retake_HgAr(show=True, nframes=1)
hvimg.opts(width=400,height=400)
print(sb.calibration["HgAr_pic"].max())
hvimg

255.0

sb.update_smile_shifts()

Map the spectral axis to wavelengths

To do this, peaks in the HgAr spectrum are found, refined by curve-fitting with Gaussians. The location of the peaks then allow for interpolation to get the map from array (column) index to wavelength (nm).

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SettingsBuilderMixin.fit_emission_lines

 SettingsBuilderMixin.fit_emission_lines (brightest_peaks:list,
                                          emission_lines:list,
                                          top_k:int=10,
                                          filter_window:int=1,
                                          interactive_peak_id:bool=False,
                                          find_peaks_height:int=10,
                                          prominence:float=0.2,
                                          width:float=1.5,
                                          distance:int=10,
                                          max_match_error:float=2.0,
                                          verbose:bool=False)

Finds the index to wavelength map given a spectra and a list of emission lines. To filter the spectra, set filter_window to an odd number > 1.

	Type	Default	Details
brightest_peaks	list		list of wavelength for the brightest peaks in spectral lines image
emission_lines	list		list of emission lines to match
top_k	int	10	how many peaks to use in fit
filter_window	int	1	filter window for scipy.signal.savgol_filter. Needs to be odd.
interactive_peak_id	bool	False	flag to interactively confirm wavelength of peaks
find_peaks_height	int	10	anything above this value is free game for a peak
prominence	float	0.2	prominence for scipy.signal.find_peaks
width	float	1.5	peak width for scipy.signal.find_peaks
distance	int	10	distance for scipy.signal.find_peaks
max_match_error	float	2.0	max diff between peak estimate wavelength and wavelength from line list
verbose	bool	False	more detailed diagnostic messages
Returns	Curve

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SettingsBuilderMixin.fit_HgAr_lines

 SettingsBuilderMixin.fit_HgAr_lines (brightest_peaks:list=[435.833,
                                      546.074, 763.511], top_k:int=10,
                                      filter_window:int=1,
                                      interactive_peak_id:bool=False,
                                      find_peaks_height:int=10,
                                      prominence:float=0.2,
                                      width:float=1.5, distance:int=10,
                                      max_match_error:float=2.0,
                                      verbose:bool=False)

Finds the index to wavelength map given a spectra and a list of emission lines. To filter the spectra, set filter_window to an odd number > 1.

	Type	Default	Details
brightest_peaks	list	[435.833, 546.074, 763.511]	list of wavelength for the brightest peaks in spectral lines image
top_k	int	10	how many peaks to use in fit
filter_window	int	1	filter window for scipy.signal.savgol_filter. Needs to be odd.
interactive_peak_id	bool	False	flag to interactively confirm wavelength of peaks
find_peaks_height	int	10	anything above this value is free game for a peak
prominence	float	0.2	prominence for scipy.signal.find_peaks
width	float	1.5	peak width for scipy.signal.find_peaks
distance	int	10	distance for scipy.signal.find_peaks
max_match_error	float	2.0	max diff between peak estimate wavelength and wavelength from line list
verbose	bool	False	more detailed diagnostic messages
Returns	Curve

sb.fit_HgAr_lines(top_k=10)

Each column in our camera frame (after smile correction) corresponds to a particular wavelength. The interpolation between column index and wavelength is slightly nonlinear which is to be expected from the diffraction grating - however it is linear to good approximation. Applying a linear interpolation gives an absolute error of $$3 nm whereas the a cubic interpolation used here gives an absolute error of \(\pm\) 0.3 nm (approximately the spacing between each column). Using higher order polynomials doesn’t improve the error due to overfitting.

For fast real time processing, the fast binning procedure assumes a linear interpolation because the binning algorithm consists of a single broadcasted summation with no additional memory allocation overhead. A slower more accurate spectral binning procedure is also provided using the cubic interpolation described here and requires hundreds of temporary arrays to be allocated each time. Binning can also be done in post processing after collecting raw data.

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SettingsBuilderMixin.update_intsphere_fit

 SettingsBuilderMixin.update_intsphere_fit
                                            (spec_rad_ref_data:str='../ass
                                            ets/112704-1-1_1nm_data.csv', 
                                            spec_rad_ref_luminance:int=520
                                            20, show:bool=True)

	Type	Default	Details
spec_rad_ref_data	str	../assets/112704-1-1_1nm_data.csv	path to integrating sphere cal file
spec_rad_ref_luminance	int	52020	reference luminance for integrating sphere
show	bool	True	flag to show plot
Returns	Curve

fig = sb.update_intsphere_fit()
#sb.dump() # resave the settings and calibration files

Integrating Sphere data

4D datacube with coordinates of cross-track, wavelength, exposure, and luminance.

Warning

Needs testing!

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SettingsBuilderMixin.update_intsphere_cube

 SettingsBuilderMixin.update_intsphere_cube (exposures:List,
                                             luminances:List,
                                             nframes:int=10,
                                             lum_chg_func:Callable=<built-
                                             in function print>,
                                             interactive:bool=False)

	Type	Default	Details
exposures	typing.List		exposure times for the camera to iterate over
luminances	typing.List		luminance values for the integrating sphere to iterate over
nframes	int	10	how many frames to average over
lum_chg_func	typing.Callable	print	called on each luminance value before collection starts
interactive	bool	False	if you want to manually press enter each luminance iteration

luminances=[0, 1_000, 5_000, 10_000, 20_000, 40_000]
exposures = [0, 5, 8, 10, 15, 20]
sb.calibration["rad_ref"] = cam.update_intsphere_cube(exposures, luminances, noframe=50, lum_chg_func=spt.selectPreset)

# remove saturated images
cam.calibration["rad_ref"] = cam.calibration["rad_ref"].where(
    ~(np.sum((cam.calibration["rad_ref"][:, :, :, :, :] == 255), axis=(1, 2)) > 1000)
)

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Input In [25], in <cell line: 6>()
      4 luminances=[0, 1_000, 5_000, 10_000, 20_000, 40_000]
      5 exposures = [0, 5, 8, 10, 15, 20]
----> 6 sb.calibration["rad_ref"] = cam.update_intsphere_cube(exposures, luminances, noframe=50, lum_chg_func=spt.selectPreset)
      8 # remove saturated images
      9 cam.calibration["rad_ref"] = cam.calibration["rad_ref"].where(
     10     ~(np.sum((cam.calibration["rad_ref"][:, :, :, :, :] == 255), axis=(1, 2)) > 1000)
     11 )

NameError: name 'cam' is not defined

When you are happy with the calibration, dump the updates.

# save at the end
cam.dump(json_path=json_path_target, pkl_path=pkl_path_target)

SpectraPT TCP Client

Class to interact with the Spectra PT integrating sphere.

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SpectraPTController

 SpectraPTController (lum_preset_dict:Dict[int,int]={0: 1, 1000: 2, 2000:
                      3, 3000: 4, 4000: 5, 5000: 6, 6000: 7, 7000: 8,
                      8000: 9, 9000: 10, 10000: 11, 20000: 12, 25000: 13,
                      30000: 14, 35000: 15, 40000: 16},
                      host:str='localhost', port:int=3434)

Initialize self. See help(type(self)) for accurate signature.

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SpectraPTController.client

 SpectraPTController.client (msg:str)

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SpectraPTController.selectPreset

 SpectraPTController.selectPreset (lumtarget:float)

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SpectraPTController.turnOnLamp

 SpectraPTController.turnOnLamp ()

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SpectraPTController.turnOffLamp

 SpectraPTController.turnOffLamp ()