Generating Calibration Files

A notebook example for generating settings and calibration files for the OpenHSI camera.

Warning

This is not for general use. Requires technical expertise.

Tools required: - An integrating sphere (we use a Spectra PT from LabSphere) - A HgAr lamp

Adjust the camera class as needed. This example uses the LucidCamera. The are some LucidCamera specifc items in the below code that would need to be removed.

#all_hardware

import os

import holoviews as hv
import numpy as np

from openhsi.calibrate import SettingsBuilderMixin, SpectraPTController, sum_gaussians
from openhsi.cameras import LucidCamera

hv.extension("bokeh", logo=False)
import panel as pn


class CalibrateCamera(SettingsBuilderMixin, LucidCamera):
    pass

json_path_template = "../cals/cam_settings_lucid_template.json"
cal_path = ""

modelno = 18

print("".format(modelno))

json_path_target = "../cals/OpenHSI-{0:02d}/OpenHSI-{0:02d}_settings_Mono8_bin1.json".format(
    modelno
)
cal_path_target = "../cals/OpenHSI-{0:02d}/OpenHSI-{0:02d}_calibration_Mono8_bin1.pkl".format(
    modelno
)

if not os.path.isdir(os.path.dirname(json_path_target)):
    os.mkdir(os.path.dirname(json_path_target))

spt = SpectraPTController()

Find illuminated sensor area

The vertical directon/y axis of the detector array corrspeonds the across-track direction of the sensor. If the image of slit is shorter then the heigh we can crop the top and bottom to save bandwidth/disk space (similar to letterboxing video).

There are two ways to do this, croping after the fact using row_minmax or by setting up a window on the sensor. Setting up a window will reduce the ammount of data transfered from the sensor and can improve maximum framerate depending on the sensor so is recomended.

1. Take a flat field

First step is to provide a uniform illumination to the slit, ideally spectrally broadband, like a halogen lamp or the sun.

# Select luminance value 10000 on the SpectraPT
spt.selectPreset(10000)

# Initialize the CalibrateCamera class with specified parameters
with CalibrateCamera(
    json_path=json_path_template,  # Path to a JSON file containing camera settings template
    cal_path="",                  # Path to a pickle file (not used here since it's an empty string)
    processing_lvl=-1,            # Processing level (specific to CalibrateCamera, meaning unknown)
    exposure_ms=20                # Exposure time in milliseconds
) as cam:
    
    # Retake the flat field image and display it using Holoviews (hvim_flat)
    hvim_flat = cam.retake_flat_field(show=True)
    hvim_flat.opts(width=600, height=600, axiswise=True)

    # Update the row min/max values and display them (hvim_row_minmax)
    hvim_row_minmax = cam.update_row_minmax(edgezone=0)
    hvim_row_minmax.opts(width=600, height=600, axiswise=True)

    # Calculate the window height based on the row slice and ensure it's a multiple of 4 (required for LucidCameras)
    windowheight = int(
        np.ceil((cam.settings["row_slice"][1] - cam.settings["row_slice"][0]) / 4.0) * 4
    )
    print("Windowheight {}".format(windowheight))
    
    # Update camera settings based on the calculated window height:
    # - Set the window resolution (height, width)
    cam.settings["win_resolution"] = [windowheight + 16, cam.settings["resolution"][1]]
    
    # - Set the window offset (adjusting for potential padding)
    cam.settings["win_offset"] = [
        int(np.ceil((cam.settings["row_slice"][0]) / 4.0) * 4) - 8,
        cam.settings["win_offset"][1],
    ]
    
    # - Update the row slice (region of interest)
    cam.settings["row_slice"] = [16, windowheight - 8]

    # Set the overall camera resolution to match the window resolution
    cam.settings["resolution"] = cam.settings["win_resolution"]

    # Save the updated camera settings to JSON and pickle files
    cam.dump(json_path=json_path_target, cal_path=cal_path_target)
    
# Display the row min/max and flat field images side-by-side using Panel
pn.Column(hvim_row_minmax, hvim_flat)

# Initialize the CalibrateCamera class with specified parameters. and setting from previous cell.
with CalibrateCamera(
    n_lines=50,
    processing_lvl=0,
    cal_path=cal_path_target,
    json_path=json_path_target,
    exposure_ms=10,
) as cam:
    # cam.collect()
    cam.start_cam()
    img = cam.get_img()
    img = cam.crop(img)
    cam.stop_cam()
    # cam.show(hist_eq=True)

# check the window looks ok.
hv.Image(img, bounds=(0, 0, *img.shape)).opts(
    xlabel="wavelength index",
    ylabel="cross-track",
    cmap="gray",
    title="test frame",
    width=400,
    height=400,
)

2. Take Arc and setup wavelength scale, and get window for 430 to 900nm

with CalibrateCamera(
    json_path=json_path_target,  # Path to the JSON file with camera settings
    cal_path="",                  # Path to a pickle file (not used here)
    processing_lvl=-1            # Processing level (specific to CalibrateCamera)
) as cam:
    
    # Set the camera gain value to 10.0 - LUCIDCAMERA ONLY
    cam.deviceSettings["Gain"].value = 10.0  

    # Capture a HgAr (Mercury-Argon) spectrum image and display it
    hvimg = cam.retake_HgAr(show=True, nframes=18)  # Capture 18 frames and average them
    hvimg.opts(width=600, height=600)  # Set display options for the image

    # Print the maximum pixel value in the captured HgAr image
    print(cam.calibration["HgAr_pic"].max()) 

    # Calculate and update the "smile" shifts (geometric distortion correction)
    smile_fit_hv = cam.update_smile_shifts()  

    # Reset the smile shifts to zero (likely for testing or specific calibration purposes)
    cam.calibration["smile_shifts"] = cam.calibration["smile_shifts"] * 0 

    # Perform wavelength calibration using the HgAr spectrum
    wavefit_hv = cam.fit_HgAr_lines(
        top_k=15,                  # Use the top 15 brightest peaks for fitting
        brightest_peaks=[546.96, 435.833, (579.960 + 579.066) / 2, 763.511],  # Known HgAr peak wavelengths
        find_peaks_height=10,     # Parameters for peak detection 
        prominence=1,
        width=1.5,
        interactive_peak_id=True,  # Allow interactive selection of peaks
    ) 

    # Define the desired wavelength range for the "window"
    waveminmax = [430, 900]  # Wavelength range in nanometers

    # Find the corresponding indices in the wavelength array
    waveminmax_ind = [
        np.argmin(np.abs(cam.calibration["wavelengths_linear"] - λ)) for λ in waveminmax
    ]

    # Calculate the window width and offset based on the wavelength indices
    window_width = int(np.ceil((waveminmax_ind[1] - waveminmax_ind[0] + 8) / 4.0) * 4)
    offset_x = int(np.floor((waveminmax_ind[0] - 4) / 4.0) * 4)
    print("Window Width {}, offset x {}".format(window_width, offset_x))

    # Update camera settings with the new window parameters
    cam.settings["win_resolution"][1] = window_width  # Set window width
    cam.settings["win_offset"][1] = offset_x        # Set horizontal offset
    cam.settings["resolution"] = cam.settings["win_resolution"]  # Update overall resolution

    # Display the HgAr image, smile fit data, and wavelength calibration results using Panel
    pn.Column(
        hvimg,
        smile_fit_hv,
        wavefit_hv.opts(xlim=(390, 1000), ylim=(-10, 255)).opts(shared_axes=False),
    )

# check the window looks ok.
pn.Column(
    hvimg.opts(shared_axes=False),
    smile_fit_hv.opts(shared_axes=False),
    wavefit_hv.opts(xlim=(400, 900), ylim=(-10, 255)).opts(shared_axes=False),
)

# save wavefit if things look ok
cam.dump(json_path=json_path_target, cal_path=cal_path_target)

3. Retake flat field and arc with windows

spt.selectPreset(10000)

# retake flat frame with wavelegth window set.
with CalibrateCamera(
    json_path=json_path_target, cal_path=cal_path_target, processing_lvl=-1
) as cam:
    hvim_flat = cam.retake_flat_field(show=True)
    hvim_flat.opts(width=600, height=600, axiswise=True)

    hvim_row_minmax = cam.update_row_minmax(edgezone=8)
    hvim_row_minmax.opts(width=600, height=600, axiswise=True)

    cam.update_resolution()
    cam.dump(json_path=json_path_target, cal_path=cal_path_target)

spt.turnOffLamp()

# display and check all looks ok.
hvim_row_minmax + hvim_flat

Redo Arc with window.

# retake arc frames and set wavelength scale foir window.

with CalibrateCamera(
    json_path=json_path_target, cal_path=cal_path_target, processing_lvl=-1
) as cam:
    cam.deviceSettings["Gain"].value = 15.0
    hvimg = cam.retake_HgAr(show=True)

    hvimg.opts(width=400, height=400)
    print(cam.calibration["HgAr_pic"].max())
    smile_fit_hv = cam.update_smile_shifts()

    wavefit_hv = cam.fit_HgAr_lines(
        top_k=12,
        brightest_peaks=[546.96, 435.833, (579.960 + 579.066) / 2, 871.66, 763.511],
        find_peaks_height=10,
        prominence=1,
        width=1.5,
        max_match_error=2,
        interactive_peak_id=True,
    )  # [435.833,546.074,(579.960+579.066)/2,763.511]
    
    cam.update_intsphere_fit()

    cam.dump(json_path=json_path_target, cal_path=cal_path_target)

(hvimg + smile_fit_hv + wavefit_hv.opts(xlim=(400, 900), ylim=(-10, 255))).opts(
    shared_axes=False
)

3. Get Integrating Sphere data for radiance calibration

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

luminances = np.fromiter(lum_preset_dict.keys(), dtype=int)
# luminances = np.append(luminances,0)
exposures = [0, 5, 8, 10, 15, 20]

with CalibrateCamera(
    json_path=json_path_target, cal_path=cal_path_target, processing_lvl=-1
) as cam:

    cam.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
        )
    )
    cam.dump(json_path=json_path_target, cal_path=cal_path_target)

spt.turnOffLamp()

cam.calibration["rad_ref"].plot(
    y="cross_track", x="wavelength_index", col="exposure", row="luminance", cmap="gray"
)

print("rad_ref is {} MB".format(cam.calibration["rad_ref"].size / 1024 / 1024 * 4))

cam.update_intsphere_fit()
cam.dump(json_path=json_path_target, cal_path=cal_path_target)