crikit package

Subpackages

Submodules

crikit.CRIkitUI module

CRIKit2: Hyperspectral imaging toolkit

CRIKit2, formerly the Coherent Raman Imaging toolKit, is a hyperspectral imaging (HSI) platform (user interface, UI).

HSI Processing:
  • Dark subtraction

  • Detrending

  • Denoising

Coherent Raman-Specific Processing:
  • Kramers-Kronig phase retrieval

  • Phase- and scale-error correction

Analysis:
  • Coming soon

Usage

From ./crikit2 directory python3 main.py

Authors

class crikit.CRIkitUI.CRIkitUI_process(**kwargs)[source]

Bases: PyQt5.QtWidgets.QMainWindow

CRIkitUI_process : CRIkitUI for image (pre-)processing

References

[1] C H Camp Jr, Y J Lee, and M T Cicerone, “Quantitative, Comparable Coherent Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting Errors in Phase Retrieval,” Journal of Raman Spectroscopy (2016). arXiv:1507.06543.

NUMCOLORS = 4
anscombe()[source]

Performance Anscombe transformation

calcAnscombeParams()[source]

Calculate Anscombe Parameters

calibrate()[source]

Calibrate spectra

calibrationReset()[source]

Set self.hsi.freqcalib back to self.hsi.freqcaliborig

changeSlider()[source]

Respond to change in frequency slider

checkCompositeUpdate(num)[source]

Update color composite only if appropriate tab is selected.

checkShowOverlays()[source]
closeEvent(self, QCloseEvent)[source]
condInEqualityChange()[source]

Conditional inequality changed.

condOpChange()[source]

Conditional math operation performed on single-color images changed.

createImgBW(img)[source]

Generate the single-frequency grayscale image

cutEveryNSpectra()[source]

Cut m spectra every n spectra

deNoise()[source]

SVD

deNoiseDark()[source]

Denoise Dark with Savitky-Golay

deNoiseNRB()[source]

Denoise NRB with Savitky-Golay

deleteOverlays()[source]
delete_preview_rois()[source]
doComposite()[source]

Update color composite image.

doKK()[source]

Pop-up Kramers-Kronig parameter entry dialog and perform the Kramers-Kronig phase retrieval algorithm.

doMath()[source]

Perform selected math operation on single-color imagery.

doUndo()[source]

Undo last operation back to last backup point

errorCorrectAmp()[source]

Error Correction: Amp aka Baseline Detrending

Notes

If data is complex, amplitude detrending occurs on and only on the imaginary portion

errorCorrectPhase()[source]

Error Correction: Phase

errorCorrectScale()[source]

Error Correction: Scale

fileOpenDLMNIST()[source]

Open and load DLM File

fileOpenHDFMacroRasterNIST(*args, dialog=True)[source]

Open and load multiple datasets from HDF file that describe a single image. Used for a macrostage rastering mode at NIST.

dialogbool

Present a gui for file and dataset selection

fileOpenHDFNIST(*args, dialog=True)[source]

Open and load HDF5 File

dialogbool

Present a gui for file and dataset selection

fileOpenHDFNISTOOC(*args)[source]

Open and load HDF5 File OUT-OF-CORE

dialogbool

Present a gui for file and dataset selection

fileOpenSuccess(success)[source]

Executed after a file is loaded. Checks success and appropriately activates or deactivates action (buttons)

freqWindow()[source]

Limit the frequency window displayed and analyzed

get_preview_spectra(full=False)[source]

If self.preview_rois is set, output the mean spectra from thos regions

inverseAnscombe()[source]

Performance an Inverse Anscombe transformation

lineEditFreqChanged()[source]

Frequency manually entered in frequency-slider-display

lineEditPixChanged()[source]

Frequency in pixel units manually entered in frequency-slider-display

loadDark()[source]

Open HDF file and load dark spectrum(a)

loadDarkDLM()[source]

Open DLM file and load dark spectrum(a)

loadNRB()[source]

Open HDF file and load NRB spectrum(a)

loadNRBDLM()[source]

Open DLM file and load NRB spectrum(a)

makeBCARSPhantom()[source]

Generate a numerical phantom for BCARS

makeRamanPhantom()[source]

Generate a numerical phantom for Raman

mergeNRBs()[source]

Interactive merge of the left- and right-side NRB

mosaicTool()[source]
nrbFromROI()[source]

Acquire an average spectrum from a user-selected ROI and apply to the NRB– either as the new NRB or averaged with the existing (sender- dependent)

Note: This function just sets up the signal-slot connection for the MPL window. It executes all the way through

opChange()[source]

Math operation performed on single-color images changed.

plotDarkSpectrum()[source]

Plot dark spectrum

plotLeftNRBSpectrum()[source]

Plot Left-Side NRB spectrum

plotNRBSpectrum()[source]

Plot NRB spectrum

plotRightNRBSpectrum()[source]

Plot NRB spectrum

plotter_show()[source]
pointSpectrum()[source]

Get spectrum of selected point.

Note: This function just sets up the signal-slot connection for the MPL window. It executes all the way through

Action:

Left mouse-click : Select vertex point

roiSpectrum()[source]

Plot spectrum over selected region-of-interest (ROI).

Note: This function just sets up the signal-slot connection for the MPL window. It executes all the way through

Action:

Left mouse-click : Select vertex point Right mouse-click : Close polygon

save()[source]
setCondFreq1()[source]

Set color math conditional frequency #1

setCondFreq2()[source]

Set color math conditional frequency #2

setCondFreq3()[source]

Set color math conditional frequency #1

setOpFreq1()[source]

Set color math frequency #1 (the primary frequency)

setOpFreq2()[source]

Set color math frequency #2 (e.g., freq #1 + freq #2)

setOpFreq3()[source]

Set color math frequency #3 (e.g., Amplitude at freq #1 - interpolation [freq #2, freq #3])

set_preview_rois()[source]

Set the preview ROIs. NOTE: this function just sets the signal for the MPL window

settings()[source]

Go to settings tab

showPreviewRois()[source]
sliderPressed()[source]

Respond to press of frequency slider (set tracking of location)

sliderReleased()[source]

Respond to release of frequency slider (end tracking of location)

specialDemosaicRGB()[source]
specialEstCalibration1()[source]

For NIST BCARS 2, maximum raw spectrum occurs at approximately 745.8 nm (18/07/11)

spectrumColorImg()[source]

Generate plot of mean

spinBoxInEqualityChange()[source]

Conditional inequality value changed.

subDark()[source]

Subtract loaded dark spectrum from HSI data.

subResidual()[source]

Subtract a linear residual over range

subtractROIStart()[source]

Acquire an average spectrum from a user-selected ROI and subtract.

Note: This function just sets up the signal-slot connection for the MPL window. It executes all the way through

tabMainChange()[source]
toolbarSetting()[source]

Set the toolbar ribbon view

toolbarSetup()[source]

Setup the tool ribbon icons

updateHistory()[source]
updateOverlays()[source]
zeroFirstColumn()[source]

Zero first non-all-zero column. (Rather than crop)

zeroFirstRow()[source]

Zero first non-all-zero row. (Rather than crop)

zeroLastColumn()[source]

Zero first non-all-zero column. (Rather than crop)

zeroLastRow()[source]

Zero first non-all-zero row. (Rather than crop)

crikit.CRIkitUI.crikit_launch(**kwargs)[source]

Command line launching of CRIkitUI.

hsicrikit.data.spectra.Hsi

Hsi instance

datandarray (3D)

Numpy array (Y,X,Freq) hsi

xndarray (1D)

x-array

x_unitsstr

Units of x (e.g. r’$mu$m’)

x_labelstr

Label of x (e.g. ‘X’)

yndarray (1D)

y-array

y_unitsstr

Units of y (e.g. r’$mu$m’)

y_labelstr

Label of y (e.g. ‘Y’)

fndarray (1D)

frequency-array

f_unitsstr

Units of frequency (e.g. r’cm$^{-1}$’)

f_labelstr

Label of frequency (e.g. ‘Wavenumber’)

filenamestr

Filename of HDF data to auto-load (requires path and dataset_name as well)

pathstr

Path of HDF data to auto-load (requires filename and dataset_name as well)

dataset_namestr

Dataset name(s) of HDF data to auto-load (requires path and filename as well)

Module contents

CRIKit2: Hyperspectral imaging toolkit

CRIKit2, formerly the Coherent Raman Imaging toolKit, is a hyperspectral imaging (HSI) platform (user interface, UI).

Usage

python -m crikit

Authors