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.
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NUMCOLORS = 4
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anscombe()[source]
Performance Anscombe transformation
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calcAnscombeParams()[source]
Calculate Anscombe Parameters
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calibrate()[source]
Calibrate spectra
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calibrationReset()[source]
Set self.hsi.freqcalib back to self.hsi.freqcaliborig
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changeSlider()[source]
Respond to change in frequency slider
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checkCompositeUpdate(num)[source]
Update color composite only if appropriate tab is selected.
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checkShowOverlays()[source]
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closeEvent(self, QCloseEvent)[source]
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condInEqualityChange()[source]
Conditional inequality changed.
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condOpChange()[source]
Conditional math operation performed on single-color images changed.
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createImgBW(img)[source]
Generate the single-frequency grayscale image
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cutEveryNSpectra()[source]
Cut m spectra every n spectra
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deNoise()[source]
SVD
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deNoiseDark()[source]
Denoise Dark with Savitky-Golay
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deNoiseNRB()[source]
Denoise NRB with Savitky-Golay
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deleteOverlays()[source]
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delete_preview_rois()[source]
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doComposite()[source]
Update color composite image.
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doKK()[source]
Pop-up Kramers-Kronig parameter entry dialog and perform
the Kramers-Kronig phase retrieval algorithm.
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doMath()[source]
Perform selected math operation on single-color imagery.
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doUndo()[source]
Undo last operation back to last backup point
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errorCorrectAmp()[source]
Error Correction: Amp aka Baseline Detrending
Notes
If data is complex, amplitude detrending occurs on and only on the imaginary portion
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errorCorrectPhase()[source]
Error Correction: Phase
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errorCorrectScale()[source]
Error Correction: Scale
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fileOpenDLMNIST()[source]
Open and load DLM File
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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
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fileOpenHDFNIST(*args, dialog=True)[source]
Open and load HDF5 File
- dialogbool
Present a gui for file and dataset selection
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fileOpenHDFNISTOOC(*args)[source]
Open and load HDF5 File OUT-OF-CORE
- dialogbool
Present a gui for file and dataset selection
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fileOpenSuccess(success)[source]
Executed after a file is loaded. Checks success and appropriately
activates or deactivates action (buttons)
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freqWindow()[source]
Limit the frequency window displayed and analyzed
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get_preview_spectra(full=False)[source]
If self.preview_rois is set, output the mean spectra from thos regions
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inverseAnscombe()[source]
Performance an Inverse Anscombe transformation
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lineEditFreqChanged()[source]
Frequency manually entered in frequency-slider-display
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lineEditPixChanged()[source]
Frequency in pixel units manually entered in frequency-slider-display
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loadDark()[source]
Open HDF file and load dark spectrum(a)
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loadDarkDLM()[source]
Open DLM file and load dark spectrum(a)
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loadNRB()[source]
Open HDF file and load NRB spectrum(a)
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loadNRBDLM()[source]
Open DLM file and load NRB spectrum(a)
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makeBCARSPhantom()[source]
Generate a numerical phantom for BCARS
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makeRamanPhantom()[source]
Generate a numerical phantom for Raman
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mergeNRBs()[source]
Interactive merge of the left- and right-side NRB
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mosaicTool()[source]
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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
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opChange()[source]
Math operation performed on single-color images changed.
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plotDarkSpectrum()[source]
Plot dark spectrum
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plotLeftNRBSpectrum()[source]
Plot Left-Side NRB spectrum
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plotNRBSpectrum()[source]
Plot NRB spectrum
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plotRightNRBSpectrum()[source]
Plot NRB spectrum
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plotter_show()[source]
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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
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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
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save()[source]
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setCondFreq1()[source]
Set color math conditional frequency #1
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setCondFreq2()[source]
Set color math conditional frequency #2
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setCondFreq3()[source]
Set color math conditional frequency #1
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setOpFreq1()[source]
Set color math frequency #1 (the primary frequency)
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setOpFreq2()[source]
Set color math frequency #2 (e.g., freq #1 + freq #2)
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setOpFreq3()[source]
Set color math frequency #3 (e.g., Amplitude at freq #1 - interpolation [freq #2, freq #3])
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set_preview_rois()[source]
Set the preview ROIs. NOTE: this function just sets the signal for the MPL window
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settings()[source]
Go to settings tab
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showPreviewRois()[source]
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sliderPressed()[source]
Respond to press of frequency slider (set tracking of location)
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sliderReleased()[source]
Respond to release of frequency slider (end tracking of location)
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specialDemosaicRGB()[source]
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specialEstCalibration1()[source]
For NIST BCARS 2, maximum raw spectrum occurs at approximately
745.8 nm (18/07/11)
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spectrumColorImg()[source]
Generate plot of mean
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spinBoxInEqualityChange()[source]
Conditional inequality value changed.
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subDark()[source]
Subtract loaded dark spectrum from HSI data.
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subResidual()[source]
Subtract a linear residual over range
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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
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tabMainChange()[source]
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toolbarSetting()[source]
Set the toolbar ribbon view
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toolbarSetup()[source]
Setup the tool ribbon icons
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updateHistory()[source]
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updateOverlays()[source]
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zeroFirstColumn()[source]
Zero first non-all-zero column. (Rather than crop)
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zeroFirstRow()[source]
Zero first non-all-zero row. (Rather than crop)
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zeroLastColumn()[source]
Zero first non-all-zero column. (Rather than crop)
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zeroLastRow()[source]
Zero first non-all-zero row. (Rather than crop)