crikit package¶
Subpackages¶
- crikit.cri package
- crikit.data package
- crikit.datasets package
- crikit.io package
- crikit.measurement package
- crikit.preprocess package
- Subpackages
- Submodules
- crikit.preprocess.crop module
- crikit.preprocess.denoise module
- crikit.preprocess.standardize module
- crikit.preprocess.subtract_baseline module
- crikit.preprocess.subtract_dark module
- crikit.preprocess.subtract_mean module
- Module contents
- crikit.transform package
- crikit.ui package
- Subpackages
- Submodules
- crikit.ui.classes_ui module
- crikit.ui.dialog_AbstractFactorization module
- crikit.ui.dialog_AbstractPlotEffect module
- crikit.ui.dialog_SVD module
- crikit.ui.dialog_kkOptions module
- crikit.ui.dialog_model module
- crikit.ui.dialog_ploteffect module
- crikit.ui.dialog_save module
- crikit.ui.dialog_subResidualOptions module
- crikit.ui.dialog_varstabAnscombeOptions module
- crikit.ui.helper_plotOptions module
- crikit.ui.helper_roiselect module
- crikit.ui.main_Mosaic module
- crikit.ui.widget_ALS module
- crikit.ui.widget_ArPLS module
- crikit.ui.widget_Calibrate module
- crikit.ui.widget_DeTrending module
- crikit.ui.widget_Jupyter module
- crikit.ui.widget_KK module
- crikit.ui.widget_SG module
- crikit.ui.widget_images module
- crikit.ui.widget_mergeNRBs module
- crikit.ui.widget_scientificspin module
- Module contents
- crikit.utils package
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¶
Charles H. Camp Jr. <charles.camp@nist.gov>
-
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¶
-
_pointClick
(event, pass_fcn)[source]¶ Capture single mouse click location in MPL window.
After this function completes, it sends the data (x_pt, y_pt) on to the pass_fcn function.
-
_roiClick
(event, pass_fcn, *args)[source]¶ Capture region-of-interest mouse click locations in MPL window.
-
_roiPreviewClick
(event, *args)[source]¶ Capture region-of-interest mouse click locations in MPL window.
-
doKK
()[source]¶ Pop-up Kramers-Kronig parameter entry dialog and perform the Kramers-Kronig phase retrieval algorithm.
-
errorCorrectAmp
()[source]¶ Error Correction: Amp aka Baseline Detrending
Notes
If data is complex, amplitude detrending occurs on and only on the imaginary portion
-
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)
-
get_preview_spectra
(full=False)[source]¶ If self.preview_rois is set, output the mean spectra from thos regions
-
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
-
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
-
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
-
specialEstCalibration1
()[source]¶ For NIST BCARS 2, maximum raw spectrum occurs at approximately 745.8 nm (18/07/11)
-
-
crikit.CRIkitUI.
crikit_launch
(**kwargs)[source]¶ Command line launching of CRIkitUI.
- hsicrikit.data.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¶
Charles H. Camp Jr. <charles.camp@nist.gov>