CRIKit2, formerly the Coherent Raman Imaging toolKit, is a hyperspectral imaging (HSI) platform. It is composed of command line tools, interactive tools, and a user interface.

HSI Processing:

• Dark subtraction
• Detrending
• Denoising via SVD

Coherent Raman-Specific Processing:

• Kramers-Kronig phase retrieval
• Phase- and scale-error correction

Coming Soon:

• SVD automated selection tools
• Analysis toolkit (separate UI)
• Interactive Raman database
• Much more

Note: These are the developmental system specs. Older versions of certain packages may work.

• python >= 3.4
  • Tested with 3.4.4, 3.5.2, 3.6.1
• SciPlot-PyQt >= 0.1.3 (>=0.1.4 for MPL2)
  • https://github.com/CCampJr/SciPlot-PyQt/releases
• numpy (1.9.3)
  • Tested with 1.11.3+mkl
• PyQT5 (5.5.* or 5.6.*)
  • Tested with 5.6, 5.8.1
• matplotlib (1.5.0rc3, 2.0.0) (see below for MPL2)
  • Tested with 1.5.2, 2.0.0
• cvxopt (1.1.7)
  • Tested with 1.1.7, 1.1.9
• h5py (2.5)
  • Tested with 2.6, 2.7
• Sphinx (1.5.2) (Only for building documentation)
  • Tested with 1.4.5, 1.6.4

You will need to use SciPlot-PyQT v0.1.4

• Matplotlib 2 made numerous changes and deprecations that are being resolved
• See the installation instruction in the README.md file at https://github.com/CCampJr/SciPlot-PyQt

You will need to manually install PyQt5 and Qt5 or get it through a distribution

• PyQt5: https://www.riverbankcomputing.com/software/pyqt/download5
• Qt: https://www.qt.io/

pip3 install pyqt5

There is a bug in PyQt 5.7.* that will prevent SciPlot's tables from showing the individual plot entries (see https://www.riverbankcomputing.com/pipermail/pyqt/2017-January/038483.html). Apparently, this will be fixed in 5.7.2.

• As WinPython 3.5.2.3Qt5 and 3.5.2.2Qt5 use PyQt 5.7.*, it is advised to use WinPython 3.5.2.1Qt5 or 3.4.4.5Qt5 until the matter is sorted out.
• Alternatively, one can uninstall pyqt5.7.* and force an install of <= 5.6.*.

Currently, SciPlot >= 0.1.3 is not available through pip. You can however clone the repository from github. (see https://github.com/CCampJr/SciPlot-PyQt)

# Make new directory for crikit2 and enter it
# Clone from github
git clone https://github.com/CoherentRamanNIST/crikit2.git

# Within install directory
pip3 install -e .

# To update installation, from within crikit2 directory
git pull

# Make new directory for crikit2 and enter it
# Clone from github
git clone https://github.com/CoherentRamanNIST/crikit2.git

# or download a copy from https://github.com/CoherentRamanNIST/crikit2

# Within install directory
pip3 install .

# You can now delete the source files you downloaded

The documentation was built using Sphinx. A pre-built version of the html files is included with this module, but you may wish to rebuild on your own system.

# Build all APIs
# From within the docs/ directory
sphinx-apidoc -o ./source/ ../crikit/

# Build API w/o pyuic5-generated files
sphinx-apidoc -f -o .\source\ ..\crikit\ ..\crikit\ui\qt_* ..\crikit\ui\*_rc* ..\crikit\ui\old\**

make html  
# On Windows
make.bat html

python3 -m crikit 

# or

python -m crikit

• The SVD visualization tool uses a complex-valued SVD for complex values; thus, there are a few things to avoid
  • If your spectra are PURELY IMAGINARY, convert them to PURELY REAL
  • If your real and imaginary parts of your spectra are IDENTICAL, then consider using just the real or imaginary portion
  • NOTE: this does not affect the accuracy or performance of SVD or the returned results, but you will see unexpected visualizations of the spatial and spectral components.

This software was developed at the National Institute of Standards and Technology (NIST) by employees of the Federal Government in the course of their official duties. Pursuant to Title 17 Section 105 of the United States Code, this software is not subject to copyright protection and is in the public domain. NIST assumes no responsibility whatsoever for use by other parties of its source code, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic.

Specific software products identified in this open source project were used in order to perform technology transfer and collaboration. In no case does such identification imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the products identified are necessarily the best available for the purpose.

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 47, 408-416 (2016). DOI: 10.1002/jrs.4824

Charles H Camp Jr: charles.camp@nist.gov