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CRIKit2: Hyperspectral imaging toolkit

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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.

Github Repository: https://github.com/CCampJr/CRIkit2 Docs Website: Coming Soon...

Note: Help Documentation available via the Help header within the CRIkit2 GUI (only for git installs, not pip)

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

Notices

• Major bug fix in 0.2.1 (Issue #84 <https://github.com/CCampJr/CRIkit2/issues/84>_)

Dependencies

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

• python >= 3.4

• NumPy

• SciPy

• matplotlib (1., 2., 3.*)

• packaging

• PyQT5

• CVXOPT

  • Requires H5Py (>= 2.6)

• SciPlot-PyQt >= 0.2.2

  • https://github.com/CCampJr/SciPlot-PyQt/releases
  • Requires Matplotlib (v1., 2., or 3.*)

• Sphinx (optional)

IMPORTANT: For Python 3.4

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/

For Python 3.5, installation through pip available

.. code::

pip3 install pyqt5

Known Issues

Windows 10 with High-Resolution Monitors

The GUI may appear squashed with small font. There is a work-around described at https://github.com/CCampJr/CRIkit2/issues/79

PyQt 5.7.*
~~~~~~~~~~~

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.*.


Installation
-------------

It is advisable to clone CRIkit2 via git (https://git-scm.com/) and install
in a *developmental* mode via *pip* or *conda* as this will enable you to
easily (relatively) update your copy of CRIkit2 as new functionality
is *pushed*.

**Note** If you choose to clone an updatable copy of CRIkit2, do not
clone to a directory within your Python installation. Rather, create a new
directory elsewhere. That way if you update your Python distribution, you won't
lose your copy of CRIkit2.

Option 1: Dynamic, Updatable Clone of CRIkit2

.. code::

# Note: in Windows, commands will be followed by .exe
# Note: On multi-python systems, you should probably append a 3 to end
# the end of commands, e.g., pip is pip3, python is python3

# Assume the new directory will be CRIkit2 (it can be anything)
# Clone from github
git clone https://github.com/CCampJr/crikit2.git CRIkit2

# Within install directory
pip install -e .

# To update installation, from within the CRIkit2 directory
git pull

# If you receive an error trying to update via git pull
# See https://github.com/CCampJr/CRIkit2/issues/82

Option 2: Static Copy

The static copy will copy the CRIkit2 install into your Python distribution
and will not be updatable without re-installing CRIkit2

.. code::

    # Note: in Windows, commands will be followed by .exe
    # Note: On multi-python systems, you should probably append a 3 to end
    # the end of commands, e.g., pip is pip3, python is python3

    # Assume the new directory will be CRIkit2 (it can be anything)
    # Clone from github
    git clone https://github.com/CCampJr/crikit2.git CRIkit2

    # Within install directory
    pip install .

    # You can now delete the source files you downloaded if so desired

    # To update installation, from within the CRIkit2 directory
    git pull
    pip install .

Option 3: Installation via pip

.. code::

pip install CRIkit2

(Re-) Building Documentation

A pre-built version of the documentation is included with the installation;
thus, this step should not be necessary unless you are making modifications
to the software.

The documentation is accessible from within CRIkit2 under the *Help* header.
It is displayed in a web browser.

.. code::

    # From within the CRIkit2 directory (not crikit)
    cd docs

    # Clean out old docs (optional)
    make clean  # On Windows make.bat clean

    # Build API w/o pyuic5-generated files
    # Windows add .exe
    sphinx-apidoc -f -o ./source/ ../ ../crikit/ui/qt_* ../crikit/ui/*_rc* ../crikit/ui/old/** ../setup.py

    make html  # On Windows make.bat html


Starting the CRIkit2 UI
------------------------

.. code::

    python3 -m crikit 

    # or

    python -m crikit

Known Operational Nuances
--------------------------

-   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.

LICENSE
----------
This software was developed by employees of the National Institute of Standards 
and Technology (NIST), an agency of the Federal Government. Pursuant to 
`title 17 United States Code Section 105 <http://www.copyright.gov/title17/92chap1.html#105>`_, 
works of NIST employees are not subject to copyright protection in the United States and are 
considered to be in the public domain. Permission to freely use, copy, modify, 
and distribute this software and its documentation without fee is hereby granted, 
provided that this notice and disclaimer of warranty appears in all copies.

THE SOFTWARE IS PROVIDED 'AS IS' WITHOUT ANY WARRANTY OF ANY KIND, EITHER 
EXPRESSED, IMPLIED, OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTY 
THAT THE SOFTWARE WILL CONFORM TO SPECIFICATIONS, ANY IMPLIED WARRANTIES OF 
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND FREEDOM FROM INFRINGEMENT, 
AND ANY WARRANTY THAT THE DOCUMENTATION WILL CONFORM TO THE SOFTWARE, OR ANY 
WARRANTY THAT THE SOFTWARE WILL BE ERROR FREE. IN NO EVENT SHALL NIST BE LIABLE 
FOR ANY DAMAGES, INCLUDING, BUT NOT LIMITED TO, DIRECT, INDIRECT, SPECIAL OR 
CONSEQUENTIAL DAMAGES, ARISING OUT OF, RESULTING FROM, OR IN ANY WAY CONNECTED 
WITH THIS SOFTWARE, WHETHER OR NOT BASED UPON WARRANTY, CONTRACT, TORT, OR 
OTHERWISE, WHETHER OR NOT INJURY WAS SUSTAINED BY PERSONS OR PROPERTY OR 
OTHERWISE, AND WHETHER OR NOT LOSS WAS SUSTAINED FROM, OR AROSE OUT OF THE 
RESULTS OF, OR USE OF, THE SOFTWARE OR SERVICES PROVIDED HEREUNDER.

CITATION
---------

`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). <https://www.ncbi.nlm.nih.gov/pubmed/28819335>`_


Contact
--------

Charles H Camp Jr: `[email protected] <mailto:[email protected]>`_

Contributors
-------------

Charles H. Camp Jr., Xavier Audier