Merge branch 'ghactions'

.github/workflows/python-publish.yml

@@ -0,0 +1,36 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/python-testing.yml

@@ -0,0 +1,46 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: pytest
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pip install pytest
+        pip install pytest-cov
+        pytest --cov=./ --cov-report=xml
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v2
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        directory: ./coverage/reports/
+        env_vars: runs-on,python-version
+        fail_ci_if_error: true
+        files: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+        path_to_write_report: ./coverage/codecov_report.txt
+        verbose: true

CHANGELOG.rst

@@ -8,6 +8,10 @@ This document records all notable changes to
 This project adheres to `PEP 440 -- Version Identification 
 and Dependency Specification <https://www.python.org/dev/peps/pep-0440/>`_.
 
+0.4 (22-03-11)
+---------------
+- **Important**: PhaseErrCorrectALS now has parameter for whether wavenumber is increasing left-to-right. This is important to set correctly. This should match the `conjugate` parameter in the KramersKronig.
+
 0.3.1 (21-11-29)
 -----------------
 - Updated h5py deprecated syntax from .value to [:] (@XavierAutier)

README.rst

@@ -1,5 +1,13 @@
 .. -*- mode: rst -*-
 
+.. image:: https://github.com/CCampJr/CRIkit2/actions/workflows/python-testing.yml/badge.svg
+    :alt: pytest
+    :target: https://github.com/CCampJr/CRIkit2/actions/workflows/python-testing.yml
+
+.. image:: https://codecov.io/gh/CCampJr/CRIkit2/branch/master/graph/badge.svg
+    :alt: Codecov
+    :target: https://codecov.io/gh/CCampJr/CRIkit2
+
 .. image:: https://img.shields.io/pypi/pyversions/CRIkit2.svg
     :alt: PyPI - Python Version
     :target: https://pypi.org/project/CRIkit2/
@@ -58,8 +66,6 @@ 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, 3.7.2
-
 -   NumPy
 -   SciPy
 -   matplotlib (1.*, 2.*, 3.*)

crikit/__init__.py

@@ -14,4 +14,4 @@
 * Charles H. Camp Jr. <[email protected]>
 """
 
-__version__ = '0.3.1'
+__version__ = '0.4.0'

crikit/cri/error_correction.py

@@ -18,13 +18,83 @@
 
 class PhaseErrCorrectALS:
     """
-    Phase error correction using alternating least squares (ALS)
+    Phase error correction (PEC) using asymmetric least squares (ALS).
+
+    Parameters
+    ----------
+
+    wavenumber_increasing : bool, optional (default=True)
+        Are the wavenumbers increasing from left-to-right? This setting should 
+        match the conjugate setting of the previously performed KramersKronig.
+
+    smoothness_param : float, optional (default=1.0)
+        ALS smoothness parameter. See Ref [2].
+
+    asym_param : float, optional (default=1e-2)
+        ALS asymmetry parameter. See Ref [2].
+
+    redux : int, optional (default=10)
+        Factor to sub-sample each spectrum. This reduces computational burnden. 
+        Sub-sample phase error is then interpolated to match input signal 
+        length.
+
+    order : int, optional (default=2)
+        ALS derivative order number. See Ref [2].
+
+    rng : array-like, optional (default=None)
+        Only perform PEC on specific pixel range.
+
+    fix_end_points : bool, optional (default=False)
+        Phase error at extrema points is equal to input phase extrema points.
+
+    fix_rng : array-like, optional (default=None)
+        Phase error over given range is pushed to be equal to input phase. To 
+        prevent discontinuities, it is not enforced in an exact manner, but 
+        rather the algorithm is weighted to try to match.
+
+    fix_const : float, optional (default=1.)
+        For fix_rng, this is the weighting term. Higher value will force the
+        phase error to be more equal to the input.
+
+    max_iter : int, optional (default=100)
+        Maximum number of ALS iterations
+        
+    min_diff : float, optional (default=1e-5)
+        Minimum difference between ALS phase error values. If difference is 
+        less than min_diff, considered static and iterations are ceased.
+        
+    verbose : bool, optional (default=True)
+        Verbose PEC output
+
+
+    Returns
+    -------
+    ndarray
+        Phase-error corrected signal from CARS.
+
+    Notes
+    -----
+    
+    -   This module assumes the spectra are oriented as such that the frequency 
+         (wavenumber) increases with increasing index.  If this is not the case for
+         your spectra(um), set wavenumber_increasing=False.
+    -   The wavenumber_increasing setting should match that of the conjugate 
+        setting for the previously-performed KramersKronig.
 
     References
-    -----------
-    * C H Camp Jr, Y J Lee, and M T Cicerone, JRS (2016).
+    ----------
+
+    [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 47, 408-415 (2016). arXiv:1507.06543.
+
+    [2] P. H. C. Eilers and H. F. M. Boelens, "Baseline Correction with \
+    Asymmetric Least Squares Smoothing," (2005).
+
     """
-    def __init__(self, smoothness_param=1, asym_param=1e-2,
+    def __init__(self, wavenumber_increasing=True, 
+                 smoothness_param=1, asym_param=1e-2,
                  redux=10, order=2, rng=None, fix_end_points=False,
                  fix_rng=None, fix_const=1, max_iter=100, min_diff=1e-5,
                  verbose=True, **kwargs):
@@ -33,7 +103,8 @@ def __init__(self, smoothness_param=1, asym_param=1e-2,
         self.rng = _rng_is_pix_vec(rng)
         self._k = kwargs
 
-        self._k.update({'smoothness_param' : smoothness_param,
+        self._k.update({'wavenumber_increasing' : wavenumber_increasing,
+                        'smoothness_param' : smoothness_param,
                         'asym_param' : asym_param,
                         'redux' : redux,
                         'order' : order,
@@ -73,7 +144,10 @@ def _calc(self, data, ret_obj, **kwargs):
                 h = _np.zeros(err_phase[..., self.rng].shape)
                 h += _hilbert(err_phase[..., self.rng])
 
-                correction_factor = _np.exp(h) * _np.exp(-1j*err_phase[...,self.rng])
+                if self._k['wavenumber_increasing']:
+                    correction_factor = _np.exp(h) * _np.exp(-1j*err_phase[...,self.rng])
+                else:
+                    correction_factor = _np.exp(-h) * _np.exp(-1j*err_phase[...,self.rng])
 
                 # if self.rng is None:
                 #     ret_obj[idx] *= correction_factor

crikit/io/meta_process.py

@@ -113,7 +113,7 @@ def meta_process(rosetta, output_cls_instance):
         output_cls_instance.freq.calib_fcn = _calib_pix_wl
 
     output_cls_instance.freq.update()
-    
+
     # See if an original calibration is found
     try:
         calib_orig_dict = {}
@@ -130,7 +130,7 @@ def meta_process(rosetta, output_cls_instance):
         calib_orig_dict['ctr_wl0'] = rosetta_query('OrigColorCalibWL',rosetta, output_cls_instance)[0]
         if calib_orig_dict['ctr_wl0'] is None:
             raise ValueError
-        
+
         # Probe and Units are not necessary for calibration
         # Probe is only needed for wavelength-to-wavenumber conversion
         calib_orig_dict['probe'] = rosetta_query('OrigColorProbe',rosetta, output_cls_instance)[0]
@@ -141,7 +141,7 @@ def meta_process(rosetta, output_cls_instance):
     else:
         print('Original calibration found.')
         output_cls_instance.freq.calib_orig = calib_orig_dict
-    
+
     # Spatial for HSI
     if type(output_cls_instance) == _Hsi:
         print('Type Hsi')
@@ -268,18 +268,19 @@ def meta_process(rosetta, output_cls_instance):
                                             as _snb)
 
     from crikit.io.hdf5 import hdf_import_data as _hdf_import_data
+    import os as _os
     rosetta = _snb()
 
     filename = _os.path.abspath('../../../mP2_w_small.h5')
 
     spect_dark = _Spectra()
-    _hdf_import_data(filename,'/Spectra/Dark_3_5ms_2',spect_dark)
+    _hdf_import_data(filename, '/Spectra/Dark_3_5ms_2',spect_dark)
     meta_process(rosetta, spect_dark)
     print(spect_dark.reps)
 
     print('')
     img = _Hsi()
-    _hdf_import_data(filename,'/BCARSImage/mP2_3_5ms_Pos_2_0/mP2_3_5ms_Pos_2_0_small',img)
+    _hdf_import_data(filename, '/BCARSImage/mP2_3_5ms_Pos_2_0/mP2_3_5ms_Pos_2_0_small',img)
     meta_process(rosetta, img)
     print(img.freq.__dict__)
 

docs/build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: ab213400e0c5b629c3fbbc81887e1f87
+config: 680b288bd642a5606b1d094f16f72345
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_modules/crikit/CRIkitUI.html

@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>crikit.CRIkitUI &#8212; CRIKit2 0.3.1 documentation</title>
+    <title>crikit.CRIkitUI &#8212; CRIKit2 0.4.0 documentation</title>
     <link rel="stylesheet" href="../../_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
     <script id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
@@ -26,7 +26,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../index.html">CRIKit2 0.3.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">CRIKit2 0.4.0 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">crikit.CRIkitUI</a></li> 
       </ul>
@@ -3864,7 +3864,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../index.html">CRIKit2 0.3.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">CRIKit2 0.4.0 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">crikit.CRIkitUI</a></li> 
       </ul>

docs/build/html/_modules/crikit/cri/algorithms/kk.html

@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>crikit.cri.algorithms.kk &#8212; CRIKit2 0.3.1 documentation</title>
+    <title>crikit.cri.algorithms.kk &#8212; CRIKit2 0.4.0 documentation</title>
     <link rel="stylesheet" href="../../../../_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="../../../../_static/pygments.css" type="text/css" />
     <script id="documentation_options" data-url_root="../../../../" src="../../../../_static/documentation_options.js"></script>
@@ -26,7 +26,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../../index.html">CRIKit2 0.3.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">CRIKit2 0.4.0 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">crikit.cri.algorithms.kk</a></li> 
       </ul>
@@ -276,7 +276,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../../index.html">CRIKit2 0.3.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">CRIKit2 0.4.0 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../index.html" >Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">crikit.cri.algorithms.kk</a></li> 
       </ul>