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# Spectro function and classes

This module supports the functions convex_hull_removal and the classes SpectrumConvexHullQuotient, FeaturesConvexHullQuotient and USGS06SpecLib.

See the file `test_hull.py` for a SpectrumConvexHullQuotient and FeaturesConvexHullQuotient example. The file `test_spectro.py` is the example for the USGS06SpecLib class.

Note

The ENVI file reader is not available for Python 3.3 and make the USGS library reader useless. To turn around the problem you can use a JSON version of the USGS library. Following is the explaination on how to do this.

To run the USGS06SpecLib class on Python 3.3 you need a JSON version of the library:

- Download the ENVI version of the library.
- Run the program USGS_ENVI_to_JSON.py on it. You can find the program in the util folder.
- And use the class spectro.JSONReader to load the JSON file, see test_hull.py for an example.

## FeaturesConvexHullQuotient

class `spectro.``FeaturesConvexHullQuotient`(spectrum, wvl, startContinuum=None, stopContinuum=None, baseline=0)

  Remove the convex-hull of the signal by hull quotient. Auto-extract the features and calculate their associated statistics. A baseline can be applied to avoid non-significant features. If you want to restrict the analysis to one continuum, just set the intervale with the startContinuum and stopContinuum parameters. It is up to you to ascertain that the continuum interval defined by startContinuum and stopContinuum do not cross the spectrum. The bilateral function can be use to remove small spectrum noises before extracting the features.

  Parameters:
    spectrum: list
      1D HSI data (p), a spectrum.
    wvl: list
      Wavelength of each band (p x 1).
    startContinuum: float
      The wavelength value of the starting left continuum.
    stopContinuum: float
      The wavelength value of the ending right continuum.
    baseline: float
      Features extracted above the baseline are rejected, features extracted below the baseline are kept.
  Reference:
    Kokaly F. Raymond, PRISM: Processing Routines in IDL for Spectroscopic Measurements (Installation Manual and User’s Guide, Version 1.0), U.S. Geological Survey,Reston, Virginia: 2011.
  `display`(plot_name, feature='all')

    Display the hull quotient graph of the feature to the IPython Notebook using matplotlib.

    Parameters:
      plot_name: string
        Title name.
      suffix: string
        Add a suffix to the title.
  `display_convex_hull_quotient`(plot_name, suffix=None)

    Display the hull quotient graph to the IPython Notebook using matplotlib.

    Parameters:
      plot_name: string
        Title name.
      suffix: string
        Add a suffix to the title.
  `get_absorbtion_depth`(feat_no)
    Returns: float
      The absorbtion value at the feature minimum.
  `get_absorbtion_wavelength`(feat_no)
    Returns: float
      The wavelength at the feature minimum.
  `get_area`(feat_no)
    Returns: float
      The feature area.
  `get_continuum_removed_spectrum`(feat_no)
    Returns: list
      Feature spectrum with convex hull removed (p).
  `get_continuum_slope`(feat_no)
    Returns: float
      The feature continuum slope.
  `get_continuum_start_wavelength`(feat_no)
    Returns: float
      The continuum left start wavelength value.
  `get_continuum_stop_wavelength`(feat_no)
    Returns: float
      The continuum right end wavelength value.
  `get_full_width_at_half_maximum`(feat_no)
    Returns: float
      Width at half maximum.
  `get_number_of_kept_features`()
    Returns: int
      The number of features that are kept (below the baseline). Only theses features have a statistic report.
  `plot`(path, plot_name, feature='all')

    Plot the hull quotient graph of the feature using matplotlib.

    Parameters:
      path: string
        The path where to put the plot.
      plot_name: string
        File name.
      suffix: string
        Add a suffix to the file name.
  `plot_convex_hull_quotient`(path, plot_name, suffix=None)

    Plot the hull quotient graph using matplotlib.

    Parameters:
      path: string
        The path where to put the plot.
      plot_name: string
        File name.
      suffix: string
        Add a suffix to the file name.
  `print_stats`(feat_no)

    Print a statistic summary for a kept feature.

    Parameters:
      feat_no: int or ‘all’
        The feature number, if feat_no=’all’, print stats for all the kept features.

## SpectrumConvexHullQuotient

class `spectro.``SpectrumConvexHullQuotient`(spectrum, wvl, normalize=False)

  Remove the convex-hull of the signal by hull quotient.

  Parameters:
    spectrum: list
      1D HSI data (p), a spectrum.
    wvl: list
      Wavelength of each band (p x 1).
  Reference:
    Clark, R.N. and T.L. Roush (1984) Reflectance Spectroscopy: Quantitative Analysis Techniques for Remote Sensing Applications, J. Geophys. Res., 89, 6329-6340.
  `display`(plot_name, suffix=None)

    Display the hull quotient graph to the IPython Notebook using matplotlib.

    Parameters:
      plot_name: string
        File name.
      suffix: string
        Add a suffix to the title.
  `get_continuum_removed_spectrum`()
    Returns: list
      Spectrum with convex hull removed (p).
  `get_hull_x`()
    Returns: list
      Convex hull x values (p).
  `get_hull_y`()
    Returns: list
      Convex hull y values (p).
  `plot`(path, plot_name, suffix=None)

    Plot the hull quotient graph using matplotlib.

    Parameters:
      path: string
        The path where to put the plot.
      plot_name: string
        File name.
      suffix: string
        Add a suffix to the file name.

## convex_hull_removal

`spectro.``convex_hull_removal`(pixel, wvl)

  Remove the convex-hull of the signal by hull quotient.

  Parameters:
    pixel: list
      1D HSI data (p), a pixel.
    wvl: list
      Wavelength of each band (p x 1).
  Results: list
    Data with convex hull removed (p).
  Reference:
    Clark, R.N. and T.L. Roush (1984) Reflectance Spectroscopy: Quantitative Analysis Techniques for Remote Sensing Applications, J. Geophys. Res., 89, 6329-6340.

## USGS06SpecLib

class `spectro.``EnviReader`(fname)

  Open a ENVI version of the USGS library and return the data and the header.

  The ENVI version is made of two files:
    - s06av95a_envi.hdr
    - s06av95a_envi.sli
  You create the reader this way (on Windows):
    rd = EnviReader(r’c:\somepath\s06av95a_envi.hdr’)
  And pass it to the SpecLib class this way:
    lib = SpecLib(rd)

class `spectro.``JSONReader`(fname)

  Open a JSON version of the USGS library and return the data and the header.

  The JSON version is made of two files:
    - s06av95a_envi.jdata
    - s06av95a_envi.jhead
  You create the reader this way (on Windows):
    rd = JSONReader(r’c:\somepath\s06av95a_envi’)
  And pass it to the SpecLib class this way:
    lib = SpecLib(rd)

class `spectro.``USGS06SpecLib`(reader)

  Load the library and add get and search functionnality.

  Parameters:
    reader: EnviReader or JSONReader instance
  `distance_match`(s, distfn='SAM')

    Scan the library and return the index of the spectrum that have the smallest distance to ‘s’.

    Parameters:
      s: list
        A spectrum.
      distfn: function [default ‘SAM’]
        One of the function: SAM, SID, chebyshev, NormXCorr.
    Returns: tuple
      Spectrum, index.
  `get`(idx)

    Return the spectrum at index idx. Indexing start at zero.

    Parameters:
      idx: int
        The index of the spectrum to fetch.
    Returns: list
      Spectrum (p).
  `get_next`()

    Iterator, scan the library and return at each step: spectrum, mineral, sample_id, description and index.

    Return: tuple
      Spectrum, mineral, sample_id, description and index.
  `get_substance`(substance, sample=None)

    Iterator, scan the library, verify the conditions ‘substance’ and/or ‘sample’ and if true return: spectrum, sample_id, description and index.

    Parameters:
      substance: string
        A substance name.
      sample: string [default None]
        A sample.
    Returns: tuple
      Spectrum, mineral, sample_id, description and index.

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