readEcostressSig

Read data from ECOSTRESS spectral library

Syntax

libData = readEcostressSig(filenames)

libData = readEcostressSig(dirname)

libData = readEcostressSig(dirname,keyword)

Description

libData = readEcostressSig(filenames) reads spectral data from the specified ECOSTRESS spectrum files.

The function supports only ECOSTRESS spectrum files. All inputs must be text files with suffix spectrum.txt.

libData = readEcostressSig(dirname) reads spectral data from the ECOSTRESS spectrum files stored in the specified directory.

libData = readEcostressSig(dirname,keyword) reads spectral data from only those ECOSTRESS spectrum files stored in the specified directory with the specified keyword in their file names.

Note

This function requires the Image Processing Toolbox™ Hyperspectral Imaging Library. You can install the Image Processing Toolbox Hyperspectral Imaging Library from Add-On Explorer. For more information about installing add-ons, see Get and Manage Add-Ons.

Examples

Read ECOSTRESS Spectrum Files

Specify the names of the spectrum files to read from the ECOSTRESS spectral library as a cell array of character vectors.

ecostressfiles = [{'soil.utisol.hapludult.none.all.87p707.jhu.becknic.spectrum.txt'},...
             {'water.seawater.none.liquid.tir.seafoam.jhu.becknic.spectrum.txt'},...
             {'vegetation.tree.eucalyptus.maculata.vswir.jpl087.jpl.asd.spectrum.txt'},...
             {'manmade.road.tar.solid.all.0099uuutar.jhu.becknic.spectrum.txt'}];

Read and display the data from the specified ECOSTRESS spectrum files. The function returns a structure array with a row for each specified ECOSTRESS spectrum file. Each row stores the spectral data read from the associated file.

libData = readEcostressSig(ecostressfiles)

libData=1×4 struct array with fields:
    Name
    Type
    Class
    SubClass
    ParticleSize
    Genus
    Species
    SampleNo
    Owner
    WavelengthRange
    Origin
    CollectionDate
    Description
    Measurement
    FirstColumn
    SecondColumn
    WavelengthUnit
    DataUnit
    FirstXValue
    LastXValue
    NumberOfXValues
    AdditionalInformation
    Wavelength
    Reflectance
      ⋮

Extract the details of the spectral data of the second file from the structure array.

libData(2)

ans = struct with fields:
                     Name: "Sea Foam"
                     Type: "Water"
                    Class: "Sea Water"
                 SubClass: "none"
             ParticleSize: "Liquid"
                    Genus: [0x0 string]
                  Species: [0x0 string]
                 SampleNo: "seafoam"
                    Owner: "Dept. of Earth and Planetary Science, John Hopkins University"
          WavelengthRange: "TIR"
                   Origin: "JHU IR Spectroscopy Lab."
           CollectionDate: "N/A"
              Description: "Sea foam water. Original filename FOAM Original ASTER Spectral Library name was jhu.becknic.water.sea.none.liquid.seafoam.spectrum.txt"
              Measurement: "Directional (10 Degree) Hemispherical Reflectance"
              FirstColumn: "X"
             SecondColumn: "Y"
           WavelengthUnit: "micrometer"
                 DataUnit: "Reflectance (percent)"
              FirstXValue: "14.0112"
               LastXValue: "2.0795"
          NumberOfXValues: "2110"
    AdditionalInformation: "none"
               Wavelength: [2110x1 double]
              Reflectance: [2110x1 double]

Extract the reflectance and the wavelength values from the spectral data of the second file.

reflectance = libData(2).Reflectance;
wavelength = libData(2).Wavelength;

Plot the spectral signature using the wavelength and reflectance values.

figure
plot(wavelength,reflectance)
title(['Spectra of ' libData(2).Name])
xlabel('Wavelength')
ylabel('Reflectance Value')

Read All ECOSTRESS Spectrum Files in Directory

Specify the full path of the directory that contains the ECOSTRESS spectrum files.

fileroot = matlabshared.supportpkg.getSupportPackageRoot();
dirname = fullfile(fileroot,'toolbox','images','supportpackages','hyperspectral','hyperdata','ECOSTRESSSpectraFiles');

Read and display the spectral data from all the files in the directory. The function returns a structure array with a row for each ECOSTRESS spectrum file in the specified directory.

libData = readEcostressSig(dirname)

libData=1×15 struct array with fields:
    Name
    Type
    Class
    SubClass
    ParticleSize
    Genus
    Species
    SampleNo
    Owner
    WavelengthRange
    Origin
    CollectionDate
    Description
    Measurement
    FirstColumn
    SecondColumn
    WavelengthUnit
    DataUnit
    FirstXValue
    LastXValue
    NumberOfXValues
    AdditionalInformation
    Wavelength
    Reflectance
      ⋮

Extract the details of the spectral data of the 15th file.

libData(15)

ans = struct with fields:
                     Name: "Tap water"
                     Type: "Water"
                    Class: "Tap Water"
                 SubClass: "none"
             ParticleSize: "Liquid"
                    Genus: [0×0 string]
                  Species: [0×0 string]
                 SampleNo: "tapwater"
                    Owner: "Dept. of Earth and Planetary Science, John Hopkins University"
          WavelengthRange: "All"
                   Origin: "JHU IR Spectroscopy Lab. Original filename TAPWATER."
           CollectionDate: "N/A"
              Description: "Tap water. Original ASTER Spectral Library name was jhu.becknic.water.tap.none.liquid.tapwater.spectrum.txt"
              Measurement: "Directional (10 Degree) Hemispherical Reflectance"
              FirstColumn: "X"
             SecondColumn: "Y"
           WavelengthUnit: "micrometer"
                 DataUnit: "Reflectance (percent)"
              FirstXValue: "14.0110"
               LastXValue: "0.4000"
          NumberOfXValues: "2844"
    AdditionalInformation: "none"
               Wavelength: [2844×1 double]
              Reflectance: [2844×1 double]

Search ECOSTRESS Spectrum Files Using Keyword

Specify full path of the directory that contains the ECOSTRESS spectrum files.

fileroot = matlabshared.supportpkg.getSupportPackageRoot();
dirname = fullfile(fileroot,'toolbox','images','supportpackages','hyperspectral','hyperdata','ECOSTRESSSpectraFiles');

Read and display the spectral data of the ECOSTRESS spectrum files with a specific keyword in their file names. The function returns a structure array with a row for each spectrum file in the specified directory with the keyword in their file names.

keyword = 'water';
libData = readEcostressSig(dirname,keyword)

libData=1×3 struct array with fields:
    Name
    Type
    Class
    SubClass
    ParticleSize
    Genus
    Species
    SampleNo
    Owner
    WavelengthRange
    Origin
    CollectionDate
    Description
    Measurement
    FirstColumn
    SecondColumn
    WavelengthUnit
    DataUnit
    FirstXValue
    LastXValue
    NumberOfXValues
    AdditionalInformation
    Wavelength
    Reflectance
      ⋮

Input Arguments

filenames — Names of ECOSTRESS files

character vector | string scalar | cell array of character vectors | vector of strings

Names of the ECOSTRESS files, specified as a character vector, string scalar, cell array of character vectors, or vector of strings. To read the data from multiple ECOSTRESS files simultaneously, use a cell array of character vectors or vector of strings. The function reads data from the files in the order in which you specify them. If the ECOSTRESS files are not in the current folder, you must specify the full path of each file.

Data Types: char | string

dirname — Name of directory

character vector | string scalar

Name of the directory containing the ECOSTRESS files, specified as a character vector or string scalar. If the directory is not in the current folder, you must specify the full path of the directory.

Data Types: char | string

keyword — File search keyword

character vector | string scalar

File search keyword, specified as a character vector or string scalar. The function returns data from only the ECOSTRESS spectrum files with the specified keyword in their file names. You cannot specify multiple keywords simultaneously.

Data Types: char | string

Output Arguments

libData — Spectral data from ECOSTRESS files

structure array

Spectral data from ECOSTRESS files, returned as a 1-by-K structure array. K is the number of spectrum files read by the function. Each element of the structure array has 24 fields that contain the header information of the spectrum files.

Field Names	Description
Name	Name of the measured sample or material
Type	Type of sample, such as "mineral", "rock", "tree", or "manmade"
Class	Class of the sample type For example, if the sample type is "mineral" then the class can be: "native elements","silicates", "oxides", "sulfides", "sulfates", "halides", "carbonates", "phosphates", or "mineraloids".
SubClass	Subclass of the sample type This field contains an empty array or "none", unless the Type value is "mineral", "rock", "manmade", "soil", "lunar", or "meteorite".
ParticleSize	Particle size of the sample type This field contains an empty array unless the Type value is "mineral", "rock", "manmade", "soil", "lunar", or "meteorite".
Genus	Genus of the sample This field contains an empty array unless the Type value is "vegetation" or "nonphotosynthetic".
Species	Species of the sample This field contains an empty array unless the Type value is "vegetation" or "nonphotosynthetic".
SampleNo	Sample number This value is an identifier for the associated sample.
Owner	Owner of the sample
WavelengthRange	Wavelength range of the measured sample The value must be "All", "TIR", or "VSWIR".
Origin	Location from which the data was obtained
CollectionDate	Date on which the sample was collected This value is in mm/dd/yy format.
Description	Description of the measured sample This field provides additional information about the characteristics of the sample.
Measurement	Spectral measurement mode used to measure the sample
FirstColumn	First column of data values in the spectrum file
SecondColumn	Second column of data values in the spectrum file
WavelengthUnit	Measuring unit for the spectral wavelengths of the samples The value for every sample type is "micrometer". This field corresponds to the X Units field of the header data in the ECOSTRESS spectrum file.
DataUnit	Unit of the spectral measurement mode Spectral measurement mode includes reflectance, transmittance, transittance, and transmission. The unit is percentage. This field corresponds to the Y Units field of the header data in the ECOSTRESS spectrum file.
FirstXValue	First value in the first column of data values in the spectrum file
LastXValue	Last value in the first column of data values in the spectrum file
NumberofXValues	Total number of data values in the first column of the spectrum file
AdditionalInformation	Additional information about the sample This field includes information that is not part of the spectral data.
Wavelength	Wavelength values at which the reflectances were measured
Reflectance	Reflectance values measured at each wavelengths

References

[1] Meerdink, Susan K., Simon J. Hook, Dar A. Roberts, and Elsa A. Abbott. “The ECOSTRESS Spectral Library Version 1.0.” Remote Sensing of Environment 230 (September 2019): 111196. https://doi.org/10.1016/j.rse.2019.05.015.

[2] Download the ECOSTRESS Spectral Library: https://speclib.jpl.nasa.gov/download