# spectralMatch

## Syntax

## Description

identifies a region or material by matching its spectral reflectance values, specified as
`score`

= spectralMatch(`libData`

,`reflectance`

,`wavelength`

)`reflectance`

and `wavelength`

, with the values
available in the ECOSTRESS spectral library `libData`

.

specifies options using one or more name-value pair arguments in addition to any combination
of input arguments in previous syntaxes.`score`

= spectralMatch(___,`Name,Value`

)

**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.

The Image Processing Toolbox Hyperspectral Imaging Library requires desktop MATLAB^{®}, as MATLAB
Online™ or MATLAB
Mobile™ do not support the library.

## Examples

### Segment Vegetation Regions in Hyperspectral Data Using Spectral Matching

The spectral matching method compares the spectral signature of each pixel in the hyperspectral data cube with a reference spectral signature for vegetation from an ECOSTRESS spectrum file.

Read the spectral signature of vegetation from the ECOSTRESS spectral library.

```
filename = 'vegetation.tree.tsuga.canadensis.vswir.tsca-1-47.ucsb.asd.spectrum.txt';
libData = readEcostressSig(filename);
```

Read the hyperspectral data into the workspace.

`hcube = hypercube('paviaU.hdr');`

Compute the distance scores of the spectrum of the hyperspectral data pixels with respect to the reference spectrum.

score = spectralMatch(libData,hcube);

Display the distance scores. The pixels with low distance scores are stronger matches to the reference spectrum and are more likely to belong to the vegetation region.

figure imagesc(score) colorbar

Define a threshold for detecting distance scores that correspond to the vegetation region.

threshold = 0.3;

Generate a binary image by assigning a intensity value `1`

for pixels with score less than a specified threshold. Other regions are assigned the intensity value 0. The maximum intensity regions in the binary image correspond to the vegetation regions in the hyperspectral data cube.

bw = score < threshold;

Segment the vegetation regions of the hyperspectral data cube by using the indices of the maximum intensity regions in the binary image.

T = reshape(hcube.DataCube,[size(hcube.DataCube,1)*size(hcube.DataCube,2) size(hcube.DataCube,3)]); Ts = zeros(size(T)); Ts(bw == 1,:) = T( bw==1 ,:); Ts = reshape(Ts,[size(hcube.DataCube,1) size(hcube.DataCube,2) size(hcube.DataCube,3)]);

. Create a new `hypercube`

object that contains only the segmented vegetation regions.

segmentedDataCube = hypercube(Ts,hcube.Wavelength);

Estimate the RGB colour image of the original data cube and the segmented data cube by using the `colorize`

function.

rgbImg = colorize(hcube,'Method','rgb','ContrastStretching',true); segmentedImg = colorize(segmentedDataCube,'Method','rgb','ContrastStretching',true);

Overlay the binary image on the RGB version of the original data cube by using the `imoverlay`

function.

`B = imoverlay(rgbImg,bw,'Yellow');`

Display the RGB colour images of the original data cube and the segmented data cube along with the overlaid image. The segmented image contains only the vegetation regions that are segmented from the original data cube.

figure montage({rgbImg segmentedImg B},'Size',[1 3]) title(['Original Image | ' 'Segmented Image | ' 'Overlayed Image'])

### Identify Unknown Spectral Signature Using Spectral Matching

Read reference spectral signatures from the ECOSTRESS spectral library. The library consists of 15 spectral signatures belonging to manmade materials, soil, water, and vegetation. The output is a structure array that stores the spectral data read from ECOSTRESS library files.

dirname = fullfile(matlabroot,'toolbox','images','supportpackages','hyperspectral','hyperdata','ECOSTRESSSpectraFiles'); libData = readEcostressSig(dirname);

Load a `.mat`

file that contains the reflectance and the wavelength values of an unknown material into the workspace. The reflectance and the wavelength values together comprise the test spectrum.

load spectralData 'reflectance' 'wavelength'

Compute the spectral match between the reference spectrum and test spectrum using spectral information divergence (SID) method. The function computes the distance score for only those reference spectra that have bandwidth overlap with the test spectrum. The function displays a warning message for all other spectra.

score = spectralMatch(libData,reflectance,wavelength,'Method','SID');

Display the distance scores of the test spectrum. The pixels with lower distance scores are stronger matches to the reference spectrum. A distance score value of `NaN`

indicates that the corresponding reference spectrum and the test spectrum do not meet the overlap bandwidth threshold.

score

`score = `*1×15*
297.8016 122.5567 203.5864 103.3351 288.7747 275.5321 294.2341 NaN NaN 290.4887 NaN 299.5762 171.6919 46.2072 176.6637

Find the minimum distance score and the corresponding index. The returned index value indicates the row of the structure array `libData`

that contains the reference spectrum that most closely matches a test spectrum.

[value,ind] = min(score);

Find the matching reference spectrum by using the index of the minimum distance score, and display the details of the matching spectral data in the ECOSTRESS library. The result shows that the test spectrum match most closely with the spectral signature of sea water.

matchingSpectra = libData(ind)

`matchingSpectra = `*struct with fields:*
Name: "Sea Foam"
Type: "Water"
Class: "Sea Water"
SubClass: "none"
ParticleSize: "Liquid"
Genus: [0×0 string]
Species: [0×0 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: [2110×1 double]
Reflectance: [2110×1 double]

Plot the reflectance values of the test spectrum and the corresponding reference spectrum. For the purpose of plotting and visualizing the shape of the reflectance curves, rescale the reflectance values to the range [0, 1] and interpolate test reflectance values to match the reference reflectance values in number.

figure testReflectance = rescale(reflectance,0,1); refReflectance = rescale(matchingSpectra.Reflectance,0,1); testLength = length(testReflectance); newLength = length(testReflectance)/length(refReflectance); testReflectance = interp1(1:testLength,testReflectance,1:newLength:testLength); plot(refReflectance) hold on plot(testReflectance,'r') hold off legend('Matching reference reflectance','Test reflectance') xlabel('Number of samples') ylabel('Reflectance value')

## Input Arguments

`libData`

— Spectral signature from library

structure | structure array

Spectral data from spectral library, specified as a structure or a
1-by-*K* structure array. *K* is the number of
spectral signatures from the library to be used for spectral matching. Each spectral
library structure must contain `Reflectance`

and
`Wavelength`

fields consisting of numeric vectors of equal length,
such as a spectral signature read from the ECOSTRESS library using the `readEcostressSig`

function.

`hcube`

— Input hyperspectral data

`hypercube`

object

Input hyperspectral data, specified as a `hypercube`

object. The
`DataCube`

property of the `hypercube`

object
contains the hyperspectral datacube.

`reflectance`

— Reflectance values

*C*-element vector

Reflectance values, specified as a *C*-element vector.
*C* is the number of wavelengths for which the reflectance values
have been measured.

`wavelength`

— Wavelength values

*C*-element vector

Wavelength values, specified as a *C*-element vector.
*C* is the number of wavelengths for which the reflectance values
have been measured.

### Name-Value Arguments

Specify optional pairs of arguments as
`Name1=Value1,...,NameN=ValueN`

, where `Name`

is
the argument name and `Value`

is the corresponding value.
Name-value arguments must appear after other arguments, but the order of the
pairs does not matter.

*
Before R2021a, use commas to separate each name and value, and enclose*
`Name`

*in quotes.*

**Example: **`spectralMatch(libData,hcube,'MinBandWidth',0.5)`

`Method`

— Spectral matching method

`'sam'`

(default) | `'sid'`

| `'sidsam'`

| `'jmsam'`

| `'ns3'`

Spectral matching method, specified as the comma-separated pair consisting of
`'Method'`

and one of these values:

`'sam'`

— Spectral angle mapper (SAM) method, which measures the similarity between two spectra by computing the angular distance between them.`'sid'`

— Spectral information divergence (SID) method, which measures the similarity between two spectra by computing the difference between their probability distribution values.`'sidsam'`

— Mixed spectral similarity method, which measures the similarity between two spectra by combining the SID and SAM distance measures.`'jmsam'`

— Jeffries Matusita-Spectral Angle Mapper (JMSAM), which measures the similarity between two spectra by combining the Jeffries Matusita (JM) and SAM distance measures.`'ns3'`

— Normalized spectral similarity score (NS3) method, which measures the similarity between two spectra by combining the Euclidean and SAM distance measures.

For details about these spectral matching methods, see Algorithm.

**Data Types: **`char`

| `string`

`MinBandWidth`

— Minimum overlap bandwidth

`300`

(default) | positive scalar

Minimum overlap bandwidth, specified as the comma-separated pair consisting of
`'MinBandWidth'`

and a positive scalar in nanometers. The overlap
bandwidth between the reference spectrum and the test spectra is defined as:

*BW*_{overlap} =
*W*_{max} −
*W*_{min}

*W*_{min} is the maximum of minimum
wavelengths in the reference and test spectra.

*W*_{max} is the maximum of maximum
wavelengths in the reference and test spectra.

The `'MinBandWidth'`

argument defines the minimum expected value
for the overlap bandwidth between the spectral values of the test material and the
ECOSTRESS spectral data.

**Data Types: **`single`

| `double`

| `int8`

| `int16`

| `int32`

| `int64`

| `uint8`

| `uint16`

| `uint32`

| `uint64`

## Output Arguments

`score`

— Distance scores

3-D numeric array | matrix | *K*-element column vector | scalar

Distance scores, returned as a 3-D numeric array, matrix,
*K*-element column vector, or scalar. The dimensions of the output
score depend on the dimensions of the `libData`

and whether the test
data is a `hypercube`

object or a `wavelength`

and
`reflectance`

pair.

**If the test spectral signatures are specified as a hypercube
object, hcube and the data cube is of size
**

*M*-by-

*N*-by-

*C*:

Dimension of input argument,
`libData` | Dimension of output,
`score` |

1-by-K, containing K reference
signatures read from K number of spectrum files | 3-D numeric array of size
The values in each
channel of |

1-by-1, containing reference signature read from one spectrum file
(K = 1) | matrix of size M-by-N, The matrix
contains the distance score for each pixel's spectra with respect to a
reference signature. |

**If the test spectral signature is specified as reflectance
and wavelength values:**

Dimension of input argument,
`libData` | Dimension of output,
`score` |

1-by-K, containing K reference
signatures read from K number of spectrum files | K-element vector containing the distance score of the
test spectra with respect to K reference signatures. Each
element of the vector is the distance score of the test reflectance values
with respect to the spectral data in the corresponding row of
`libData` . |

1-by-1, containing reference signature read from one spectrum file
(K = 1) | scalar |

**Data Types: **`double`

## Limitations

This function does not support `parfor`

loops when the `Method`

is specified as
`"sam"`

, `"sid"`

, `"jmsam"`

, or
`"ns3"`

, as its performance is already optimized.* (since R2023a)*

## Algorithms

### Spectral Angle Mapper (SAM)

For the `"sam"`

method, the `spectralMatch`

function
computes the SAM score *α* using this formula.

$$\alpha =\text{\hspace{0.17em}}{\mathrm{cos}}^{-1}\left(\frac{{\displaystyle \sum _{i=1}^{C}{t}_{i}{r}_{i}}}{\sqrt{{\displaystyle \sum _{i=1}^{C}{t}_{i}^{2}}}\sqrt{{\displaystyle \sum _{i=1}^{C}{r}_{i}^{2}}}}\right).$$

where, *r* and *t* are the reference
and test spectra, respectively. *r _{i}* and

*t*are the

_{i}*i*

^{th}elements of the vectors

*r*and

*t*, respectively.

*C*is the length of vectors

*r*and

*t*.

### Spectral Information Divergence (SID)

For the `"sid"`

method, the `spectralMatch`

function
normalizes the reference spectra `refSpectra`

and test spectra
`testSpectra`

and computes the SID value using this formula.

$$\text{\hspace{0.17em}}\text{\hspace{0.17em}}SID={\displaystyle \sum _{i=1}^{C}{p}_{i}\mathrm{log}\left(\frac{{p}_{i}}{{q}_{i}}\right)+}{\displaystyle \sum _{i=1}^{C}{q}_{i}\mathrm{log}\left(\frac{{q}_{i}}{{p}_{i}}\right)}.$$

*q* and *p* are the vectors of
normalized reference and test spectra, respectively.
*q _{i}* and

*p*are the

_{i}*i*

^{th}elements of the vectors

*q*and

*p*, respectively.

*C*is the length of vectors

*q*and

*p*.

### SID-SAM

For the `"sidsam"`

method, the
`spectralMatch`

function computes the SID-SAM value using this formula.

$$SIDSAM\text{\hspace{0.17em}}=\text{\hspace{0.17em}}SID\times \mathrm{tan}\left(\alpha \right)$$

*SID* is the SID value, and *α* is the
SAM score.

### Jeffries Matusita-Spectral Angle Mapper (JMSAM)

For the `"jmsam"`

method, the
`spectralMatch`

function computes the JMSAM score using this formula.

$$JMSAM\text{\hspace{0.17em}}=\text{\hspace{0.17em}}\text{\hspace{0.17em}}J{M}_{distance}\times \mathrm{tan}\left(\alpha \right)\text{\hspace{0.17em}}$$

*JM _{distance}* is the JM distance,
and

*α*is the SAM score. This method computes the JM distance using this formula.

$$J{M}_{\text{distance}}=2\left(1-{e}^{-B}\right)$$

*B* is the Bhattacharyya distance:

$$B=\frac{1}{8}{\left({\mu}_{t}-{\mu}_{r}\right)}^{T}{\left[\frac{{\sigma}_{t}+{\sigma}_{r}}{2}\right]}^{-1}\left({\mu}_{t}-{\mu}_{r}\right)\text{\hspace{0.17em}}+\text{\hspace{0.17em}}\frac{1}{2}\mathrm{ln}\left[\frac{\left|\frac{{\sigma}_{t}+{\sigma}_{r}}{2}\right|}{\sqrt{\left|{\sigma}_{t}\right|\left|{\sigma}_{r}\right|}}\right]$$

*μ _{r}* and

*μ*are the mean values of the reference and test spectra, respectively.

_{t}*σ*and

_{r}*σ*are the covariance values of the reference and test spectra, respectively.

_{t}### Normalized Spectral Similarity Score (NS3)

For the `"ns3"`

method, the
`spectralMatch`

function computes the NS3 score using this formula.

$$NS3\text{\hspace{0.17em}}=\text{\hspace{0.17em}}\sqrt{{A}_{Euclidean}{}^{2}+{\left(1-\mathrm{cos}\left(\alpha \right)\right)}^{2}}$$

*A _{Euclidean}* is the Euclidean
distance, and

*α*is the SAM score. This method computes the Euclidean distance using this formula.

$${A}_{Euclidean}=\text{\hspace{0.17em}}\sqrt{\frac{1}{C}{\displaystyle \sum _{i=1}^{C}{\left({t}_{i}-{r}_{i}\right)}^{2}}}$$

*r* and *t* are the vectors of
reference and test spectra, respectively. *r _{i}* and

*t*are the

_{i}*i*

^{th}elements of the vectors

*r*and

*t*, respectively.

*C*is the length of vectors

*r*and

*t*.

## Version History

**Introduced in R2020a**

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