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hypercube

Read hyperspectral data

Since R2020a

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    Description

    The hypercube function reads hyperspectral data and returns a hypercube object. The object contains the hyperspectral data cube and its related properties. Use the object functions to remove or select a desired hyperspectral band, assign new pixels values, generate colored image, and write hyperspectral data to the ENVI (environment for visualizing images) file format.

    Creation

    Syntax

    hcube = hypercube(filename)
    hcube = hypercube(img,hdr)
    hcube = hypercube(___,wavelength)
    hcube = hypercube(tifFile,wavelength)
    hcube = hypercube(image,wavelength)
    hcube = hypercube(image,wavelength,metadata)
    hcube = hypercube(___,BlockSize=blockSize)

    Description

    hcube = hypercube(filename) reads hyperspectral data from the specified input file filename. The input file can be a national imagery transmission format (NITF) file, Hyperion level 1R (L1R) file stored in hierarchical data format (HDF), ENVI header or image file, or metadata text extension (MTL) file that contains satellite data from earth observing (EO) satellites. The hypercube object supports hyperspectral and multispectral data acquired by these satellites.

    • EO-1 Hyperion — Hyperspectral data

    • EO-1 Advanced Land Imager (EO-1 ALI) — Multispectral data

    • Landsat Multispectral Scanner (Landsat MSS) — Multispectral data

    • Landsat Thematic Mapper (Landsat TM) — Multispectral data

    • Landsat Enhanced Thematic Mapper Plus (Landsat ETM+) — Multispectral data

    • Landsat Operational Land Imager / Thermal Infrared Scanner (Landsat OLI / TIRS) — Multispectral data

    • Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) — Hyperspectral data

    Note

    The hypercube function reads satellite data stored in the georeferenced tagged image file format (GeoTIFF).

    example

    hcube = hypercube(img,hdr) reads hyperspectral data from the data file img. The data file can be an ENVI image file or Hyperion L1R file. The function uses the metadata in the header file hdr to interpret the data from img.

    example

    hcube = hypercube(___,wavelength) specifies the wavelength for each spectral band in the input data and sets the Wavelength property of the output hypercube object.

    example

    hcube = hypercube(tifFile,wavelength) reads hyperspectral data from a tagged image file format (TIFF) file tifFile.

    hcube = hypercube(image,wavelength) creates a hypercube object from the hyperspectral data cube image and the specified center wavelength values wavelength.

    example

    hcube = hypercube(image,wavelength,metadata) creates a hypercube object from the hyperspectral data cube image, specified center wavelength values wavelength, and the metadata metadata. You can use this syntax to modify the Metadata property of a hypercube object.

    example

    hcube = hypercube(___,BlockSize=blockSize) specifies the block size for loading the hyperspectral data cube, in addition to any combination of input arguments from previous syntaxes.

    Note

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

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

    Input Arguments

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    Input filename, specified as a character vector or string scalar. The input filename must be one of these file types.

    File FormatExtensionsAdditional Requirements
    NITF files

    .ntf

    .nsf

    		None
    GeoTIFF metadata files from EO satellites.txtFilename must end with suffix "MTL".

    ENVI image files

    ENVI header files

    Image files:

    • .dat

    • .img

    • .raw

    • .bsq (since R2023b)

    • .bil (since R2023b)

    • .bip (since R2023b)

    Header files:

    • .hdr

    		Image and header file must be in the same folder and have the same filename.

    Hyperion level 1R image files

    Hyperion header files

    Image files:

    • .L1R

    Header files:

    • .hdr

    		Image and header file must be in the same folder and have the same filename.

    Multipage TIFF files (since R2023b)

    .tif

    		File must be a multipage TIFF file containing a volume or time series image stack.

    Data Types: char | string

    Image filename, specified as a character vector or string scalar. The input file must be a flat binary raster file with one of these file extensions.

    • .dat

    • .raw

    • .L1R

    • .bsq (since R2023b)

    • .bil (since R2023b)

    • .bip (since R2023b)

    The binary data must be in band sequential (BSQ), band-interleaved-by-pixel (BIP), or band-interleaved-by-line (BIL) interleave format.

    Data Types: char | string

    Header filename, specified as a character vector or string scalar. The header file contains the metadata for the image file img and must have the extension .hdr. The header file must contain at least these fields.

    FieldDescription
    HeightHeight of the image or number of rows in the image, specified as a positive integer.
    WidthWidth of the image or number of columns in the image, specified as a positive integer.
    BandsNumber of spectral bands, specified as a positive integer.
    DataType

    Data type of data in the ENVI file, specified as any of these values:

    • "single"

    • "double"

    • "uint8"

    • "uint16"

    • "int16"

    • "uint32"

    • "int32"

    • "uint64"

    • "int64"

    HeaderOffsetZero-based location of the first element in the image file,specified as a positive integer. The header offset represents the number of bytes from the beginning of the image file to the start of the image data.
    ByteOrderEndianness of the data, specified as the string "ieee-le" for little endian or "ieee-be" for big endian.

    The hypercube function also requires data interleave information to read the hyperspectral image associated with the header. If the image file does not have a .bsq (band-sequential), .bil (band-interleaved-by-line), or .bip (band-interleaved-by-pixel) extension, then your header file must include an Interleave field with one of these values.

    • "bsq" — Band-sequential

    • "bil" — Band-interleaved-by-line

    • "bip" — Band-interleaved-by-pixel

    Data Types: char | string

    Center wavelength values of each spectral band, specified as C-element vector. C is the spectral dimension, defined as the number of spectral bands, of the input hyperspectral data.

    Data Types: single | double | int8 | int16 | int32 | int64 | uint8 | uint16 | uint32 | uint64

    TIFF file name, specified as a character vector or string scalar. The file name must include the extension .tiff or .tif.

    Data Types: char | string

    Input hyperspectral data, specified as a 3-D numeric array of size M-by-N-by-C. M and N are the number of rows and columns in the hyperspectral data, respectively. C is the number of spectral bands in the hyperspectral data.

    Data Types: single | double | int8 | int16 | int32 | int64 | uint8 | uint16 | uint32 | uint64

    Metadata of hyperspectral data, specified as a structure array.

    Data Types: struct

    Size of the data blocks, specified as a 2-element vector of positive integers. The elements of the vector correspond to the number of rows and columns in each block, respectively. This argument sets the BlockSize property of the hypercube object.

    Data Types: single | double | int8 | int16 | int32 | int64 | uint8 | uint16 | uint32 | uint64

    Properties

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    This property is read-only.

    Hyperspectral data cube, stored as a 3-D numeric array of size M-by-N-by-C. The data cube stores the hyperspectral data read from a file or numeric array as an array of 2-D monochromatic images. C is the number of images or spectral bands, M and N are the spatial resolution of the images in pixels. The data cube is of the same size and data type as the input data.

    Data Types: single | double | int8 | int16 | int32 | int64 | uint8 | uint16 | uint32 | uint64

    This property is read-only.

    Center wavelength values of each spectral band, specified as a C-element vector. C is the spectral dimension, defined as the number of spectral bands, of the input hyperspectral data. You can set this property by using wavelength input argument.

    Data Types: single | double | int8 | int16 | int32 | int64 | uint8 | uint16 | uint32 | uint64

    This property is read-only.

    Metadata of hyperspectral data, stored as a structure array with these fields as defaults.

    FieldDescription
    HeightHeight of the image or number of rows in the data cube, specified as a positive integer
    WidthWidth of the image or number of columns in the data cube, specified as a positive integer
    BandsNumber of spectral bands comprising the data cube, specified as a positive integer
    DataType

    Data type of data, specified as any of these values:

    • "single"

    • "double"

    • "uint8"

    • "uint16"

    • "int16"

    • "uint32"

    • "int32"

    • "uint64"

    • "int64"

    Interleave

    Data interleave, specified as any one of these values:

    • "bsq" — Band-sequential

    • "bil" — Band-interleaved-by-line

    • "bip" — Band-interleaved-by-pixel

    HeaderOffset

    Zero-based location of the first element in the image file, specified as a positive integer

    The header offset represents the number of bytes from the beginning of the image file to the start of the image data. The default value is 0.

    ByteOrderEndianness of the data, specified as the string "ieee-le" for little endian or "ieee-be" for big endian.
    WavelengthUnits

    Units for the wavelengths of spectral bands, stored as one of these strings.

    • "Nanometers" — If all wavelengths are in nanometers (greater than 200 and less than 100000)

    • "Micrometers" — If all wavelengths are in micrometers (greater than 0.2 and less than 100)

    • "" — If all the wavelengths are neither in nanometers, nor in micrometers.

    Note

    The Metadata property of hypercube object can have one or more additional fields depending on the parameter values stored in the header file of the input hyperspectral data. You can modify the parameters values of the Metadata property or add new Metadata to the hypercube object by specifying the input argument metadata.

    Data Types: struct

    Size of the data blocks, stored as a 2-element vector of positive integers. The elements of the vector correspond to the number of rows and columns in each block, respectively. Loading the hyperspectral data cube using blocks enables you to load smaller regions of large data sets without running out of memory.

    • A small value for BlockSize reduces the memory usage of the function at the cost of increased execution time.

    • A large value for BlockSize reduces the execution time at the cost of increased memory usage.

    You can set this property using the blockSize name-value argument.

    • The number of rows in each block must be less than or equal to the number of rows in the hyperspectral image. If you specify a value greater than the number of rows in the hyperspectral image, BlockSize uses the number of rows in the hyperspectral image, instead.

    • The number of columns in each block must be less than or equal to the number of columns in the hyperspectral image. If you specify a value greater than the number of columns in the hyperspectral image, BlockSize uses the number of columns in the hyperspectral image, instead.

    Data Types: double

    Object Functions

    assignDataAssign new data to hyperspectral data cube
    cropDataCrop regions-of-interest
    enviwriteWrite hyperspectral data to ENVI file format
    selectBandsSelect most informative bands
    removeBandsRemove spectral bands from data cube
    colorizeEstimate color image of hyperspectral data

    Examples

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    This example uses:

    Open Live Script

    Read hyperspectral data stored in the ENVI format into the workspace. Create a hypercube object by specifying an ENVI data file and the associated ENVI header file. 

    hcube = hypercube('paviaU.dat','paviaU.hdr');

    Display the properties of the hypercube object.

    hcube
    hcube = 
  hypercube with properties:

      DataCube: "[610x340x103 double]"
    Wavelength: [103x1 double]
      Metadata: [1x1 struct]
     BlockSize: [610 340]

    Estimate an RGB image from the hyperspectral data by using the colorize function. Visualize the RGB image. 

    rgbImg = colorize(hcube,'Method','RGB');
figure
imagesc(rgbImg)
title('RGB Image of Data Cube')

    Figure contains an axes object. The axes object with title RGB Image of Data Cube contains an object of type image.

    Inspect the metadata of the hypercube object.

    hcube.Metadata
    ans = struct with fields:
             Filename: "/mathworks/devel/bat/filer/batfs2566-0/Bdoc24b.2855429/build/runnable/matlab/toolbox/images/supportpackages/hyperspectral/hyperdata/mavendata/paviaU.hdr"
          FileModDate: "21-Jun-2024 16:13:21"
             FileSize: 654
               Format: "HDR"
        FormatVersion: ''
           SensorType: [0x0 string]
          Description: [0x0 string]
      AcquisitionTime: [0x0 string]
         RasterFormat: "ENVI"
               Height: 610
                Width: 340
                Bands: 103
             DataType: "double"
           Interleave: "bsq"
         HeaderOffset: 0
            ByteOrder: "ieee-le"
            BandNames: [0x0 string]
                 FWHM: []
                 Gain: []
               Offset: []
      ReflectanceGain: []
    ReflectanceOffset: []
             BadBands: []
           CloudCover: []
           SunAzimuth: []
         SunElevation: []
      SolarIrradiance: []
     EarthSunDistance: []
      WavelengthUnits: "Nanometers"

    This example uses:

    Open Live Script

    Read ENVI format data into the workspace by specifying a header file that contains information about hyperspectral data. The associated ENVI binary data file must be stored in the same folder as the ENVI header file.

    hcube = hypercube('paviaU.hdr');

    Display the properties of the hypercube object.

    hcube
    hcube = 
  hypercube with properties:

      DataCube: "[610x340x103 double]"
    Wavelength: [103x1 double]
      Metadata: [1x1 struct]
     BlockSize: [610 340]

    Estimate an RGB image from the data cube by using the colorize function. Increase the contrast of the RGB image using contrast stretching. Visualize the RGB image. 

    rgbImg = colorize(hcube,'Method','RGB','ContrastStretching',true);
figure
imagesc(rgbImg)
title('RGB Image of Data Cube')

    Figure contains an axes object. The axes object with title RGB Image of Data Cube contains an object of type image.

    Assign new center wavelength values for the hyperspectral data. The number of wavelength values must be equal to the number of bands in the hyperspectral data cube. Each wavelength value must be unique values.

    minWavelength = 500;
maxWavelength = 1010;
newWavelength = minWavelength:5:maxWavelength;

    Create a new hypercube object with the new wavelength values.

    newhcube = hypercube('paviaU.hdr',newWavelength);

    Plot the old and the new wavelength values. Display the wavelength range.

    figure
plot(hcube.Wavelength,'o')
hold on
plot(newhcube.Wavelength,'or')
xlabel('Band Number')
ylabel('Wavelength')
str1 = ['Original wavelength range: ' num2str(min(hcube.Wavelength))  'nm to ' num2str(max(hcube.Wavelength)) 'nm'];
text(5,1075,str1)
str2 = ['New wavelength range: ' num2str(min(newhcube.Wavelength))  'nm to ' num2str(max(newhcube.Wavelength)) 'nm'];
text(5,1035,str2)
legend('Original Values','New Values','Location','SouthEast')

    Figure contains an axes object. The axes object with xlabel Band Number, ylabel Wavelength contains 4 objects of type line, text. One or more of the lines displays its values using only markers These objects represent Original Values, New Values.

    This example uses:

    Open Live Script

    Read an RGB image into the workspace. An RGB image contains three spectral channels: red, green, and blue channels.

    image = imread('peppers.png');

    Specify the center wavelength values for the red, green, and blue channels as 700, 530, and 470 nanometers (nm) respectively.

    wavelength = [700 530 470];

    Create a hypercube object using the image and the wavelength values. 

    hcube = hypercube(image,wavelength)
    hcube = 
  hypercube with properties:

      DataCube: "[384x512x3 uint8]"
    Wavelength: [3x1 double]
      Metadata: [1x1 struct]
     BlockSize: [384 512]

    This example uses:

    Open Live Script

    Read a hyperspectral data into the workspace and inspect its properties.

    hcube = hypercube('paviaU.dat');

    Inspect the Metadata property of the hypercube object. 

    hcube.Metadata
    ans = struct with fields:
             Filename: "/mathworks/devel/bat/filer/batfs2566-0/Bdoc24b.2855429/build/runnable/matlab/toolbox/images/supportpackages/hyperspectral/hyperdata/mavendata/paviaU.hdr"
          FileModDate: "21-Jun-2024 16:13:21"
             FileSize: 654
               Format: "HDR"
        FormatVersion: ''
           SensorType: [0x0 string]
          Description: [0x0 string]
      AcquisitionTime: [0x0 string]
         RasterFormat: "ENVI"
               Height: 610
                Width: 340
                Bands: 103
             DataType: "double"
           Interleave: "bsq"
         HeaderOffset: 0
            ByteOrder: "ieee-le"
            BandNames: [0x0 string]
                 FWHM: []
                 Gain: []
               Offset: []
      ReflectanceGain: []
    ReflectanceOffset: []
             BadBands: []
           CloudCover: []
           SunAzimuth: []
         SunElevation: []
      SolarIrradiance: []
     EarthSunDistance: []
      WavelengthUnits: "Nanometers"

    Find and remove the empty fields from the metadata.

    metadata = hcube.Metadata;
fields = fieldnames(metadata);
indx = find(structfun(@isempty,metadata)==1);
newMetadata = rmfield(metadata,fields(indx));

    Set the value for the AcquistionTime field to current date.

    currentDate = string(datetime("now",Format="yyyy-MM-dd"));
newMetadata.AcquistionTime = currentDate;

    Create a hypercube object with the new metadata. The DataCube and Wavelength properties of the new hypercube object is same as that of the input data.

    nhcube = hypercube(hcube.DataCube,hcube.Wavelength,newMetadata);

    Inspect the Metadata property of the new hypercube object.

    nhcube.Metadata
    ans = struct with fields:
             Height: 610
              Width: 340
              Bands: 103
           DataType: "double"
         Interleave: "bsq"
       HeaderOffset: 0
          ByteOrder: "ieee-le"
     AcquistionTime: "2025-01-23"
    WavelengthUnits: "Nanometers"

    More About

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    Version History

    Introduced in R2020a

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    See Also

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