Creating/Editing a Spectral Library

So far, QGIS has no functionality for creating, viewing or editing spectral libraries. For that reason, we had to build this tool ourselves. It has several functions:

  • Create a Spectral Library by manually selecting spectra from an image
  • Create a Spectral Library by using Regions Of Interest (polygons/points)
  • Open and inspect a Spectral Library
  • Edit the metadata of a Spectral Library
  • Remove profiles from the Spectral Library
  • …

It speaks for itself that a thorough understanding of the research area is required to be able to build a Spectral Library from it.

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The table below gives a short overview of all Spectral Library specific buttons and their function:

select Select a new profile from a (hyperspectral) image
add Add the currently overlaid profiles to the Spectral Library
auto Automatically add selected profiles to the Spectral Library
import Import Spectral Library
polygon Import profiles from raster + vector source
save Save the current Spectral Library to file
color Use colors from map vector symbology

All other buttons are inherent to QGIS, but here is a short overview:

m_edit Toggle editing mode
m_edit_m Toggle multi-edit mode
m_save Save edits
m_reload Reload the table
m_add_ft Add feature
m_delete Delete selected features
m_cut Cut selected rows to clipboard
m_copy Copy selected rows to clipboard
m_paste Paste features from clipboard
m_expr Select features using an expression
m_select Select all
m_invert Invert selection
m_deselect Deselect all
m_top Move selection to top
m_filter Select/filter features using form
m_pan Pan map to the selected rows
m_zoom Zoom map to the selected rows
m_add New field
m_rem Delete field
m_format Conditional formatting
m_action Actions
m_form Form View
m_table Table View
m_prop Show Spectral Library Properties

Note

This is a highly interactive tool and has no command line equivalent.

Create Spectral Library manually

In order to select spectra from an image, first load an hyperspectral image in QGIS.

  • Toggle the Select Profile button select.
  • Click on a random pixel in the image to view a profile in the plot window. This profile is not automatically kept, and you can click as many times as you want in the image, until you find a good profile.
  • Click on the Add button add to add the last profile to your Spectral Library.
  • If you check the Auto button auto all selected profiles are automatically added to the spectral library.
  • To remove a profile, select it in the attribute table and use the Delete button m_delete. In order to do so, you must first toggle editing mode m_edit and afterwards save your edits by clicking again on m_edit.
  • You can now edit the profile metadata, add or remove non-compulsory fields and zoom/pan to your selection on the image.
  • Use the settings tool m_prop to change the colors of your profiles (according to a metadata element).

Hint

You can view a subset of your data by only setting layer properties for a subset of classes! The spectral library behaves like a point shape file and so the styling behaves accordingly.

Create Spectral Library from ROI’s

To start with this step, you need a ROI (Regions Of Interest) file. This is a QGIS Vector Layer, with each feature representing an unmixing class (e.g. Pine trees). These classes, and other metadata, should be included in the attribute table.

  • Make sure both the image and ROI file are open in QGIS.
  • Click on Import profiles from raster + vector source polygon: a small popup window will ask you to select the correct raster and vector files. The All touched options allows the user to choose between importing only pixels that lie completely within the ROI’s, or also import pixels that are partly touched by the ROI’s boundaries.
  • You can now edit the profile metadata, add or remove non-compulsory fields and zoom/pan to the selection on the image.

Note

A Spectral Library will copy the attribute table of the ROI Vector Layer, it is therefore essential that it does not contain the following protected fields: ‘fid’, ‘name’, ‘source’, ‘values’ or ‘style’.

The attribute table of the ROI Vector Layer must contain an ‘ID’ field (spelled with all capitals) with unique integer values.

Open existing Spectral Library

To open an existing Spectral Library, use the Open Library button import.

Save Spectral Library to file

To save the current Spectral Library use the Save Library button save.

Note

All changes made to the Spectral Library exist in memory only, until they are saved to file.

ACKNOWLEDGMENTS

This user guide is very loosely based on the VIPER Tools 2.0 user guide (UC Santa Barbara, VIPER Lab): Roberts, D. A., Halligan, K., Dennison, P., Dudley, K., Somers, B., Crabbe, A., 2018, Viper Tools User Manual, Version 2, 91 pp.

The Spectral Library tool was created for the most part at HU Berlin, by B. Jakimow. More information on the source code: https://bitbucket.org/jakimowb/qgispluginsupport.

For issues, bugs, proposals or remarks, visit the issue tracker.