Spectral Libraries

A Spectral Library is a library is a vector layer with a layer field designated to store spectral profiles.

Overview

Spectral Library Window viewlist_spectrumdock

The Spectral Library Window offers (almost) the same tools like the standard QGIS attribute table. In addition, it provides views and features specifically to visualize and manage spectral profiles. It directly interacts with the Map View(s), which means spectra can be directly collected from an image. Furthermore, external libraries (e.g. ENVI Spectral Library) can be imported.

Add a new spectral library view by using the Add Spectral Library Window viewlist_spectrumdock button in the toolbar or open a new window from the menu View ‣ Add Spectral Library Window.

../../_images/SpecLib_overview.PNG

Overview of the Spectral Library view with several collected and labeled spectra and main tools

Buttons of the Spectral Library Window

Button Description Button Description
plus_green Add currently overlaid profiles to the spectral library profile_add_auto Activate to add profiles automatically into the spectral library
speclib_add Import Spectral Library speclib_save Save Spectral Library
legend Activate to change spectra representation speclib_usevectorrenderer Activate to use colors from map vector symbology
system Enter the Spectral Library Layer Properties mActionToggleEditing Toggle editing mode
mActionMultiEdit Toggle multi editing mode mActionSaveAllEdits Save edits
mActionRefresh Reload the table mActionNewTableRow Add feature
mActionDeleteSelected Delete selected features mActionEditCut Cut selected rows to clipboard
mActionEditCopy Copy selected rows to clipboard mActionEditPaste Paste features from clipboard
mIconExpressionSelect Select by Expression mActionSelectAll Select all elements in the spectral library
mActionInvertSelection Invert the current selection mActionDeselectAll Remove selection (deselect everything)
mActionSelectedToTop Move selection to the top mActionFilter2 Select / filter features using form
mActionPanToSelected Pan map to selected rows mActionZoomToSelected Zoom map to selected rows
mActionNewAttribute Add New field mActionDeleteAttribute Delete field
mActionConditionalFormatting Conditional formatting mAction Actions
mActionFormView Switch to form view mActionOpenTable Switch to table view
profile_processing Spectral Processing Dialog mActionCalculateField Enable to calculate new attribute fields

Spectral Profile Sources

This menu manages the connection between raster sources and spectral library windows. When collecting profiles, the Identify tool select_location selects profiles from the top-most raster layer by default. The Profile Source panel allows to change this behaviour and to control:

  • the profile source, i.e., the raster layer to collect profiles from,
  • the style how they appear in the profile plot as profile candidate,
  • the sampling method, for example to aggregate multiple pixel into a single profile first,
  • the scaling of profile value.
../../_images/SpectralProfileSources.png

Overview of the Spectral Profile Sources Window with two labeled spectra and main functionalities

Buttons of the Profile Sources

Profiles
  • Define the input data from where to take the spectral information from.
Style
  • Change style of displayed spectra, i.e. symbol and color
../../_images/SpecProfile_style.png
Source
  • Specify a source raster dataset
  • Double-clicking in the cell will open up a dropdown menu where you can select from all loaded raster datasets.
Sampling
  • Select Single Profile or Kernel by double-clicking into the cell.
Scaling
  • Choose how spectra are sampled.
  • Define the scaling factors by setting the Offset and Scale value.
Option Description
SingleProfile Extracts the spectral signature of the pixel at the selected location
Sample3x3 Extracts spectral signatures of the pixel at the selected location and its adjacent pixels in a 3x3 neighborhood.
Sample5x5 Extracts spectral signatures of the pixel at the selected location and its adjacent pixels in a 5x5 neighborhood.
Sample3x3Mean Extracts the mean spectral signature of the pixel at the selected location and its adjacent pixels in a 3x3 neighborhood.
Sample5x5Mean Extracts the mean spectral signature of the pixel at the selected location and its adjacent pixels in a 5x5 neighborhood.

Working with the Spectral Library

Collect profiles

  1. Make sure to enable the profile and select_location button in the menu bar and open a raster from which you want to collect spectra in a new Map View.

    ../../_images/collectProfiles.png

  2. Click on a desired pixel position in the opened raster image and a new Spectral Library window opens with the spectral profile of the respective pixel.

  3. Profiles obtained from pixel positions are considered as current or temporary profile candidates. The last profile candidate will be replaced by a new one each time you click on a new pixel position.

  4. Click on Add Profile(s) plus_green to keep the candidate profile in the spectral library. Activate Add profiles automatically profile_add_auto to collect multiple profiles and display them all in the same spectral library.

    ../../_images/profile_types.png

As an alternative to the mouse you can also identify and select pixel profiles using the shortcuts to change, select and add pixel profiles to the Spectral Library.

  • First activate the crosshair for the respective image. Click with the right mouse button in the image. Select Crosshair > Pixel Grid > desired raster image.

  • Now you should see a red square around your pixel and a red dot indicating the position of the pixel profile.

    ../../_images/crosshair.png

  • To identify, select and add a pixel profile, use the following key combinations:

Shortcut Action
Arrow Move the map
CTRL + Arrow Select next pixel in arrow direction
CTRL + S Add the selected pixel profile candidate

Add profiles from another raster image

Sometimes, you want to compare spectral profiles from different raster sources. The Spectral Profile Source panel allows you to change the default settings of the Identify tool so that you can select profiles from different images at the same time.

  1. If the Spectral Profile Source Panel is not already visible, open it via View ‣ Panels ‣ Spectral Profile Sources.

  2. Add another profile source relation with plus_green and change the Source to the desired raster images.

  3. If you now collect new spectral information, two profiles will appear in the same Spectral Library Window.

    ../../_images/TwoProfileSources.png

Tip

Change the color of one of the profile by changing the Style in the Spectral Profile Sources.

In a similar way you can compare profiles from the same raster image but using a different sampling methods.

  1. In the second relation set the Source to the same image as the first relation.
  2. Change the Sampling to e.g. a 3x3 Kernel mean profile.
  3. Collect new pixel profiles.
../../_images/KernelProfile.png

Spectral Profile Sources Sampling Example

Adding information

The attribute table

You can also add more information to your spectral library by using the attribute table. Add additional fields to the table, e.g. in order to add information to every spectrum (id, name, classification label, …).

  1. Activate the Table view mActionOpenTable and enable the Editing mode mActionToggleEditing.

  2. Now you can use the Add Field mActionNewAttribute dialog to add a new column.

    ../../_images/SpecLib_addNewField.png

  3. Select a data type of your choice.

  4. A new column is added to the attribute table, which you can edit with a double click.

  5. To delete a column, use the Delete field button mActionDeleteAttribute.

Tip

When you add a new attribute to the table, you can also choose to use it to store new spectral profiles by checking the Use to store spectral profiles checkbox. String, text and binary format can be used to store spectral profiles.

Add information in the layer properties window

It is also possible to add new information to the attribute table in the Layer Properties of the Spectral Library.

  • Click on system to open the spectral library properties.

  • Navigate to the Fields tab and add a new field. Note: This view does not allow you to set the option Use to store spectral profiles.

    ../../_images/LayerProperties_addField.png

Overview of the Layer Properties / Fields section

In addition, the Layer Properties panel allows you to set a certain widget for a specific column.

  • Switch to the Attributes Form tab in the Layer Properties, select the desired column and choose a certain widget type, e.g. a default range, color, spectral profiles etc.

    ../../_images/SpecLib_AddWidget.png

Selecting widget types for specific columns

The field calculator

The field calculator allows you to modify or assess spectra and calculate new columns or modify existing ones using an expression.

../../_images/fieldCalculator.png

Overview of the Field Calculator

Selecting spectra

Spectra can be selected in the attribute table and in the plot window itself. Selected spectra will be highlighted (blue background in the table; thicker line in a different color in the plot window).

  • Hold the Shift key to select multiple spectra.
  • A selection can be removed by clicking the mActionDeselectAll button.
../../_images/SpecLib_SelectSpectra.png
  • Selected spectra can be removed by using the mActionDeleteSelected button.

Tip

You can inspect an individual value of a spectrum by holding the Alt key and clicking some position along the spectrum

It is also possible to select and filter profiles with the common vector filter and selection tools, e.g. select spectra by expression:

../../_images/SpecLib_SelectByExpr.png

Select profiles using an expression

Show coordinates of profiles

Locations of spectra (if available) can be visualized as a point layer by right-clicking into the map window, and selecting Add Spectral Library > SpectralLibrary #

../../_images/SpecLib_AddCoords.png

Advanced options

Create / Modify profiles with the Field Calculator

As already mentioned, the Field Calculator can modify attribute values of all or selected features. In addition, the field calculator can be used to calculate spectral profiles.

  1. Create a new Spectral Profile field based with Add Field mActionNewAttribute, use string, text or binary format and tick the Ise to store Spectral Profiles box.
  2. Open the field calculator mActionCalculateField and search for spectralData or spectralMath in the Spectral Libraries tab.

SpectralMath allows you to modify spectral profiles with Python code.

  • To use the SpectralMath function, select a field from which to take the spectral profiles, define an expression and the format.
spectralMath("<profile field 1>", ..., "<profile field n>", '<python code>', '<output format>')

Note: The last argument defines the output format. It must correspond to the type you assigned when creating the new column.

../../_images/SpecLib_FieldCalc.png

Example of calculating new spectral profiles

SpectralData returns spectral profile values.

The following table shows some examples of how spectralMath and spectralData can be used.

Description Example
Multiply the existing profiles spectralMath(“profiles”, ‘y *=2’, ‘text’)
Create a new profile with x and y values spectralMath(‘x,y=[1,2,3],[20,30,25]’)
Return spectral profile values from map with spectral data from spectral profiles in field column “profiles” spectralData(“profiles”)
Return xUnit string of the spectral profile e.g. ‘nm’ for wavelength unit spectralData(“profiles”)[‘xUnit’]

Spectral Processing

../../_images/SpecLib_spectralProcessing.png

Overview of the spectral processing idea

The Spectral Processing framework allows you to use raster processing algorithms to create new profiles. Field values of your spectral library will be converted into artificial one-line raster images. In principally, this can be done with most of the field types:

Field Type Raster Size (band, height, n) type
Spectral Profile nb, 1, n int/float
integer 1, 1, n integer
float 1, 1, n float
text 1, 1, n int (classification)

These temporary raster images are input to standard QGIS processing algorithms or QGIS processing models. If they generate raster outputs, these outputs can be converted back into field values of the spectral library:

Raster Output Spectral library Field Type
(>1, 1, n) int/float Spectral Profile
(1, 1, n) int integer
(1, 1, n) float float

This allows you to use the same algorithms to modify spectral profiles as you may want to use to manipulate raster images. Furthermore, you can make use the QGIS model builder to create (potentially very large and complex) models and use them for both, spectral libraries and raster image processing.

  • To use the Spectral Processing tool open profile_processing and choose the desired algorithm, e.g. Spectral resampling.

  • Select the input profiles to be translated to the temporary raster layer and specify the outputs. Select an existing field or enter a name to create a new field.

    ../../_images/SpecLib_specProDialog.png

Spectral Processing Example

Visualization settings

General profile plot settings

The Profile Plot displays spectral profiles. Toggling the Profile View icon profile shows or hides the plot panel. This can be useful, for example to enlarge the attribute table and focus on attribute modifications.

You can adjust the extent of the visualized data range and units

  • in the plot context menu
  • using the mouse cursor while keeping the right mouse button pressed
  • in the visualization settings view
../../_images/SpecLib_units.png

You can also export the entire plot scene or visible view box by clicking into the plot and select Export.

../../_images/SpecLib_export.png

Export options of the spectral library

Visualizing profiles

The visualization settings of the spectral library allow you to customize the view according to your needs. You can define multiple visualization groups that describe how profiles from a specific field and with specific attributes should be visualized.

../../_images/SpecLib_VisualSettings.png

Overview of the visualization settings in the Spectral Library window

  • It is also possible, to change the appearance of the Spectral Library window, i.e., bright or dark.

  • Moreover, activate or deactivate the crosshair and choose a color.

    ../../_images/SpecLib_themes.png

  • The Current Profiles section shows you all the spectra that have been collected but do not yet appear in the attribute table. Change the color and symbol, or add a line between the points by double clicking the profile below the Current Profile section and adjust the style settings.

Working with multiple visualization groups

The spectral library visualization settings also allow you to add several profile Groups with different style settings.

  • Add a second visualization group with plus_green.
  • If you want rename Group “profiles”.
  • Change the color for both groups in the Color.
  • Under Field you can specify which spectral profile column of the attribute table you want to use.

If you have more than one column that stores spectral information, you can have different visualization groups using different profiles.

../../_images/SpecLib_visualization1.png

If you have only one column where spectral information is stored, but you have another column storing e.g. class names, you can use the Filter field to define an expression and select only specific class names, e.g. Impervious and Vegetation and visualize these profiles in different colors.

img/SpecLib_visualization2.png

Colorize spectra by attribute

Spectra can be colorized according to their attributes, e.g. their class name.

  1. In the Data Views panel on the left, right click on the spectral library that we are currently using and select the Layer Properties.
  2. Switch to the Symbology symbology tab and select the Categorized renderer at the top.
  3. In the Column droplist select the desired column and click Classify.
  4. Confirm with Ok and close the window.
../../_images/SpecLib_visualization.gif
  1. In the Spectral Library Window activate the visualization settings with the mActionAddLegend button.
  2. Right-click on Color and select Use vector symbol colors speclib_usevectorrenderer.

Loading, Saving and Importing / Exporting

Load and Save Spectral Libraries

Loading or Saving a spectral library means to load or save vector files.

  • Load any vector source in the Data Source Panel into a :guilabel:`Spectral Library Viewer.
  • The vector layer does not need to contain any Spectral Profile fields. You can add or define them afterwards.
../../_images/Load_SpecLib.png

If your spectral library uses an in-memory vector layer backend, all data will be lost if the layer is closed. This is the case if the Spectral Library Viewer was opened from scratch with an empty spectral library. In this case, don’t forget to export collected profiles before closing the Spectral Library Viewer.

If your spectral library already uses a file backend (e.g. *.gpkg, *.geojson), Style and other layer specific information are not saved in the data source file, but the QGIS project or a QGIS specific sidecar .qml file.

  • Open Layer properties > Symbology > Style > Save Default to create or update the .qml file and ensure that the Spectral Profile fields will be restored when re-opening the data set.
../../_images/SpecLib_defaultStyle.png

Exporting Profiles

The Export dialog speclib_save allows you to export all or selected profiles as Geopackage (.gpkg), GeoJSON (.geoson) or ENVI Spectral Library (*.sli).

../../_images/SpecLib_exportProfiles.png

The ENVI Spectral Library does not allow saving profiles with different spectral settings (number of bands, wavelength units, FWHM, …) in the same file. Therefore, you need to select one (out of multiple) profile fields. Profiles with different spectral settings will be exported into different ENVI files.

Importing Profiles

  • To import none-vector files into an existing spectral librar use the Import Spectral Library speclib_add button.

  • Possible formats to be imported: ENVI Spectral Library, Geopackage, ASD Field Spectrometer measurements, Raster Layer.

    ../../_images/SpecLib_ImportFormts.png

  • You can also import ASD Field Spectrometer measurements and map and modify the imported profiles and attributes accordingly.

    ../../_images/SpecLib_addASDProfiles.png

Spectral Profile JSON format

The EnMAP-Box stores the minimum data to plot a single profile in a JSON object. In its most simple way, this JSON object contains a single array “y” of length n, with n = number of spectral profile values:

{
     "y": [43, 23, 45, 63,45]
}

In this case it can be assumed that the corresponding ‘x’ values are an increasing band index “x”: [0, 1, 2, 3, 4].

The JSON object can describe the “x”, the axis units and a vector of bad band values explicitly:

Member Content
y An array with n profile values
x An array with n profile value locations
yUnit String that describes the unit of y values
xUnit String that describes the x value unit
bbl A bad band list

Other metadata to describe spectra profiles are stored in additional vector layer fields.

As JSON object, a single hyperspectral EnMAP profile may therefore look like:

{
   "bbl":[1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],
   "x":[0.46,0.465,0.47,0.475,0.479,0.484,0.489,0.494,0.499,0.503,0.508,0.513,0.518,0.523,0.528,0.533,0.538,0.543,0.549,0.554,0.559,0.565,0.57,0.575,0.581,0.587,0.592,0.598,0.604,0.61,0.616,0.622,0.628,0.634,0.64,0.646,0.653,0.659,0.665,0.672,0.679,0.685,0.692,0.699,0.706,0.713,0.72,0.727,0.734,0.741,0.749,0.756,0.763,0.771,0.778,0.786,0.793,0.801,0.809,0.817,0.824,0.832,0.84,0.848,0.856,0.864,0.872,0.88,0.888,0.896,0.915,0.924,0.934,0.944,0.955,0.965,0.975,0.986,0.997,1.007,1.018,1.029,1.04,1.051,1.063,1.074,1.086,1.097,1.109,1.12,1.132,1.144,1.155,1.167,1.179,1.191,1.203,1.215,1.227,1.239,1.251,1.263,1.275,1.287,1.299,1.311,1.323,1.522,1.534,1.545,1.557,1.568,1.579,1.59,1.601,1.612,1.624,1.634,1.645,1.656,1.667,1.678,1.689,1.699,1.71,1.721,1.731,1.742,1.752,1.763,1.773,1.783,2.044,2.053,2.062,2.071,2.08,2.089,2.098,2.107,2.115,2.124,2.133,2.141,2.15,2.159,2.167,2.176,2.184,2.193,2.201,2.21,2.218,2.226,2.234,2.243,2.251,2.259,2.267,2.275,2.283,2.292,2.3,2.308,2.315,2.323,2.331,2.339,2.347,2.355,2.363,2.37,2.378,2.386,2.393,2.401,2.409],
   "xUnit":"Micrometers",
   "y":[405,397,412,410,402,413,421,427,444,446,445,445,476,491,495,504,504,519,532,530,536,539,533,527,529,527,529,526,530,524,520,521,522,523,507,514,505,502,494,497,543,603,703,769,845,930,1007,1096,1178,1249,1314,1359,1388,1386,1419,1432,1432,1435,1471,1498,1479,1487,1482,1499,1507,1517,1509,1534,1532,1507,1557,1527,1552,1605,1534,1555,1577,1564,1582,1600,1611,1643,1659,1678,1684,1672,1687,1659,1697,1624,1612,1602,1576,1515,1508,1513,1522,1542,1575,1602,1632,1649,1663,1639,1602,1587,1530,977,996,1026,1063,1086,1108,1123,1169,1177,1191,1194,1210,1222,1208,1201,1187,1182,1146,1157,1112,1093,1085,1096,1058,1041,754,781,804,796,780,792,812,825,851,803,812,836,834,818,823,842,842,860,851,880,844,856,847,846,819,842,820,754,768,731,728,750,695,735,675,718,640,601,684,744,635,568,696,637,592]}
}

Note that conceptually profile objects can differ in its wavelength etc.