Spectral Collection

Command:

Tools > Spectral Collection

Sometimes it is convenient to store spectra of selected pixels or mean spectra of particular areas for later use. Epina ImageLab supports this by offering spectral collections which are linked to a particular dataset. Each dataset contains exactly one spectral collection. A spectral collection can only contain spectra of the associated dataset.

The spectral collection can store three types of spectra: (1) single pixel spectra, (2) mean spectra obtained from a center pixel and the pixels in a circular area around this pixel, and (3) mean spectra of an arbitrary contiguous region which is defined by a user drawn polygon. Please note that the spectra stored in spectral collections are actually stored in the collection (in contrast to bookmarks which are only pointers to particular pixels). This means that an entry of the spectral collection always reflects the state of the spectrum at the time when it has been added to the collection, later changes are not reflected unless you add the changed spectra as well.

Each spectrum in the spectral collection is augmented by additional information, such as the type of the spectrum, a caption, a class number, user-defined categories and user-defined flags. This additional information can be used to retrieve specific spectra from the collection later-on.

Spectra can be added to the spectral collection in the following ways:

• 2D Imager: click the "add to spectral collection" button in order to add a particular spectrum to the collection.
• Dataset Editor: you can add the entire set of specified data points, including the class information.
• Principal Component Analysis: you can add marked spectra by using the context menu of the PCA scores plot.
• Import individual spectra: use one of the commands "File > Import ..." and select one or more suitable files on your harddisk. Imported spectra will be stored as reference spectra exhibiting a default class of 127. Reference spectra are displayed in the table on the tab "Reference Spectra".

The collected spectra are displayed both in tabular and graphic form. In the collection table you can select any spectrum by clicking the corresponding line. Further you can make a selection permanent by ticking the checkbox in the first column of the table. All selected spectra are displayed in the spectral window below the table, the current selection is always displayed using a thicker line. In order to edit the properties of the selected spectra you have to click the edit button . You can delete the selected spectra by clicking the delete button .

	Undo	The Undo button reverts the spectral collection to the state which it had when clicking the Open button.
	Filter	If you have a large spectral collection, it might be helpful to filter the list of entries. You can narrow down the list by entering a substring in the filter field. All entries showing (partial) matches with the filter string are displayed in the list in a normal (enabled) state, all other entries are disabled and displayed at the end of the list. The filter is based on the following entries: "Type", "Caption", "Categories", "Status Flags". Please note that there are two different modes of filtering: simple substring search and logical search (see Preferences (option "Filter Mode for Text Filters") and Logical Combinations in Filter Expressions for more). You can store and remove preferred search terms by clicking the plus and minus button at the right side of the filter expression. Preferred search terms can be selected by clicking the drop-down button in the filter expression field.
	Remove all permanent selections	Removes all permanent selections in the entire collection (including disabled filtered spectra)
	Invert the permanent selections	Inverts all permanent selections in the entire collection (including disabled filtered spectra)
	Edit the properties of the selected spectra.	See the Property Editor for details.
	Delete selected entries	Deletes the selected spectra after confirmation.
	Spec1/2/3/4	Switch between different spectral groups.
	Standardize Spectra	If you activate this option, all displayed spectra are standardized, which may greatly help to visually compare spectra (especially if the spectra show largely differing intensities).

Command Menu

File > Export as Text File	Exports the selected spectra of the collection as a CSV file. See Export of Spectral Collection Data for details.
File > Export as Training/Test Dataset	This command generates a training or test daseset from selected spectra of the spectral collection. The generated dataset can be opened by the Dataset Editor.
File > Import JCAMP/DX	You can import one or more reference spectra in JCAMP/DX format by using this command. Imported reference spectra always receive zero coordinates (X/Y/T) and have the type "Reference" assigned to it. Reference spectra are displayed in the table on the tab "Reference Spectra".
File > Import ENVI SLI	This command allows to import an ENVI spectral library. After opening the library you have to select which spectra to import and the type of spectra (the ENVI format does not fully specify the type of the spectra, thus you have specify it manually). Imported reference spectra always receive zero coordinates (X/Y/T) and have the type "Reference" assigned to it. Reference spectra are displayed in the table on the tab "Reference Spectra". Hint: please ensure that the data part of the ENVI library has either the file extension '.sli' or '.esl'.
File > Import Renishaw WiRE	Import a spectrum in WiRE format (as defined by Renishaw). Imported reference spectra always receive zero coordinates (X/Y/T) and have the type "Reference" assigned to it. Reference spectra are displayed in the table on the tab "Reference Spectra".
File > Import From Another Collection	This command allows to load reference spectra from another specral collection. After activating this command you have to select the spectra to be imported by ticking the corresponding check boxes.
Spectra > Edit Selected Spectra	Edit the properties of the selected spectra. See Property Editor of Spectral Collections for details.
Spectra > Delete Selected Spectra	Deletes the selected spectra after confirmation.
Spectra > Add Selected Spectra to Database	Adds the selected spectra to a database of your choice. After activating this command you have to select the database and a few additional parameters. See Add Spectral Collection Data to a Database for details.
Spectra > Copy Captions of Selected Spectra to Category	Creates a category "caption" and copies the text of the captions into this category. Please note that this command is only available from the context menu of the spectral list.
Setup > Edit Flag Names	Edit or define the identifiers of the state flags (see section State Flags in Spectral Collections for more).
Setup > Edit Class Names	Edit or define the class names and the unique class identifiers. See the section Class Names and Unique Class Identifiers for details.
Setup > Categories	You can define new categories, or edit or delete existing ones. See the section Definition of Categories for details.

Hint:

Please note that in the case of multisensor images the collected spectra always consist of the entire set of spectra (i.e. a collected spectrum actually consists of several spectra). In the case you extend the data cube later-on the new parts of the data cube are not updated in the spectral collection (the spectral collection actually stores the current spectrum as it is when you press the "Add" button).