Customising and sharing luminescence databases
Adding lines to the database
Users may add lines to the luminescence database for later reference by three methods:
Any lines added to the database are stored in user-created databases, which are seamlessly integrated in the luminescence database search interface for later reference, and may also be easily or shared with other researchers, if desired.Please note also that when storing a line in the luminescence database, the spectrum in OpticalFit from which the line was measured is automatically saved in the user-created database also, and may also be displayed for comparison with other measured spectra using the luminescence database window (see 'spectra in the luminescence database' section.)
Add fitted peaks to database
If peaks have been fitted to a spectrum, they may be added to the luminescence database by right-clicking on the peak in the peak table and selecting the ‘Add to CL database’ menu option, as shown below:
This will open the 'Edit line' window, shown below, in which the user may enter the relevant information about the specimen and luminescence emitter. Note that for fitted peaks, the values in the 'Edit line' window for peak position, FWHM and relative height are automatically populated from the peak table. Please read the ‘database entry fields’ section for a description of the data fields in this window, and advice on appropriate values.
The 'Edit line' window, when adding a fitted peak to the luminescence database.
Adding a line from the spectrum cursor
To add a peak in the spectrum to the luminescence database, without fitting the peak (see above), double-click in the OpticalFit spectrum plot to set the inspection marker at the desired position in the spectrum, then select the ‘Database→Add line from cursor...’ item from the OpticalFit menu, as shown below.
The 'Database→Add line from cursor' item in the OpticalFit menu.
This will open the 'Edit line' window, shown below, in which the user may enter the relevant information about the specimen and luminescence emitter. Note that the values of the peak position and relative height fields will be automatically populated from the marker position, but the FWHM value will not be set. Please read the ‘database entry fields’ section for a description of the data fields in this window, and advice on appropriate values.
The 'Edit line' window, when adding a line to the luminescence database using the inspection marker.
Adding an emission band
To add an emission band, rather than a distinct peak, to the luminescence database, use the ‘Edit→Select region...’ menu item to set the start and end of the emission band (see selecting spectrum regions section.) Once the selected region is appropriately set, select the ‘Database→Add band from selection...’ item from the OpticalFit menu, as shown below.
The 'Database→Add band from selection' item in the OpticalFit menu.
This will open the 'Edit line' window, shown below, in which the user may enter the relevant information about the specimen and luminescence emitter. Note that the start and end positions of the band will be automatically populated from the selected region, as will the relative height. Please read the ‘database entry fields’ section for a description of the data fields in this window, and advice on appropriate values.
The 'Edit line' window, when adding an emission band to the luminescence database using a selected region.
Database entry fields
Each entry in the luminescence database contains a number of fields that describe the luminescent material and emission centre, the energy/wavelength of the emission line, and the attribution / citation for the luminescence line. These fields must be set when adding a new to the database, and can be seen in the 'Edit line' window, shown below:
The 'Edit line' window when adding a line to the luminescence database.
The meaning of the database fields are described below.
'Material and emitter' fields
The 'Material and emitter' fields, in the upper left corner of the 'Edit line' window, are where the user enters details of the luminescence emitter and the host material. These are the values by which users search the database.
| Material | The name of the luminescent material. Please do not include variants or formulas in material names, as there are separate fields for that information. |
|---|---|
| Variant | The name of the variant of the luminescent material, if any. For example, a mineral from a specific location (e.g. Material = “Apatite”, Variant = “Durango”) or formation process (e.g. Material = “Quartz”, Variant = “Radiolaria”). The variant field may also be used to denote natural or synthetic doping (e.g. Material = “Apatite”, Variant = “chloro”, or Material = “Zircon”, Variant = “Dy doped”), or other treatment or modification (e.g. “Ion irradiated”). Note the 'Variant' drop-down list will be automatically populated with variant values from the database entries that match the given value in the 'Material' field. |
| Formula | The nominal chemical formula of the luminescent material. Note trace dopants may be denoted in the 'formula' field by appending a colon and the dopant symbol, like “SiO2:Ti”, and/or may be stated in the 'variant' field (e.g. “Ti doped”). If the 'Formula' field is left empty, users will not find this line reference when using the search by formula mode in the Luminescence database window. Note the 'Formula' drop-down list will be automatically populated with formula values from the database entries that match the given value in the 'Material' and 'Variant' (if used) fields. |
| Emitter | The name of the emission centre. If an element or ion, use chemical symbol(s) (e.g. “Dy”, “VO4”). If charged, please specify charge in the 'Charge' field, not in the 'Emitter' field. If the emitter is unknown, please use an 'Emitter' value of “Unspecified” (this is the default value). Note the 'Emitter' drop-down list will be automatically populated with emitter values from the database entries that match the given value in the 'Material' and 'Variant' (if used) fields. |
| Charge | The chemical charge of the emitter, if known (e.g. “3+”, “2-”). Note the 'Charge' drop-down list will be automatically populated with charges values from the database entries that match the given values in the 'Material' and 'Emitter' fields. |
| Shell | The electronic shell responsible for luminescence, if known (e.g. “3d5”, “4f1”). |
| Site | If the luminescence emission comes from an atom in a specific site in the lattice, it may be specified in the 'Site' field (e.g. “Ca II site”) |
'Emission line' fields
The 'Emission line' fields, in the upper right corner of the 'Edit line' window, are where the user enters the location and height of the luminescence line. These are the values that determine where and how lines are displayed on the spectrum plot.
| Line type | Luminescence database entries may be either 'lines' (with a definite central emission energy/wavelength) or 'bands' (with an emission range, but no specific maximum in emission). The type of emission may be selected using the 'Line type' drop-down list. |
|---|---|
| Peak pos. | The maximum in intensity from an emission (if 'Line type' field = 'Line'). The position units are specified in the 'Units' drop-down list. |
| FWHM | The full width at half maximum of the emission (if 'Line type' field = 'Line'). The FWHM units are specified in the 'Units' drop-down list. Note this value is optional; if the FWHM is not known or well-defined, check the 'Not set' check-box to the right of the 'FWHM' field. |
| Band start | The start of the emission band (if 'Line type' field = 'Band'). The position units are specified in the 'Units' drop-down list. |
| Band end | The end of the emission band (if 'Line type' field = 'Band'). The position units are specified in the 'Units' drop-down list. |
| Units | The physical units associated with the 'Peak pos.' / 'FWHM' or 'Band start' / 'Band end' fields. The luminescence database only supports units of eV (for energy) and nm (for wavelength). The default value is taken from the current x-axis units in the OpticalFit spectrum plot. |
| Rel. height | The relative height of the emission peak, if known. If the line is being defined from a fitted peak in the peak table, the relative height will be the height of the peak relative to the greatest height of any peak in the peak table. If the line is being defined from the current cursor position in the spectrum plot (i.e. not a fitted peak), the relative height will be the intensity of the spectrum channel at the current cursor position relative to the greatest intensity of any channel in the spectrum. If the relative height is not known or well-defined, check the 'Not set' check-box to the right of the 'Rel. height' field. |
| Technique | The technique used to measure the luminescence line, e.g. “Cathodoluminescence”. The 'Technique' drop-down list is automatically populated with all the technique values defined in the database. |
| Temperature | The temperature of the specimen during analysis, if known. The default value is “Ambient”, implying no specific temperature control. The 'Temperature' drop-down list is automatically populated with all the temperature values defined in the database (e.g. “4K”, “77K”, etc.). |
'Citation' fields
The 'Citation' fields, in the lower portion of the 'Edit line' window, are used to give appropriate attribution to the publication in which the emission line was reported. For unpublished emission line measurements, such as those one may add to a user database, the citation fields may be used to document when and by whom the measurements were made.
| Short form | A shortened form of the citation given in the 'Long form' field (below). This text should be as short as practicable, as it may be displayed as part of the line marker overlay in the OpticalFit spectrum plot. For publications, this should take the form of “Gaft et al. (2005)”, for example. For unpublished works in a user database, this should take the form of “Bloggs, J. (2018), unpub.”. |
|---|---|
| Long form | The full citation for the source of the emission line. For publications, this should include at least the full list of authors, the journal name, year of publication, volume, and page numbers. For unpublished works, this should include at least the name(s) of the researcher(s) that made the measurement, when it was made, and that it is unpublished (e.g. “Bloggs, J. (2018), unpublished work.”) |
'Database' field
The 'database' field, at the bottom left corner of the 'Edit line' window, is where the user enters the name of the user-created database that will contain the new line entry and associated spectrum. The 'database' drop-down list will be automatically populated with a list of the names of all user-created databases currently loaded, if any. If a new database name is given in the 'database field', a new database will be automatically created.
Databases
The Luminescence Database used with OpticalFit is a composite of the OEM database that is installed with OpticalFit (and is available on-line), as well as zero or more user-created databases that are created by users themselves, and may be readily added to, modified, and shared. The search interface in the Luminescence Database window presents results from all databases (OEM and user-created), but the data is stored separately to that users' lines and spectra can be easily backed up or shared, and also so that the OEM database can be updated without overwriting any users' database entries.
OEM database
The 'original equipment manufacturer' (OEM) database, for lack of a better term, is the official luminescence database that is included in the OpticalFit installer, and is the same as the on-line luminescence database. The OEM line database and spectra are stored on disk in the following path:
C:\Users\Public\CL database (OEM)
Note that the contents of this directory will be automatically overwritten by OpticalFit installers, and will be removed by the uninstaller. No user data should be stored in the OEM database path.
User-created databases
User-created databases are stored in a sub-directory of the user's home directory, at:
C:\Users\[username]\CL database
Within the path given above, users will find CSV files, which are the user-created database files. There may also be subdirectories within the 'CL database' directory, containing the spectra associated with the line entries in the user-created luminescence database files.
Users should not manually edit the database CSV files, nor rename files or folders within the 'CL database' directory. Users may, however, wish to back-up the database directory from time to time, and may share the contents with other users by providing them with a copy of the appropriate files (see sharing user-created databases, below).
Sharing user-created databases
If users would like to share their user-created databases with other researchers, they may do so by opening the following path in the Windows File Explorer:
C:\Users\[username]\CL database
In this path, they should make a copy of the user-created database file they wish to share (it will have a CSV file extension), and also copy the correspondingly-named subdirectory in that path, which contains the spectra associated with the database entries. These files and folders can be zipped and e-mailed to the intended recipient, who can then copy the files and folders into their “C:\Users\[username]\CL database” directory. The user-generated database will be automatically loaded next time OpticalFit is started.
To contribute lines and spectra to the OEM database, so that it may be shared with all OpticalFit users in the next software update, please e-mail the CSV database files and associated folders to luminescence@csiro.au. All contributions will be most gratefully appreciated and acknowledged.
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