Raman Data Search and Storage (RDSS)

Complete Documentation

A Raman spectra library software using peaks position for fast and accurate identification of unknown inorganic compounds.



Description: D:\Faculty\!RDRS - SITE files\SOFT\!RDSS new version\sigla noua\RDSS_400H_300dpi.tif

v2013.09.01

 

 

 

 

 

I wish you resonant, clean and non fluorescent spectra!

                                                            ©2012 – 2013 - PhD. stud. Andrei Ionut APOPEI
andrei[dot]apopei[at]geology[dot]uaic[dot]ro

 

 

RDSS website: http://rdss.sf.net

RDSS forum: http://rdrs.uaic.ro/forum/


 

TABLE OF CONTENT

 

 

1. ABSTRACT 1

2. GENERAL DESCRIPTION 2

2.1. Description 2

2.2. System Requirements & Installation 2

2.2.1. Terms of Use / Before start 2

2.2.2. Download 2

2.2.3. Installation 2

2.3. Scientific citation 2

3. THE GUI (GRAPHICAL USER INTERFACE) 3

3.1. Menus 3

3.2. Main window 3

3.2.1. Data entries, ChartView and tentative assignment of the Raman peaks 4

3.3. New Spectrum window 4

3.3.1. Analyze 4

3.3.1.1. Manual 4

3.3.1.2. Automatic 5

3.3.2. Relative Intensity Assignment (RIA) 6

3.3.3. Appearance 8

3.4. Spectra menu and properties 9

4. FUTURE DEVELOPMENT 10

 


1. ABSTRACT

 

Raman spectroscopy is widely used in the field of geosciences because it is very fast, non-destructive, noninvasive and does not require sample preparation. The Raman spectra often provide unique fingerprint of the sample that can be used to identify any unknown minerals.

Raman Data Search and Storage (RDSS) software was developed as an analytical tool for a fast and accurate identification of unknown minerals by comparison of their spectra with the indexed library of data. RDSS is a freeware, user-friendly software, written in Java, not OS dependent, available for use by anyone who has an Internet connection and can be accessed at the following link:  http://rdss.sf.net. A search function was implemented to enable users to find a specific peak value. Using the asterisk character (*) as a placeholder for one or more unknown peak value(s), the software will return the best match(es). Besides the search utility by the Raman band positions, which was proven to be priceless in the interpretation of Raman spectra, the RDSS software gives the user the ability to display and inspect the Raman spectra quickly and very efficiently. Users can zoom into the Raman spectrum, shift in any direction the wavenumber and the intensity axes, and if any part of the spectral display is clicked, that region will be highlighted and the specific wavenumber returned. A photo for every sample entry stored in the database is also available. For the raw Raman spectra, the RDSS software can open any .txt file format with XY data format, delimited by different delimiters: tab, space, comma, semicolon, and it can also ignore rows with ##comments.

The RDSS software allows users to easily find the Raman peaks of a raw spectrum obtained from a single crystal or from a mixture where multiple peaks are expected to arise. The only disadvantage encountered in most applications which use a spectral matching system is usually the insufficient number of spectra in the database. However, even with a limited number of records in the database, the user can obtain a first impression of the mineral class of the unknown compound.

 


 

2. GENERAL DESCRIPTION

 

2.1. Description

Raman Data Search and Storage (RDSS) software was developed as an analytical tool for a fast and accurate identification of unknown minerals by comparison of their spectra with the indexed library of data. This application derives from an online database entitled Romanian Database of Raman Spectroscopy (RDRS). RDSS is freeware, enjoy!

 

2.2. System Requirements & Installation

2.2.1. Terms of Use / before start (takes 10 seconds)

Please, read END-USER LICENSE AGREEMENT (EULA) carefully before copying, installing or using the RDSS software. By using all or any portion of the Software you accept all the terms and conditions of this Agreement. If you do not agree, do not use this Software.
You can read the EULA online, at this URL
http://rdss.sf.net/license.html; or, you can read the full EULA which is in the root directory of the application (LICENSE.txt).

 

2.2.2. Download

You can download it from application website (http://rdss.sf.net/download.html), or from the sourceforge website (http://sourceforge.net/projects/rdss/).

 

2.2.3. Installation

This is written in Java, so you don't need to install it, just take care if you have JAVA Runtime Environment. You can find Sun's Java here (http://java.com/download/). By the nature of what it does and for what it’s used, it is not portable at all, and only runs on Windows (tested on XP, Vista 32/64, Windows 7 32/64). It works on Linux OS, but not fully functional! Minimum hardware requirements: RAM 512 MB (1GB recommended).

 

            2.3. Scientific citation

If you use RDSS in your scientific work, please reference to the software as:

 

"RDSS - A Raman spectra library software using peaks position for fast and accurate identification of unknown inorganic compounds", Version 201x.xx.xx, http://rdss.sourceforge.net.

 

Important! Please insert the current version number which is presented as date format yyyy.mm.dd.

 

 


 

3. THE GUI (GRAPHICAL USER INTERFACE)

 

3.1. Menus

General functions are accessed via the Menus.

 

Main Window //Menu

New Spectrum //Menu

Function

Shortcut

Action event

Function

Shortcut

Action event

File > Login

F5

Disabled at this moment*

File > Clear Spectrum

Ctrl + R

Clear the spectrum from the ChartView

File > Open Spectrum

Ctrl + N

Open a new file spectrum

File > Exit

Ctrl + Q

Close the window

File > Save Spectrum

Ctrl + S

Save the current spectrum

Spectra > Properties

Ctrl + E

Properties of the spectrum

File > Refresh

Ctrl + Alt + R

Restart the application

Spectra > RIA

Baseline adjusted

Ctrl + B

Open ‘baseline adjusted’ tab for RIA

File > Exit

Ctrl + Alt + Q

Quit without prompt message

High fluorescence

Ctrl + H

Open ‘high fluorescence’ tab for RIA

Window > Reset Layout

F3

Reset all panels

 

 

 

Help > Help

F1

Open this file

 

 

 

Help > Quick Start Guide

Ctrl + G

Open a quick start guide

 

 

 

Help > Support Forum

F11

Open the Forum webpage

 

 

 

Help > License

Alt + L

Open License file

 

 

 

Help > Change Log

F12

Open Change log

 

 

 

Help > Roadmap

 

Open Roadmap page

 

 

 

Help > Check for update

Ctrl + U

It checks for any updates

 

 

 

Help > Donate

 

Open donation page

 

 

 

Help > About

F2

Open About window

 

 

 

* - Login function is disabled at this moment because administrator panel require some technical adjustments.

 

3.2. Main window

 

Figure 1 - Main window of the Raman Data Search and Storage application: a) – ChartView panel; b) – data entries panel; and c) – panel with the details of the selected entry from panel 2

 

 

3.2.1. Data entries, ChartView and tentative assignment of the Raman peaks

The core of the RDSS application GUI is the bottom, where two tabbed panels contain two tables. First tab named Primary Table contain a table designed to have commons columns like: sample no., mineral name, chemical formulae, main peaks, other peaks, reference, external link and comments. The second tab named Secondary Table, contain a table designed to have a more specific columns for specific domain search: mineral name, 200 - 600 cm-1, 600 - 900 cm-1, 900 - 1200 cm-1, 1200 - 1500 cm-1, 1500 - 2000 cm-1, 2000 - 3000 cm-1, 3000 - 4000 cm-1, external link, comments and reference (see figure 1). The first and the last three columns are linked with those from Primary table for structure reasons.

In the left-upper part of the main window of RDSS application, a Raman spectrum shows when a specific row is clicked in the Primary and Secondary Table. In other words, each mineral row is linked with its own Raman spectrum.

 

3.3. New Spectrum window

 

Figure 2 – New Spectrum window of the Raman Data Search and Storage application: a) – ChartView panel; and b) – a panel which contain tabs with specific functions

 

 

            3.3.1. Analyze

            In this tab user can manually extract the interested peaks or automatically which is a great function for Raman spectra with multiple peaks. See bellow discussions for both options.

 

            3.3.1.1. Manual

            When “Manual” radio button is pressed, a panel with manual search function of the Raman peaks becomes active (figure 3).

            After the "Get Peaks" checkbox is checked, on the Raman spectra chart panel appear a crosshair which moves with the mouse crosshair. In other words it's like a real-time mouse tracing which help the user to get the exact peak position. Furthermore, the user can zoom in before get the desired peak. All peaks appear in a list with different options: delete a single peak, multiple or even all peaks from the list.

To compare selected peak(s), after selection, press “Go” button from the bottom of the entire panel.

 

Figure 3 – Manual search function of the Raman peaks

 

 

 

            3.3.1.2. Automatic

When “Automatic” radio button is pressed, a panel with automatic search function of the Raman peaks becomes active (figure 4).

 

Figure 4 – Automatic search function of the Raman peaks while set the value of the “Threshold”

 

To use the automatic search function, the user needs to fill two variables before obtaining peak values.

First variable is the “threshold”. Specify the 'threshold' heigh, 'findpeaks' only returns peaks that exceed at least the Y-value of 'Threshold' (figure 4).

 

Second variable is the “Gap”. Specify the 'gap' width. This function affects number of peaks. Density of the peaks is directly correlated with this variable. Most recommended values are between 50 and 300. In this example (figures 4 and 5), was used a value of 200. Don’t forget to press “Find” button after you filled the second variable.

All peaks appear in a list with different options: delete a single peak, multiple or even all peaks from the list. To compare selected peak(s), after selection, press “Go” button from the bottom of the entire panel.

 

Figure 5 – Automatic search function of the Raman peaks after was set the value of the “Gap” and “Find” button was pressed

 

 

3.3.2. Relative Intensity Assignment (RIA)

            This function is performed for both the Baseline Adjusted Raman spectra and for Raman spectra with High fluorescence. For both functions is used a 5 steps of intensity assignment and are divided as follow:

 

Intensity

Assignment

between 0 – 10%

very weak (vw)

between 10 – 30%

weak (w)

between 30 – 60%

medium (m)

between 60 – 90%

strong (s)

between 90 – 100%

very strong (vs)

 

            The Baseline adjusted Raman spectra (figures 6 and 7) works very well with baseline-removed spectra. After the checkbox "On/Off | Intensity Assignment" is checked, the user must extract the strongest peak by moving the crosshair and press first mouse-button on that peak (figure 6). Afterwards, the lowest peaks (in terms of intensity) can be assignet based on the strongest peak.

            The High fluorescence Raman spectra (figures 8 and 9) works very well with the Raman spectra which has no baseline-removed spectra. After checkbox "On/Off | Intensity Assignment" is checked, the user must extract the strongest peak in two steps:

(i)                           first identify the highest peak from the Raman spectrum and check the “Min” (which stands from “minimum”) radiobutton, afterwards the user must extract the minimum of the strongest peak by moving the crosshair and press first mouse-button on that minimum of the peak (figure 8);

(ii)                        the second step is similar to the first, the difference being that the user must to check the “Max” (which stands from “maximum”) radiobuutton, afterwards the user must extract the maximum of the strongest peak by moving the crosshairr and press first mouse-button on the maximum of the peak.

For the Peak 1 assignment, the procedure is similar to that of the extraction intensity value for the “Strongest peak” (discussed above).

 

Figure 6 – Relative Intensity Assignment (RIA) in action for a Baseline adjusted Raman spectrum. Obtaining the “Strongest peak” intensity value

 

Figure 7 – Relative Intensity Assignment (RIA) in action for a Baseline adjusted Raman spectrum. Obtaining the “Peak 1” Intensity Assignment based on the “Strongest peak” intensity

 

 

 

Figure 8 – Relative Intensity Assignment (RIA) in action for a High fluorescence Raman spectrum. Obtaining the minimum intensity value of the “Strongest peak”

 

Figure 9 – Relative Intensity Assignment (RIA) in action for a High fluorescence Raman spectrum. Obtaining the maximum intensity value of the “Strongest peak”

 

            3.3.3. Appearance

            The Appearance panel (figure 10) contains a lot of tools to manipulate the Raman spectrum in terms of appearance. These tools are described in the following table:

 

Tool

Action

Tick spacing

Fill the textbox with the desired space between ticks for both axes (Wavenumber and Intensity)

Gridlines

Check or uncheck the checkboxes for the desired axis to show or hide the gridlines

Range

Fill the textboxes from x (start number) to y (end number). Don’t confuse y with Y axis. This range can be used just for the Wavenumber axis.

Spectrum color

User can choose a color from 7 available colors (black, red, green, blue, orange, yellow and cyan). Default is black.

Spectrum width

Width of the Spectrum line

Spectrum points/lines

Convert the Raman spectrum line in points linked by a thin line and default Raman spectrum line

Reverse axes

Checkbox to reverse X-axis (Wavenumber) and checkbox to reverse Y-axis (Intensity)

 

           

Figure 10 – Functions from the Appearance panel tab in action

 

3.4. Spectra menu and properties

            The Chart Panel where is shown the Raman spectrum has some functionalities and properties which can be archieved by mouse actions.

            Right mouse click activates a popup menu with the following items:

 

Item

Action

Copy

Copy the Raman spectrum (you can paste it in photo editors)

Save as…

Save the Raman spectrum in .png format

Print…

Print it

Zoom in > Both Axes

Zoom in perserving the ratio of both axes

              > Domain Axis

Zoom in perserving just the Intensity ratio

              > Range Axis

Zoom in perserving just the Wavenumber ratio

Zoom out > Both Axes

Zoom out perserving the ratio of both axes

                 > Domain Axis

Zoom out perserving just the Intensity ratio

                 > Range Axis

Zoom out perserving just the Wavenumber ratio

Auto Range > Both Axes

Auto Range both axes

                   > Domain Axis

Auto Range Wavenumber axis

                   > Range Axis

Auto Range Intensity axis

Reverse X-axis

Reverse Wavenumber axis

Help/Shortcuts

Opens a window with explainations of how to use mouse for a fast and easy controlls of the Raman spectrum

 

           

Figure 11 – Spectra menu and properties

 

 

Action

How to do it

Zoom in/out

Use the scroollwheel-up/down of the mouse

Zoom in on a desired region

Use the left mouse button to drag a selection rectangle

Restore X-axis / Y-axis

Press right mouse button and drag the mouse up/down

Translate X-axis / Y-axis

Ctrl + left mouse button and drag the mouse to move the whole Raman spectrum

Get X value

press left mouse button on the Raman spectrum and hover the mouse to see the specific value of the X axis

 

 

4. FUTURE DEVELOPMENT

           

- to populate the application with new Raman spectra;
- integrate 3D crystal structure for every entry;
- save spectra in .csv / .xls format
- drag and drop spectrum file;
- add clear button for RIA panel;
- mineral classes description;
- Raman introduction/tutorial/short presentation;
- google maps api, for GIS coordinates of the samples.