Mineral Spectral Library_CI

Transcription

1 MINERAL RESOURCES Mineral Spectral Library_CI Manual Ian C Lau, Peter Warren, Peter Mason, Victor Tey and Carsten Laukamp Epublish Report Number: EP th of January 2018 National Virtual Core Library NCRIS project

2 Mineral resources Citation Lau IC, Warren P, Mason P, Tey V and Laukamp C. (2018) Mineral Library CI: Manual. CSIRO Open File Report, Australia. EP175214, 36p. Copyright Commonwealth Scientific and Industrial Research Organisation To the extent permitted by law, all rights are reserved and no part of this publication covered by copyright may be reproduced or copied in any form or by any means except with the written permission of CSIRO. Important disclaimer CSIRO advises that the information contained in this publication comprises general statements based on scientific research. The reader is advised and needs to be aware that such information may be incomplete or unable to be used in any specific situation. No reliance or actions must therefore be made on that information without seeking prior expert professional, scientific and technical advice. To the extent permitted by law, CSIRO (including its employees and consultants) excludes all liability to any person for any consequences, including but not limited to all losses, damages, costs, expenses and any other compensation, arising directly or indirectly from using this publication (in part or in whole) and any information or material contained in it. CSIRO is committed to providing web accessible content wherever possible. If you are having difficulties with accessing this document please contact csiroenquiries@csiro.au. Document Control Sheet version Date Created by: Approved by /01/2017 Ian C Lau. Commenced document /1/2017 Ian C Lau: finishing document /1/2017 Ian C Lau: figure links /2/2017 Carsten: review 0.5 9/3/2017 Ian Corrections 0.6 7/6/2017 Ian checking edits and login added /6/2017 Ian final edits 0.8 3/1/2018 Applied reviewers comments

3 Contents Acknowledgments... iv Executive summary... v 1 Introduction Installation Adding users Populating the Library Adding new SUPPORT DATA Adding new Sample data: Adding validation data to Physical Samples Recovering from mistakes Adding Spectra to the library, reviewing data and downloading Viewing the Spectra Online Mineral Library page Mineral Spectral Library_CI i

4 Figures Figure 1 Webpage for the desktop client web installer for the backend software for The Mineral Spectral Library Figure 2 Webpage to download the installer for Silverlight Figure 3 Splash screen for Microsoft Silverlight installer Figure 4 Webpage link to the installer once Microsoft Silverlight is installed (example is using Mozilla Firefox). Note the version has been updated since this screenshot was taken Figure 5 Popup security warning when MineralLibrary_CI is being installed (Example is using Windows 10) Figure 6 Icon on the desktop for the Mineral Library CI desktop client Figure 7 Example of the login screen for MineralLibrary_CI (example is using Windows 10) Figure 8 First screen shown after logging into the MineralLibrary_CI (Data->samples) Figure 9 Users window for adding new users and accounts Figure 10 Editing the Roles of Users using the Administration menu Figure 11 The opening screen of Mineral Library CI. The red oval shows the interactive buttons for creating, editing and deleting samples, as well as exporting data and searching Figure 12 Sample Sources screen Figure 13 Pop up window for adding a new sample source Figure 14 Minerals tab in the Support Data menu Figure 15 Add New Mineral pop up box Figure 16 Validation Instruments tab in the Support Data menu Figure 17 Adding a new validation Instrument Figure 18 Spectrum Types tab Figure 19 New Spectrum Type window Figure 20 Example of a webpage that converts column data to comma separated list Figure 21 TSA Minerals tab in Support Data Figure 22 Add new physical sample window Figure 23 Validation data of a physical sample is located in the bottom right corner of the right scroll window on the Physical Sample tab Figure 24 Add validation data window Figure 25 Add validation spectrum to a physical sample Figure 26 Exiting the program without saving will show this pop up box. Discard can be selected to exit and not add the changes if a mistake has been made, such as deleting a sample unwantedly ii Mineral Spectral Library_CI

5 Figure 27 Adding a spectrum in the Spectrum Menu Figure 28 Spectrum Collections (libraries) Figure 29 Spectrum pop up Figure 30 CSIRO Mineral Spectral Libraries web page opening screen Figure 31 Spectra Screen for the online content Figure 32 Spectral Libraries screen for the online content Figure 33 Inside the Spectral Libraries, showing the individual spectra and associated samples for the online content Mineral Spectral Library_CI iii

6 Acknowledgments This work was supported by AuScope Pty Ltd and the National Virtual Core Library (NVCL) project and CSIRO s Mineral Resources Business Unit. iv Mineral Spectral Library_CI

7 Executive summary This document is a manual for The Mineral Spectral Library, consisting of both a web-based viewing interface, and an installed executable that provides an editing function for authorised users. The Mineral Spectral Library website ( has an associated backend software program which allows the import and editing of data associated with mineral spectra. The purpose of the web-based Mineral Spectral Library is to allow the sharing of pure mineral spectral data and their associated validation data. The web site has similar spectral viewing functionality to the backend software, but does not allow the upload of new data. Data can be viewed and downloaded from the website by anyone, whereas the software requires a user to have a login and password assigned to them. Users can be assigned different levels of access, which allows them to edit different at levels. Currently, the thermal infrared wavelength region spectral library used in The Spectral Geologist has been placed in the database, with plans to put the renewed shortwave infrared and visible libraries when they are completed. Mineral Spectral Library_CI v

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9 1 Introduction This manual supports The Mineral Spectral Library backend software and website. The manual demonstrates the backend software s installation procedure, login process how to update and access data, and explains the structure of the database. It also overviews the website. The Mineral Spectral Library has been constructed to allow a spectral community to share and curate spectral data of mineral samples. The software has the flexibility to be able to hold different types of spectral data in ASCII format, as well as attach validation data and photos to each sample. The structure of the database consists of three main areas, which are located in tabs in the menu bar. These consist of: 1. Administration; 2. Support Data, and; 3. Data. The Administration tab is for creating the users and their access level. There are two levels of user: administrator and external. Support Data is used to create some automatic fields of information for the data. The support data consists of the following inputs: 1. Minerals; 2. Sample Sources; 3. TSA (The Spectral Assistant, from The Spectral Geologist) Minerals; 4. Spectrum Types, and; 5. Validation Sources. Each of the Support Data has two to four input fields of information. Once the Users and Support Data are sorted out, the data can be added. The data area contains three sections: 1. Samples; 2. Spectra, and; 3. Spectral Libraries. Generally, the entering of Samples is performed first and they are linked to the Support Data fields. Photographs, spectral data and validation data can then be added to the Samples. The Spectra tab allows the spectra entered in the Samples tab to be listed and plotted. Spectral data can be entered in this area as well and linked to a Physical Sample. Once spectral data has been added, they can be made into Spectral Libraries based on the Spectrum Type. The Spectral Libraries require the TSA Mineral to be linked to each spectrum. Mineral Spectral Library_CI 1

10 The data uploaded using The Mineral Spectral Library backend software can immediately be seen online after it has been saved ( 2 Mineral Spectral Library_CI

11 2 Installation NOTE BEFORE STARTING: These instructions will not work with Google Chrome and have been tested with Internet Explorer and Mozilla Firefox. No testing has been done with Microsoft Edge, Safari or Opera web browsers. Initial testing using OS X found Safari unable to install the MineralLibrary_CI software. Installation of The Mineral Spectral Library requires Microsoft Silverlight. Click on the link below, to go to the back-end client installer using Internet Explorer or Mozilla Firefox. The web page will show the button as shown in Figure 1. Figure 1 Webpage for the desktop client web installer for the backend software for The Mineral Spectral Library. Click on the button and a download the installer screen will be displayed (Figure 2). Mineral Spectral Library_CI 3

12 Figure 2 Webpage to download the installer for Silverlight. Click on the Install for windows link and the Silverlight_x64.exe file will download. Once the installer has downloaded open it (and click yes to any security questions), click on Install now button, as shown in Figure 3. You may wish to uncheck the boxes regarding the installation of BING Search Engine and MSN homepage. Windows may ask you if you want to enable updates. Figure 3 Splash screen for Microsoft Silverlight installer. 4 Mineral Spectral Library_CI

13 One Silverlight has installed the web page should change to show MineralLibrary_CI Version (as of January 2018) and a message to click on the Install MineralLibraryCI button (as shown in Figure 4). Figure 4 Webpage link to the installer once Microsoft Silverlight is installed (example is using Mozilla Firefox). Note the version has been updated since this screenshot was taken. A security warning will pop up asking if you want to install the application from CSIRO (Figure 5). Figure 5 Popup security warning when MineralLibrary_CI is being installed (Example is using Windows 10). Click Install and a shortcut will be placed on the desktop (Figure 6) to run the desktop client. Mineral Spectral Library_CI 5

14 Figure 6 Icon on the desktop for the Mineral Library CI desktop client. On clicking the desktop icon The Mineral Spectral Library client will start with a login screen, as shown in Figure 7. Enter your given username and password and click Log In. Figure 7 Example of the login screen for MineralLibrary_CI (example is using Windows 10). A user name and password can be obtained by ing Peter.Warren@csiro.au or Ian.lau@csiro.au. 6 Mineral Spectral Library_CI

15 If this is your first time logging in, it is advised that you change your password by clicking on the Change Password link in the top right of the first screen, which is shown in Figure 8. Figure 8 First screen shown after logging into the MineralLibrary_CI (Data->samples). 2.1 Adding users New Users can be added under the Administration menu. The Users window, as shown in Figure 9. The username, their full name and password fields are required to be added. Passwords need to have a seven characters and require at least one non-number or letter (i.e.!@#$% etc). Once the name and password has been correctly entered a role must be assigned to the user. This is done on the Role screen, as shown in Figure 10. The two options are Administrator or ExternalUser. The Administrator allows the full use of the software whereas the ExternalUser only allows collections to be written. An administrator can also write Data, write support data and modify the administration data. The administrator could also increase the privileges to the ExternalUser, or create another role, such as a super user, which could, for example allow data to be written, but no administrator tasks could be performed.. Mineral Spectral Library_CI 7

16 Figure 9 Users window for adding new users and accounts. Figure 10 Editing the Roles of Users using the Administration menu. 8 Mineral Spectral Library_CI

17 3 Populating the Library To populate The Mineral Spectral Library with minerals and spectra, there must be Support Data associated with the information that is going in. The Support Data dropdown menu consists of TSA Minerals, Minerals, Validation Instruments, Sample Sources and Spectrum Types. The addition of the Support Data should be done in the following order: Firstly, the Mineral needs to be entered, then the Validation Instruments for obtaining the validation data, the Source of the sample and the Spectrum Types. Figure 11 highlights the buttons used for editing in the MineralLibrary_CI software. Add new item to the list and displays the dialog to edit it. Displays a dialog to edit the current item in the list (once something is selected). Deletes the current item in the list (once something is selected). Export data to a MS Excel file (once something is selected). Search bar. Figure 11 The opening screen of Mineral Library CI. The red oval shows the interactive buttons for creating, editing and deleting samples, as well as exporting data and searching. Mineral Spectral Library_CI 9

18 3.1 Adding new SUPPORT DATA Source of sample: Click on the SUPPORT DATA->Sample Sources drop down menu item to add sources of samples. The Sample Sources tab will open, as shown in Figure 12. Figure 12 Sample Sources screen. To add to the existing sources, click on the icon in the Sample Sources tab, as shown in Figure 11, which will open a popup window as shown in Figure Mineral Spectral Library_CI

19 Figure 13 Pop up window for adding a new sample source. The following fields can be populated: Organisation name; Department name; Web site. Once the new source has been added to Sample Sources and has to the left of the name, click on the icon to save the entry New Minerals: Click on the SUPPORT DATA->Minerals drop down menu item to add new minerals. The Minerals tab will pop up (Figure 14). Mineral Spectral Library_CI 11

20 Figure 14 Minerals tab in the Support Data menu. Click on the (Figure 15). icon in the Minerals tab to open the editing box for adding a new mineral Figure 15 Add New Mineral pop up box. The following fields can be populated: Name; 12 Mineral Spectral Library_CI

21 Group; Subgroup; Chemical Formula. Once the mineral has been added to the Minerals list and has to the left of the name click on the icon to save the entry Validation Instruments Click on the SUPPORT DATA->Validation Instruments drop down menu item to add new minerals. The Validation Instruments tab will pop up (Figure 16). Figure 16 Validation Instruments tab in the Support Data menu. Click on the icon in the Validation Instruments tab to open the editing box for adding a new instrument (Figure 17). Mineral Spectral Library_CI 13

22 Figure 17 Adding a new validation Instrument. The following fields can be populated: Name; Type. Once the instrument has been added to the Validation Instruments list and has to the left of the name click on the icon to save the entry Spectrum Types Click on the SUPPORT DATA->Spectrum Types drop down menu item to add new Spectrum types. The Spectrum Types tab will pop up (Figure 18). 14 Mineral Spectral Library_CI

23 Figure 18 Spectrum Types tab. Click on the Type (Figure 19). icon in the Instruments tab to open the editing box for adding a new Spectrum Figure 19 New Spectrum Type window. The following fields can be populated: Name. Mineral Spectral Library_CI 15

24 Wavelengths. The wavelength data needs to be in text format as a comma separated string, such as: This can be done by copying a column of wavelengths from a spreadsheet into this web page (Figure 20): Figure 20 Example of a webpage that converts column data to comma separated list. Once the Spectrum Type been added to the list and has to the left of the name click on the icon to save the entry. 16 Mineral Spectral Library_CI

25 3.1.5 TSA Minerals Currently the TSA Minerals are linked to Peter Mason s data in TSG. Editing these minerals should not be done without consultation and can only be done by administrators. The TSA Minerals tab is opened by selecting SUPPORT DATA->TSA Minerals (Figure 21). Figure 21 TSA Minerals tab in Support Data. 3.2 Adding new Sample data: New Samples To add new samples, Click on the DATA->Samples menu to add new samples (Error! Reference source not found.). Click on the icon in the Physical Samples tab, or open a Samples tab by clicking DATA->Samples. A window called Add New Physical Sample will appear (Figure 22). Mineral Spectral Library_CI 17

26 Figure 22 Add new physical sample window. Once the data have been entered for the sample, click OK. It will now show up in the Physical Samples list with to the left of the name. This means that it has not been saved in the database yet. Click on the icon to save the entry. If some of the fields are not known at the time of entry, they can be edited later using the icon and then saving the data. 3.3 Adding validation data to Physical Samples There are multiple types of validation data that can be attached to a physical sample. This is found at the bottom of the right hand column, under the Physical Samples metadata (Figure 23). 18 Mineral Spectral Library_CI

27 Figure 23 Validation data of a physical sample is located in the bottom right corner of the right scroll window on the Physical Sample tab. Photos can be uploaded using the icon (maximum size of ~4MB). Validation data (as defined in the SUPPORT DATA->Validation Instruments) can be added (as shown in Figure 24). Figure 24 Add validation data window. New validation spectra can be uploaded (as shown in Figure 25). Mineral Spectral Library_CI 19

28 Figure 25 Add validation spectrum to a physical sample. The Spectrum type must be defined in the SUPPORT DATA->Spectrum Types field. Each instrument with different wavelengths needs to be defined separately. The data is entered as comma separated in the Spectrum box. Such as: 3.4 Recovering from mistakes If you make a mistake in the database and do not want the information updated, such as accidently deleting an entry, click on the refresh button and click Discard (as shown in Figure 26). This will discard any unsaved changes. This makes it important to save regularly to minimise the amount of work that is lost. 20 Mineral Spectral Library_CI

29 Figure 26 Exiting the program without saving will show this pop up box. Discard can be selected to exit and not add the changes if a mistake has been made, such as deleting a sample unwantedly. Mineral Spectral Library_CI 21

30 3.5 Adding Spectra to the library, reviewing data and downloading Adding Spectra Spectra can be added to a Physical sample by going to the DATA->Spectra menu and clicking on the icon. A popup window will appear (Figure 27). Figure 27 Adding a spectrum in the Spectrum Menu. The spectrum type must be in the SUPPORT DATA->Spectrum Type. The spectrum is entered as comma separated values in a single line Adding Spectral Libraries Spectral Libraries can be created in the DATA->Spectral Libraries menu, as shown in Figure Mineral Spectral Library_CI

31 Figure 28 Spectrum Collections (libraries). Spectra can be added to the Spectral Library by selecting the Spectrum Collections in the left hand list and then clicking on the icon. The spectra need to be the same type (i.e. HyLogger TIR or ASD etc.), which is selected in the top right box (Spectrum Type). 3.6 Viewing the Spectra To view the spectra, go to the DATA->Samples tab and select a sample. Then scroll down on the right hand side, below the metadata, and select the Spectra Collection tab. Select a blue coloured text under the NAME column to view that spectra. A new tab should pop up of that spectrum type (Figure 29). Mineral Spectral Library_CI 23

32 Figure 29 Spectrum pop up. The data can be linked to a Spectral Library and TSA Mineral by editing the right hand columns under the blue text of Collections Real Spectra Collection, as shown in Figure Mineral Spectral Library_CI

33 4 Online Mineral Library page By using the following link ( the CSIRO Mineral Spectral Libraries page can be accessed. The Samples page opens by default, as shown in Figure 30. Figure 30 CSIRO Mineral Spectral Libraries web page opening screen. Under the Content drop down menu, the Spectral Libraries and Spectra can be viewed and downloaded. In the Samples window (as shown in Figure 30), if the Details link is clicked, a new page opens containing the metadata, spectra, photos and validation data for that sample Spectra The Spectra page (Figure 31) accessed by the Content drop down menu, shows the spectrum names, plot, sample associated with the spectrum and the type of spectrum. Mineral Spectral Library_CI 25

34 Figure 31 Spectra Screen for the online content. By clicking on the Sample name in the Spectra page, the Sample Details page is opened up, which shows the metadata as well as the attached validation photos, spectra and data Spectral Libraries The Spectral Libraries page (Figure 32), accessed by the Content drop down menu, allows the opening of the individual libraries. Figure 32 Spectral Libraries screen for the online content. 26 Mineral Spectral Library_CI

35 Once opened, the library can be downloaded or each spectra can be viewed (Figure 33). Each spectral library has a page with all their associated spectra, and a download link, which produces zipped ENVI Spectral Library files. Figure 33 Inside the Spectral Libraries, showing the individual spectra and associated samples for the online content. Mineral Spectral Library_CI 27

36 CONTACT US t e csiroenquiries@csiro.au w AT CSIRO, WE DO THE EXTRAORDINARY EVERY DAY We innovate for tomorrow and help improve today for our customers, all Australians and the world. Our innovations contribute billions of dollars to the Australian economy every year. As the largest patent holder in the nation, our vast wealth of intellectual property has led to more than 150 spin-off companies. With more than 5,000 experts and a burning desire to get things done, we are Australia s catalyst for innovation. CSIRO. WE IMAGINE. WE COLLABORATE. WE INNOVATE. FOR FURTHER INFORMATION CSIRO Mineral Resources Ian C Lau t e ian.lau@csiro.au w CSIRO Mineral Resources Peter Warren t e Peter.warren@csiro.au CSIRO Mineral Resources Peter Mason t e Peter.mason@csiro.au CSIRO Mineral Resources Victor Tey t e Victor.tey@csiro.au CSIRO Mineral Resources Carsten Laukamp t e Carsten.laukamp@csiro.au 28 Mineral Spectral Library_CI