Reformatting and merging of geochemical data analyzed with ICPMS for geospatial application

Reformatting and merging of geochemical data analyzed with ICPMS for geospatial application - Customization in ArcGIS

A.M.V. Raghava Rao
Geological Survey of India Training Institute, Bandlaguda, Hyderabad 500068
Phone: 040-24221679, 040-24220682, Fax: 040-24220680
Email: amvrao@sancharnet.in

Abstract:
Geochemical analysis of rock/sediment/soil/water samples by ICPMS (Inductively Coupled Plasma Mass Spectrometer) instrument records 2 or 3 sets of data. The analysis is about 32 elements for rock/sediment/soil and 61 elements for water samples respectively. There are suggested detection limits for all the elements, if the concentration of an element in the sample is below the detection limits, the analyzed value may show as negative or irregular. For analyzing water sample it is some times required to dilute the sample for number of times to limit the Total Dissolved Solids (TDS) to 1000 micrograms per milliliter.

A Macro named IcpmsGeoSpatial has been developed in IcpmsMap.mxt template in ESRI’s ArcMap application to reformat and merge the ICPMS analysed data into suitable geospatial format. Running this macro opens different forms at different levels. Two comma separated value (*.csv) files one for rock/sediment/soil sample and another for Water sample containing entries for two fields 1.Element Name and 2.Detection Limit was used as input for this Macro. From these files the detection limit values are loaded in the respective form. Running the Macro does 1) Applying detection limits to various elements. i.e., the value is eliminated if it falls below the detection limit. 2) Takes care of the dilution factor for water sample 3) merging different sets of data 4) Creating table for all the elements with XY locations 5) Creating a point layer and plotting. The macro designed in such a way that to meet the future demands of reordering the elements or changing the number of elements in any of the inputted files.

Introduction:
Inductively Coupled Plasma Mass Spectrometer installed at Geological Survey of India, Southern Region, Hyderabad is used for geochemical analysis of rock, sediment, soil and water samples. The analysis involves presently about 32 elements (Be, Co, Ga, Ge, As, Y, Zr, Nb, Mo, Cd, Sb, Cs, Hf, Ta, W, Bi, Th, U, La, Ce, Pr, Nd, Eu, Sm, Tb, Gd, Dy, Ho, Er, Tm, Yb, Lu ) for rock/sediment/soil and 61 elements (Li, Be, Al, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Ga, As, Se, Rb, Sr, Ag, Cd, In, Cs, Ba, Tl, Pb, Bi, U, B, Ti, Ge, Zr, Nb, Mo, Ru, Rh, Pd, Sn, Sb,Te, Hf, Ta, W, Re, Ir, Pt, Au, Sc, Y, La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Th) for water samples respectively. Presently the analysis in the laboratory is being carried out as 2 packages (i)Be(Beryllium) group (Be to U ) and (ii)REE(Rare Earth Elements) group ( La to Lu) for rock/sediment/soil and 3 packages (i) Al(Aluminium) group (Li to U) (ii) B&PGE(Boran and Planium Group Elements) group (B to Au) (iii) REE(Rare Earth Elements) group (Sc to Th) for water sample respectively. In future there are plans to include another package for rock/sediment/soil sample.

Necessity:
Analysis of samples with ICPMS (Inductively Coupled Plasma Mass Spectrometer) instrument records data into 2 to 3 individual packages as samples are analysed separately for each package. The data obtained from the instrumental software is not in the report format because it contains so many headers and several other details. Analysts are manually reentering the data by combining all the elemental data obtained from separate packages. This is consuming lot of man hours and also prone to several mistakes. Thus, there is an urgent need for development of suitable software to reformat and merge the data obtained from different packages so that all the elemental data is present in one file. This will facilitate and make possible to load as a layer in any GIS application.

Format of recorded data:
There are many formats of analysed recorded data of ICPMS and one of them is given below:

Format of REE group package for water sample:

All the formats contain some standard headers like “Sample ID:”, "Analyte", "Conc. Mean" and names of elements “Sc”, ”Y”, “La” etc., which are used to pickup the relevant value from any format. Each package results (input file) contain analysis results of many samples and same number of samples is repeated in each package (2 for rock/sediment/soil and 3 for water).

Required output:
Technicality in development of the software package demands to

Facilitate the user to know the nature of the data by very look of the improvised column names of the elements, as detection unit of the element is added as tag to the element with an underscore (ex: Sc_ppb). The element and tag to the elements are acquired from “Analyte” and next to “Conc. Mean” sections of the comma separated data stream.
The opened form/window should accommodate all elements and their detection limits into one complete list for analysed samples at the laboratory in 2 series of elements for solids ( i.e., rock/sediment/soil) and 3 series of elements for water samples. The macro controls the data being fed by 2 or 3 files in such a manner that concentration mean (“Conc. Mean”) of different elements of the same sample identified by “Sample ID” loaded into same row.
To take care of those values of concentration mean, which are recorded as negative/irregular into the data stream due to the fact that those have concentration below the detection limit of the ICPMS instrument, and eliminate such values in post loading steps on running merging tool of the package.
For analyzing water sample it is some times required to dilute the sample for number of times to limit the Total Dissolved Solids (TDS) to 1000 micrograms per milliliter. Macro has special catching eye to identify such samples from its last 3 characters of “Sample ID” and manipulate the concentration mean by multiplying it by that factor.
The package designing has to fulfill the future demands of reordering the elements or changing the number of elements in any of the inputted files.

With all these aspects the output should look like the following (Fig. 1):

Fig.1: Required output
IcpmsGeoSpatial Macro:
IcpmsGeoSpatial macro is developed in IcpmsMap.mxt template using Visual Basic editor in ArcMap to merge and reformat ICPMS analysed data. Considering the aspects mentioned in the above section, it creates

file1, a comma separated value (csv) file with user specified name containing Sample ID’s and respective element concentrations. For the water sample, if the last three characters of Sample ID are figures, implies the level of dilution that the sample has undergone, and the element concentration mean is multiplied by that number. If any slash (“/”) character is found during the process, it is replaced with “p” because ArcGIS application does not accept this character for working within it. The slash is found in string “mg/L” and replaced with “mgpL”.
file2, with the name XY is added at the end of file1 name, containing additional information of XY co-ordinates compared to file1 (this needs another csv file containing minimum three columns of Sample ID and respective X,Y co-ordinates)
Plots with geographic coordinates as point layer in ArcMap with the name adding “_lyr” at the end of file2 name.

Input Requirements:
Two files SedRokSoilDecLimits.csv for sediment/rock/soil and WaterDecLimits.csv for water containing element names and corresponding detection limits of various elements inside the folder C:\IcpmsDL are required for input to the software. The format of the files is given below:

SRSelement, Deteclimits
In,0.0
Be,0.3
Co,1
Ga,0.5
………
………
………
Lu,0.01

The first row is headers, and the second row contains a standard element name as first field for geochemical analysis and 0.0 as detection limit. This standard element is for checking the accuracy of the analytes, and is eliminated at the time of merging. User can open these files in any text editor, change the standard name and edit the detection limits if they need to change and save it.

How IcpmsGeoSpatial works:
Clicking Tools->Macros->IcpmsGeospatial opens the following form (Fig. 2).

Fig 2: Type of Sample and no. of files selection form
User needs to click one of the six options 1) Sediment/Rock/Soil Sample (*** three files) 2) Sediment/Rock/Soil Sample (** two files) 3) Sediment/Rock/Soil Sample (* Single file) 4) Water Sample (*** three files) 5) Water Sample (** two files) 6) Water Sample (*single file). Suppose if the user clicks the 4th option, a form as shown in Fig. 3 opens.

Fig. 3: Form opened when Water sample with 3 files option is clicked
Because the user clicked to merge three files, three file browsing buttons and three corresponding label boxes are appeared in this form. If the user clicks options to merge two files, only two file browsing buttons and two corresponding label boxes will appear and clicks options to merge single file, only single file browsing buttons and single corresponding label box will appear respectively. OutputFile Browse button appear every time. Apply Dilution Factor check box will not appear for merging of rock/sediment/soil samples.

Initially Merge, Add Coordinates, Plot buttons are disabled. As a first step the user needs to select the proper input files by clicking the browse buttons and also select the folder and give a name for output file by clicking OutputFile browse button. Secondly clicking Load Detec. Limits button reads the file formats, loads the elements containing in the files and corresponding detection limits in to the form as shown in Fig. 4. “Load Detec. Limits” button is disabled and “Merge” button is activated.

Fig. 4: Form loaded with detec. Limits after clicking “Load Detec. Limits” button.
Clicking the “Merge” button will merge the data in three/two/one files and a message will appear whether the user needs to merge another set of files of similar format to the same output file. If the user clicks “yes” the label boxes are cleared and the user needs to add another set of files by clicking the corresponding browse button. The process will repeat till the user clicks “no”. If the user clicks “no”, “Merge” button is deactivated “Add Coordinates” button is activated.

Thirdly clicking the “Add Coordinates” button asks the user to specify the coordinates file containing Sample IDs and related X and Y-coordinates. Fourthly the structure of the coordinates file is read and “Coordinate Details” form (Fig. 5) is opened. User needs to select “Sample ID”, “X-coordinate” and “Y-coordinate” fields/columns from the drop down lists of corresponding boxes. Clicking “Prepare Merged file with XY Coordinates” will create the merged file with X and Y Coordinates. “Add Coordinates” button is disabled and “Plot” button is activated in the form shown in Fig. 4. Clicking the plot button will plot the file in ArcMap as shown Fig. 6 and the attributed table of this layer is shown in Fig. 7. User can get out of the application at any stage by clicking the “close” button.

Fig. 5: Coordinate details input form

Fig. 6: Geochemical data plotted with geographic XY coordinates

Fig. 7: Attributed table of the plotted layer
Utility:
Geochemists can supply raw ICPMS analysed data to geologists/geophysicists. Utilizing this software, merged file with XY coordinates can be straight away created. From this, a point feature class and there by a Raster and contour utilizing conversion tools and 3D Analyst tools in ArcToolbox can be prepared. Mineral concentrations can be best visualized overlying geology layer with Raster/Contour layer of different elements chemical concentrations.

Conclusions:
The software is extremely useful, saves enormous amount of time there by helping the analysts to concentrate on the new methodologies and new packages. It is a handy software tool for the field geologists/geophysicists, because the merged data can be directly used for the preparation of maps and a point layer is automatically created in the ArcGIS platform. Further as GSI is in the process of procuring 3 more ICPMS instruments at Kolkata, Lucknow and Jaipur and the same software can be used for all those ICPMS recorded data. Finally it is worthwhile to note that the present software package has been developed at an appropriate time and it will be immensely beneficial to our NGCM (National Geochemical Mapping) Program, which is the most prestigious project of the country.

Acknowledgement:
The author is thankful to Director General, Geological Survey of India and Deputy Director General, Geological Survey of India, Training Institute for granting permission to present this paper. The authors are also thankful to Dr. C.R.M. Rao, Director, Chemical Division, and Sri M. Venkata Ramaiah, Chemist (Sr) of Geological Survey of India, Southern Region for their valuable interaction while developing this software.