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sfadschm edited this page Mar 19, 2022 · 48 revisions 
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Using

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Spectral Analysis with OriginC

Last Update: 19.03.2022 (v1.2.3)

This is an OriginC library providing several scripts for importing, handling, and evaluating spectroscopic data. No warranty is given for functionality or correctness, please verify all results generated with this script manually.

All methods have been tested with OriginPro 2021-2022; older program versions should be updated anyways.

1   Installation

  1. Copy the file build/Spectral Analysis.opx to a location on your computer.

  2. Run OriginPro.

  3. Drag and drop Spectral Analysis.opx into OriginPro. The installation process will start automatically and add all required files to the User Folder Workspace.

    If any errors occur, the script will show a prompt. Please contact the script provider with the displayed error code.

  4. All scripts will now be available after each start of OriginPro.

2   Usage

  1. Open the Script Window.

    (Window / Script Window or Shortcut Alt + Shift + 3)

  2. Type the name of a script (see Methods) into the window and confirm with Enter.

    (Each Enter inside the Script Window will be interpreted as a command call. If the current row does not contain a valid script name, an error will be printed.)

3   Extending

This package can easily be extended by other code modules.

See the Developer Guide and the Example Plugin code in the src directory.

4   Debugging

If you need to debug the runtime of any function from this library or your own, you can use the timer(string label) method.

  1. Skipping the label parameter resets the timer without output:

    timer();
// no output

  2. To generate output, pass a descriptor to the label parameter:

    timer("Transpose Sheet");
// output: "Transpose Sheet: 19 ms"

5   Methods

All callable methods can be looked up in the file main.c and do not require any parameters to be passed when calling them.

Helper methods are in the header files ( *.h ) in the corresponding subfolders. They can in principle also be called from the Script Window, however, in this case the function parameters must be passed immediately.

5.1   Data Handling

5.1.1   import

Automates data import from a variety of sources. The import functions for spectra, 3D-maps and XY-λ-I data support pushing header lines to the OriginPro worksheet user parameters with the pseudo-syntax ParamName:{TAB}Value.

Parameters
Parameter Description
Target Workbook Name of the workbook to append the imported data to. If not set, will create a new workbook.
Target Worksheet Name of the worksheet to append the imported data to. If not set, will create a new worksheet.
Data Type The source type of the data (see b).
Delimiter The column value delimiter of the source file (usually Tab, sometimes Whitespace).
Dec. Separator The decimal separator of the source file.
Constant X-Axes If checked, removes the X-columns of all imported files except the first.
Create Sparklines? If checked, creates sparklines for all imported data columns. (Use with caution, creates heavy CPU load!)
Datatypes
Data Type Description
Spectra Files E.g., spectra from LabSpec or UVProbe. Imported file names will be written to the column comments.
3D-Maps E.g., time traces from LabSpec, peak maps from NT-MDT or Raman images generated with the Raman Live Tool Set. The file structure must be XY-I ... File names are used as worksheet names. XY-coordinates and other axes are written to the user parameters.
4D-Maps E.g., raw map data from NT-MDT (XY-λ-I ...). File names are used as worksheet names. XY-coordinates are written to the user parameters. Note that NT-MDT data must be exported from Image Analysis as a MATLAB file (*.m)!
Tracks XML-Files generated via ImageJ TrackMate containing particle tracking information. Metadata (e.g., time axis and XY-coordinates) are written to the user parameters.

5.1.2   correct

Manipulates all datasets in a selectable worksheet of the active workbook. For each selected method, the results are stored in a new worksheet, which is then used as the data source worksheet for the subsequent correction method.

Parameters (vary depending on the chosen method)
Parameter Description
Data Source Dropdown field to select the source data worksheet.
Worksheet Dropdown field to select the reference data worksheet (only in selected methods).
Parameter Dropdown field to select the user parameter containing the reference data (in the current worksheet) or connecting the data and reference worksheets (only in selected methods).
Methods (selected via checkboxes in initial dialog)
Method Description
Masked Data Removal Clears all cells of the source worksheet that have been masked (e.g., in a graph window) and fills them with mean values (averaging window: 10 data points).
Background Subtraction

Subtracts reference data from all datasets.

The Reference mode uses reference spectra connected via a selectable user parameter.

Parameters: Worksheet, Parameter

The Median mode uses the median value of the user defined spectral subregion.

Parameters: Start, Stop

The Constant mode uses a fixed value.

Parameters: Value
Spike Removal

Automatically removes spikes from the worksheet. This method is based on the Whitaker-Hayer algorithm, see Chemolab 2018.

Parameters: Z-Threshold, Averaging Width
Setup Correction

Applies a setup calibration curve to the source data by division. If no reference user label is selected, this method defaults to the first two columns of the reference worksheet.

Parameters: Worksheet, Parameter
Filter Correction

Corrects the source data with a set of neutral density filter transmission curves by division. The transmission data of the filters must be absolute values.

Parameters: Worksheet, Parameter
Integration Correction

Divides all datasets by the integration time provided in a user parameter of the source worksheet. The selected user label must only contain numerical data!

Parameters: Parameter
Jacobian Transformation

Performs a Jacobian Transformation to the energy space on all source datasets (Caution! Not to be used for PLE or absorption data.).

Parameters: none
Normalisation

Normalises all source datasets by dividing them by their respective maximum value.

Parameters: none

5.1.3   analyze

Executes simple spectroscopic analytics on the current worksheet.

Parameters
Parameter Description
Dataset Name The name that will appear in the long name of the result column in the evaluation sheet.
Method The mathematical evaluation method to apply to the data.
Skip Abscissae? If checked, does not generate new abscissa in the result sheet, e.g., if they have already been generated with the last run of the method.
X-Abscissa The name of the user label that holds the data representing the new X values of the evaluation result.
Y-Abscissa See X-Abscissa . If set to none, values in the result sheet will be assigned Y, if set, values will be assigned Z (e.g., for map analysis).
X Start Value The lower bound of X values to evaluate; if 0, will default to the first data row.
X Stop Value The upper bound of X values to evaluate; if 0, will default to the last data row.
Methods
Method Description
Peak Position Finds the point with the highest Y value in the given range.
Mass Centre Calculates the centroid in the given range.
Peak Intensity Returns the highest Y value in the given range.
Peak Area Summarizes all Y values in the given range (pseudo-area)
Peak FWHM Calculates the full width at half maximum by finding the Peak Position Ymax in the given range and iterating to higher and lower X values until Y ≤ 0.5 × Ymax in both directions.

5.1.4   map

Transforms the datasets in the currently active worksheet to a different representation (e.g., generate 3D-Map from XYZ columns).

Parameters
Parameter Description
Method Dropdown field to select the data conversion method.
Methods
Method Description
XYZ-Data to Matrix Transforms a Z dataset into an XYZ-Map. XY data can be extracted from the column designations or from user input.
4D-Linescan Extracts a line scan along one axis from an imported XY-λ-I map (e.g., from NT-MDT or LabView).

5.1.5   interpolate

Interpolates all XY-datasets in the currently active worksheet onto a new X-axis. The new axis must be included in the same worksheet.

Parameters
Parameter Description
New X-Axis The source column containing the new X-axis data.

5.1.6   peaks

Convenience method for peak fitting that collects a selected column from all PeakProperties* worksheets in the currently active workbook. The data are collected in a new sheet, transposed and some basic statistics (mean and standard deviation) are calculated. All results are auto-updated such that adjustments to individual fittings will directly be reflected.

Parameters
Parameter Description
Name The dataset identifier used to name the result sheets.
Target Column The source column from the PeakProperties sheet.

5.1.7   setLowerBound

Replaces all values in the active worksheet smaller than lowerBound with 0.

lowerBound defaults to 0 if omitted (all negative data are set to 0).

Parameters
Parameter Description
lowerBound (0) This parameter must be passed when calling the method, there is no user dialog.

5.2   Miscellaneous

5.2.1   renameWbs

Renames the Short Name field of all workbooks in the current folder based on their Long Names (e.g., to enable sorting in the Horiba Fluoressence software).

5.2.2   reduce

Reduces the project's CPU load by deleting (!) all sparklines in the project and hiding all windows.

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© 2017-2022 Alexander Schmitz-Wunderlich, University of Duisburg-Essen

 
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