11.3 The Quick Peaks Gadget

From

The beginning of X scale.

To

The ending of X scale.

Fixed (Prevent moving by ROI)

Fix the X scale to prevent from moving by ROI box.

• None (Y=0)

  Use Y=0 as baseline.

• Constant

  Use a horizontal line for baseline. You can specify the intercept of the horizontal line in the Constant control below.

• 2nd Derivative

  Use the 2nd Derivative method to create baseline.

• Use Existing Dataset

  Select an existing dataset as the baseline.

• Min&Max

  Use minimum Y as baseline to find positive peaks. Use maximum Y as baseline to find negative peaks.

• End Points Weighted

  Create a smoothed curve using data points from two ends.

• Straight Line

  Connect two end points of the data plot and connect them as baseline.

• Full Plot Range

  Create the baseline for the full plot range.

• Curve Within ROI

  Create the baseline only for the plot range within the ROI box.

• Entire Data

  The end points of the data plot are used

• Rectangle

  The end points at the boundaries of ROI box are used

• Scale

  The end points at the X axis scale are used

• Adjacent-Averaging

  Please refer to algorithm of smoothing.

• Savitzky-Golay

  Please refer to algorithm of smoothing.

Window Size: Specify the desired window size (a positive integer) in the moving window for the Savitzky-Golay or Adjacent-Averaging smoothing.

Threshold: Specify threshold for the Savitzky-Golay or Adjacent_Averaging smoothing.

Polynomial Order: This parameter is available only when Savitzky-Golay is selected for Smoothing Method. It specifies the polynomial order (1 through 9).

• Minimum

  Set the intercept to the minimum value of the data.

• Maximum

  Set the intercept to the maximum value of the data.

• Mean

  Set the intercept to the mean of the data.

• Median

  Set the intercept to the median of the data.

• Custom

  When this option is chosen, specify the desired intercept for the horizontal line as baseline.

• Positive

  Find positive peaks only.

• Negative

  Find negative peaks only.

• Both

  Find both positive and negative peaks.

Method: Use this drop-down list to select the method to find the peaks.

• Local Maximum

  Use the Local Maximum method to find the peaks.

• Window Search

  Use the Window Search method to find the peaks.

• 1st Derivative

  Use the first derivative method to find the peaks.

• 2nd Derivative (Search Hidden Peaks)

  Use the 2nd Derivative method to find the peaks. This method is capable of detecting hidden peaks in the data.

• Residual (Search Hidden Peaks)

  Use the Residual after 1st Derivative method to find the peaks. This method is capable of detecting hidden peaks in the data.

Local Points: This is available only when Local Maximum is selected in the Method drop-down list. It specifies the number of points in the local area, which will be used for finding the peaks with the Local Maximum method.

Size Option: This is available only when Window Search is selected in the Method drop-down list. This drop-down list specifies how the Height and Width values (see below) are interpreted.

• Raw Size

  The values will be interpreted as raw sizes.

• Percent of Raw Data

  The values will be interpreted as the percentages with respect to the total width or maximum height of the spectrum data.

Height: This is available only when Window Search is selected in the Method drop-down list. It specifies the height of the rectangle, which is used to find the peaks. There is an Auto check box to the right. If it is selected, it will determine the value automatically. Therefore, if you want to edit the value, please uncheck this check box.

Width: This is available only when Window Search is selected in the Method drop-down list. It specifies the width of the rectangle, which is used to find the peaks. There is an Auto check box to the right. If it is selected, it will determine the value automatically. Therefore, if you want to edit the value, please uncheck this check box.

Smooth Derivative: This is available only when 1st Derivative, 2nd Derivative (Search Hidden Peaks) or Residual (Search Hidden Peaks) is selected in the Method drop-down list. Specify the method to smooth the derivative of data (1st derivative or 2nd derivative).

Method: Specify the smoothing method.

• None

  Do not use any smoothing method.

• Savitzky-Golay

  Specify the Savitzky-Golay method to get smooth derivative.

• FFT Filter

  Specify the FFT Filter method to smooth derivative. It is only available for 2nd Derivative (Search Hidden Peaks).

• Adjacent-Averaging

  Specify the Adjacent-Averaging method to smooth derivative. It is only available for 2nd Derivative (Search Hidden Peaks).

• Quadratic Savitzky-Golay

  Specifies the Quadratic Savitzky-Golay method to smooth derivative. It is only available for 2nd Derivative (Search Hidden Peaks).

Polynomial Order: It is available for Savitzky-Golay and Quadratic Savitzky-Golay methods to specify the polynomial order.

Points of Window: It is available for Savitzky-Golay, Adjacent-Averaging and Quadratic Savitzky-Golay methods. The greater this value, the greater the degree of smoothing. A value of zero for this parameter will leave the data unsmoothed.

Cut Off Frequence: It is available only for FFT Filter method. It specifies the cutoff frequency.

Method: Use this drop-down list to specify whether you want to limit the number of found peaks or the height of the peaks.

• None

  Select this option if you do not want to limit the number of found peaks nor the heights of the peaks.

• By Height

  When you select this option and specify a threshold height with the Threshold Height(%) text box, only the peaks whose heights are not less than the threshold height will be found.

• By Number

  If you select this option and enter a value in the Number of Peaks text box, you can limit the number of peaks that will be found.

Threshold Height(%): This text box is available only when By Height is selected in the filter Method drop-down list. You can use it to specify the minimum height of the found peaks. It is a percent of a reference value, which is defined as follows: First, get the maximum value and the minimum value of the data (if a baseline has been subtracted from it, use the data after subtraction). Then compare the absolute values of the maximum value and the minimum value. The greater one will be regarded as the reference value of the Threshold Height. There is an Auto check box to the right. When it is selected, the smooth points will be determined automatically. If you want to specify the height, make sure the clear this check box.

Number of Peaks: This text box is available only when By Number is selected in the filter Method drop-down list. You can use it to specify the maximum number of the found peaks. There is an Auto check box to the right. When it is selected, the smooth points will be determined automatically. If you want to specify the number of peaks, make sure the clear this check box.

Peak Marker: Whether to show peak marker.

Color: The color of peak marker.

Size: The size of peak marker. This drop-down list allows typing a number not listed there.

Peak Label: Whether to show peak label.

Label: What label of the peak to show, includes three options:

X of Peaks: Show only X scale of the peak as peak label.

Y of Peaks: Show only Y scale of the peak as peak label.

(X,Y) of Peaks: Show both X and Y scales of the peak as peak label.

If you have applied a Formula to axis tick labels, you can display the formula-adjusted tick value as opposed to the actual data (scale) value using the Numeric Display Format box on the Plot Details Label tab.

Base Marker: Whether to show base marker. Note that when more than 100 peaks are found, no base marker will show even though it is checked.

Color: The color of base marker.

Size: The size of base marker. This drop-down list allows typing a number not listed there.

• Data Plot

  If this is selected, later if you select Tag Peaks from the gadget fly-out menu, the tagged peak labels will be automatically created as a data plot and added to the original graph.

• Marker

  If this is selected, later if you select Tag Peaks from the gadget fly-out menu, the tagged peak labels will be only added as data marker. But you can right click on the data marker(move mouse over and right click when mouse turn to crossing) and choose Convert to Data Plot to convert data marker into data plot.

Select how to integrate the peaks, from Beaseline or Y=0.

Select if show the integration area of found peaks in the ROI box. Note that when more than 100 peaks are found, no integration area will show even though it is checked.

Specify whether to output the results to the Script Window.

Specify whether to append the results to a worksheet.

This is only available when Append to Worksheet is selected. It is used to specify the name of the worksheet.

• When you generate new output, results are output to [%H-QkPeak]Result by default (here %H means the Short Name of source graph), but other books and sheets can be specified. If the book and sheet do not exist, they will be created on output.
• Alternately, you can click the flyout button to the right of Result Worksheet Name and choose Sheet in Input Book. This fills the edit box with [<input>]Result. When you generate new output, results are output to a sheet named Result in the source book.

Specify the output sheet name to store the tag information.

If on the Find Peak tab:

• Tag Peak and Base as is set to Data Plot, a new worksheet with specified name will be created with tag info data when output is generated. Accept the default [%H-QkPeak]Tag or click the flyout button to the right of Tag Info Worksheet Name and choose Sheet in Input Book. This fills the edit box with [<input>]Tag. When you choose New Output (O), results will be output to a sheet named Tag in either the QkPeak book, or in the source book. Alternately, you can type a [BookName]SheetName into the field. If the book and sheet do not exist, they will be created when you generate new output.
• Tag Peak and Base as is set to Marker, the worksheet will not be created because Marker does not have associated data.

Specify to output the baseline to worksheet.

• When you generate new output, results are output to [%H-QkPeak]Baseline by default, but other books and sheets can be specified. If the book and sheet do not exist, they will be created on output.
• Alternately, you can click the flyout button to the right of Result Worksheet Name and choose Sheet in Input Book. This fills the edit box with [<input>]Baseline. When you generate new output, results are output to a sheet named Baseline in the source book.

Dataset Identifier

Specify a dataset identifier in the drop-down list.

Peak ID

Peak ID, something like "Peak 1", "Peak 2", etc.

Peak Row

The row index of the peak center.

Peak X

The X scale of the peak.

Peak Y

The Y scale of the peak.

Height

The height of peak, calculated from baseline.

Peak Area

The peak area that is calculated by integrating the raw peak data from the baseline or Y=0 (depending on the selection in the Integrate From drop-down list under the Area tab). The integration range is marked out by Base Marker on Find Peak tab, which is not identical to the range covered by ROI box.

FWHM

The full width at half maximum height or the peak width at half the peak's maximum value.

Centroid

The peak centroid or gravity center, which is defined as:

Left Half Width

The left half width. If we draw a line for , this line will intercept with the input data at two points. Let's denote them as and , where . Also, we denote the peak center as . Then we can compute the left half width as:

Right Half Width

The righthalf width. If we draw a line for , this line will intercept with the input data at two points. Let's denote them as and , where . Also, we denote the peak center as . Then we can compute the right half width as:

Left Base Marker Row

The row index of the left base marker.

Left Base Marker X

The X scale of the left base marker.

Left Base Marker Y

The Y scale of the left base marker.

Right Base Marker Row

The row index of the right base marker.

Right Base Marker X

The X scale of the right base marker.

Right Base Marker Y

The Y scale of the right base marker.

Info

The information of the baseline, which is an embedded notes window. ‘’’Note’’’: when input data is larger than 1000 points, baseline data will not output to Notes. Please select ‘’’Output Baseline to Worksheet’’’ to see the baseline data.

• Click on any plot to select.
• Click Select... or More... to open the Select Plot(s) browser.
• By default, the Auto mode will be checked in the fly-out menu, which means the target data/plot will follow the data plot selection/highlighting outside the ROI box on the graph. In Origin 2019 and earlier versions, Origin doesn't support this auto behavior; to change the target plot/data, you have to select from the fly-out list or the Select Plot(s) dialog.

Please note, when you change the source data/target plot, the peak markers and peak labels of found peaks will automatically show on the newly-selected plot, following the settings in the Find Peaks tab. If you need keep the peak markers and labels on current plot, please select Tag Peaks from the fly-out menu.