Quick Peaks Gadget

The Quick Peaks gadget provides a quick tool to pick peaks, subtract baseline and integrate the peaks in the ROI (Region of Interest) range. To use this tool, select Gadgets: Quick Peaks from the Origin menu, when a graph is active.

This dialog can be opened from Gadgets: Quick Peaks in the Origin menu, or by selecting Preferences from the ROI fly-out menu.

1 ROI Box Tab
2 Baseline Tab
3 Find Peak Tab
4 Area Tab
5 Output to Tab
6 Quantities Tab
7 Fly-out Menu

ROI Box Tab

X Scale	Specify the X Data range for the ROI. 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.
Show Tool Name	Specify whether to show the tool's name near the top of the ROI.
Show Number of Peaks on Center-Top	Specify whether to show the number of peaks on center-top of the ROI.
Fill Color	Specify the filled color of the ROI.

Baseline Tab

Mode	Specify the baseline mode, options include: None No 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 and maximum Y as baseline separately to find peak twice, minimum Y as baseline to find positive peaks and maximum Y as baseline to find negative peaks. End Points Weighted Create a smoothed curve using data points from two ends.
Range	Specify how the baseline range show on the ROI. 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.
Smoothing Method	Select smoothing method to create baseline. This option is only available when the Mode is set as 2nd Derivative. 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).
Maximum Anchor Points	Specify the maximum of baseline anchor points. This option is only available when you set Mode as 2nd Derivative.
Connected Method	Specify connect method for the anchor points. This option is only available when you set Mode as 2nd Derivative.
Constant	Use drop-down list to specify the intercept for the horizontal line, which will be used as the baseline. 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, it will allow you to enter the desired intercept for the horizontal line as baseline.
Y=	Specify the customized intercept for the horizontal line as baseline. This option is only available when Constant is Custom.
Dataset	Specify a dataset as baseline. This option is only available when Mode is set to Use Existing Dataset.
End Points(%)	Specify the percentage of end points to create baseline. This option is only available when you set Mode as End Points Weighted.

Find Peak Tab

Direction	Specify whether or not to find peaks with a specified direction only. Positive Find positive peaks only. Negative Find negative peaks only. Both Find both positive and negative peaks.
Peak Finding Settings	Specify the settings for finding 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.
Peak Filtering	Specify how to filter peaks. 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 Display	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. Base Marker: Whether to show base marker. Color: The color of base marker. Size: The size of base marker. This drop-down list allows typing a number not listed there.

Area Tab

Integration from	Select how to integrate the peaks, from Beaseline or Y=0.
Show Integrated Area	Select if show the integration area of found peaks in the ROI box.

Output to Tab

Script Window	Specify whether to output the results to the Script Window.
Results Log	Specify whether to output the result to the Results Log.
Append to Worksheet	Specify whether to append the results to a worksheet.
Result Worksheet Name	This is only available when Append to Worksheet is selected. It is used to specify the name of the worksheet.
Output Baseline to Worksheet	Specify if output the baseline to worksheet.

Quantities Tab

Output Quantities	Specify what data to output. Dataset Name The name of dataset where the peak comes from. 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 peak data from the baseline or Y=0 (depending on the selection in the Integrate From drop-down list under the Area tab). 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: $C=\frac{\int_{0}^{\infty}xF(x)dx}{\int_{0}^{\infty}F(x)dx}$ Left Half Width The left half width. If we draw a line for $y = M a x i m u m H e i g h t / 2$ , this line will intercept with the input data at two points. Let's denote them as Failed to parse (Missing texvc executable; please see math/README to configure.): (x1, y1) and $(x 2, y 2)$ , where $x 1 < x 2$ . Also, we denote the peak center as $(x c, y c)$ . Then we can compute the left half width as: $L e f t H a l f W i d t h = x c - x 1$ Right Half Width The righthalf width. If we draw a line for $y = M a x i m u m H e i g h t / 2$ , this line will intercept with the input data at two points. Let's denote them as Failed to parse (Missing texvc executable; please see math/README to configure.): (x1, y1) and $(x 2, y 2)$ , where $x 1 < x 2$ . Also, we denote the peak center as $(x c, y c)$ . Then we can compute the right half width as: $R i g h t H a l f W i d t h = x 2 - x c$ 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.

Output Quantities

Specify what data to output.

Dataset Name

The name of dataset where the peak comes from.

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 peak data from the baseline or Y=0 (depending on the selection in the Integrate From drop-down list under the Area tab).

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: $C=\frac{\int_{0}^{\infty}xF(x)dx}{\int_{0}^{\infty}F(x)dx}$

Left Half Width

The left half width. If we draw a line for

y = M a x i m u m H e i g h t / 2

, this line will intercept with the input data at two points. Let's denote them as Failed to parse (Missing texvc executable; please see math/README to configure.): (x1, y1)

and  $(x 2, y 2)$ , where  $x 1 < x 2$ . Also, we denote the peak center as  $(x c, y c)$ . Then we can compute the left half width as:  $L e f t H a l f W i d t h = x c - x 1$

Right Half Width

The righthalf width. If we draw a line for

y = M a x i m u m H e i g h t / 2

, this line will intercept with the input data at two points. Let's denote them as Failed to parse (Missing texvc executable; please see math/README to configure.): (x1, y1)

and  $(x 2, y 2)$ , where  $x 1 < x 2$ . Also, we denote the peak center as  $(x c, y c)$ . Then we can compute the right half width as:  $R i g h t H a l f W i d t h = x 2 - x c$

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.

Fly-out Menu

New Output	Output results to the specified worksheet (if not empty, append the results).
Subtract Baseline	Subtract the specified baseline from source data in the ROI box.
Tag Peaks	Tag the found peaks. Then even close the gadget, the found peaks are with peak labels, and these peaks can be used by the Multiple Peak Fit (menu is Analysis: Peaks and Baseline: Multiple Peak Fit) tool.
Fit Peaks(Pro)	Fit the found peaks by specifying a fitting function. This feature is only available in Pro version.
Switch to Peak Analyzer	Switch to Peak Analyzer to fit the found peaks. More details about fitting peaks in Peak Analyzer, please refer to this help page.
Update Output	Update the output, and the original results will be clear, then add the current results. This is applicable only when you have output the peak values.
Go to Report Worksheet	Activate the report worksheet, if there is one.
Change Data	Change the source data set. This is applicable only when there are multiple curves on the graph layer.
Expand to Full Plot(s) Range	Expand the ROI box to full plot range.
Fix ROI Position	Fix the ROI position, then you cannot move it any more.
Save Theme	Save theme for the dialog settings.
Save as <default>	Save the current dialog settings as default theme.
Load Theme	Load the existed theme to apply the dialog settings.
Preferences	Open the Quick Peaks Preferences dialog, which is similar with the one when starting the gadget by selecting menu Gadgets: Quick Peaks.