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11.3 The Quick Peaks Gadget

Video Image.png See more related video:Quick Peaks Gadget

Overview

The Quick Peaks Gadget provides a quick and interactive way to perform peak analysis on data plotted in a graph. You can select an arbitrary range of the data plot using the region of interest (ROI) object displayed in the graph. Peak analysis results will update as the ROI is moved or resized.

Quick Peaks Gadget.png

With the Quick Peaks gadget, you can:


To Open Quick Peaks Gadget

To use this tool, select Gadgets: Quick Peaks from the Origin menu, when a graph is active. If the tool has already been activated, you can re-open the Quick Peaks dialog by clicking on the arrow in the upper-right corner of the ROI and choosing Preferences.

To Show or Hide Gadget Tool

To toggle the display of all gadget ROI boxes in a graph at the same time, click the H button H Button.png in the top right corner of the graph, which enables users to export the graph with gadget results.

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 (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.
Range This is not available when the Mode is Straight Line. Specify how the baseline range shows 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.
Fix x to This is only available when the Mode is Straight Line. Specify how the straight line end points are decided.
  • 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
Y Offset of Left This is only available when the Mode is Straight Line. Specify the left end point offset on the Y axis scale.
Y Offset of Right This is only available when the Mode is Straight Line. Specify the right end point offset on the Y axis scale.
Smoothing Method Select smoothing method to create baseline. This option is only available when the Mode is set as 2nd Derivative.
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 to 2nd Derivative.
Connected Method Specify connect method for the anchor points. This option is only available when you set Mode to 2nd Derivative.
Constant Use drop-down list to specify the intercept for the horizontal line to 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, specify 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.
Tag Peak and Base as
  • 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.

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.

Tag Info Worksheet Name

Specify the output sheet name to store the tag information. If Data Plot is chosen for Tag Peak and Base as in the Find Peaks tab, a new worksheet with specified name will be created with tag info data when output the results; Otherwise, if Marker is chosen for Tag Peak and Base as, the worksheet will not be created because Marker does not have associated data.

Output Baseline to Worksheet

Specify if output the baseline to worksheet.

Quantities Tab

Output Quantities Specify what data to output.
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: 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 = MaximumHeight / 2, this line will intercept with the input data at two points. Let's denote them as (x1, y1) and (x2, y2), where x1 < x2. Also, we denote the peak center as (xc, yc). Then we can compute the left half width as: LeftHalfWidth = xc - x1
Right Half Width
The righthalf width. If we draw a line for y = MaximumHeight / 2, this line will intercept with the input data at two points. Let's denote them as (x1, y1) and (x2, y2), where x1 < x2. Also, we denote the peak center as (xc, yc). Then we can compute the right half width as: RightHalfWidth = x2 - xc
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).
New Output for Entire Curve Output results for all peaks in the active plot to the specified worksheet (if not empty, append the results).
New Output for All Curves (N) Output the results for all curves in the current layer to the specified worksheet (if not empty, append the results).
New Output for All Layers (L) Output the results for all curves in all layers within the current graph 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 and add the peak labels for found peaks as a label plot or data markers into the original graph. The labels will still exist even after closing the gadget. When the peaks are added as data marker, they can be used by the Multiple Peak Fit (menu is Analysis: Peaks and Baseline: Multiple Peak Fit) tool.
Fit Peaks Fit the found peaks by specifying a fitting function.
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.
 

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