abbreviation:

• LMB : left mouse button
• RMB : right mouse button

The instruction plot for a SeqIm instance generate a plot window as shown in figure 1

xx.plot() or xx.plot(1) for logarithm scale The figure is used to visualize the images take some measurements and determine peaks positions. The figure contains several buttons and widgets with which interact.

The first element of the figure is the representation of the current image with its filename, if any widget is activated the position of the cursor is specified in rectangle 2 (light green) x, y positionS in pixel, distance from the center (d_spacing) in pixel and nm^-1. The intensity value of the pixel below the cursor is shown between square brackets [ ]. It is generally better if only one window is open, the windows could be closed at any moment the peaks selected will be conserved.

contains several buttons related to zoom color setting margins and the possibility to save the figure as jpg more information could be found here

contains two buttons that allows to pass from an image to the previous or the following image

contain the buttons related to the management of the peaks:
switch the representation as red dots of the peaks taken in account
allows to remove one peak by clicking over, the tools remain active till the RMB is pressed. ATTENTION this tool is quite buggy if some buttons are used before than it has been deactivated. In such case press several times the RMB and close the windows
it will allow to remove peaks in a rectangle. One time the button is pressed the first time that the LMB is pressed on the image will start a red line that represents the first axis of the rectangle, which could be defined by the release of the button, second LMB click define the wide of the rectangle. The tool deactivated automatically

contain the buttons related to measurements on the image:
allows tracing a line on the image, on the shell will appear the length of such line and a supplementary window will show the intensity profile along the line.
allows tracing two lines on the image and measuring the angle between them.

contain the slider and button related to peak detection on the image, this is an interface to the commands self.ima.find_peaks() or self.find_peaks() both command could be used to obtain a more precise control on the parameters. The parameters of find_command are the following and could be controlled by moving the slides:

• int: minimum intensity count for the maximum of the peak. In the slider and the command, the value is on a relative scale in respect to the maximum
• dis: maximum distance from the center acceptable for a peak. In the command the unit is pixels, however, for the sliders, the value is the fraction on a horizontal number of pixels. dis = 0 correspond to any constrain
• rad: minimal distance between peaks, generally this parameter is not necessary to be used
• sym: centrosymmetric filter for peaks. Only peaks for which exist a symmetric peak in respect to the center are considered. The numerical value is a tolerance limit for the symmetric peak position. If the tolerance is 0 the symmetric filter is not applied.
• apply to all button that applies the selected parameter for peak searching for all images.

The max slider allows controlling the contrast for the images