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Array of Circles Tool

This tool puts an adjustable array of circles on an image.

If the image is from a data cube or spectral image, Lispix will save spectra averaged over each circle.  The Data Cube Tool and the Mosaic Tool are also designed to work with spectral images.


AOC Tool as opened.

Parameters to right of Set Circles button are in pixels.  Area is number of pixels in each circle.

  • Help - shows this file.
  • Note - opens the text window for taking notes.
  • Data Cube - sets spectral image for deriving spectra.
  • Sum Image - displays sum image for whole cube.
  • Plot Spectrum - plots EMSA spectrum file, which Save Spectrum recorded.
  • Rectangle On / Off - shows / hides the array of circles on the front image, eg. the spectral image or the sum image.
  • Set Circles - set number of rows & number in each row, and diameter.
  • Label Circles - temporarily displays circle indices on the image.  Indices are used in info file and spectrum file names.
  • Make Mask - makes image showing where circles are.  Overlay with sum image to see exact pixel locations for spectra.
  • Save Spectra - saves sum or max spectra from each circle in a MSA format text file.  Also writes the AOC-info file.


Green circles are handles to position the array.

Yellow circles show where spectra are taken.



You specify the size of the circles (in pixels), the number of circles in each row and the number of rows.  You then adjust the position and tilt of the array with the center and right green handle, respectively.  The horizontal and vertical circle spacings (of the untilted array) are the same, so the width of the rectangle follows the length as you change it with the right handle.  In other words, the over-all aspect ratio of the rectangle is set by the number of rows and the number of circles in each row.


How to Use

  • Open Array of Circles Tool  (AOC)
  • Open your data cube.  Click on Data Cube button.
  • Lispix generates data from the Data Cube, but displays the array of circles either on the cube itself, or on an image which you derive from the cube.  Derived images, such as a sum or max image, may make positioning the array easier.   The Sum Image Button in this tool is a shortcut of Image / Sum Image of Whole Cube in the Data Cube Tool..  You can also make a sum image or other derived images with the Image Button in the Data Cube Tool.
  • Click on Rectangle On Button.  Rectangle (array of circles) appears on image or on cube.
  • Adjust circle diameter and number as necessary, using the Set Circles button.
    • Diameter -  Set the diameter of the circles, in pixels.  Circles can overlap.
    • Number - Set the number of circles in each row (n) and the number of rows (m).  Displayed to right of Set Circles Buttons as Number: n x m.
    • Load From File - If spectra have been saved previously with the Save Spectra Button, Lispix will have made an AOC-info.txt file in the same folder with the spectra.  Selecting this file restores the positions and size of the circles to those when the spectra were saved.
  • Adjust array of circles with the two circular green handles by moving (clicking on and dragging) either circle.  Moving the green handle in the center moves the array without changing its size or orientation.  Moving the green handle on the right changes the size and orientation of the array.  Notes:  The aspect ration of the rectangle is controlled by n and m in Number, above.  Circles can be partially or entirely out of the image boundaries.
  • Save Spectra makes a folder in the same folder as your spectral image named "max spectra" or "sum spectra" and the date and time.  The folder contains the AOC-info file and the MSA formatted spectra for each circle.  The info file lists the spectrum files with summary data.  Spectra are labeled with their (n m) indices, which are in their file name, in the spectrum list in the info file, and are shown with the Label Circles Button.
  • Plot Spectrum plots a spectrum saved as an EMSA Standard ASCII (text) file.  This is a shortcut of Plots / Plot EMSA Spectrum in the Lispix Menu Bar.


Note - Lispix does not check that the derived image actually came from or corresponds to the data cube.  It's up to you to do that.