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
- 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
- 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
- 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
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.