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This utility is for displaying intensity profiles along a straight line. This utility plots intensity profiles using values in the original image arrays. The plots are not affected by scaling, false coloring, etc. There is an option for averaged line profiles, that is where pixels are averaged along a line (usually) perpendicular to the scan line or line profile direction.

Profiles can be plotted (either single pixel or averaged) in the 3rd dimension when using stacks.

Popup menu Summary of commands.

Summary details

• Profiles Menu
• First, mouse a straight line on the image.
  • Then, if desired, mouse across the line to set the width.
  • If desired, the end points and the width can be adjusted with the mouse.
  • If the end point is outside the image, it will be moved to the closest point on the edge of the image.
  • If parts of the rectangle ('fat line' or averaged mode) are outside of the image, only appropriate points along the 'averaging perpendicular' that are inside the image will be used. In other words, fewer pixels will be in the average for these cases, which are near the end of the main line. The effect is usually not noticable.
  • When done, close the message bar. The line (or rectangle) is now fixed. It can be adjusted via the scan_line parameter, using the Parameters button
• Select the images for the plots.
• The plot window can be resized. If it is clicked on, the y value will appear in the window, and the location of the clicked point will be shown in the image.
• The plot can be rescaled using other menues in the Profile... button. (These menus will be moved to the title bar of the profile plot window, to be more like other plot windows. 6/97 DSB)

Profile plot annotation

When the profile plot is clicked on, annotation like this appears in the lower left of the plot. There are three lines of annotation: x coordinte: y value pixel location in image, value profile line length and width

There are three lines in the annotation of a profile plot, which changes when the plot is clicked on.

The first line shows the (x,y) coordinates of the plot for the clicked point- that is, the x location for the click is shown, along with the corresponding y values that are in the plot.

The second line shows the pixel coordinates and value for the image corresponding to the clicked point. Note that when the line is 'fat', that is, when averaging is performed, then this value (that for the single pixel right on the line) will be different from the above plot value (which has been averaged).

The third line just shows the height and width of the rectangle representing the line profile location in the image. The length corresponds to the number of points in the profile, and the width the number of pixels (along a line perpendicular to the profile line) that were averaged for each point.

Details Summary

To mouse the line - click and hold down the mouse on one end of the line in the window desired. The window need not be the front window - it will become the front window when you click on it. While holding the mouse down, move the cursor to the other end of the line. You will see the message bar at the top of the image, and the rubber band line while you are doing this. When you let up on the cursor, a new message appears indicating that the line can be adjusted by moving the end points and by changing its width. The width is initially one pixel, and is changed by wiping the mouse across the scan line. Adjust the width by mousing either edge of the resulting rectangle. Close the message bar to proceed to select the images to be profiled, and to plot the results.

Selecting Images - Images are selected as usual - the images to choose from have the same dimensions as the image on which the line is being 'moused'. This image may be zoomed at the time - the dimensions refer to the image data (image array), not the window size. The selected images need not be shown.

Examples top

This is an image of part of a disk with noise added.

The yellow line shows the locations (along a one pixel line) for the values which are plotted below:

This plot shows the default, with ymin = 0.

The object is barely visible - it has been enhanced as much as practical for display. The step in average across the boundary is not visible in the above plot, but can be seen if the data are averaged. This next figures show the same horizontal line in the center of a rectangle that indicates the area of the image used in the averaging process:

This is the message bar that appeared over the image below while the line was being adjusted.

For each point along the yellow central horizontal line, 284 pixels were averaged along the vertical line through the point. (If the initial line were not horizontal, the line for the pixel averages would be perpendicular to the initial line.)

The averaged plot looks like this:

where the transition is easily seen. The scale has been expanded by using the ymin=min for the proile.

The numbers at the top give the range for the data in the plot.

The blue numbers at the bottom give information about the last point clicked in the plot window:

1. the distance along the line in pixels, ie. the abscissa of the clicked position in the window. (323.0)
2. the relative intensity of that pixel, ie. the ordinate of the plot - as seen (146.0)
3. the absolute or real intensity of the pixel. (10056)

The black numbers across the bottom give the length and width of the yellow rectangle in the previous image. The title bar of the plot window gives the coordinates of the end point of the line, and the width of the rectangle (not shown here).

1. The color of the outline of the scanned area of the image is controlled by the mouse_draw_color parameter: Parameters button.
2. The progress of the calculation is shown by drawing (temporarily) on the window. Note that the direction of the data averaging follows the direction that the line was originally 'moused'. If you 'mouse' the original line from right to left, for example, then the plot will be backwards.
3. The line will remain in the image window until another profile is drawn. To get rid of the line, use the clear button when the window with the line is in the front.
4. If the end points are adjusted AFTER the thickness is set, the direction of averaging remains fixed so that the rectangle becomes a parallogram. If one wants the averaging direction to be perpendicular to the scan line, just adjust the thickness by a small amount, and the parallelogram will snap into rectangular shape.
5. The plots are scaled 0 - max for each image array as the default. Negative values plot below the x axis (they are not plotted). The scaling can be changed at any time.
6. The plot window can be resized. If you are planning to resize the plot after capture for inclusion into slides or viewgraphs or papers, best to make the plot the size that you wish before capturing to retain the appearance of the annotation.
7. Click on the plot (only the x-coordinate of the click is used) to see location in the image and print the coordinates in the Listener. Move the plot off of the image and enlarge it if desired, so that locations (such as peaks or valleys) on the line profiles can be clicked, and the circles on the image can be seen at the same time. The printed locations in the listener can, as usual, be cut and pasted into other text windows.
8. Click on the lower right of image to make the small circles disappear. Use the Clear... graphics button when the image is the front window to make the line disappear.

Doit: Mouse a line. Mouse the line width if desired. Choose images for plotting the results. Re-Doit: Select images. Plot the intensity profile for the selected images using the existing line - which has been 'moused' with the Doit button. Show Line: Show the position of the line in the front image window. Can be erased or cleared using the Clear... button (graphics option). Print data: Prints the y values of the intensity profiles to the Listener or Monitor window, from whence they can be cut and pasted to a text file or directly to the spreadsheet of a plotting program such as Kalidagraph (change the collumn format from text to float. Close Closes some/all of the profile plots. Scaling Options for the minimum value of the y-axis (ymin). Ymin 0: ymin=0, the default. Ymin each line: each profile is plotted using its own minimum as ymin. This expands each plot by the maximum amount (if the ymax each line option, again the default, is used.) Ymin global: the minimum of the minima for all of the profiles. Ymin fixed: user input of ymin. Options for the maximum value of the y-axis (ymax). Ymax each line: the default. Ymax global: the maximum of the maxima of all the profiles. Ymax fixed: user input of ymax.