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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.
- 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
- 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.
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.
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:
- the distance along the line in pixels, ie. the abscissa of the clicked
position in the window. (323.0)
- the relative intensity of that pixel, ie. the ordinate of the plot
- as seen (146.0)
- 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).
Notes: ------ top
- The color of the outline of the scanned area of the image is controlled
by the mouse_draw_color parameter: Parameters button.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
The Profiles... button gives
this popup menu: top
- 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
- 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.
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.