Roi Application

• Invocation
• Roi Application Window
• Control Panel
• List Output Window
• Slice Image Window

Invocation

java RoiApp [ <plist file> [ROI image file] ]

Roi Application Window

• Plist file
  Enter the full pathname of the plist file (CCN lab nisroi.c format) or select it thru the browse button. You may leave this field blank and just enter the ROI image filename in the ROI Image file field; RoiApp will automatically replace a .img extension with a .plist extension to get the plist filename. All files must be uncompressed.
• ROI Image file
  Enter the full pathname of the ROI image file (ANALYZE format) or select it thru the browse button. You may leave this field blank and just enter the plist filename in the plist field; RoiApp will automatically replace a .plist extension with a .img extension to get the image filename. All files must be uncompressed.
• Run
  Hit run to bring up the ROI viewing windows (Control Panel, Image window, Output window).
• Cancel
  Cancel will kill the entire application.
• Help
  Help will start up netscape on whatever machine you are running the application on, with the html help document for Roi Application. All CCN lab java help documents are also available at a kraeplin java doc site.

Control Panel

• ROI
  When you click on a pixel that is part of a ROI, the ROI number will be displayed in this box. You may enter a ROI number in this box, and hit return, to select a ROI as if you had clicked on it. Entering 0 will clear any ROI selection.
• (x,y,z)
  When you click (any mouse button) in a slice image, this box will display the (x,y,z) coordinates of the location you clicked. The upper left pixel of the first slice is location (0,0,0).
• Brighten
  The original colormapping is a linear mapping of disk values to a grayscale in the range of 0-255. Use brighten to scale the mapping such that high disk values are all set to 255 and lower disk values get better grayscale range.
• Darken
  The original colormapping is a linear mapping of disk values to a grayscale in the range of 0-255. Use darken to scale the mapping such that low disk values are all set to 0 and higher disk values get better grayscale range.
• List
  Select one of the three choices to display in the List Output Window:
  • A summary description of all ROI in this image.
  • A summary description of the selected ROI.
  • A listing of each pixel in the selected ROI (disk # followed by (x,y,z) location.)
• Timeseries
  Selecting a timeseries viewer will pop up an interactive graph that displays ROI/pixel values over time. Once one or more interactive graphs are up, clicking on an ROI with the middle mouse button will cause timeseries data for that ROI/pixel to be added to the graphs. Two timeseries formats are allowed:
  • nis
    Timeseries data for the average value of an ROI. Enter the name of a CCN lab ascii "time-series" file. The values in the AVERAGE column of this file will be plotted. Note: Because these are ascii files, and the data is not in time order, there may be a several second delay in plotting these timeseries.
  • pgh1
    Binary per-pixel timeseries data. Enter the name of a pgh1.0 txyz int16 file. Use the java Permute program to generate this data from a directory of ANALYZE image files. Clicking on a pixel in an ROI will plot the timeseries data for that pixel.
• Quit
  Kill the RoiWindow.

List Output Window

Slice Image Window

• Menubar
• Toolbar
• Output window