% ALEX (Matlab SFM Image Processing Toolbox) 
%
% Beta version
%
% Start and Quit
%   alex             - M FILE TO START ALEX
%   alexlogo         - Display the Alex logo image
%   exitalex         - Quit Alex
%   load_setup       - M file to load some global variables
%   save_setup       - M file to save some global variables
%
% Image input/output
%   flipbytes        - Flip the 2 bytes integer (PC/Unix conversion)
%   load_image       - Load an image file with a specified format
%   nano2read        - Read the header and the image from a nanoscope 2 file
%   nano2write       - Write the header and the image to a nanoscope 2 file
%   nano3read        - Read the header and the image from a nanoscope file
%   nano3write       - Write the header and the image to a nanoscope file
%   readBMP          - Import a Microsoft Windows Bitmap file
%   readGIF          - Import a gif file
%   readMATLAB       - Import a Matlab image file
%   readPCX          - Import a pcx file
%   readSPIDER       - Import a SPIDER file
%   readTIFF         - Import a tiff file
%   save_image       - Save the image in the file FullFname
%   spiread          - Read the image from Spider format
%   spiwrite         - Write the image in the Spider format
%   writeASCII       - Write the image in a ascii file
%   writeBMP         - Write the image in a bit map file
%   writeGIF         - Write the image in a gif file format
%   writeMATLAB      - Save the image in MATLAB file formart
%   writeNANO2       - Write the image in a nano2 file format
%   writePCX         - Write the image in a pcx file format
%   writeSPIDER      - Write the image in a spider file format
%   writeTIFF        - Write the image in a tiff file format
%
% Image display
%   cbar             - Inizialize the menu bar
%   closeimage       - Close the actual image
%   clearzrange      - Clear the Z range controls
%   cmaps            - Allows to load, save and modify the 30 colormaps
%   createimgax      - Create the image axes
%   fillc            - Fill the image contours
%   fullscreen       - Set the window size to the screen size
%   getcontrast      - Return the value of the actua contrast setting
%   getmap           - Get the image colormap number
%   getoffset        - Return the value of the actual offset setting
%   getviewmode      - Return the current view mode
%   getzoom          - Get the actual zoom
%   getzoomstatus    - Get the zoom status for the current figure
% * icol             - External program to modify the colormap
%   imagenote        - Set the note edit uicontrol
%   imagetitle       - Set the image title
%   isimage          - Check if the image axes exist
%   lineplot_buttons - Inizialize the uicontrols for the line plot
%   makecolorbar     - Display color bar (color scale)
%   mapcontrast      - Contrast the colormap
%   mapoffset        - Move the colormap offset
%   meshc_buttons    - Inizialize the surface uicontrols
%   scaleimage       - Scale the image to a specified z-range
%   screencenter     - Return the coordinates of the screen center in pixels
%   screensize       - Return the size of the screen in pixels
%   setcontrast      - Set the contrast panel and slider to the specified value
%   setimage         - Set and display the global variable I
%   setmap           - Set the image colormap
%   setoffset        - Set the   offset panel and slider to the specified value
%   setviewmode      - Set the view mode
%   setzoomstatus    - Set the zoom status for the current figure
%   showimage        - displays the image in the mode set in the Views menu
%   snapshot         - Set the figure for a picture
%   viewer           - Tool to modify 3D views orientation
%   zrange           - Return or define the image zrange
%
% Cut/Paste and Clipboard
%   copyimage        - Copy a specified position area defined with the mouse
%   cutimage         - Cut a specified position area defined with the mouse
%   getclipboard     - Get the Clipboard
%   pasteimage       - Paste the CutPaste variable in the specified position
%   setclipboard     - Store the passed argument in the clipboard
%   undo             - Revert the last command
%
% Image Transformation
%   doflatten        - Flat an image
%   flatten_buttons  - Start the flatten uicontrols
%   getview          - Returns the image submatrix on the current view
%   image_binary     - Trasform the image in binary mode
%   image_blur       - Compute the Blur filter of the current image
%   image_dilate     - Dilate the current binary image
%   image_edge       - Find the edges of the image
%   image_emboss     - Emboss the actual image
%   image_erode      - Erode the current binary image
%   image_flip       - Flip the actual image
%   image_gray       - Trasform the image in grayscale (scale 0<I<1)
%   image_invert     - Invert the actual image
%   image_median     - Compute the median filter of the current image
%   image_morph      - Morfological operations on binary images
%   image_perim      - Find the perimeter of the image
%   image_recon      - preform the image/tip reconstruction
%   image_resize     - resizes the current view to be the current image
%   image_rotate     - Rotates the image
%   image_snoise     - Add salt noise to the image
%   image_wiener     - Compute the Wiener filter of the current image
%   image_wnoise     - Add white noise to the image
%   maketip          - Make the tip matrix from a profile
%   mexconvol        - Mex file for the image/tip convolution
%   mexrecon         - Mex file for the image/tip reconstruction
%
% Image Analysis
%   countmolecules   - Counts the molecules clicked by the user
%   display_header   - Display the Image Header parameters
%   findcoords       - Returns rows of Coords with the specified identifier
%   image_contour    - Analyze the Image contours
%   imagehist        - Display the image Histogram
%   image_stat       - Computes and display some Image statistic values
%   langle           - Determines angles of a line
%   llength          - Length of a line
%   measure          - Get the coordinates of the clicked pixels
%   profile          - Analyze the image profile
%
% Header Parameters
%   getparameter     - Return the value of a specified header parameter
%   scansize         - Return the image scan size
%   setparameter     - Set the value of a specified header parameter
%   xoffset          - Return the image X offset
%   yoffset          - Return the image Y offset
%
% Get/Set Options
%   asknumber        - Ask to input a number in the rigth corner of the figure
%   definergb        - User Graphical Interface to define any RGB color
%   getfillcolor     - Return the current filling color
%   getfont          - Return the current font
%   getfontsize      - Return the current fontsize
%   getfontstyle     - Return the current fontstyle
%   getlinestyle     - Return the current line style
%   getlinewidth     - Return the current line width
%   getpencolor      - Return the current pen color
%   preferences      - Set the ALEX preferences
%   setaxcolor       - Set the image axes background color
%   setbarscale      - Set the colorbar scale
%   setfigcolor      - Set the window background color
%   setimagescale    - Set the image x axis scale
%   setoption        - Set the SelOBj (selected object) properties
%   swd              - User Graphical Interface to define default directories
%
% Conversion
%   height2ind       - Convert the height values in nm into image data
%   ind2height       - Convert the image data into heigth values in nm
%   ind2nm           - Converts the matrix indexes into coordinates (nm)
%   nm2ind           - Converts the matrix indexes into coordinates (nm)
%   onoff            - Switch between on->1, 1->on; off->0, 0->off
%   pix2axes         - Convert pixel units in the axes scale units
%   sec2time         - Converts the seconds in hours, min, sec
%   time             - Returns a string containing the time in hh:mm:ss format
%   time2sec         - Converts the time in seconds
%
% Uimenu and Uicontrols
%   alexmenu         - Initializes the ALEX menubar
%   amenu            - Turn on the menu bar
%   buttonframe      - Inizialize the buttonframe box
%   checkuncheck     - Check or uncheck a menu item
%   clearobject      - Clear the objects inside the rect
%   closebuttons     - Eval the Done button callback and deletes the
%   finduicontrols   - Find all the uicontrols in the figure
%   finduimenu       - Find all the uimenu in the figure
%   initbuttons      - Inizialize the uicontrol in the control frame
%   ischildren       - Check if an object exists
% * isobj            - True for objects
%   setalexmenu      - Enable/Disable the menu items
%   setuicontrols    - Turn on/off the uicontrols
%   setuimenu        - Turn on/off the menubar
%   showmenubotton   - Show a button to reactivate the menubar
%
% Dialog Boxes
%   alexdlg          - Open a dialog box
%   alexerror        - Open an error dialog box
%   alexhelp         - Display an help file in a scrolling text window
%   clearstatusbar   - Clear the message in the statusbar
%   display_text     - Display a scrolling text window
%   edit_mfile       - Display an Mfile in a scrolling text window
%   message          - Display a message box
% * pgsetup          - Open the printer setup window
%   progressbar      - Display wait bar in the statusbar
% * scrledit         - Multiline edit uicontrol with scroll bar
%   sendmail         - Send comments via e-mail to the alex group
%   statusbar        - Display a message in the statusbar
%
% Miscellaneus
%   backup           - Makes a backup of the files *  , *.c, *  exsg *  at
%   edit             - Call the selected editor to edit the file
%   editstr2value    - Set the value of an edit obj to its str2num (string)
%   getfile          - Retrieve the filelist and the pathname
% * readstr          - Read a text file
%   writestr         - Write a string to a text file
%
% See readme.txt for more information.
%

% * functions written by other people. See README for more detailes.
% Copyright (c) 1995 by Claudio Rivetti and Mark Young
% claudio@alice.uoregon.edu,    mark@alice.uoregon.edu