7#,V+o@    """*Lv(x 0( H* ^m*B ABOUT THE IMAGE PROGRAMS There are several image programs contained in this CD. The two programs that are used in the exercises are NIH Image and MacSigma0. Documentation for these has been included. Additional public domain programs have been included for possible use in applications that the teacher may design (such as converting images from PC format to Macintosh format). The basic requirements to run the programs are a Macintosh computer that will support an eight bit color monitor and that has at least 4 megabytes of RAM. The following instructions presuppose basic knowledge of Macintosh functions, such as copying, scrolling, and opening programs. Although these programs will work with System 6, we have assumed in writing the instructions and the Lesson Guides that System 7 will be available for most computers.(If you are uncertain of what System you are running, click and hold on the Apple  at the top left of the Menu bar. The first line should read: About this Mac. If this does not appear, you are running System 6.) These instructions are meant only to get you started on the programs.The best way to go through them is with a computer and the CD readily to hand. Complete instructions are included in the documentation files in the Software directory. NIH Image NIH Image was developed by the National Institutes of Health to allow scientists to study medical and biological systems. It has since been adopted for other scientific applications, such as in the Planetary Data Systems CD series. Many of its features are quite specialized but many are similar to standard Macintosh paint programs. 1. Getting started. We suggest that you copy NIH Image and MacSigma0 to the hard disks of all computers that will be used with the Modules. You will notice that when you copy the programs, NIH Image assumes the name Image whereas MacSigma0 retains its name. You will also notice that NIH Image has two versions - Image 1.51 and Image 1.51(nonFPU). If Image 1.51 will run on your computer, it will be faster. Many computers, however, will need to use the nonFPU version. This will work more than adequately for almost all applications. You can find out quickly which version to use by opening Image 1.51 and then attempting to open TestImag.pic (located in Module01 Images). If it does not run, then you will need to run Image 1.51non FPU. The Lesson Guides presuppose that you have followed the next instructions. We have designed them to make it as easy as possible for you and your students to locate the programs and the images that will be used. You should make an alias of the two principal programs and place the aliases on the desktop (System 7 only). This helps students locate the programs immediately and it also helps keep them from inadvertently crashing the system by poking around looking for the programs. You will notice that the Image icon is a microscope and the MacSigma0 icon looks a bit like a happy snail. To make an alias: Click on the name or icon of the program; Go to the Menu Bar; Click on File; Drag the mouse to Make Alias and click. The alias will appear directly adjacent to the icon for the original file. Drag the alias to the desktop. When you double-click on the alias it will open the original file. 2. Opening an image. You also need to place a folder on the desk top labeled Today's Images and copy the images for any module into that folder. To make a folder: File: New Folder. A new folder will appear labeled "untitled folder". Drag this to the desktop. Click once on its name and wait. A box will eventually appear around it. Type the name Today's Images in the box. Copy the images in the Module01 folder Images (Documents:Module01.txt:Image) into the folder Today's Images. Double click on the folder . You should see several image icons. Double click on the icon GalOptic.pic. This will open both the Image program and the image of earth taken from Galileo. To open a second image File:Open. You will be presented with a window which shows several images. Open as many as the memory can handle. Close them by clicking in the box in the upper left hand corner or by going to File:Close. 3. Image too Large for Screen. Image and screen sizes vary. Some images may be too large to fit on the available screen. In this case, you have two options: a) You can shrink the image by going to the Menu bar: Options: Scale to Fit Window. Or you may click once in the small box at the top right of the title bar (the bar that says GalOptic.pic). b) You may prefer to keep the image the same size and move it around on the screen. To do this, go to Tools (on the left hand side of the screen). Click the mouse on  (second icon down on the left). Now bring the mouse to the center of the screen, click and hold it, and drag it up and to the left. The image should move with it.   4. Enhancing an image Open TestImag.pic NIH Image displays images as 256 shades of gray or as 256 colors. In either case, each shade or color has its own digital number (DN). Go to the Look Up Table or LUT (left side of screen) and bring the cursor from the bottom of the LUT to the top. Look at the Values window as you do this. (If it is hidden, you may bring it up by clicking on Windows:Values.) You should see the DNs next to the word Values vary from 0 to 255 as you move the cursor up and down the table. Move your cursor around TestImag.pic. This is an image of an area of tropical rain forest in Belize, Central America. Notice that the DNs are very high in the dark portions and they come close to zero in the very light portions. Notice also that the Values window also shows the X and Y coordinates of the tip of the cursor (or the center of the crossbar). This allows you to reference a particular pixel in the image. Often it is the case that most of the gray shades have DN values bunched together and it is difficult to see much contrast. To see how heavily the pixel values are clustered you may go to Analyze: Show Histogram. You will see a histogram showing the number of pixels that have the DNs from 0 to 255, as below:  Now run the cursor along the base of the histogram and look at the Values window. Notice how the values are clustered between DNs 167 and 187. You will often want to improve the amount of contrast on your images by spreading out the DN values. You may do this in several ways. Go to Tools and double click on the rectangular selection tool  (top right). This selects the entire image (you should see "ants" marching around the outside of the image.) Now go to Enhance: Enhance Contrast. This will change the contrast just a little. Try Enhance: Equalize. Is there a more dramatic change? Now click on the image. The ants should disappear. Then, go to Enhance:Apply LUT. Try Analyze:Show Histogram again. Notice how the histogram has changed. Image spreads out the number of pixels allocated to each gray value to make an image easier to read. You may experiment with enhancing contrast by doing several things. Draw out a box (click and hold the mouse as you move down and to the right) in an area where you would like to see more contrast. Look at the histogram before and after you Apply LUT. You may also move the graphic tools around by fooling with the Map at bottom left. 5. Getting back to an original image. Often you will find that you or your student has made undesired changes in an image. You will be happy to know that you will never change the original as stored in the CD. Usually, however, you can recover the original image by going to: File:Revert to Saved. If this does not work, get it from the CD. 6. Finding images to open. Occasionally, you will be in the Image program and you will need to move from one folder to another. For example, you may be in the NIH Image folder and need to get a desktop folder or to the CD. Go to File:Open and this box will come up on the screen:  Notice that there are no choices shown in the window. To find your way to folders which will offer you choices, you should bring the cursor to the arrow next to the the words NIH Image, and click and hold. A menu will pop down. Continue to hold while pulling down to the desired folder, such as Today's Images (or you may click on the Desktop icon next to the window). You should see a selection of folders. Continue to open them (double click) until you reach the folder and image you wish. You may have as many images open as you have available memory. An efficient way of viewing several images is to go to Windows:Tile Windows or Stack Windows. TIFF and PICT. These are the two file formats that are opened directly by the command Open as used in NIH Image. Many other sorts of images can be opened as well, by using the command Import, as you will see later in Module 3 activities. 7. Enlarging an image. Bring up an image, go to Tools, and click on the magnifying glass . Now bring the cursor to a section of the image that you would like to enlarge. Click on that section. You can see the image has enlarged. If you click several times, you will note that the image gets larger and larger until you reach the limit of its resolution. Notice that the pixel itself enlarges. Move the mouse around and verify that the DN remains the same for the entire pixel as it is enlarged. Returning to the original size. Hold down the Option key on the keyboard as you click in the window or double click on . Deselecting the magnifying glass. Click on another tool icon to get out of the magnifying glass mode. 8 Changing from grayscale to color Bring up TestImag.pic Go to Options: Color Tables. Move the cursor to the right and click on Fire 1. Then try the other available selections. Select a pixel and check its DN as you go from one Color Table to another. Now bring up earthgal.pic. Go to Options:Grayscale. Now check the other color tables. 9. Saving changes Image will not save changes unless you tell it to do so. If you would like to save an altered version of the image you have been working with, go to File:Save As. A window will pop up that will ask you to give the file a name and will give you several choices. Name the file and consider where you wish to save. it. You may wish to establish a Desktop folder named Saved Images for students to put their work into. (Click on Desktop on the left of the Image window. Click on Saved Images. Then click on Open. Finally Click on Save.) Closing images and exiting the program. File: Close and File:Quit. If you have forgotton to save your changes, Image will give you a prompt. You will discover many features to NIH image as you go along. We urge you to read the documentation (About Image) and to explore the features. If you encounter problems with memory, be sure to read the next section as well as the section in the documentaion on memory thoroughly. Memory management in NIH IMAGE Image processing, by its nature, is very memory intensive. Sooner or later you will get a message that memory is low. You will get this message for one of two reasons: there is a problem with "External Memory" or a problem with "Internal Memory". Dealing with these problems can be extremely frustrating. What follows is first a description of what the various memory terms mean and steps to follow in setting the memory and trouble shooting the problems. Then we will address some common memory messages and give some steps. 1) External Memory We use this term to refer to the amount of memory that the program occupies on your computer when it is open. Typically, when you have a problem with this you will receive the following sort of Memory Message:  Since images tend to be very large, programs that work with them often need to occupy lots of memory. If you have a problem with external memory, you will need to make more memory available to the program or you will need to reduce the amount of memory the program needs. Ideally, you should have at least three times as much memory available for Image as the size of the largest image you will use. However, you can run the program with substantially less. There are a number of steps you should follow. a) Sometimes there is a simple solution. You may have several other programs open. Close everything that is open but Image. ( You can find out what else is running by clicking and holding on the icon at the top right of your screen., next to the question mark). b) Sometimes, due to the fact that memory can be "split" by previous applications, you will need to close everything, restart the computer, and then open Image. b) You may still have a problem because your computer does not have enough RAM. You can find out how much memory Image is currently using by closing the program, highlighting the Image icon, and going to: File: Get Info. (If you have clicked on the Alias, you must now click on Find Original and then on File:Get Info again.) You will see two boxes at the bottom: Suggested Size: 2500K Current Size: 2500K * * This is called Preferred Size in Image 1.51NonFPU You may change the size of the memory the program requires by changing the number in the Current Size box. You may change this number up or down, according to your needs. Be sure to hit the Return button on your keyboard after you have typed in the new number! 2) Internal Memory You will occasionally receive the following message:  We are referring to the Clipboard and Undo buffers when we refer to Internal Memory. Image processing programs have many tools with which you can change the appearance of images that are being displayed. NIH Image keeps a copy of the original image in a buffer within the program, in order to provide you the opportunity to Undo any changes you make. It also keeps space to put items into the Clipboard for standard Copy and Paste operations. If your buffers are too small, you may be unable to complete an operation or, after completing the operation, you may be unable to return to the original image. On the other hand, if you have set the buffers too large, you may receive threatening messages when you open the program. In general, you may ignore the latter. To set the Internal Memory, do the following. After opening Image you should go to Options: Preferences. Then go to Undo & Clipboard buffer, double click in the box, and change the number. Recall that ideally your buffer should be at least the size of the largest image you are working with (but seee below about PICT images). If you are low on RAM, you will not be able to get that high but you will increase what you are able to do by increasing the size of the buffers as much as you can. Then go to File: Record Preferences and quit Image (you must quit Image in order for the changes to take effect). Increasing the Internal Memory changes the External Memory requirements. Thus, you should consider whether you will need to increase the Current Memory to get rid of those annoying message boxes. Now, open up the program again. You should now be able to display most images. 3) Typical problems a) The program won't open. Try: i) Closing all other applications ii) Closing all applications and restarting the computer iii) Reducing Current Memory iv) Running Virtual Memory (Check your System Manual or Control Panels:Memory) for this. If you are able to run virtual memory it will slow your computer considerably but it will allow you to do some things you would not otherwise be able to do. b) You get messages that your Undo&Clipboard Buffers are too small. You increase their size and you get messages saying "Can't Allocate the Undo & Clipboard Buffers". This will not be a problem if you only wish to look at an image. If you wish to process it you need to increase the size of the Current Memory. c) You changed the size of the Current Memory and it hasn't had any effect. Did you hit Return after you typed in the size change? If so, try increasing it again. d) You open a few images and then run out of memory. Quit Image and increase the Current Memory. e) You attempt to use one of the Tools and nothing happens. You need to increase the size of the buffers. f) The memory seems to have been set right. Then you attempt to open a PICT image that should be 300K in size and you can't open it. PICT images are compressed - that is , they occupy less space when stored on your disk than they do when opened up and displayed In fact, they can occupy as much as 16 times as much memory when they are opened up. if you are having a problem with them, you need to increase the Current Memory. g) Nothing works. Quit the program and go to the beach. MacSigma0 MacSigma0 was developed in order for scientists to be able to easily interact with and display radar images. Two versions of MacSigma0 have been included here, MacSigma0 and Macsigma0_II. The former is used for computers without a coprocessor and the latter is for computers with a coprocessor. Computers without a coprocessor will be very slow with large images, but otherwise both programs will serve you about equally well. It is possible to take images from MacSigma0 to NIH Image. Procedures to do that will be developed in Module 2 and need not concern you here. 1. DIsplaying an Image Go to File:Open. You will see that four typesof images may be displayed (opened) in MacSigma0. These are:  Open Compressed Stokes - images from the US Space Imaging Radar program Byte - images whose size must be specified to the computer in order to be opened properly. (J)-ERS-1 lo res - low resolution images from the Japanese and European Space Imaging Radar programs. Magellan MIDR format - images from the Magellan satellite's flights over Venus The images on the SIR-CED CD are in Compressed Stokes files and are identified as Filename.stk. Double click on Open compressed Stokes. A list of files will come up. Open TestImag.stk. Notice that a menu of choices appears. The meaning of these choices is explained in Module 2. Just now, choose HH and click OK. You will now be presented with a histogram. Click OK. You will recognize the image that comes up on the screen as similar to TestImag.pic. It is the same image of Belize but displayed in a different format. Bring the mouse to the small box at the bottom right of the window. Click and hold the mouse and draw the box down and to the right. The size of the window that comes up in MacSigma0 is always the same, regardless of image size. It is frequently necessary to draw out the box in order to see the entire image. You may also accomplish this by clicking in the box at the top right. Place the cursor on a dark portion and look at the bottom left of the image. You will see numbers representing the X and Y coordinates as well as a number representing the radar backscatter value or so. These numbers tell you your location in the image and how reflective the surface was to the radar. A large negative so indicates very low reflectivity and appears as quite dark whereas a number close to zero indicates very high reflectivity and will be quite light. so in the program MacSigma0 is similar to gray scale value in NIH Image. The so values are used by scientists who analyze radar images. Move the cursor to a very dark area, such as at 100, 260 and look at the so value. Compare this to the reading at 184, 31. Close the file (File:Close) and then open it again. Again select HH and the histogram will appear. This time, however, move the tip of the cursor to the gray bar underneath the histogram:  Click and hold the cursor while moving it to the left, until it is located about one half to two thirds of the way from the left of the bar. Click OK. Notice how much more contrast is evident in this image. Moving the cursor under the histogram in MacSigma0 is similar to using the Enhance Contrast or Equalize tools in NIH Image. Look again at the two areas you checked before (X,Y coordinates 184,31 and 100,260). Has the value of so changed? Now let's draw out a box around one of those areas. Move the cursor to a location left and above the area you want to study. Click and hold the mouse and move it downward and to the right. You should see a box with "ants" marching around it. Go to Image:Zoom In. Notice that this acts like a magnifying glass. Zoom in several times. You will continue to enlarge the area of interest. Draw out the window (box on bottom right) so that you can still see a lot of the image. After you have zoomed several times, you will notice that the command Image: Display_Sigma 0s becomes darkened. Click on it. You will now see all the so's printed in the boxes. Zoom out now using Image: Normal Size or Image: Zoom Out. You will find that Zoom Out is especially useful for large images - it is the equivalent of Scale to Fit Window in NIH Image. Draw a small box again in a dark area. Go to Statistics: Mean and std dev. This produces a window which gives the mean value of so in the selected box as well as the standard deviation. You will note that this can be saved as text and printed. There are two last utilities that may be of interest to you. One is File:About this data. This tells you the size of the image displayed (lines three and four) and other bits of information. The other is Get Info. You may change memory up or down as needed, using the Get Info window. We believe these instructions should get you up and running. Please be sure to read the user's guide, MacSigma.txt, for further information. 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 440@0@0@0@0@0@0@0@0@0@0@0@0@0@0@0@0@0@0@0@0@0@0@0@0@000@ 0@@@ π (for the MAC) (for the MAC) in the0 folder IMDISP (for the PC) Software in the PC folder on the SIR-CED CD-ROM is designed for use with IBM-compatible computers. The software included in the folder are: IMDISP.EXE - program for display and interaction with images Also included in the PC folder are documentation for the IMDISP program and a help library. Please refer to the file IMDISP.TXT for complete instructions on how to use IMDISP.EXE. Copy the executable file *H!+tw3<OT]f M ^ a f  & 1 ?MUceoq;Gbgz    @   @VS^zQV:;>?CFXZ^kmv*+WZtzesIQ./syOTPb%* 7;< @ @ @E( @ X @x   N<Sv{ ! * T U!!!#!&!!!!""""""""#>#B#N#W#####$ $$4$5%%%%&J&K&M&n&&&&&&' '6'='''''(((!(#(()))***!*%*9*?*A**  @   @L @, @   L****+6+A+, ,,.'.6/ / 0l0q111112223,313n3s33345A5555566669)9/9@9T9b9s:(:,:I:M:j:k:;;;; ;; ;&;;GKG]GwGGHHH(H*H+H-HXHZH`HbHHKLKMKNKKKKL]L^L_LoLyLLLLLM/M0M2MtM~MMN&N'NNOEOUOYOaOkOtOOOPPRR-R=R@RgRhRjRRRRRRSS/ @cL     @` TS/SnSSSST|TUUUGUOUUUUV"0>EFMOXefgwxý̗̰̾*01FHjp͍͊ͦͰ͵;%'DYbhvwz{} @  00    T%!t ` q(:<=¸tk^N>h$ t)h$ t !qh t!h   !0  !0  !0 !0  !0   !0 !0 !0 !0 !0 !0 !D0 =>@ABC.0I7 T V""#%ȷxmbTI>3 !q0  !0  !0  !/0P 0  !0  !0  !0  !0P !0P 0T  @$@9($@$ 0P 0 D.$ h t%&M&(*A*+++,.$/ / 1 2234-4^455øsfYLC:!0H!0H !4 !4 !04 @ !04  !04  !j04!04!04 ! 0  !0 !0 !0  !0  !0  !0  !+0 5558?S?@\@BxBBEEEEEEF6FŷrhbVJAAAAl @A@$ @A@$!0 !0 ! 0  !0  !0  !0  !0  !0  !0H!00H !0H!0H !j0HFFFHfJMdN&N(ORS@T7UXUUUVNf1;·™zuzkaWMCka !0 !0 !0 !0 0 !0 !0 !0 !E0 !0 !o0 !0 !0 !0 !0 !0 ll! 9 0 IMDISP.EXE over to your own computer to install it. With IMDISP.EXE you should be able to open most of the .gif type files contained on the CD-ROM. You will not be able to open Stokes matrix format (AIRSAR) files (which end in .stk), PICT format files, (which end in .pic), or text files (which end in .txt). A commercially available program called PC-CEOS, which is marketed by a company called PCI [Tel: (703) 243 3700 in the USA or (416) 764 0614 in Canada] should be able to read and display the .stk files. The .pic files are duplicates of the .gif files. We recommend that you use the commercially available program Microsoft Word for Windows to read the text (.txt) files. To use the data on the SIR-CED CD-ROM, first be sure that you have copied IMDISP.EXE to your hard drive. If do not have a program to display the .stk format files, don't worry. Just skip those sections in the SIR-CED program which use .stk files or refer to using the program Macsigma0. You will need to be able to read the text files, however. To use the IMDISP program from your hard disk first create a directory to hold the IMDISP files. Use the MS-DOS command "MKDIR \IMDISP" to create a directory to hold the programs. Use the "CHDIR \IMDISP" command to make IMDISP the default directory. Copy the files you want to display from the CD-ROM to your hard disk. You should now be able to run all examples from that directory on your hard disk. IMDISP is invoked by typing "IMDISP". The program will blank the display screen and display a welcome logo, then the prompt "COMMAND:" will appear in the lower left portion of the screen. Type "FILE filename.gif" in response to the COMMAND prompt, followed by "DISPLAY" to display the image contained in the file "filename.gif". Please refer to the documentation in IMDISP.TXT for complete instructions on how to use IMDISP. XV and Reader.bin (for the SUN) Software in the SUN folder on the SIR-CED CD-ROM is designed for use with SUN-Unix computers. The software included in the folder are: XV.SU4 - program for display and interaction with images Reader.bin - program for display and interaction with images Also included in the SUN folder are documentation for XV and Reader.bin in the files XVDOCS.PS and SOFTINFO.TXT. Please refer to the file SOFTINFO.TXT for complete instructions on how to use Reader.bin. Copy the executable file XV.SU4 over to your own computer to install it. With XV you should be able to open most of the .gif type files contained on the CD-ROM. You will not be able to open Stokes matrix format (AIRSAR) files (which end in .stk), PICT format files, (which end in .pic), or text files (which end in .txt). A program called RAVEN which should be able to read and display the .stk files is currently being developed by JPL and the University of Colorado at Boulder, but was not ready for release at the time this CD-ROM was generated. The .pic files are duplicates of the .gif files. We recommend that you use the commercially available program Microsoft Word for Windows to read the text (.txt) files. To use the data on the SIR-CED CD-ROM, first be sure that you have copied XV.SU4 to your hard drive. Rename as XV for convenience. If you do not have a program to display the .stk format files, don't worry. Just skip those sections in the SIR-CED program which use .stk files or refer to using the program Macsigma0. You will need to be able to read the text files, however. To use the XV program first mount the CD using the mount command. Copy the XV.SU4 file to your hard drive. Rename as XV for convenience. Use the cd command to change your working directory to the one containing the XV software. Type XV to run the program. A welcome sign will appear (with a fish) to to show that XV is running. Click the right button on the mouse to bring up the XV Controls window. Select an image of file type "filename.gif" from the CD-ROM for display. Use the Load button to display the filename.gif file of your choice. Please refer to the documentation in XVDOCS.PS for complete instructions on how to use XV. XV (for Indigo) Software in the INDIGO folder on the SIR-CED CD-ROM is designed for use with Indigo computers. The software included in the folder are: XV.IND - program for display and interaction with images Also included in the INDIGO folder documentation for XV in the files README.XV and SOFTINFO.TXT. Please refer to the file README.XV for complete instructions on how to use XV.IND. Copy the executable file XV.IND over to your own computer to install it. With XV you should be able to open most of the .gif type files contained on the CD-ROM. You will not be able to open Stokes matrix format (AIRSAR) files (which end in .stk), PICT format files, (which end in .pic), or text files (which end in .txt). The .pic files are duplicates of the .gif files. We recommend that you use the commercially available program Microsoft Word for Windows to read the text (.txt) files. To use the data on the SIR-CED CD-ROM, first be sure that you have copied XV.IND to your hard drive. Rename as XV for convenience. If you do not have a program to display the .stk format files, don't worry. Just skip those sections in the SIR-CED program which use .stk files or refer to using the program Macsigma0. You will need to be able to read the text files, however. To use the XV program first mount the CD using the mount command. Copy the XV.IND file to your hard drive. Rename as XV for convenience. Use the cd command to change your working directory to the one containing the XV software. Type XV to run the program. A welcome sign will appear (with a fish) to to show that XV is running. Click the right button on the mouse to bring up the XV Controls window. Select an image of file type "filename.gif" from the CD-ROM for display. Use the Load button to display the filename.gif file of your choice. Please refer to the documentation in README.XV for complete instructions on how to use XV. }}(||"#$*_#$,-.249:;<[\di)-R[ *-LTt+1OQw  `QSdeqrs  *CK` .05?@MV[gi  ;@E\bd  `"JNT8WefquyzBFtv   "?DNUW]^cx/0FHTUZy  `+:OPVWY^g$&),X^_tz ,-034Y[]bd  ,-0136OSVZ^{  `',ILOeoq 3<wxy  ~ 6FS[_  ^ %_x   gȾү !0  !0 !0 0!0 !0 !0 !0 !0on for these has been included. explicitly Additional software has been include for the PC, SUN and Indigo computers, which should open all the files on the SIR-CED CD-ROM with names ending in .gif. Excellent documentation for these programs has also been provided. as at least 4 megabytes of RAM. computer operatrolling, and opening programs. 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