Equipoise-Image User Manual
Contents
1. kohoutec for zl 1 to length ql do begin q2 substring ql z1 1 rUserl zl1 ord q2 end UserCode EqpiLoadFile 0 0 0 End This macro will load and run automatically because it contains the autoload and autorun keywords see the online help The key that is used in this macro kohoutec must be the same key used to encrypt the target macro file that the loader will load Note that as in this example the ordinal analogs of the key characters must be stored in the rUser1 array so that the decryption routines in EqPi can access them To use this example do the following 1 Use the Objects gt New Object menu item to create a new object file Give it a name such as MySampleTargetMacros obj You will be asked if you d like to define the objects that are to be used Select Yes Create the objects that the encrypted macros will be manipulating For this example a single ROI object should be defined for the new object file by dragging the ROI icon from the list on the left of the object definition panel to the central area of the panel This object will be given the name RoiA by default and its area is selected for measurement by default You can verify this by examining the results table via the Objects gt Show Obj Results menu item 2 Type or paste the text in the sample above onto the macro card of the object you created Be sure to type the actual key that you used in encrypting the ta2. a 3 x 3 neighborhood centered on the pixel and dividing this by the mean value of the neighborhood The COV is not computed for pixels at the boundary of a image since 10 the 3 x 3 neighborhood extends beyond the image boundary Hence the maximum contrast image generated using LookDeep has a value of 0 for all edge pixels Increased macro symbol space The number of variables symbols that may be allocated in NZH Image and Object Image macro programs is limited to 236 EqPi increases this limit to 1200 This allows EqPi macro programs to use a greater number of global and local variables than was previously possible Please note that EqPi macro programs that use more variables than NIH Image and Object Image permit will not open in NIH Image or Object Image Increased number of static columns Object Image implements user created static columns in the results table that may be populated and manipulated by macro authors through several commands The maximum number of static columns allowed in Object Image is 50 this limit has been increased to 100 in EqPi Please note that macros programs that take advantage of this increased limit in EqPi may exceed the number of static columns that Object Image permits and macro commands that attempt to surpass the Object Image limit will not succeed in Object Image 6 Resources and related information NIH Image homepage http rsb info nih gov nih image the homeland of the whole Jmage fa
3. key A Save dialog will prompt the user to enter a file name for the macro and allow navigation to the location where the file will be created The key will be offered as the default file name Please note that the key text will be needed later to load and use the encrypted macro program file Be sure to note and safeguard the key text if you decide to change the name of the encrypted macro program file at any later time Use of encrypted macro program files can be limited to those who have been given the key text Loading and using encrypted macro files from a text file Encrypted macro program files are loaded using the Equipoise gt Load eqPi macros menu item When this item is selected the user is prompted for a password An Open Save dialog then appears allowing the user to navigate to and open the encrypted macros file A dialog then prompts the user to enter a valid key for the encrypted macros file if a valid key has been entered the macros in the macros file will be loaded and will be listed and available in the EqPi Special menu Loading will be terminated if the user enters an invalid key when prompted and the macros will not be loaded During encrypted macro program loading no text window containing the macro text is opened or visible Note on encrypted file filetypes Encrypted files created by EqPi can be identified by their unique icon which resembles the filmstrip icon used by NIH Image and Object Image Encrypted fi
4. or create your own go back to the loader file and replace the encryption key given there and resave the loader file 6 Now you are ready to use the loader and encrypted macros by double clicking on the sampleLoader obj icon You will be prompted to navigate to the encrypted macros file which will then be loaded Voila The encrypted macros in the file will now appear at the bottom of the Special menu The first user macro listed in the Special menu has the name autoeqpi this macro was autoexecuted when the file containing these macros was loaded Now run either the second or third macro by selecting its name in the Special menu you ll get a message that tells you that everything loaded correctly You can create objects using the tools introduced by Object Image and examine the property values measured for them by examining the results table in the Objects gt Show Results Table menu item To do this open or create an image file then select the object creation tool in the Tools palette on the left of the screen this tool looks like a crosshair with the letters OBJ at its center This will activate an ROI creation tool use this tool to draw a closed curve in the image A dashed red outline will appear on the image don t worry these object outlines do not change the image but exist in a transparent layer that lies over the image Now select the Objects gt Show Results Table menu item which will open a results table
5. window if it is already open when the command is executed with the appropriate parameter values it will remain open The command only disables attempts to open this window To close the object window use the command UserCode EqpiHideObj 0 0 0 The values of the three parameters contained in this command are ignored Note that this command does not prevent the object window from being opened thereafter it only closes it if it is already open In summary UserCode EqpiHideObj 0 0 0 closes the object window but will not keep it from being opened while UserCode EqpiUserMode 1 0 0 keeps the window from being opened but doesn t close it Use UserCode EqpiUserMode 0 1 0 to disable export or UserCode EqpiUserMode 0 1 0 to enable export of the results table 5 Other new features and commands Using the autorun mechanism in EqPi macros The autorun mechanism introduced by Object Image is available in EqPi plain text macros containing this keyword operate as usual However while encrypted macros containing this macro language keyword will load and can be run they will not autorun After testing of a plain text macro has been completed change the autorun keyword to autoeqpi just before encrypting the macro program file this will allow the macro to autorun when it is loaded using the UserCode eqpiloadfile 0 0 0 macro command in a loader macro Note that encry
6. Equipoise Image User Manual version 1 0 1 October 2002 1 Introduction Equipoise Image EqPi is a Macintosh application that adds a number of macro language features to the widely used image processing packages NIH Image and Object Image from which it is derived EqPi can run macro programs written in the MIH Image and Object Image macro languages without change and adds capabilities not available in either of these applications EqPi allows users to run encrypted macros created by others EqPi allows macro authors to create encrypted macros EqPi runs on all versions of Mac OS X in Classic mode as well as on Mac OS 8 6 and all versions of Mac OS 9 It can be freely used and distributed and the source code is available upon request About macro files and file types Macro programs in MH Image and Object Image are stored as source text in text files that are readable by any text or word processor These files may be loaded directly into NIH Image or Object Image for execution or may be opened into a text window for user editing and loading Object Image introduced object files whose names end with the extension obj These files can contain several layers and types of information and tremendously extend the power available to programmers These layers include definitions of objects defined by the user image files associated with a project and macro text on the file s macro card It also implemented a spreadsheet
7. dgeSubt but is used only with rectangular ROIs It weights boundary points using value distance weighting using only the boundary points directly above below to the left and to the right of the point in the ROI UserCode BordRectSubt vall val2 0 BordRectSubt is similar to EdgeSub4OverR since it is used only with rectangular ROIs BordRectSubt weights boundary points using the same weighting formula as EdgeSubt but uses all points on the boundary Boundary points at a distance greater than vall are given a weight of 0 UserCode LinearHoriz 0 0 0 This command ignores the parameter values PlaneSubt subtracts a linear function from each row of a rectangular ROI based on the ROI boundary points at the left and right ends of the ROI row UserCode LinearVert 0 0 0 This command uses the same algorithm as LinearHoriz but acts on vertical columns UserCode EqpiPDP 0 0 0 This command ignores the parameter values It places the average value of all of the points in a column of a rectangular ROI inter the User1 array UserCode EqpiCoordLine 0 0 0 EqpiCoordLine ignores the parameter values It makes a segline ROI using the contents of User1 and User2 as the x and y coordinates of the ROI vertices Projecting extended focus stack slices onto a new slice In image stacks constructed from a series of images acquired at different depths by confocal microscopy it is commo
8. itle bar and in the list of windows in the Windows menu Note that this name does not correspond to any existing file and that if a renamed window is closed or disposed without being saved no file with that name will have been created Also use of the File gt Save menu item will generate an error message and no save operation will be performed In order to save a renamed image window in a file use the File gt Save As menu item Background subtraction EqPi has several specialized background subtraction routines built in with supporting macro commands These include UserCode EdgeSubt vall val2 0 This command takes two real number parameters vall and val2 the third parameter value is ignored EdgeSubt performs a background subtraction on an ROI region At any point in the ROI the background value to be subtracted is computed from the weighted average of all of the points on the ROI s boundary The weight of each boundary point is computed as value of the boundary point weight of boundary point val2 square of distance to the ROI point Because a calculation using every point on the boundary must be done at each point within the ROI it is very computationally intensive This background subtraction method is very effective in reducing the impact of noise and is locally adaptive to backgrounds that may vary over an image UserCode EdgeSub40OverR vall val2 0 EdgeSub4OverkR is similar to E
9. lain text loader macro on the macro card of the loader obj file The obj definitions are also defined in the loader obj file The encrypted macros are contained in a separate encrypted macro target file While sounding complex this mechanism is quite simple in practice double click on a loader obj file icon and use the Open Save dialog that opens to navigate to the encrypted macro program file The loader mechanism makes use of a new macro language command introduced in EqPi This command uses the following syntax UserCode EqpiLoadFile 0 0 0 Whenever this command is encountered in a macro an Open Save dialog for loading encrypted macro program files is invoked This command is similar to the Equipoise gt Load EqPi macros menu item except that the user is not prompted for a key Instead the loader program must contain the key and code that prepares it The values of the three parameters contained in this command are ignored 3 Tutorial example NB The files discussed in the tutorial can be created during this tutorial preferred or can be downloaded from the following URL http www eqpi net eqpi downloads TutorialFiles sit hqx Here is the text to be placed on the macro card of the loader object file SampleMacrosLoader obj autoload filename SampleMacrosLoader obj var ql q2 string zl integer Macro autorun Begin for zl 1 to 256 do begin rUserl zl 0 end ql
10. le icons differ from these in several ways they are blue on black in color and the symbols and n are visible in the icon The filetype of these files is TOBJ even though their content is text Because their file type is not explicitly TEXT many text editors and word processors may not display these files in Open Save dialogs Many applications such as Tex Edit Plus and Nisus allow the display and opening of files whose type is not TEXT or a type native to that application An encrypted macro program file may be inspected using such a text editor or word processor in the usual manner The text content of an encrypted file however will be indistinguishable from gibberish This ensures that encrypted macro files may be made available to users while preventing the underlying text from being read Loading and using encrypted macro files from a obj file EqPi supports the use of obj files introduced in Object Image While obj files can be used in EqPi exactly as they are in Object Image there is presently no mechanism in EqPi for loading encrypted macro programs from the macro card of a obj file There is however a new macro command that can be used in a loader object file to load encrypted macro files target files This mechanism ensures that the object definitions and list of images contained in the loader obj file are available to the encrypted macros that the loader loads This mechanism entails storing a p
11. like results table that can contain measurements of objects While use of text in text files and on the macro card of obj files has the advantage of simplicity it does not provide any security to macro authors The macro code in these files can be viewed by users depriving authors of the means to prevent unauthorized use alteration or piracy of their macro program creations Using the online help viewer Much can be learned about using EqPi and programming macros by using the Online help introduced by Object Image It contains a complete description of the hundreds of programming commands and explains how many features are operated To use the online help double click on any macro language keyword while holding down the option key This will open a help window explaining the syntax and related information about the command This window can be scrolled or searched to reach descriptions of every other macro language command and other information 2 Macro authoring capabilities added in EqPi Creation and loading of encrypted macros EqPi allows macro programs stored in text and object obj files to be loaded opened and edited just as in NIH Image and Object Image EqPi additionally provides for the creation and loading of encrypted macro programs It also allows authors to limit which features of their macros are available to users through the use of a key password and through the use of several macro commands that set the u
12. mily laden with information and related software Object Image homepage http simon bio uva nl object image html especially useful for familiarization with Object Image Equipoise Imaging homepage http www egqpi net eqpi examples macros and related software 11
13. n that only part of the image in each slice is in focus This is a direct result of confocal imaging s ability to focus exclusively upon content at a particular depth While this effect is intended in confocal imaging and exploited during later reconstruction of volumes from image stacks it is sometimes desirable to effectively compress or project the stack onto a single maximum contrast image generated from the in focus regions from all of the slices in the stack EqPi contains a macro command implementing this capability The LookDeep command operates on an open active image stack and uses the following syntax LookDeep When LookDeep is executed in a macro program two additional slices are appended to the stack The maximum contrast image is calculated and appears in the first of the two appended slices i e the next to last slice of the stack In the last slice in the stack the grayscale value of each pixel contains the slice number in which the maximum contrast occurred at that pixel s position For example if the pixel with x y coordinates of 11 23 has a value of 5 in the last slice this indicates that the maximum contrast found in the stack at 11 23 occurred in slice 5 and it is the value of this pixel in slice 5 that is used in the maximum contrast image at 11 23 LookDeep calculates the best focus by using a coefficient of variation COV metric The COV of a pixel is computed by measuring the standard deviation of
14. pted macros loaded using the Equipoise gt Load eqPi macros menu item will not autorun In summary autorunning of encrypted macros is possible only if the macro uses the keyword autoeqpi and is loaded using the UserCode eqpiloadfile 0 0 0 macro command in a loader macro After creating an encrypted macro program file be sure to edit the autoeqpi keyword back to autorun in the plain text version of the macro program file that is saved for testing and further development Plain text macros containing autoeqpi in their name will load and run correctly but will not autorun except when they are used in encrypted macros However once a plain text macro containing autoeqpi in its name has been loaded the autorun mechanism for plain text macros which normally uses the keyword autorun in the macro tile is disabled until EqPi is restarted This condition is not likely to be encountered during normal use and can be prevented by ensuring that the keyword autoeqpi is not used in plain text macro names Renaming image windows In NIH Image and Object Image changing the name of an open image window entails either writing a macro to perform the task or saving the file under a new name In EqPi an image window may be renamed using the Equipoise gt Rename active image item in the menu To rename the active image window select this item and enter the new image window name in the dialog The new name will be evident in the window t
15. rget macros file in place of the sample key kohoutec given in this example 3 Save the object file The filename you choose will have the extension obj added to it NB Do not encrypt the loader object file and save it using the File gt Save menu item 4 Use the File gt New menu item and create a new text file to hold the target macros text using an arbitrary size Type or paste the plain text target macros that will be encrypted into this window Here is the sample target macro text filename SampleTargetMacros macro autoegpi begin InitStaticColumn twiceArea end macro EncryptedMacro 1 begin PutMessage Encrypted macros loaded end macro EncryptedMacro 2 begin PutMessage This one too end macro TwiceArea var intl columns rows twiceArea integer begin for intl 1 to nCount do begin twiceArea 2 GetValue RoiA intl SetValue twiceArea intl twiceArea end end 5 Encrypt this text using the Equipoise gt Encrypt macros menu item You can accept the candidate encryption key or type in one of your own choosing After noting the encryption key save the encrypted file with the name SampleEncryptedTarget The file that this creates is of type TEXT although the text within it has been encrypted Note The encryption key in the loader must match the one used during encryption Whether you use the candidate encryption key
16. sampleLoader obj file In summary encrypted macros are kept in one file the target and they are loaded by an associated loader obj file that contains the key information in the macro on its macro card 4 Control of user mode during execution of encrypted macros Authors of encrypted macros may wish to provide one level of capability to the public while restricting access to other features to those who have purchased a key EqPi allows authors to prevent users lacking a key from viewing the object window with its macro card containing the text of macros or from exporting the results table The availability of these features may be manipulated using the UserCode EqopiUserMode 0 0 0 command The first numerical parameter in this command controls whether the user may open the object window while the second controls whether the results table can be exported via the following parameter values Parameter 1 Value Action 1 Disable opening of object window 0 Enable opening of object window Parameter 2 Value Action 1 Disable export of results table 0 Enable export of results table Four different combinations of parameter 1 and parameter 2 are possible The value of the third parameter contained in this command is ignored For example the command UserCode EqpiUserMode 1 0 0 will disable opening of the object window while enabling export of the results table Note that this command does not close the object
17. ser mode This affords macro program provides macro authors a method for protecting their macro creations This mechanism does not cripple or alter any of the features of EqPi itself Creating an encrypted file and key Macros to be encrypted are first written edited and stored in text or obj files using the internal text editor as in NIH Image and Object Image A new text document may be created using the File gt New menu item or the lt command N gt keyboard combination or new text can be enetered into the macro card of Object Image in the usual manner As with any Macintosh application an existing text file may be opened using the File gt Open menu item lt command O gt Text files are saved using either the File gt Save menu item lt command S gt or File gt SaveAs menu item To create an encrypted macro program first make sure that the text window containing the macro program text is open and active in EqPi Then choose the Equipoise gt Encrypt eqPi macros menu item A dialog will open proposing a key to be used in the encryption of the macro text Initially a key consisting of 12 to 16 random characters is generated and indicated in the dialog The user may accept this key or replace the proposed key text as desired Be sure to remember this password which will be needed later to load and use the encrypted macros file Once the desired key text has been entered in the dialog hit the OK button or the return
18. that lists the ROIs that have been created Go ahead and mark several other ROIs also called cells in the image and you ll see more entries appear in the results table If you click on the cell number of a particular cell in the results table this number is in the first column of the table you ll see that a marker on the red ooutline for that cell is highlighted in the image window The second column contains the cell s area since this measurement was desgnated during the object definition operation The third column has a heading twiceArea that was created by the first macro which was autoexecuted during loading Notice that there are no measurements in this column Now go ahead and run the TwiceArea macro in the Special menu This macro uses the data in the Area column to calculate values that are then entered into the third colimn For detailed information on the many types of objects and the range of operation that can be done with them consult the Object Image manual or the online help introduced by Object Image online help can be invoked by depressing the option key while double clicking any macro language keyword visible in a macro text window You can export the results table using the Objects gt Export Obj Results menu item This creates a tab delimited spreadsheet file that can be opened in any spreadsheet or word processor Finally quit EqPi or close all of the opened files NB Do not save changes to the
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