3D-DOCTOR Scripting With 3DBasic:

3DBasic Summary

3DBasic is a Basic-like scripting language implemented to allow programming with 3D-DOCTOR’s advanced image processing functions.  This enables the user to perform sophisticated tasks in batch mode. A 3DBasic program can be created using a text editor, such as Windows NotePad or use 3D-DOCTOR’s 3DBasic/Create command. Use 3DBasic/Run to run an existing 3DBasic program directly.

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Key Features

3DBasic supports most of the standard Basic commands, including

In addition, 3DBasic provides a new set of commands to provide enhanced functionality for programming and image processing . The new commands include:

3DBasic supports different variable types, including INTEGER (32-bit long), FLOAT (64-bit double), STRING (variable length text string) and IMAGE3D (a data container for 3D images, boundaries, and other data).

The following are some examples of some commonly used 3DBasic programs.

Example for Image Segmentation:

LOGFILE "c:\output.log"

PRINT "THIS IS A 3D SEGMENTATION EXAMPLE"

STRING FILENAME

INTEGER X1, X2

X1 = 51

X2 = 186

IMAGE3D image1

INPUT "Enter image file name:", FILENAME

PRINT FILENAME

OPENIMAGE image1 FILENAME

SEGMENTIMAGE image1 X1 X2

SAVEBOUNDARY image1 "c:\test.bnd"

SHOWIMAGE image1

PRINT "FINISHED"

END

 

Example for Simple Surface Rendering:

LOGFILE "c:\ output.log"

PRINT "THIS IS A SURFACE RENDERING PROGRAM"

STRING FILENAME

IMAGE3D image1

INPUT "Enter image file name:", FILENAME

PRINT FILENAME

OPENIMAGE image1 FILENAME

REM Assuming boundary data has been generated

OPENBOUNDARY image1 "d:\test.bnd"

SURFSIMPLE image1 "d:\test.suf"

CLOSEIMAGE image1

PRINT "FINISHED"

END

Example for saving image slices to separate image files:

LOGFILE "c:\output.log"

INTEGER X

STRING FILENAME, NAME1, NAME

IMAGE3D image1

NAME = "testimg"

INPUT "Enter image file name:", FILENAME

PRINT FILENAME

OPENIMAGE image1 FILENAME

REM saves image slices 1 to 10 to files testimage1 to testimage10

FOR X = 1 TO 10

NAME1 = NAME + X

PRINT NAME1

SAVEIMAGE image1 X X NAME1

NEXT

END

 

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1. REM statement

This command indicates that the entire line following REM is only comment and will not affect the program execution.

Syntax:

REM comment text

Example:

REM this is a sample comment

REM PRINT "This"

REM the above line will do nothing

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2. LOGFILE statement

This command defines the output file where it stores all information generated by the PRINT command. Besides the PRINT command, all error messages will also be saved to the log file.

Syntax:

LOGFILE "c:\output.log"

LOGFILE outputname

where, STRING outputname

This command can be used more than once in a program to define different log files for PRINT output.

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3. INTEGER statement

INTEGER is used to declare integer variables.

Syntax:

INTEGER I, J, K1

where, I, J, and K are the names of integer variables.

An integer variable is 32-bit long and must be declared before it is used in the program.

Example:

 

LOGFILE "c:\output.log"

INTEGER I, J

I = 25

J = I + 101

PRINT "I=", I, "J=", J

END

 

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4. FLOAT statement

FLOAT is used to declare float variables.

Syntax:

FLOAT X1, Y, y1

where, X1, Y, and y1 are the names of float variables.

Example:

LOGFILE "c:\output.log"

FLOAT X, Y

INPUT "Enter X", X

Y = X + 25.0

PRINT "X=", X, "Y=", Y

END

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5. STRING statement

STRING is used to declare variables that are text string.

Syntax:

STRING Name1, note, name2

where, Name1, note, and name2 are text strings.

Example:

 

LOGFILE "c:\output.log"

STRING Name1, Note

INPUT "Enter Name", Name1

Note = "The name is"

Name1 = Note + Name1

PRINT "New string is", Name1

END

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6. IMAGE3D statement

IMAGE3D is used to declare 3D image variables. IMAGE3D variables can contain image data, boundary data, and other types of data created using 3D-DOCTOR’s processing functions.

Syntax:

IMAGE3D image1, Image10, T1

where, image1, Image10, and T1 are images.

Example:

LOGFILE "c:\output.log"

IMAGE3D image1

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

SHOWIMAGE image1

END

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7 ASSIGNMENT statement

Assignment statements are used to assign a value to a declared variable, which can be an integer, float, or string.

Syntax:

<Variable> = <Expression>

Example:

LOGFILE "c:\output.log"

STRING Note

INTEGER N

FLOAT F1, F2

Note = "This is the value for Note"

N = 200

F1 = 1.2*N

F2 = F1 + N

PRINT Note, N, F1, F2

END

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8. PRINT statement

The PRINT statement prints values of variables, expressions, and text strings to the file defined by the LOGFILE statement.

Syntax:

PRINT <parameters>

Example:

INTEGER I,

FLOAT F

STRING note

I = 25

F = 25.0

note = "Just a note"

PRINT "Test Print", note, I, F

END

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9. INPUT statement

The INPUT statement allows interactive assignment of values to variables.

Syntax:

INPUT <Variable>

INPUT "Prompt Text", <Variable>

Example:

INTEGER I,

FLOAT F

STRING note

INPUT "Enter I", I

INPUT "Enter F", F

INPUT "Enter Note", note

PRINT "Test Input", note, I, F

END

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10. GOTO statement

The GOTO statement is one of several ways implemented in 3DBasic to control program flow.

Syntax:

GOTO <Label>

where, the Label is a numeric value indicating the line where the program continues. 3DBasic does not require a Label for each line. Only a line that is a target line of a GOTO statement must have a label.

Example:

INTEGER I

INPUT "Enter I", I

GOTO 200

I = I*I

200 I = I+I

PRINT "I =", I

END

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11. IF statement

The IF statement implemented in 3DBasic is slightly different from the standard Basic format. The ELSE statement is not supported and only "<", ">" and "=" can be used as operators.

Syntax:

IF <Expression> <Operator> <Expression> THEN <LineLabel>

Example:

INTEGER I

INPUT "Enter I", I

IF I > 10 THEN 200

I = I * I

PRINT "I < 10, I*I=", I

200 I = I + I

PRINT "I > 10, I+I=", I

END

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12. FOR loop statement

The FOR loop allows implementing sophisticated programs to repeat certain operations with different variable values.

Syntax:

FOR <Control Variable> = <Starting Value> TO <Ending Value>

…

Operations

…

NEXT

where, the "Control Variable" will start with the "Starting Value", and run the program through the "NEXT" statement and then increment the "Control Variable" by 1, and repeat the operation until the "Control Variable" is the same as the "Ending Value".

Example:

INTEGER I, J

FOR I = 0 TO 100

J = J*I

PRINT "J=", J

NEXT

END

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13. GOSUB and RETURN statements

Same as the standard Basic, the use of GOSUB and RETURN allows implementation of subroutines.

Syntax:

GOSUB <Label>

…

…

<Label> (Subroutine starts)

Subroutine body

RETURN

Example:

 

INTEGER I

GOSUB 200

PRINT "I=", I

END

 

200 INPUT "I=", I

RETURN

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14. OPENIMAGE statement

This command opens an image or project file for processing. It is similar to the File/Open Image function.

Syntax:

OPENIMAGE imagevar "filename"

OPENIMAGE imagevar filename

 

where, IMAGE3D imagevar

STRING filename

Example:

IMAGE3D image1

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

SHOWIMAGE image1

END

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15. SAVEIMAGE statement

This command saves specified image planes to a file where both start and end planes are included. The image must be currently open and the start and end planes must exist. If the start plane is the same as the end plane, then only this plane is saved. This command is similar to File/Save Image As command.

Syntax:

SAVEIMAGE imagevar "filename" startplane endplane

SAVEIMAGE imagevar filename startplane endplane

 

where, IMAGE3D imagevar, STRING filename, INTEGER startplane endplane

Example:

LOGFILE "c:output.log"

IMAGE3D image1

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

SAVEIMAGE image1 "c:\newfile.tif" 1 3

END

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16. SAVEIMAGEPLANE statement

This command saves the current active image plane to a file. An image plane can be set to active by using the SETIMAGEPLANE command.

Syntax:

SAVEIMAGEPLANE imagevar "filename"

SAVEIMAGEPLANE imagevar filename

where, IMAGE3D imagevar, STRING filename

Example:

LOGFILE "c:output.log"

IMAGE3D image1

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

SETIMAGEPLANE image1 3

REM save image plane 3 to file

SAVEIMAGEPLANE image1 "c:\3ddoctor\plane3.tif"

END

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17. SETIMAGEPLANE statement

This command sets a specified image plane as current for processing functions like GETPIXEL, SETPIXEL, and SAVEIMAGEPLANE. The image plane number must exist.

Syntax:

SETIMAGEPLANE image planenum

where, IMAGE3D image, INTEGER planenum

Example:

LOGFILE "c:output.log"

IMAGE3D image1

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

REM set image plane to 3

SETIMAGEPLANE image1 3

REM save image plane 3 to file

SAVEIMAGEPLANE image1 "c:\3ddoctor\plane3.tif"

END

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18. IMAGEDIM statement

This function retrieves the image dimension values, including the number of columns, number of rows, and number of planes. The image must be opened before this command is used. This command is similar to Image/Information but with less parameters.

Syntax:

IMAGEDIM image x y z

where, IMAGE3D image, INTEGER x y z

Example:

LOGFILE "c:output.log"

IMAGE3D image1

INTEGER cols, rows, planes

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

IMAGEDIM image1 cols rows planes

PRINT "Cols=", cols, "Rows=", rows, "Planes=", planes

END

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19. GETPIXEL statement

This function retrieves a pixel from the current plane of an opened image. The image must be opened before this command is used. To work on another image plane, use SETIMAGEPLANE to set the plane as current first and then use the GETPIXEL function.

Syntax:

GETPIXEL image col row value

where, IMAGE3D image, INTEGER col row value, the col and row defines the pixel location.

Example:

LOGFILE "c:output.log"

IMAGE3D image1

INTEGER col, row, pix

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

SETIMAGEPLANE image1 2

FOR col = 0 TO 20

FOR row = 0 TO 20

GETPIXEL image1 col row pix

PRINT "pixel (", col, ",", row, ")=", pix

NEXT

END

 

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20. SETPIXEL statement

This function sets a pixel value in the current plane of an opened image. The image must be open before this command is used. To work on another image plane, use SETIMAGEPLANE to set the plane as current first and then use this function.

Syntax:

SETPIXEL image col row value

where, IMAGE3D image, INTEGER col row value, the col and row defines the pixel location.

Example:

LOGFILE "c:output.log"

IMAGE3D image1

INTEGER col, row, pix

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

SETIMAGEPLANE image1 2

pix = 255

FOR col = 0 TO 20

FOR row = 0 TO 20

SETPIXEL image1 col row pix

NEXT

END

 

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21. SHOWIMAGE statement

This command sends the currently opened image to display. Once an image is used by this command, it will be automatically closed and will no longer be available to the same program. It should be opened again if the image needs to be used by the same program.

Syntax:

SHOWIMAGE imagevar

where, IMAGE3D imagevar

Example:

IMAGE3D image1

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

SHOWIMAGE image1

END

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22. CLOSEIMAGE statement

This command closes a currently opened image when it is no longer needed. This will free up all memory allocated by the image.

Syntax:

CLOSEIMAGE imagevar

where, IMAGE3D imagevar

Example:

IMAGE3D image1

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

CLOSEIMAGE image1

END

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23. SIZEIMAGEUP statement

This command enlarges an image by a specified scaling factor. For example, if the scaling factor is 2, then the resized image will be doubled in all three dimensions. This command is similar to Image/Resize Volume command.

Syntax:

SIZEIMAGEUP imagevar "filename" 2

SIZEIMAGEUP imagevar filename scalar

 

where, IMAGE3D imagevar, STRING filename, INTEGER scalar

Example:

IMAGE3D image1

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

SIZEIMAGEUP image1 "c:\size2.tif" 2

END

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24. SIZEIMAGEDOWN statement

This command reduces the size of an image by a specified scaling factor. For example, if the scaling factor is 2, then the resized image will be scaled down by 2 in all three dimensions. This command is similar to Image/Resize Volume command.

Syntax:

SIZEIMAGEDOWN imagevar "filename" 2

SIZEIMAGEDOWN imagevar filename scalar

where, IMAGE3D imagevar, STRING filename, INTEGER scalar

Example:

IMAGE3D image1

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

SIZEIMAGEDOWN image1 "c:\size2.tif" 2

END

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25. ROTATEIMAGEX and ROTATEIMAGEY statements

The ROTATEIMAGEX and ROTATEIMAGEY commands rotate a 3D volume around the X-axis and Y-axis, respectively. They are similar to Image/Reslice/Reslice X Axis and Image/Reslice/Reslice Y Axis commands.

Syntax:

ROTATEIMAGEX imagevar "filename"

ROTATEIMAGEX imagevar filename

ROTATEIMAGEY imagevar "filename"

ROTATEIMAGEY imagevar filename

where, IMAGE3D imagevar, STRING filename

Example:

IMAGE3D image1

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

ROTATEIMAGEX image1 "c:\topview.tif"

ROTATEIMAGEY image1 "c:\sizeview.tif"

END

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26. CROPIMAGE statement

This command crops a sub-volume from an image and save the volume to a new image file. This command is similar to the Image/Crop Image/Crop Volume command.

Syntax:

CROPIMAGE imagevar "filename" x1 x2 y1 y2 z1 z2

CROPIMAGE imagevar filename x1 x2 y1 y2 z1 z2

where, IMAGE3D imagevar, STRING outputfile

INTEGER x1 x2 y1 y2 z1 z2; defines the volume

Example:

IMAGE3D image1

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

CROPIMAGE image1 "c:\crop.tif" 10 50 10 50 1 15

END

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27. SEGMENTIMAGE statement

This command segments an image using specified low and high thresholds. The generated object boundary lines are stored in the IMAGE3D variable and can be used by surface or volume rendering commands. This command is similar to the 3D Rendering/Interactive Segment command.

Syntax:

SEGMENTIMAGE image low high alllines

SEGMENTIMAGE image 50 189 0

where, IMAGE3D image, INTEGER low high

INTEGER alllines (0: only outline, 1: all boundaries)

Example:

IMAGE3D image1

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

SEGMENTIMAGE image1 50 189 0

SAVEBOUNDARY image1 "c:\object1.bnd"

SHOWIMAGE image1

END

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28. OPENBOUNDARY statement

This command loads object boundary data into an IMAGE3D variable from a boundary file. This command is similar to the File/Boundary/Import Boundary command.

Syntax:

OPENBOUNDARY imagevar "filename"

OPENBOUNDARY imagevar filename

where, IMAGE3D imagevar, STRING filename

Example:

IMAGE3D image1

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

OPENBOUNDARY image1 "c:\3ddoctor\head3d.bnd"

SHOWIMAGE image1

END

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29. SAVEBOUNDARY statement

This command saves object boundary data into a boundary file. This command is similar to the File/Boundary/Export Boundary command.

Syntax:

SAVEboundary imagevar "filename"

SAVEboundary imagevar filename

where, IMAGE3D imagevar, STRING filename

Example:

IMAGE3D image1

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

SEGMENTIMAGE image1 50 189 0

SAVEBOUNDARY image1 "c:\object1.bnd"

SHOWIMAGE image1

END

 

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30. DECONVNN statement

This command performs a nearest neighbor deconvolution. It is similar to the Image/Deconvolution//Fast Nearest Neighbor command.

Syntax:

DECONVNN "sourcefile" "psffile" "outputfile" areasize kernelsize scalar

DECONVNN sourcefile psffile outputfile 32 11 0.0001

where, STRING sourcefile, psffile, outputfile, INTEGER areasize, kernelsize, FLOAT scalar

Example:

LOGFILE "c:\output.log"

DECONVNN "c:\image.tif" "c:\psf.tif" "c:\output.tif" 32 11 0.0001

END

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31. DECONVMAX statement

This command performs a maximum entropy based deconvolution. It is similar to the Image/Deconvolution/Maximum Entropy command.

Syntax:

DECONVMAX "sourcefile" "psffile" "outputfile" iterations feedback

DECONVMAX sourcefile psffile outputfile 15 0.05

where, STRING sourcefile, psffile, outputfile, INTEGER iterations, FLOAT feedback; this value should be less than 1.

Example:

LOGFILE "c:\output.log"

DECONVMAX "c:\image.tif" "c:\psf.tif" "c:\output.tif" 15 0.05

END

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32. SURFSIMPLE statement

This command performs a simple surface rendering using boundary data stored in an IMAGE3D object. It is similar to the 3D Rendering/Surface Rendering/Simple Surface command, but the surface modeling data is saved directly to a file, instead of being displayed in a window.

Syntax:

SURFSIMPLE imagevar "filename"

SURFSIMPLE imagevar filename

where, IMAGE3D imagevar, STRING filename

Example:

IMAGE3D image1

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

SEGMENTIMAGE image1 50 189 0

surfsimple image1 "c:\3ddoctor\head3d.suf"

END

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33. SURFCOMPLEX statement

This command performs a complex surface rendering using boundary data stored in an IMAGE3D object. It is similar to the 3D Rendering/Surface Rendering/(Fast or Full) Complex Surface command, but the surface modeling data is saved directly to a file, instead of being displayed in a window.

Syntax:

SURFCOMPLEX imagevar "filename"

SURFCOMPLEX imagevar filename

where, IMAGE3D imagevar, STRING filename

Example:

IMAGE3D image1

OPENIMAGE image1 "c:\3ddoctor\head3d.tif"

SEGMENTIMAGE image1 50 189 0

surfCOMPLEX image1 "c:\3ddoctor\head3d.suf"

END

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34. END statement

This command indicates the end of the program.

Syntax:

END

Example:

PRINT"This is a test"
END

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