Execution

Since the 3dma code has many different functionalities, we have adopted a convention for naming the 2 main input/output files associated with each different option. Typically an input file is labelled caseN.M.in and the associated output file is caseN.M.out where N and M are the integer options chosen on the first two menus provided by the 3dma executable.

The first menu asked is

Input Data Options
	tomographic data (1)
	segmented data (2)
	burn data (3)
	Medial Axis data (4)
Enter choice: 1

and refers to the data set on which the desired analysis is to be preformed. The second menu depends on the selection in the first menu. These second menus are listed in sections 8, 9, 10, 11.

The 3dma executable is built to read user provided input from either the screen or from an input file (caseN.M.in), and produce an output file (caseN.M.out) containing a record of the input and a text record of the desired output statistics, as well as associated files containing requested graphs and images.

Input from the screen

	% 3dma_sun > case1.1_ras.out

Inputting answers from the screen can be mildly tedious. Additionally, the input format has bad error recovery when a wrong answer is issued, input must be entered all over again. However once prepared, an output file can be converted to an input file, it can be edited to change responses, and rerun.

eg:
	% mv case1.1_ras.out case1.1_ras.in
	% vi case1.1_ras.in		/* edit input file, change answers */
	% stripcomm_sun -b < case1.1_ras.in | 3dma_sun > case1.1_ras.out

The stripcomm facility is provided for the purpose of running from an input file. It scans the input file searching for the next occurrance of the string ``: ''. The remainder of the line is taken to be the next required answer and is passed to the 3dma executable.

As the stripcomm command line is rather lengthy, we provide the shell script runcase to shorten the typing. Thus

	% runcase sun case1.1_ras

is equivalent to typing

	% stripcomm_sun -b < case1.1_ras.in | 3dma_sun > case1.1_ras.out