Jadrian Miles: /* Command Line Options */

2010-01-26T23:14:03Z

Command Line Options

← Older revision		Revision as of 23:14, 26 January 2010
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	=== Command Line Options ===		=== Command Line Options ===

	The design of the command line options for this program will be very important. The Unix "<tt>find</tt>" utility has a simple syntax for specifying boolean operations as command-line arguments, but it can be unwieldy and has weird escaping problems. Another option might be to first specify the streamline collection, then a list of ROIs, and then a simple text string with boolean operations among the ROIs, which are named by the order in which they were specified; ''e.g.'' <code>"(1 \| 2) & !3"</code>.		The design of the command line options for this program will be very important. The Unix "<tt>find</tt>" utility has a simple syntax for specifying boolean operations as command-line arguments, but it can be unwieldy and has weird escaping problems. Another option might be to first specify the streamline collection, then a list of ROIs, and then a simple text string with boolean operations among the ROIs, which are named by the order in which they were specified; ''e.g.'' <code>"(1 \| 3) & !2"</code>.

	ROIs are typically specified either as rectangular prisms (by the coordinates of two opposite corners), spheres (by a radius and the coordinates of the center), or binary masks (raster images in [[NIfTI]] format, in which each voxel has a value 0 ['''not in'''] or 1 ['''in''']). One additional difficulty is that collections of masks are sometimes specified by indices in a raster image: a value of 0 means "not in any ROI", a value of 1 means "in ROI 1", a value of 2 means "in ROI 2", and so on.		ROIs are typically specified either as rectangular prisms (by the coordinates of two opposite corners), spheres (by a radius and the coordinates of the center), or binary masks (raster images in [[NIfTI]] format, in which each voxel has a value 0 ['''not in'''] or 1 ['''in''']). One additional difficulty is that collections of masks are sometimes specified by indices in a raster image: a value of 0 means "not in any ROI", a value of 1 means "in ROI 1", a value of 2 means "in ROI 2", and so on.

Jadrian Miles: New page: This Job Jar task is to create a non-interactive command-line program that reads in a collection of streamlines, one or more regions of interest (ROIs; more ...

2010-01-26T20:49:14Z

New page: This Job Jar task is to create a non-interactive command-line program that reads in a collection of streamlines, one or more regions of interest (ROIs; more ...

New page

This Job Jar task is to create a non-interactive command-line program that reads in a [[Job Jar/Streamline library|collection of streamlines]], one or more regions of interest (ROIs; more on these below), and a description of boolean operations among the ROIs, and outputs the resulting subset of streamlines.

=== ROIs ===

An ROI is a binary partitioning of space: for a given ROI, every point in space either is '''in''' the ROI, or '''not in''' it. For example, you could specify an ROI as a cube with two corners at (0,0,0) and (1,1,1); every point inside the cube (including its boundary) is '''in''' the ROI; every other point is '''not in''' the ROI. Another example of an ROI specification is a binary mask, in which every point in a discretized space is labeled as either 0 ('''not in''') or 1 ('''in''').

A streamline for which any point on it is '''in''' a given ROI is said to "pass through" that ROI. What this program should do is create a [[Job Jar/Streamline library|collection]] of every streamline that passes through the specified ROIs according to the given boolean operations on them. For example, if the user specifies streamline set ''Q'' and the operation "''ROI_A'' '''and''' '''not''' ''ROI_B''", then the result should be all those streamlines in ''Q'' that pass through ''ROI_A'' and not ''ROI_B''.

=== Command Line Options ===

The design of the command line options for this program will be very important. The Unix "<tt>find</tt>" utility has a simple syntax for specifying boolean operations as command-line arguments, but it can be unwieldy and has weird escaping problems. Another option might be to first specify the streamline collection, then a list of ROIs, and then a simple text string with boolean operations among the ROIs, which are named by the order in which they were specified; ''e.g.'' <code>"(1 | 2) & !3"</code>.

ROIs are typically specified either as rectangular prisms (by the coordinates of two opposite corners), spheres (by a radius and the coordinates of the center), or binary masks (raster images in [[NIfTI]] format, in which each voxel has a value 0 ['''not in'''] or 1 ['''in''']). One additional difficulty is that collections of masks are sometimes specified by indices in a raster image: a value of 0 means "not in any ROI", a value of 1 means "in ROI 1", a value of 2 means "in ROI 2", and so on.

=== Development Notes ===

For an initial version of this program, it would be sufficient to only support one type of ROI specification, as long as the software (and command-line interface) were designed for extensibility for future support of all others listed above.

[[Jadrian]] proposed this job and could collaborate to design the command line options.

=== Dependencies ===
This job depends on the completion of [[Job Jar/Streamline library]].

Job Jar/Streamline boolean ROI selection program - Revision history

Jadrian Miles: /* Command Line Options */

Jadrian Miles: New page: This Job Jar task is to create a non-interactive command-line program that reads in a collection of streamlines, one or more regions of interest (ROIs; more ...