Gap sampling - Revision history

Mjeppesen at 04:58, 20 January 2022

2022-01-20T04:58:02Z

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	= Introduction =		= Introduction =
			Gap sampling came into vogue in the field of Nuclear Magnetic Resonance (NMR) when Hyberts and Wagner introduced their Poisson-gap (PG) sampler for building Nonuniform Sampling (NUS) schedules. This project is the software realization of a full generalization of their PG method to admit any gap equation.

			Initial versions of gaputil contained hard-coded Poisson-gap, sine-gap, and sine-burst (cf. Worley and Powers, above) gap equations. The generality of the proposed framework was a tempting opportunity for me to embed the Julia programming language into one of my software projects. By embedding Julia into my existing gap sampling algorithm, this utility enables the construction of NUS schedules from completely arbitrary gap equations.
	== Obtaining ''gaputil'' ==		== Obtaining ''gaputil'' ==
	You can download the ''gaputil'' source code on its [http://github.com/geekysuavo/gaputil GitHub page].		You can download the ''gaputil'' source code on its [http://github.com/geekysuavo/gaputil GitHub page].

	== Installing ''gaputil'' ==		== Installing ''gaputil'' ==
	The ''gaputil'' binary is a command-line open-source C program. The software will run basically anywhere. Once you have the source code, run these commands to install it:		<!--The ''gaputil'' binary is a command-line open-source C program. The software will run basically anywhere. Once you have the source code, run these commands to install it:-->
			You will need to have Julia 0.4.0-dev compiled and installed in order to build nusutils. It is recommended that you compile and install from the latest GitHub nightly commit.

	git clone git://github.com/geekysuavo/~~gaputil~~.git		Once Julia is installed into the path, you can compile and install gaputil, rejutil and jitutil as follows:
	cd ~~gaputil~~
	make		git clone git://github.com/geekysuavo/nusutils.git
	sudo make install		cd nusutils
			make
			sudo make install

	== Using ''gaputil'' ==		== Using ''gaputil'' ==
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	All the utilities have the same argument syntax: the first argument is the sampling density, and the remaining arguments specify the size of the sampling grid. The final argument is the gap equation string to use when constructing the schedule. The code is currently soft-limited to generating 3D grids, but you can remove this restriction by editing '''term.c''' and recompiling/reinstalling.		All the utilities have the same argument syntax: the first argument is the sampling density, and the remaining arguments specify the size of the sampling grid. The final argument is the gap equation string to use when constructing the schedule. The code is currently soft-limited to generating 3D grids, but you can remove this restriction by editing '''term.c''' and recompiling/reinstalling.

			==Package Info==
			A set of command-line utilities for deterministically (i.e. without pseudorandom numbers) constructing nonuniform sampling schedules on multidimensional Nyquist grids. The gaputil is a utility to construct schedules using the generalized gap sampling framework published in:

			''Worley, B., Powers, R., Deterministic Multidimensional Nonuniform Gap Sampling, Journal of Magnetic Resonance, 2015, 261: 19-26.''

			The rejutil and jitutil are utilities to construct schedules from density functions using a quasirandom accept-reject sampling method published in:

			''Worley, B., Subrandom Methods for Multidimensional Nonuniform Sampling, Journal of Magnetic Resonance, 2016, 269: 128-137.''

	[[category:Data_Collection]]		[[category:Data_Collection]]

Mjeppesen at 04:32, 20 January 2022

2022-01-20T04:32:11Z

← Older revision		Revision as of 04:32, 20 January 2022
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	All the utilities have the same argument syntax: the first argument is the sampling density, and the remaining arguments specify the size of the sampling grid. The final argument is the gap equation string to use when constructing the schedule. The code is currently soft-limited to generating 3D grids, but you can remove this restriction by editing '''term.c''' and recompiling/reinstalling.		All the utilities have the same argument syntax: the first argument is the sampling density, and the remaining arguments specify the size of the sampling grid. The final argument is the gap equation string to use when constructing the schedule. The code is currently soft-limited to generating 3D grids, but you can remove this restriction by editing '''term.c''' and recompiling/reinstalling.

	~~[[category:Protocols]]~~
	[[category:Data_Collection]]		[[category:Data_Collection]]

Mjeppesen: Added to Category

2021-09-11T05:12:06Z

Added to Category

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	[[category:Protocols]]		[[category:Protocols]]
	[[category:~~Data_Processing_and_Analysis~~]]		[[category:Data_Collection]]

Mjeppesen: Added to Category

2021-09-11T05:10:21Z

Added to Category

← Older revision		Revision as of 05:10, 11 September 2021
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	[[category:Protocols]]		[[category:Protocols]]
			[[category:Data_Processing_and_Analysis]]

Jcatazaro at 19:38, 14 March 2017

2017-03-14T19:38:19Z

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	[[category:Protocols]]		[[category:Protocols]]
	~~[[test]]~~

Jcatazaro at 19:37, 14 March 2017

2017-03-14T19:37:46Z

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	[[category:Protocols]]		[[category:Protocols]]
			[[test]]

MediaWiki default at 18:46, 13 July 2015

2015-07-13T18:46:34Z

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	The ~~DGS~~ package provides a few small command-line utilities for generating deterministic Poisson-gap, stochastic Poisson-gap, and deterministic burst-augmented gap sampling schedules over multidimensional grids. This page outlines how to install and use the ~~DGS~~ utilities.		The ''gaputil'' package provides a few small command-line utilities for generating deterministic Poisson-gap, stochastic Poisson-gap, and deterministic burst-augmented gap sampling schedules over multidimensional grids. This page outlines how to install and use the gap utilities.

	= Introduction =		= Introduction =

MediaWiki default at 18:46, 13 July 2015

2015-07-13T18:46:04Z

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	= Introduction =		= Introduction =

	== Obtaining ''~~dgs~~'' ==		== Obtaining ''gaputil'' ==
	You can download the ''~~dgs~~'' source code ~~by clicking~~ [http://~~bionmr~~.~~unl.edu~~/~~dgs.php here~~].		You can download the ''gaputil'' source code on its [http://github.com/geekysuavo/gaputil GitHub page].

	== Installing ''~~dgs~~'' ==		== Installing ''gaputil'' ==
	The ~~utilities in~~ ''~~dgs~~'' ~~are~~ a ~~set of~~ command-line open-source C ~~programs~~. The software will run basically anywhere. Once you have the source code, run these commands to install it:		The ''gaputil'' binary is a command-line open-source C program. The software will run basically anywhere. Once you have the source code, run these commands to install it:

	cd /~~path~~/to/~~source~~/~~tarball~~		git clone git://github.com/geekysuavo/gaputil.git
	~~tar xf dgs-YYYYMMDD.tar~~.gz		cd gaputil
	cd ~~dgs-YYYYMMDD~~
	make		make
	sudo install ~~-v -m 755 -o root -g root spg dpg dbag /usr/local/bin/~~		sudo make install

	== Using a ''~~dgs~~'' ~~utility~~ ==		== Using ''gaputil'' ==
	Once the programs are compiled and installed, you can run them from anywhere, ''e.g.'':		Once the programs are compiled and installed, you can run them from anywhere, ''e.g.'':

	~~dpg~~ 0.1 512 512		gaputil 0.1 512 512 'L*x'

	All the utilities have the same argument syntax: the first argument is the sampling density, and the remaining arguments specify the size of the sampling grid. The code is currently soft-limited to generating 3D grids, but you can remove this restriction by editing '''~~dgs~~.c''' and recompiling/reinstalling.		All the utilities have the same argument syntax: the first argument is the sampling density, and the remaining arguments specify the size of the sampling grid. The final argument is the gap equation string to use when constructing the schedule. The code is currently soft-limited to generating 3D grids, but you can remove this restriction by editing '''term.c''' and recompiling/reinstalling.

	[[category:Protocols]]		[[category:Protocols]]

MediaWiki default: Created page with "The DGS package provides a few small command-line utilities for generating deterministic Poisson-gap, stochastic Poisson-gap, and deterministic burst-augmented gap sampling sc..."

2015-01-11T19:22:52Z

Created page with "The DGS package provides a few small command-line utilities for generating deterministic Poisson-gap, stochastic Poisson-gap, and deterministic burst-augmented gap sampling sc..."

New page

The DGS package provides a few small command-line utilities for generating deterministic Poisson-gap, stochastic Poisson-gap, and deterministic burst-augmented gap sampling schedules over multidimensional grids. This page outlines how to install and use the DGS utilities.

= Introduction =

== Obtaining ''dgs'' ==
You can download the ''dgs'' source code by clicking [http://bionmr.unl.edu/dgs.php here].

== Installing ''dgs'' ==
The utilities in ''dgs'' are a set of command-line open-source C programs. The software will run basically anywhere. Once you have the source code, run these commands to install it:

cd /path/to/source/tarball
tar xf dgs-YYYYMMDD.tar.gz
cd dgs-YYYYMMDD
make
sudo install -v -m 755 -o root -g root spg dpg dbag /usr/local/bin/

== Using a ''dgs'' utility ==
Once the programs are compiled and installed, you can run them from anywhere, ''e.g.'':

dpg 0.1 512 512

All the utilities have the same argument syntax: the first argument is the sampling density, and the remaining arguments specify the size of the sampling grid. The code is currently soft-limited to generating 3D grids, but you can remove this restriction by editing '''dgs.c''' and recompiling/reinstalling.

[[category:Protocols]]