Guide to madagascar programs - Revision history

Fomels: ahay.org

2024-11-19T00:13:20Z

ahay.org

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	<math>\\|\mathbf{d - L\,m}\\|^2</math> for the given input data vector <math>\mathbf{d}</math>.		<math>\\|\mathbf{d - L\,m}\\|^2</math> for the given input data vector <math>\mathbf{d}</math>.

	The pseudocode for <tt>sfconjgrad</tt> is given at the end of the [~~http~~://~~www.reproducibility~~.org/RSF/book/gee/lsq/paper.pdf "Model fitting with least squares" chapter] of ''Imaging Estimation by Example'' by Jon Claerbout, with the earliest form published in [http://sepwww.stanford.edu/data/media/public/oldreports/sep48/48_25.pdf "Conjugate Gradient Tutorial"] (SEP-48, 1986, same author). A simple toy implementation with a small matrix shows that this algorithm produces the same steps as the algorithm described in equations 45-49 of [http://www.cs.cmu.edu/~quake-papers/painless-conjugate-gradient.pdf "An introduction to the Conjugate Gradient Method Without the Agonizing Pain"] by J.R. Shewchuk, 1994, when the equation <math>A^T A x = A^T b</math> (in Shewchuk's notation) is solved. Multiplying with the transpose ensures a correct solution even when matrix A is square but not symmetric at all. The program [~~http~~://~~www.reproducibility~~.org/RSF/sfcconjgrad.html sfcconjgrad] implements this algorithm for the case when inputs are complex.		The pseudocode for <tt>sfconjgrad</tt> is given at the end of the [https://ahay.org/RSF/book/gee/lsq/paper.pdf "Model fitting with least squares" chapter] of ''Imaging Estimation by Example'' by Jon Claerbout, with the earliest form published in [http://sepwww.stanford.edu/data/media/public/oldreports/sep48/48_25.pdf "Conjugate Gradient Tutorial"] (SEP-48, 1986, same author). A simple toy implementation with a small matrix shows that this algorithm produces the same steps as the algorithm described in equations 45-49 of [http://www.cs.cmu.edu/~quake-papers/painless-conjugate-gradient.pdf "An introduction to the Conjugate Gradient Method Without the Agonizing Pain"] by J.R. Shewchuk, 1994, when the equation <math>A^T A x = A^T b</math> (in Shewchuk's notation) is solved. Multiplying with the transpose ensures a correct solution even when matrix A is square but not symmetric at all. The program [https://ahay.org/RSF/sfcconjgrad.html sfcconjgrad] implements this algorithm for the case when inputs are complex.

	Here is an example. The <tt>sfhelicon</tt> program implements Claerbout's multidimensional helical filtering		Here is an example. The <tt>sfhelicon</tt> program implements Claerbout's multidimensional helical filtering
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	The misfit decreased by an order of magnitude in 10 iterations. Running the program for more iterations can improve the result.		The misfit decreased by an order of magnitude in 10 iterations. Running the program for more iterations can improve the result.

	An equivalent implementation for complex-valued inputs is [~~http~~://~~www.reproducibility~~.org/RSF/sfcconjgrad.html sfcconjgrad]. A lightweight Python implementation can be found in [https://github.com/ahay/src/blob/master/user/fomels/conjgrad.py $PYTHONPATH/rsf/conjgrad.py].		An equivalent implementation for complex-valued inputs is [https://ahay.org/RSF/sfcconjgrad.html sfcconjgrad]. A lightweight Python implementation can be found in [https://github.com/ahay/src/blob/master/user/fomels/conjgrad.py $PYTHONPATH/rsf/conjgrad.py].

	==sfcp==		==sfcp==
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	\|}		\|}

	Different [~~http~~://~~reproducibility~~.org/~~rsflog~~/~~index.php?~~/~~archives~~/~~14-Color~~-schemes~~.html~~ color schemes] are available		Different [https://ahay.org/blog/2005/03/28/color-schemes/ color schemes] are available
	for sfgrey and sfgrey3. Examples are in the book at [~~http~~://~~reproducibility~~.org/RSF/book/rsf/rsf/sfgrey.html rsf/rsf/sfgrey].		for sfgrey and sfgrey3. Examples are in the book at [https://ahay.org/RSF/book/rsf/rsf/sfgrey.html rsf/rsf/sfgrey].

	==sfgrey==		==sfgrey==
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	\|}		\|}

	Different [~~http~~://~~reproducibility~~.org/~~rsflog~~/~~index.php?~~/~~archives~~/~~14-Color~~-schemes~~.html~~ color schemes] are available, and examples are in the book at [~~http~~://~~reproducibility~~.org/RSF/book/rsf/rsf/sfgrey.html rsf/rsf/sfgrey].		Different [https://ahay.org/blog/2005/03/28/color-schemes/ color schemes] are available, and examples are in the book at [https://ahay.org/RSF/book/rsf/rsf/sfgrey.html rsf/rsf/sfgrey].

	==sfplas==		==sfplas==
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	=Plotting programs (development)=		=Plotting programs (development)=
	==sfplsurf==		==sfplsurf==
	<tt>sfplsurf</tt> utilizes PLplot's surface rendering capabilities. Output is dumped to stdout in VPLOT format, so it can easily be used like <tt>sfgrey</tt> or other plotting programs. It also supports animation, if n3 > 1 in the input file. A SConstruct usage example can be found below. A [~~http~~://~~reproducibility~~.org/wikilocal/movies/sfplsurf_membrane.mpg movie of the output] is available as well.		<tt>sfplsurf</tt> utilizes PLplot's surface rendering capabilities. Output is dumped to stdout in VPLOT format, so it can easily be used like <tt>sfgrey</tt> or other plotting programs. It also supports animation, if n3 > 1 in the input file. A SConstruct usage example can be found below. A [https://ahay.org/wikilocal/movies/sfplsurf_membrane.mpg movie of the output] is available as well.

	<syntaxhighlight lang="python">		<syntaxhighlight lang="python">
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	===Usage example===		===Usage example===
	The commands below, slightly modified from [http://rsf.svn.sourceforge.net/viewvc/rsf/trunk/book/data/sigsbee/ptest/SConstruct?revision=3993&view=markup RSFSRC/book/data/sigsbee/ptest], show how to prepare the [~~http~~://~~www.reproducibility~~.org/RSF/book/data/sigsbee Sigsbee 2A] data and velocity for migration.		The commands below, slightly modified from [http://rsf.svn.sourceforge.net/viewvc/rsf/trunk/book/data/sigsbee/ptest/SConstruct?revision=3993&view=markup RSFSRC/book/data/sigsbee/ptest], show how to prepare the [https://ahay.org/RSF/book/data/sigsbee Sigsbee 2A] data and velocity for migration.

	Convert input data (shots) from SEG-Y to RSF:		Convert input data (shots) from SEG-Y to RSF:

Fomels: typos

2024-11-13T23:35:42Z

typos

Show changes

Sfomel: /* sfcsv2rsf */

2018-11-17T00:05:01Z

sfcsv2rsf

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	Notice that sfdisfil displays in column order (i.e. matrix is transposed if the number of rows is right). The dimensions of the file are actually transposed on disk:		Notice that sfdisfil displays in column order (i.e. matrix is transposed if the number of rows is right). The dimensions of the file are actually transposed on disk:

			<syntaxhighlight lang="bash">
	$ sfin junk.rsf		$ sfin junk.rsf
	junk.rsf:		junk.rsf:

Sfomel: /* sfwindow */

2016-05-06T12:59:59Z

sfwindow

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	==sfwindow==		==sfwindow==
	{\| class="wikitable" align="center" cellspacing="0" border="1"		{\| class="wikitable" align="center" cellspacing="0" border="1"
	! colspan="4" style="background:#ffdead;" \| Window a portion of ~~the~~ dataset.		! colspan="4" style="background:#ffdead;" \| Window a portion of a dataset.
	\|-		\|-
	! colspan="4" \| sfwindow < in.rsf > out.rsf verb=n squeeze=y j#=(1,...) d#=(d1,d2,...) f#=(0,...) min#=(o1,o2,,...) n#=(0,...) max#=(o1+(n1-1)d1,o2+(n1-1)d2,,...)		! colspan="4" \| sfwindow < in.rsf > out.rsf verb=n squeeze=y j#=(1,...) d#=(d1,d2,...) f#=(0,...) min#=(o1,o2,,...) n#=(0,...) max#=(o1+(n1-1)d1,o2+(n1-1)d2,,...)
			\|-
			\| colspan="4" \| <br>Other parameters from the command line are passed to the output (similar to sfput).
	\|-		\|-
	\| ''float '' \|\| '''d#=(d1,d2,...)''' \|\| \|\| sampling in #-th dimension		\| ''float '' \|\| '''d#=(d1,d2,...)''' \|\| \|\| sampling in #-th dimension
	\|-		\|-
	\| ''~~int~~ '' \|\| '''f#=(0,...)''' \|\| \|\| window start in #-th dimension		\| ''largeint'' \|\| '''f#=(0,...)''' \|\| \|\| window start in #-th dimension
	\|-		\|-
	\| ''int '' \|\| '''j#=(1,...)''' \|\| \|\| jump in #-th dimension		\| ''int '' \|\| '''j#=(1,...)''' \|\| \|\| jump in #-th dimension
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	\| ''float '' \|\| '''min#=(o1,o2,,...)''' \|\| \|\| minimum in #-th dimension		\| ''float '' \|\| '''min#=(o1,o2,,...)''' \|\| \|\| minimum in #-th dimension
	\|-		\|-
	\| ''~~int~~ '' \|\| '''n#=(0,...)''' \|\| \|\| window size in #-th dimension		\| ''largeint'' \|\| '''n#=(0,...)''' \|\| \|\| window size in #-th dimension
	\|-		\|-
	\| ''bool '' \|\| '''squeeze=y''' \|\| [y/n] \|\| if y, squeeze dimensions equal to 1 to the end		\| ''bool '' \|\| '''squeeze=y''' \|\| [y/n] \|\| if y, squeeze dimensions equal to 1 to the end

Sfomel: /* sftransp */

2016-05-06T12:59:03Z

sftransp

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	there but, if not enough memory is available, it performs a slower		there but, if not enough memory is available, it performs a slower
	transpose out of core using disk operations. You can control the		transpose out of core using disk operations. You can control the
	amount of available memory using the <b>memsize=</b> parameter or		amount of available memory using the <tt>memsize=</tt> parameter or
	the <b>RSFMEMSIZE</b> environmental variable.		the <tt>RSFMEMSIZE</tt> environmental variable.

	==sfwindow==		==sfwindow==

Sfomel: /* sftransp */

2016-05-06T12:57:05Z

sftransp

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	The <tt>sftransp</tt> program transposes the input hypercube		The <tt>sftransp</tt> program transposes the input hypercube
	exchanging the two axes specified by the <b>plane=</b> parameter.		exchanging the two axes specified by the <tt>plane=</tt> parameter.
	<pre>		<pre>
	bash$ sfspike n1=10 n2=20 n3=30 > orig123.rsf		bash$ sfspike n1=10 n2=20 n3=30 > orig123.rsf

Sfomel: /* sfstack */

2016-05-06T12:56:04Z

sfstack

← Older revision		Revision as of 12:56, 6 May 2016
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	! colspan="4" style="background:#ffdead;" \| Stack a dataset over one of the dimensions.		! colspan="4" style="background:#ffdead;" \| Stack a dataset over one of the dimensions.
	\|-		\|-
	! colspan="4" \| sfstack < in.rsf > out.rsf axis=2 rms=n norm=y min=n max=n		! colspan="4" \| sfstack < in.rsf > out.rsf scale= axis=2 rms=n norm=y min=n max=n prod=n
	\|-		\|-
	\| colspan="4" \| <br>This operation is adjoint to sfspray.		\| colspan="4" \| <br>This operation is adjoint to sfspray.
	\|-		\|-
	\| ''int '' \|\| '''axis=2''' \|\| \|\| which axis to stack		\| ''int '' \|\| '''axis=2''' \|\| \|\| which axis to stack. If axis=0, stack over all dimensions
	\|-		\|-
	\| ''bool '' \|\| '''max=n''' \|\| [y/n] \|\| If y, find maximum instead of stack. Ignores rms and norm.		\| ''bool '' \|\| '''max=n''' \|\| [y/n] \|\| If y, find maximum instead of stack. Ignores rms and norm.
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	\|-		\|-
	\| ''bool '' \|\| '''norm=y''' \|\| [y/n] \|\| If y, normalize by fold.		\| ''bool '' \|\| '''norm=y''' \|\| [y/n] \|\| If y, normalize by fold.
			\|-
			\| ''bool '' \|\| '''prod=n''' \|\| [y/n] \|\| If y, find product instead of stack. Ignores rms and norm.
	\|-		\|-
	\| ''bool '' \|\| '''rms=n''' \|\| [y/n] \|\| If y, compute the root-mean-square instead of stack.		\| ''bool '' \|\| '''rms=n''' \|\| [y/n] \|\| If y, compute the root-mean-square instead of stack.
			\|-
			\| ''floats '' \|\| '''scale=''' \|\| \|\| optionally scale before stacking [n2]
	\|}		\|}

	While <tt>sfspray</tt> adds a dimension to a hypercube,		While <tt>sfspray</tt> adds a dimension to a hypercube,
	<tt>sfstack</tt> effectively removes one of the dimensions by stacking		<tt>sfstack</tt> effectively removes one of the dimensions by stacking

Sfomel: /* sfspike */

2016-05-06T12:54:08Z

sfspike

← Older revision		Revision as of 12:54, 6 May 2016
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	! colspan="4" style="background:#ffdead;" \| Generate simple data: spikes, boxes, planes, constants.		! colspan="4" style="background:#ffdead;" \| Generate simple data: spikes, boxes, planes, constants.
	\|-		\|-
	! colspan="4" \| sfspike > spike.rsf mag= nsp=1 k#=[0,...] l#=[k1,k2,...] p#=[0,...] n#= o#=[0,0,...] d#=[0.004,0.1,0.1,...] label#=[Time,Distance,Distance,...] unit#=[s,km,km,...] title=		! colspan="4" \| sfspike < in.rsf > spike.rsf mag= nsp=1 k#=[0,...] l#=[k1,k2,...] p#=[0,...] n#= o#=[0,0,...] d#=[0.004,0.1,0.1,...] label#=[Time,Distance,Distance,...] unit#=[s,km,km,...] title=
	\|-		\|-
	\| colspan="4" \| <br>Spike positioning is given in samples and starts with 1.		\| colspan="4" \| <br>Spike positioning is given in samples and starts with 1.
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	\| ''string '' \|\| '''unit#=[s,km,km,...]''' \|\| \|\| unit on #-th axis		\| ''string '' \|\| '''unit#=[s,km,km,...]''' \|\| \|\| unit on #-th axis
	\|}		\|}


	<tt>sfspike</tt> takes no input and generates an output with		<tt>sfspike</tt> takes no input and generates an output with

Sfomel: /* sfscale */

2016-05-06T12:53:11Z

sfscale

Sfomel: /* sfrtoc */

2016-05-06T12:52:19Z

sfrtoc

← Older revision		Revision as of 12:52, 6 May 2016
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	! colspan="4" style="background:#ffdead;" \| Convert real data to complex (by adding zero imaginary part).		! colspan="4" style="background:#ffdead;" \| Convert real data to complex (by adding zero imaginary part).
	\|-		\|-
	! colspan="4" \| sfrtoc < real.rsf > cmplx.rsf		! colspan="4" \| sfrtoc < real.rsf > cmplx.rsf pair=n
	\|-		\|-
	\| colspan="4" \| <br>See also: sfcmplx		\| colspan="4" \| <br>See also: sfcmplx
			\|-
			\| ''bool '' \|\| '''pair=n''' \|\| [y/n] \|\| y - use odd elements for real part and even ones for imaginary part
	\|}		\|}

	The input to <tt>sfrtoc</tt> can be any <tt>type=float</tt> dataset:		The input to <tt>sfrtoc</tt> can be any <tt>type=float</tt> dataset:
	<pre>		<pre>

← Older revision		Revision as of 12:53, 6 May 2016
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	! colspan="4" style="background:#ffdead;" \| Scale data.		! colspan="4" style="background:#ffdead;" \| Scale data.
	\|-		\|-
	! colspan="4" \| sfscale < in.rsf > out.rsf axis=0 rscale=0. dscale=1.		! colspan="4" \| sfscale < in.rsf > out.rsf axis=0 rscale=0. pclip=100. dscale=1.
	\|-		\|-
	\| colspan="4" \| <br>To scale by a constant factor, you can also use sfmath ~~or sfheadermath~~.		\| colspan="4" \| <br>To scale by a constant factor, you can also use sfmath.
	\|-		\|-
	\| ''int '' \|\| '''axis=0''' \|\| \|\| Scale by maximum in the dimensions up to this axis.		\| ''int '' \|\| '''axis=0''' \|\| \|\| Scale by maximum in the dimensions up to this axis.
	\|-		\|-
	\| ''float '' \|\| '''dscale=1.''' \|\| \|\| Scale by this factor (works if rscale=0)		\| ''float '' \|\| '''dscale=1.''' \|\| \|\| Scale by this factor (works if rscale=0)
			\|-
			\| ''float '' \|\| '''pclip=100.''' \|\| \|\| data clip percentile
	\|-		\|-
	\| ''float '' \|\| '''rscale=0.''' \|\| \|\| Scale by this factor.		\| ''float '' \|\| '''rscale=0.''' \|\| \|\| Scale by this factor.
	\|}		\|}

	<tt>sfscale</tt> scales the input dataset by a factor. Here		<tt>sfscale</tt> scales the input dataset by a factor. Here
	are some simple examples. First, let us create a test dataset.		are some simple examples. First, let us create a test dataset.
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	equivalent to <tt>sfscale axis=1</tt>, and <tt>sfscale rscale=0</tt>		equivalent to <tt>sfscale axis=1</tt>, and <tt>sfscale rscale=0</tt>
	is equivalent to <tt>sfscale dscale=1</tt>.		is equivalent to <tt>sfscale dscale=1</tt>.







	==sfspike==		==sfspike==