Guide to madagascar programs: Difference between revisions
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<center><font size="-1">''This page was created from the LaTeX source in [ | <center><font size="-1">''This page was created from the LaTeX source in [https://github.com/ahay/src/blob/master/book/rsf/rsf/prog.tex book/rsf/rsf/prog.tex] using [[latex2wiki]]''</font></center> | ||
This guide introduces some of the most used <tt> | This guide introduces some of the most used <tt> Madagascar </tt> programs and illustrates their usage with examples. | ||
=Main programs= | =Main programs= | ||
The source files for these programs can be found under [ | The source files for these programs can be found under [https://github.com/ahay/src/blob/master/system/main system/main] in the Madagascar distribution. The "main" programs perform general-purpose operations on RSF hypercubes regardless of the data dimensionality or physical dimensions. | ||
==sfadd== | ==sfadd== | ||
| Line 47: | Line 47: | ||
</pre> | </pre> | ||
In both cases, the size and shape of <tt>data1.rsf</tt> and | In both cases, the size and shape of <tt>data1.rsf</tt> and | ||
<tt>data2.rsf</tt> hypercubes should be the same, and a warning | <tt>data2.rsf</tt> hypercubes should be the same, and a warning message is printed out if the axis sampling parameters (such as | ||
message is printed out if | |||
<tt>o1</tt> or <tt>d1</tt>) in these files are different. | <tt>o1</tt> or <tt>d1</tt>) in these files are different. | ||
====Implementation: [ | ====Implementation: [https://github.com/ahay/src/blob/master/system/main/add.c system/main/add.c]==== | ||
The first input file is either in the list or in the standard input. | The first input file is either in the list or in the standard input. | ||
<c> | <syntaxhighlight lang="c"> | ||
/* find number of input files */ | /* find number of input files */ | ||
if (isatty(fileno(stdin))) { | if (isatty(fileno(stdin))) { | ||
| Line 58: | Line 57: | ||
nin=0; | nin=0; | ||
} else { | } else { | ||
filename[0] = "in"; | |||
nin=1; | nin=1; | ||
} | } | ||
</ | </syntaxhighlight> | ||
Collect input files in the <tt>in</tt> array from all command-line | Collect input files in the <tt>in</tt> array from all command-line | ||
parameters that don't contain an "<tt>=</tt>" sign. The total number | parameters that don't contain an "<tt>=</tt>" sign. The total number | ||
of input files | of input files is <tt>nin</tt>. | ||
<c> | <syntaxhighlight lang="c"> | ||
for (i=1; i< argc; i++) { /* collect inputs */ | for (i=1; i< argc; i++) { /* collect inputs */ | ||
if (NULL != strchr(argv[i],'=')) continue; | if (NULL != strchr(argv[i],'=')) continue; /* not a file */ | ||
filename[nin] = argv[i]; | |||
nin++; | nin++; | ||
} | } | ||
if (0==nin) sf_error ("no input"); | if (0==nin) sf_error ("no input"); | ||
/* nin = no of input files*/ | /* nin = no of input files*/ | ||
</ | </syntaxhighlight> | ||
A helper function <tt>check_compat</tt> checks the compatibility of | A helper function <tt>check_compat</tt> checks the compatibility of | ||
input files. | input files. | ||
<c> | <syntaxhighlight lang="c"> | ||
static void | static void | ||
check_compat (sf_datatype type /* data type */, | check_compat (sf_datatype type /* data type */, | ||
| Line 118: | Line 117: | ||
} | } | ||
} | } | ||
</ | </syntaxhighlight> | ||
Finally, we enter the main loop, where input data are getting read | Finally, we enter the main loop, where the input data are getting read | ||
buffer by buffer and combined in the total product depending on the | buffer by buffer and combined in the total product depending on the | ||
data type. | data type. | ||
<c> | <syntaxhighlight lang="c"> | ||
for (nbuf /= sf_esize(in[0]); nsiz > 0; nsiz -= nbuf) { | for (nbuf /= sf_esize(in[0]); nsiz > 0; nsiz -= nbuf) { | ||
if (nbuf > nsiz) nbuf=nsiz; | if (nbuf > nsiz) nbuf=nsiz; | ||
| Line 146: | Line 145: | ||
exp_flag[j]); | exp_flag[j]); | ||
break; | break; | ||
</ | </syntaxhighlight> | ||
The data combination program for floating point numbers is | The data combination program for floating point numbers is | ||
<tt>add_float</tt>. | <tt>add_float</tt>. | ||
<c> | <syntaxhighlight lang="c"> | ||
static void add_float (bool collect, /* if collect */ | static void add_float (bool collect, /* if collect */ | ||
size_t nbuf, /* buffer size */ | size_t nbuf, /* buffer size */ | ||
| Line 193: | Line 192: | ||
} | } | ||
} | } | ||
</ | </syntaxhighlight> | ||
==sfattr== | ==sfattr== | ||
| Line 199: | Line 198: | ||
! colspan="4" style="background:#ffdead;" | Display dataset attributes. | ! colspan="4" style="background:#ffdead;" | Display dataset attributes. | ||
|- | |- | ||
! colspan="4" | sfattr < in.rsf want= | ! colspan="4" | sfattr < in.rsf lval=2 want= | ||
|- | |- | ||
| colspan="4" | | | colspan="4" | <br>Sample output from "sfspike n1=100 | sfbandpass fhi=60 | sfattr"<br>*******************************************<br>rms = 0.992354<br>mean = 0.987576<br>2-norm = 9.92354<br>variance = 0.00955481<br>std dev = 0.0977487<br>max = 1.12735 at 97<br>min = 0.151392 at 100<br>nonzero samples = 100<br>total samples = 100<br>*******************************************<br><br>rms = sqrt[ sum(data^2) / n ]<br>mean = sum(data) / n<br>norm = sum(abs(data)^lval)^(1/lval)<br>variance = [ sum(data^2) - n*mean^2 ] / [ n-1 ]<br>standard deviation = sqrt [ variance ] | ||
|- | |- | ||
| ''int '' || '''lval=2''' || || norm option, lval is a non-negative integer, computes the vector lval-norm | | ''int '' || '''lval=2''' || || norm option, lval is a non-negative integer, computes the vector lval-norm | ||
|- | |- | ||
| ''string '' || '''want=''' || || 'all'(default),'rms','mean','norm','var','std','max','min','nonzero','samples','short' | | ''string '' || '''want=''' || || 'all'(default), 'rms', 'mean', 'norm', 'var', <br> 'std', 'max', 'min', 'nonzero', 'samples', 'short' | ||
:want= 'rms' displays the root mean square | :want= 'rms' displays the root mean square | ||
:want= 'norm' displays the square norm, otherwise specified by lval. | :want= 'norm' displays the square norm, otherwise specified by lval. | ||
| Line 226: | Line 225: | ||
is <math>\sqrt{\sum\limits_{i=0}^n d_i^2}</math>, the variance is | is <math>\sqrt{\sum\limits_{i=0}^n d_i^2}</math>, the variance is | ||
<math>\frac{1}{n-1}\,\left[\sum\limits_{i=0}^n d_i^2 - \frac{1}{n}\left(\sum\limits_{i=0}^n d_i\right)^2\right]</math>, and the standard | <math>\frac{1}{n-1}\,\left[\sum\limits_{i=0}^n d_i^2 - \frac{1}{n}\left(\sum\limits_{i=0}^n d_i\right)^2\right]</math>, and the standard | ||
deviation is the square root of the variance. Using <tt>sfattr</tt> | deviation is the square root of the variance. Using <tt>sfattr</tt> is a quick way to see the distribution of data values and check it for anomalies. | ||
is a quick way to see the distribution of data values and check it for anomalies. | |||
The output can be parsed using utilities such as <tt>awk</tt>, to extract only a numeric value for feeding it as a parameter value into a command line interface. Notice the backticks in the example below: | The output can be parsed using utilities such as <tt>awk</tt>, to extract only a numeric value for feeding it as a parameter value into a command line interface. Notice the backticks in the example below: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
sfgrey <vel.rsf allpos=y bias=`sfattr <vel.rsf want=min | awk '{print $4}'` | sfpen | sfgrey <vel.rsf allpos=y bias=`sfattr <vel.rsf want=min | awk '{print $4}'` | sfpen | ||
</ | </syntaxhighlight> | ||
====Implementation: [ | ====Implementation: [https://github.com/ahay/src/blob/master/system/main/attr.c system/main/attr.c]==== | ||
Computations start by finding the input data (<tt>in</tt>) size | Computations start by finding the input data (<tt>in</tt>) size | ||
(<tt>nsiz</tt>) and dimensions (<tt>dim</tt>). | (<tt>nsiz</tt>) and dimensions (<tt>dim</tt>). | ||
<c> | <syntaxhighlight lang="c"> | ||
dim = (size_t) | dim = (size_t) sf_largefiledims (in,n); | ||
for (nsiz=1, i=0; i < dim; i++) { | for (nsiz=1, i=0; i < dim; i++) { | ||
nsiz *= n[i]; | nsiz *= n[i]; | ||
} | } | ||
</ | </syntaxhighlight> | ||
In the main loop, we read the input data buffer by buffer. | In the main loop, we read the input data buffer by buffer. | ||
<c> | <syntaxhighlight lang="c"> | ||
for (nleft=nsiz; nleft > 0; nleft -= nbuf) { | for (nleft=nsiz; nleft > 0; nleft -= nbuf) { | ||
nbuf = (bufsiz < nleft)? bufsiz: nleft; | nbuf = (bufsiz < nleft)? bufsiz: nleft; | ||
| Line 256: | Line 254: | ||
case SF_INT: | case SF_INT: | ||
sf_intread((int*) buf,nbuf,in); | sf_intread((int*) buf,nbuf,in); | ||
break; | |||
case SF_SHORT: | |||
sf_shortread((short*) buf,nbuf,in); | |||
break; | break; | ||
case SF_COMPLEX: | case SF_COMPLEX: | ||
| Line 268: | Line 269: | ||
break; | break; | ||
} | } | ||
</ | </syntaxhighlight> | ||
The data attributes are accumulated in corresponding double-precision | The data attributes are accumulated in corresponding double-precision variables. | ||
variables. | <syntaxhighlight lang="c"> | ||
<c> | |||
fsum += f; | fsum += f; | ||
fsqr += f*f; | fsqr += (double) f*f; | ||
</ | </syntaxhighlight> | ||
Finally, the attributes are reduced and printed out. | Finally, the attributes are reduced and printed out. | ||
<c> | <syntaxhighlight lang="c"> | ||
fmean = fsum/nsiz; | fmean = fsum/nsiz; | ||
if (lval==2) fnorm = sqrt(fsqr); | if (lval==2) fnorm = sqrt(fsqr); | ||
| Line 286: | Line 286: | ||
else fnorm = pow(flval,1./lval); | else fnorm = pow(flval,1./lval); | ||
frms = sqrt(fsqr/nsiz); | frms = sqrt(fsqr/nsiz); | ||
if (nsiz > 1) fvar = (fsqr-nsiz*fmean*fmean)/(nsiz-1); | if (nsiz > 1) fvar = fabs(fsqr-nsiz*fmean*fmean)/(nsiz-1); | ||
else fvar = 0.0; | else fvar = 0.0; | ||
fstd = sqrt(fvar); | fstd = sqrt(fvar); | ||
</ | </syntaxhighlight> | ||
<c> | <syntaxhighlight lang="c"> | ||
if(NULL==want || 0==strcmp(want,"rms")) | if(NULL==want || 0==strcmp(want,"rms")) | ||
printf("rms = % | printf("rms = %13.6g \n",(float) frms); | ||
if(NULL==want || 0==strcmp(want,"mean")) | if(NULL==want || 0==strcmp(want,"mean")) | ||
printf("mean | printf("mean = %13.6g \n",(float) fmean); | ||
if(NULL==want || 0==strcmp(want,"norm")) | if(NULL==want || 0==strcmp(want,"norm")) | ||
printf("%d-norm value = % | printf("%d-norm value = %13.6g \n",lval,(float) fnorm); | ||
if(NULL==want || 0==strcmp(want,"var")) | if(NULL==want || 0==strcmp(want,"var")) | ||
printf("variance = % | printf("variance = %13.6g \n",(float) fvar); | ||
if(NULL==want || 0==strcmp(want,"std")) | if(NULL==want || 0==strcmp(want,"std")) | ||
printf("standard deviation = % | printf("standard deviation = %13.6g \n",(float) fstd); | ||
</ | </syntaxhighlight> | ||
==sfcat== | ==sfcat== | ||
| Line 308: | Line 308: | ||
! colspan="4" style="background:#ffdead;" | Concatenate datasets. | ! colspan="4" style="background:#ffdead;" | Concatenate datasets. | ||
|- | |- | ||
! colspan="4" | sfcat > out.rsf space= axis=3 nspace=(int) (ni/(20*nin) + 1) [<file0.rsf] file1.rsf file2.rsf ... | ! colspan="4" | sfcat > out.rsf order= space= axis=3 nspace=(int) (ni/(20*nin) + 1) o= d= [<file0.rsf] file1.rsf file2.rsf ... | ||
|- | |- | ||
| colspan="4" | sfmerge inserts additional space between merged data. | | colspan="4" | sfmerge inserts additional space between merged data. | ||
|- | |- | ||
| ''int '' || '''axis=3''' || || Axis being merged | | ''int '' || '''axis=3''' || || Axis being merged | ||
|- | |||
| ''float '' || '''d=''' || || axis sampling | |||
|- | |- | ||
| ''int '' || '''nspace=(int) (ni/(20*nin) + 1)''' || || if space=y, number of traces to insert | | ''int '' || '''nspace=(int) (ni/(20*nin) + 1)''' || || if space=y, number of traces to insert | ||
|- | |||
| ''float '' || '''o=''' || || axis origin | |||
|- | |||
| ''ints '' || '''order=''' || || concatenation order [nin] | |||
|- | |- | ||
| ''bool '' || '''space=''' || [y/n] || Insert additional space. | | ''bool '' || '''space=''' || [y/n] || Insert additional space. | ||
:y is default for sfmerge, n is default for sfcat | :y is default for sfmerge, n is default for sfcat | ||
|} | |} | ||
<tt>sfcat</tt> and <tt>sfmerge</tt> concatenate two or more files | <tt>sfcat</tt> and <tt>sfmerge</tt> concatenate two or more files | ||
| Line 362: | Line 367: | ||
</pre> | </pre> | ||
====Implementation: [ | ====Implementation: [https://github.com/ahay/src/blob/master/system/main/cat.c system/main/cat.c]==== | ||
The first input file is either in the list or in the standard input. | The first input file is either in the list or in the standard input. | ||
<c> | <syntaxhighlight lang="c"> | ||
in = (sf_file*) sf_alloc ((size_t) argc,sizeof(sf_file)); | in = (sf_file*) sf_alloc ((size_t) argc,sizeof(sf_file)); | ||
| Line 370: | Line 375: | ||
nin=0; | nin=0; | ||
} else { | } else { | ||
filename[0] = "in"; | |||
nin=1; | nin=1; | ||
} | } | ||
</ | </syntaxhighlight> | ||
Everything on the command line that does not contain a "=" sign is | Everything on the command line that does not contain a "=" sign is | ||
treated as a file name, and the corresponding file object is added to the list. | treated as a file name, and the corresponding file object is added to the list. | ||
<c> | <syntaxhighlight lang="c"> | ||
for (i=1; i< argc; i++) { /* collect inputs */ | for (i=1; i< argc; i++) { /* collect inputs */ | ||
if (NULL != strchr(argv[i],'=')) | if (NULL != strchr(argv[i],'=')) | ||
continue; /* not a file */ | continue; /* not a file */ | ||
filename[nin] = argv[i]; | |||
nin++; | nin++; | ||
} | } | ||
if (0==nin) sf_error ("no input"); | if (0==nin) sf_error ("no input"); | ||
</ | </syntaxhighlight> | ||
As explained above, if the <tt>space=</tt> parameter is not set, it is | As explained above, if the <tt>space=</tt> parameter is not set, it is | ||
inferred from the program name: <tt>sfmerge</tt> corresponds to | inferred from the program name: <tt>sfmerge</tt> corresponds to | ||
<tt>space=y</tt> and <tt>sfcat</tt> corresponds to <tt>space=n</tt>. | <tt>space=y</tt> and <tt>sfcat</tt> corresponds to <tt>space=n</tt>. | ||
<c> | <syntaxhighlight lang="c"> | ||
if (!sf_getbool("space",&space)) { | if (!sf_getbool("space",&space)) { | ||
/* Insert additional space. | /* Insert additional space. | ||
| Line 405: | Line 410: | ||
} | } | ||
} | } | ||
</ | </syntaxhighlight> | ||
Find the axis for the merging (from the command line <tt>axis=</tt> | Find the axis for the merging (from the command line <tt>axis=</tt> | ||
argument) and figure out two sizes: <tt>n1</tt> for everything after | argument) and figure out two sizes: <tt>n1</tt> for everything after | ||
the axis and <tt>n2</tt> for everything before the axis. | the axis and <tt>n2</tt> for everything before the axis. | ||
<c> | <syntaxhighlight lang="c"> | ||
n1=1; | n1=1; | ||
n2=1; | n2=1; | ||
| Line 417: | Line 422: | ||
else if (i > axis) n2 *= n[i-1]; | else if (i > axis) n2 *= n[i-1]; | ||
} | } | ||
</ | </syntaxhighlight> | ||
In the output, the selected axis will get extended. | In the output, the selected axis will get extended. | ||
<c> | <syntaxhighlight lang="c"> | ||
/* figure out the length of extended axis */ | /* figure out the length of extended axis */ | ||
ni = 0; | ni = 0; | ||
| Line 436: | Line 441: | ||
(void) snprintf(key,3,"n%d",axis); | (void) snprintf(key,3,"n%d",axis); | ||
sf_putint(out,key,(int) ni); | sf_putint(out,key,(int) ni); | ||
</ | </syntaxhighlight> | ||
The rest is simple: loop through the datasets reading and writing the | The rest is simple: loop through the datasets reading and writing the | ||
data in buffer-size chunks and adding extra empty chunks if | data in buffer-size chunks and adding extra empty chunks if | ||
<tt>space=y</tt>. | <tt>space=y</tt>. | ||
<c> | <syntaxhighlight lang="c"> | ||
for (i2=0; i2 < n2; i2++) { | for (i2=0; i2 < n2; i2++) { | ||
for (j=0; j < nin; j++) { | for (j=0; j < nin; j++) { | ||
| Line 458: | Line 463: | ||
} | } | ||
} | } | ||
</ | </syntaxhighlight> | ||
==sfcdottest== | ==sfcdottest== | ||
| Line 471: | Line 476: | ||
|} | |} | ||
A simple demonstration of the program can be made taking advantage that the complex-to-complex FFT is a linear operator: | A simple demonstration of the program can be made by taking advantage that the complex-to-complex FFT is a linear operator: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
sfspike n1=100 | sfrtoc > spike.rsf | sfspike n1=100 | sfrtoc > spike.rsf | ||
< spike.rsf sffft axis=1 pad=1 > spike2.rsf | < spike.rsf sffft axis=1 pad=1 > spike2.rsf | ||
sfcdottest sffft mod=spike.rsf dat=spike2.rsf axis=1 pad=1 | sfcdottest sffft mod=spike.rsf dat=spike2.rsf axis=1 pad=1 | ||
</ | </syntaxhighlight> | ||
The output should show values identical down to the last decimal: | The output should show values identical down to the last decimal: | ||
| Line 490: | Line 495: | ||
! colspan="4" style="background:#ffdead;" | Create a complex dataset from its real and imaginary parts. | ! colspan="4" style="background:#ffdead;" | Create a complex dataset from its real and imaginary parts. | ||
|- | |- | ||
! colspan="4" | sfcmplx > cmplx.rsf real.rsf imag.rsf | ! colspan="4" | sfcmplx < real.rsf > cmplx.rsf real.rsf imag.rsf | ||
|- | |- | ||
| colspan="4" | There has to be only two input files specified and no additional parameters. | | colspan="4" | There has to be only two input files specified and no additional parameters. | ||
| Line 519: | Line 524: | ||
</pre> | </pre> | ||
====Implementation: [ | ====Implementation: [https://github.com/ahay/src/blob/master/system/main/cmplx.c system/main/cmplx.c]==== | ||
The program flow is simple. First, get the names of the input files. | The program flow is simple. First, get the names of the input files. | ||
<c> | <syntaxhighlight lang="c"> | ||
/* the first two non-parameters are real and | /* the first two non-parameters are real and imag files */ | ||
for (i=1; i< argc; i++) { | for (i=1; i< argc; i++) { | ||
if (NULL == strchr(argv[i],'=')) { | if (NULL == strchr(argv[i],'=')) { | ||
| Line 539: | Line 544: | ||
real = sf_input("in"); | real = sf_input("in"); | ||
} | } | ||
</ | </syntaxhighlight> | ||
The main part of the program reads the real and imaginary parts buffer by buffer and assembles and writes out the complex input. | The main part of the program reads the real and imaginary parts buffer by buffer and assembles and writes out the complex input. | ||
<c> | <syntaxhighlight lang="c"> | ||
for (nleft= (size_t) (rsize*resize); nleft > 0; nleft -= nbuf) { | for (nleft= (size_t) (rsize*resize); nleft > 0; nleft -= nbuf) { | ||
nbuf = (BUFSIZ < nleft)? BUFSIZ: nleft; | nbuf = (BUFSIZ < nleft)? BUFSIZ: nleft; | ||
| Line 553: | Line 558: | ||
sf_charwrite(cbuf,2*nbuf,cmplx); | sf_charwrite(cbuf,2*nbuf,cmplx); | ||
} | } | ||
</ | </syntaxhighlight> | ||
==sfconjgrad== | ==sfconjgrad== | ||
{| class="wikitable" align="center" cellspacing="0" border="1" | {| class="wikitable" align="center" cellspacing="0" border="1" | ||
! colspan="4" style="background:#ffdead;" | Generic conjugate-gradient solver for linear inversion | ! colspan="4" style="background:#ffdead;" | Generic conjugate-gradient solver for linear inversion | ||
|- | |- | ||
! colspan="4" | sfconjgrad < dat.rsf mod=mod.rsf > to.rsf < from.rsf > out.rsf niter=1 | ! colspan="4" | sfconjgrad < dat.rsf mod=mod.rsf mwt=mwt.rsf known=known.rsf x0=x0.rsf > to.rsf < from.rsf > out.rsf niter=1 | ||
|- | |||
| ''string '' || '''known=''' || || auxiliary input file name | |||
|- | |||
| ''file '' || '''mod=''' || || auxiliary input file name | |||
|- | |||
| ''string '' || '''mwt=''' || || auxiliary input file name | |||
|- | |- | ||
| ''int '' || '''niter=1''' || || number of iterations | | ''int '' || '''niter=1''' || || number of iterations | ||
|- | |||
| ''string '' || '''x0=''' || || auxiliary input file name | |||
|} | |} | ||
| Line 578: | Line 592: | ||
<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 [ | 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> | Here is an example. The <tt>sfhelicon</tt> program implements Claerbout's multidimensional helical filtering | ||
program implements Claerbout's multidimensional helical filtering | (Claerbout, 1998<ref>Claerbout, J., 1998, Multidimensional recursive filters via a helix: Geophysics, '''63''', 1532--1541.</ref>). It requires a filter to be specified in addition to the input and output vectors. We create a helical 2-D filter using the Unix <tt>echo</tt> command. | ||
(Claerbout, 1998<ref>Claerbout, J., 1998, Multidimensional recursive filters via a helix: Geophysics, '''63''', 1532--1541.</ref>). It requires a filter to be specified in | |||
addition to the input and output vectors. We create a helical | |||
2-D filter using the Unix <tt>echo</tt> command. | |||
<pre> | <pre> | ||
bash$ echo 1 19 20 n1=3 n=20,20 data_format=ascii_int in=lag.rsf > lag.rsf | bash$ echo 1 19 20 n1=3 n=20,20 data_format=ascii_int in=lag.rsf > lag.rsf | ||
| Line 596: | Line 607: | ||
check that the adjoint mode works correctly. | check that the adjoint mode works correctly. | ||
<pre> | <pre> | ||
bash$ sfdottest sfhelicon filt=flt.rsf lag=lag.rsf | bash$ sfdottest sfhelicon filt=flt.rsf lag=lag.rsf mod=vec.rsf dat=vec.rsf | ||
sfdottest: L[m]*d=5.28394 | sfdottest: L[m]*d=5.28394 | ||
sfdottest: L'[d]*m=5.28394 | sfdottest: L'[d]*m=5.28394 | ||
| Line 609: | Line 619: | ||
and try to invert the filtering operation using <tt>sfconjgrad</tt>: | and try to invert the filtering operation using <tt>sfconjgrad</tt>: | ||
<pre> | <pre> | ||
bash$ sfconjgrad sfhelicon filt=flt.rsf lag=lag.rsf | bash$ sfconjgrad sfhelicon filt=flt.rsf lag=lag.rsf mod=vec.rsf < dat.rsf > mod.rsf niter=10 | ||
mod=vec.rsf < dat.rsf > mod.rsf niter=10 | |||
sfconjgrad: iter 1 of 10 | sfconjgrad: iter 1 of 10 | ||
sfconjgrad: grad=3253.65 | sfconjgrad: grad=3253.65 | ||
| Line 640: | Line 649: | ||
and after | and after | ||
<pre> | <pre> | ||
bash$ sfhelicon filt=flt.rsf lag=lag.rsf < mod.rsf | | bash$ sfhelicon filt=flt.rsf lag=lag.rsf < mod.rsf | sfadd scale=1,-1 dat.rsf | sfattr want=norm | ||
sfadd scale=1,-1 dat.rsf | sfattr want=norm | |||
norm value = 5.73563 | norm value = 5.73563 | ||
</pre> | </pre> | ||
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 [ | 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== | ||
| Line 653: | Line 660: | ||
! colspan="4" style="background:#ffdead;" | Copy or move a dataset. | ! colspan="4" style="background:#ffdead;" | Copy or move a dataset. | ||
|- | |- | ||
! colspan="4" | sfcp in.rsf out.rsf | ! colspan="4" | sfcp < in.rsf > out.rsf in.rsf out.rsf | ||
|- | |- | ||
| colspan="4" | sfcp - copy, sfmv - move.<br>Mimics standard Unix commands. | | colspan="4" | sfcp - copy, sfmv - move.<br>Mimics standard Unix commands. | ||
| Line 681: | Line 688: | ||
</pre> | </pre> | ||
====Implementation: [ | ====Implementation: [https://github.com/ahay/src/blob/master/system/main/cp.c system/main/cp.c]==== | ||
First, we look for the two first command-line arguments that don't | First, we look for the two first command-line arguments that don't | ||
have the "=" character in them and consider them as the names of the | have the "=" character in them and consider them as the names of the input and the output files. | ||
input and the output files. | <syntaxhighlight lang="c"> | ||
<c> | |||
/* the first two non-parameters are in and out files */ | /* the first two non-parameters are in and out files */ | ||
for (i=1; i< argc; i++) { | for (i=1; i< argc; i++) { | ||
| Line 700: | Line 706: | ||
if (NULL == in || NULL == out) | if (NULL == in || NULL == out) | ||
sf_error ("not enough input"); | sf_error ("not enough input"); | ||
</ | </syntaxhighlight> | ||
Next, we use library functions <font color="#cd4b19">sf_cp</font> and <font color="#cd4b19">sf_rm</font> to do the actual work. | Next, we use library functions <font color="#cd4b19">sf_cp</font> and <font color="#cd4b19">sf_rm</font> to do the actual work. | ||
<c> | <syntaxhighlight lang="c"> | ||
sf_cp(in,out); | sf_cp(in,out); | ||
if (NULL != strstr ( | if (NULL != strstr (prog,"mv")) | ||
sf_rm(infile,false,false,false); | sf_rm(infile,false,false,false); | ||
</ | </syntaxhighlight> | ||
==sfcut== | ==sfcut== | ||
{| class="wikitable" align="center" cellspacing="0" border="1" | {| class="wikitable" align="center" cellspacing="0" border="1" | ||
! colspan="4" style="background:#ffdead;" | Zero a portion of the dataset. | ! colspan="4" style="background:#ffdead;" | Zero a portion of the dataset. | ||
|- | |||
! colspan="4" | sfcut < in.rsf > out.rsf verb=n j#=(1,...) d#=(d1,d2,...) f#=(0,...) min#=(o1,o2,,...) n#=(0,...) max#=(o1+(n1-1)*d1,o2+(n1-1)*d2,,...) | |||
|- | |- | ||
| colspan="4" | <br>Reverse of window. | |||
|- | |- | ||
| | | ''float '' || '''d#=(d1,d2,...)''' || || sampling in #-th dimension | ||
|- | |||
| ''largeint'' || '''f#=(0,...)''' || || window start in #-th dimension | |||
|- | |||
| ''int '' || '''j#=(1,...)''' || || jump in #-th dimension | |||
|- | |||
| ''float '' || '''max#=(o1+(n1-1)*d1,o2+(n1-1)*d2,,...)''' || || maximum in #-th dimension | |||
|- | |||
| ''float '' || '''min#=(o1,o2,,...)''' || || minimum in #-th dimension | |||
|- | |||
| ''int '' || '''n#=(0,...)''' || || window size in #-th dimension | |||
|- | |- | ||
| ''bool '' || '''verb=n''' || [y/n] || Verbosity flag | | ''bool '' || '''verb=n''' || [y/n] || Verbosity flag | ||
|} | |} | ||
The <tt>sfcut</tt> command is related to <tt>sfwindow</tt> and has the same | The <tt>sfcut</tt> command is related to <tt>sfwindow</tt> and has the same | ||
set of arguments only instead of extracting the selected window, it fills it | set of arguments, only instead of extracting the selected window, it fills it | ||
with zeroes. The size of the input data is preserved. | with zeroes. The size of the input data is preserved. | ||
Examples: | Examples: | ||
| Line 751: | Line 768: | ||
! colspan="4" style="background:#ffdead;" | Convert between different formats. | ! colspan="4" style="background:#ffdead;" | Convert between different formats. | ||
|- | |- | ||
! colspan="4" | sfdd < in.rsf > out.rsf line=8 form= type= format= | ! colspan="4" | sfdd < in.rsf > out.rsf trunc=n line=8 ibm=n form= type= format= | ||
|- | |- | ||
| ''string '' || '''form=''' || || ascii, native, xdr | | ''string '' || '''form=''' || || ascii, native, xdr | ||
|- | |- | ||
| ''string '' || '''format=''' || || Element format (for conversion to ASCII) | | ''string '' || '''format=''' || || Element format (for conversion to ASCII) | ||
|- | |||
| ''bool '' || '''ibm=n''' || [y/n] || Special case - assume integers actually represent IBM floats | |||
|- | |- | ||
| ''int '' || '''line=8''' || || Number of numbers per line (for conversion to ASCII) | | ''int '' || '''line=8''' || || Number of numbers per line (for conversion to ASCII) | ||
|- | |- | ||
| ''string '' || '''type=''' || || int, float, complex | | ''bool '' || '''trunc=n''' || [y/n] || Truncate or round to nearest when converting from float to int/short | ||
|- | |||
| ''string '' || '''type=''' || || int, float, complex, short, long | |||
|} | |} | ||
| Line 817: | Line 838: | ||
The <tt>sfdisfil</tt> program simply dumps the data contents to the standard | The <tt>sfdisfil</tt> program simply dumps the data contents to the standard | ||
output in a text form. It is used mostly for debugging purposes to | output in a text form. It is used mostly for debugging purposes to examine RSF files quickly. Here is an example: | ||
examine RSF files. Here is an example: | |||
<pre> | <pre> | ||
bash$ sfmath o1=0 d1=2 n1=12 output=x1 > test.rsf | bash$ sfmath o1=0 d1=2 n1=12 output=x1 > test.rsf | ||
| Line 840: | Line 860: | ||
|- | |- | ||
! colspan="4" | sfdottest mod=mod.rsf dat=dat.rsf > pip.rsf | ! colspan="4" | sfdottest mod=mod.rsf dat=dat.rsf > pip.rsf | ||
|- | |||
| ''file '' || '''dat=''' || || auxiliary input file name | |||
|- | |||
| ''file '' || '''mod=''' || || auxiliary input file name | |||
|} | |} | ||
<tt>sfdottest</tt> is a generic dot-product test program for testing | <tt>sfdottest</tt> is a generic dot-product test program for testing | ||
| Line 862: | Line 885: | ||
where <tt>mod.rsf</tt> and <tt>dat.rsf</tt> are RSF files that | where <tt>mod.rsf</tt> and <tt>dat.rsf</tt> are RSF files that | ||
represent vectors from the model and data spaces. Pay attention to the | represent vectors from the model and data spaces. Pay attention to the | ||
dimensions and size of these vectors! If the program does not respond | |||
for a very long time, | for a very long time, the dimension and size | ||
of the vectors | of the vectors may be inconsistent with the requirement of the program to be | ||
tested. <tt>sfdottest</tt> | tested. <tt>sfdottest</tt> | ||
does not create any temporary files and | does not create any temporary files and has no restrictive | ||
limitations on the size of the vectors. | limitations on the size of the vectors. | ||
Here is an example. We first | Here is an example. We first create a vector with 100 elements using | ||
<tt>sfspike</tt> and then run <tt>sfdottest</tt> to test the | <tt>sfspike</tt> and then run <tt>sfdottest</tt> to test the | ||
<tt>sfcausint</tt> program. <tt>sfcausint</tt> implements a linear | <tt>sfcausint</tt> program. <tt>sfcausint</tt> implements a linear operator of causal integration and its adjoint, the anti-causal | ||
operator of causal integration and its adjoint, the anti-causal | |||
integration. | integration. | ||
<pre> | <pre> | ||
| Line 916: | Line 938: | ||
! colspan="4" style="background:#ffdead;" | Output parameters from the header. | ! colspan="4" style="background:#ffdead;" | Output parameters from the header. | ||
|- | |- | ||
! colspan="4" | sfget | ! colspan="4" | sfget parform=y all=n par1 par2 ... | ||
|- | |||
| ''bool '' || '''all=n''' || [y/n] || If output all values. | |||
|- | |- | ||
| ''bool '' || '''parform=y''' || [y/n] || If y, print out parameter=value. If n, print out value. | | ''bool '' || '''parform=y''' || [y/n] || If y, print out parameter=value. If n, print out value. | ||
|} | |} | ||
The <tt>sfget</tt> program extracts a parameter value from an RSF file. It is | The <tt>sfget</tt> program extracts a parameter value from an RSF file. It is | ||
| Line 932: | Line 955: | ||
See also <tt>sfput</tt>. | See also <tt>sfput</tt>. | ||
====Implementation: [ | ====Implementation: [https://github.com/ahay/src/blob/master/system/main/get.c system/main/get.c]==== | ||
The implementation is trivial. Loop through all command-line parameters that contain | The implementation is trivial. Loop through all command-line parameters that contain | ||
the "=" character. | the "=" character. | ||
<c> | <syntaxhighlight lang="c"> | ||
for (i = 1; i < argc; i++) { | for (i = 1; i < argc; i++) { | ||
key = argv[i]; | key = argv[i]; | ||
if (NULL != strchr(key,'=')) continue; | if (NULL != strchr(key,'=')) continue; | ||
</ | </syntaxhighlight> | ||
Get the parameter value (as string) and output it as either | Get the parameter value (as a string) and output it as either | ||
<tt>key=value</tt> or <tt>value</tt>, depending on the | <tt>key=value</tt> or <tt>value</tt>, depending on the | ||
<tt>parform</tt> parameter. | <tt>parform</tt> parameter. | ||
<c> | <syntaxhighlight lang="c"> | ||
string = sf_histstring(in,key); | string = sf_histstring(in,key); | ||
if (NULL == string) { | if (NULL == string) { | ||
| Line 952: | Line 975: | ||
printf("%s\n",string); | printf("%s\n",string); | ||
} | } | ||
</ | </syntaxhighlight> | ||
==sfheadercut== | ==sfheadercut== | ||
| Line 961: | Line 984: | ||
|- | |- | ||
| colspan="4" | <br>The input data is a collection of traces n1xn2,<br>mask is an integer array of size n2. | | colspan="4" | <br>The input data is a collection of traces n1xn2,<br>mask is an integer array of size n2. | ||
|- | |||
| ''file '' || '''mask=''' || || auxiliary input file name | |||
|} | |} | ||
<tt>sfheadercut</tt> is close to <tt>sfheaderwindow</tt> but instead | <tt>sfheadercut</tt> is close to <tt>sfheaderwindow</tt> but instead | ||
| Line 1,008: | Line 1,032: | ||
45: 0 0 0 0 0 | 45: 0 0 0 0 0 | ||
</pre> | </pre> | ||
==sfheadersort== | ==sfheadersort== | ||
| Line 1,070: | Line 1,092: | ||
! colspan="4" style="background:#ffdead;" | Window a dataset based on a header mask. | ! colspan="4" style="background:#ffdead;" | Window a dataset based on a header mask. | ||
|- | |- | ||
! colspan="4" | sfheaderwindow mask=head.rsf < in.rsf > out.rsf | ! colspan="4" | sfheaderwindow mask=head.rsf < in.rsf > out.rsf inv=n | ||
|- | |- | ||
| colspan="4" | <br>The input data is a collection of traces n1xn2,<br>mask is an integer array os size n2, windowed is n1xm2,<br>where m2 is the number of nonzero elements in mask. | | colspan="4" | <br>The input data is a collection of traces n1xn2,<br>mask is an integer array os size n2, windowed is n1xm2,<br>where m2 is the number of nonzero elements in mask. | ||
|- | |||
| ''bool '' || '''inv=n''' || [y/n] || inversion flag | |||
|- | |||
| ''file '' || '''mask=''' || || auxiliary input file name | |||
|} | |} | ||
| Line 1,120: | Line 1,146: | ||
In this case, only three traces are selected for the output. Thanks to | In this case, only three traces are selected for the output. Thanks to | ||
the separation between headers and data, the operation of | the separation between headers and data, the operation of | ||
<tt>sfheaderwindow</tt> is optimally efficient. | <tt>sfheaderwindow</tt> is optimally efficient. | ||
==sfin== | ==sfin== | ||
| Line 1,126: | Line 1,152: | ||
! colspan="4" style="background:#ffdead;" | Display basic information about RSF files. | ! colspan="4" style="background:#ffdead;" | Display basic information about RSF files. | ||
|- | |- | ||
! colspan="4" | sfin info=y check=2. trail=y file1.rsf file2.rsf ... | ! colspan="4" | sfin info=y check=2. trail=y [<file0.rsf] file1.rsf file2.rsf ... | ||
|- | |- | ||
| colspan="4" | n1,n2,... are data dimensions<br>o1,o2,... are axis origins<br>d1,d2,... are axis sampling intervals<br>label1,label2,... are axis labels<br>unit1,unit2,... are axis units | | colspan="4" | n1,n2,... are data dimensions<br>o1,o2,... are axis origins<br>d1,d2,... are axis sampling intervals<br>label1,label2,... are axis labels<br>unit1,unit2,... are axis units | ||
| Line 1,196: | Line 1,222: | ||
</pre> | </pre> | ||
To actually eliminate annoying trailing dimensions of length one (not just stop displaying them with <tt>trail=n</tt>), you may use <tt>sed</tt>. Example for eliminating axis 6: | To actually eliminate annoying trailing dimensions of length one (not just stop displaying them with <tt>trail=n</tt>), you may use <tt>sed</tt>. Example for eliminating axis 6: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
sed -i 's/n6=1//g' file.rsf | sed -i 's/n6=1//g' file.rsf | ||
</ | </syntaxhighlight> | ||
==sfinterleave== | ==sfinterleave== | ||
| Line 1,255: | Line 1,281: | ||
! colspan="4" style="background:#ffdead;" | Create a mask. | ! colspan="4" style="background:#ffdead;" | Create a mask. | ||
|- | |- | ||
! colspan="4" | sfmask < in.rsf > out.rsf min= | ! colspan="4" | sfmask < in.rsf > out.rsf min= max= | ||
|- | |- | ||
| colspan="4" | <br>Mask is an integer data with ones and zeros. <br>Ones correspond to input values between min and max.<br><br>The output can be used with sfheaderwindow. | | colspan="4" | <br>Mask is an integer data with ones and zeros. <br>Ones correspond to input values between min and max.<br><br>The output can be used with sfheaderwindow. | ||
|- | |- | ||
| ''float '' || '''max= | | ''float '' || '''max=''' || || maximum header value | ||
|- | |- | ||
| ''float '' || '''min= | | ''float '' || '''min=''' || || minimum header value | ||
|} | |} | ||
| Line 1,282: | Line 1,308: | ||
! colspan="4" style="background:#ffdead;" | Mathematical operations on data files. | ! colspan="4" style="background:#ffdead;" | Mathematical operations on data files. | ||
|- | |- | ||
! colspan="4" | sfmath > out.rsf type= unit= output= | ! colspan="4" | sfmath > out.rsf nostdin=n n#= d#=(1,1,...) o#=(0,0,...) label#= unit#= type= label= unit= output= | ||
|- | |- | ||
| colspan="4" | <br>Known functions: cos, sin, tan, acos, asin, atan, <br> | | colspan="4" | <br>Known functions: <br>cos, sin, tan, acos, asin, atan, <br>cosh, sinh, tanh, acosh, asinh, atanh,<br>exp, log, sqrt, abs,<br>erf, erfc, sign (for float data),<br>arg, conj, real, imag (for complex data).<br><br>sfmath will work on float or complex data, but all the input and output<br>files must be of the same data type.<br><br>An alternative to sfmath is sfadd, which may be more efficient, but is<br>less versatile.<br><br>Examples:<br><br>sfmath x=file1.rsf y=file2.rsf power=file3.rsf output='sin((x+2*y)^power)' > out.rsf<br>sfmath < file1.rsf tau=file2.rsf output='exp(tau*input)' > out.rsf<br>sfmath n1=100 type=complex output="exp(I*x1)" > out.rsf<br><br>Arguments which are not treated as variables in mathematical expressions:<br>datapath=, type=, out=<br><br>See also: sfheadermath. | ||
|- | |||
| ''float '' || '''d#=(1,1,...)''' || || sampling on #-th axis | |||
|- | |||
| ''string '' || '''label=''' || || data label | |||
|- | |||
| ''string '' || '''label#=''' || || label on #-th axis | |||
|- | |||
| ''largeint'' || '''n#=''' || || size of #-th axis | |||
|- | |||
| ''bool '' || '''nostdin=n''' || [y/n] || y - ignore stdin | |||
|- | |||
| ''float '' || '''o#=(0,0,...)''' || || origin on #-th axis | |||
|- | |- | ||
| ''string '' || '''output=''' || || Mathematical description of the output | | ''string '' || '''output=''' || || Mathematical description of the output | ||
| Line 1,290: | Line 1,328: | ||
| ''string '' || '''type=''' || || output data type [float,complex] | | ''string '' || '''type=''' || || output data type [float,complex] | ||
|- | |- | ||
| ''string '' || '''unit=''' || || | | ''string '' || '''unit=''' || || data unit | ||
|- | |||
| ''string '' || '''unit#=''' || || unit on #-th axis | |||
|} | |} | ||
<tt>sfmath</tt> is a versatile program for mathematical operations | <tt>sfmath</tt> is a versatile program for mathematical operations | ||
with RSF files. It can operate with several input | with RSF files. It can operate with several input files with the | ||
same dimensions and data type. The data type can be real (floating | same dimensions and data type. The data type can be real (floating | ||
point) or complex. | point) or complex. The following example demonstrates several | ||
features of <tt>sfmath</tt>. | features of <tt>sfmath</tt>. | ||
<pre> | <pre> | ||
| Line 1,324: | Line 1,364: | ||
</pre> | </pre> | ||
Here we refer to input files by names (<tt>r</tt> and <tt>a</tt>) and combine the names in a formula. | Here we refer to input files by names (<tt>r</tt> and <tt>a</tt>) and combine the names in a formula. | ||
Functions can be nested and combined, and variable names, as well as the <tt>input</tt> keyword, may be combined with the axes keywords <tt>x1</tt>, <tt>x2</tt>, etc. Here is an example that shifts a wavelet -0.4s to t=0, computes the frequency-domain complex square root (equivalent to the convolutional square root in time), and shifts the result back to t=0.4s: | |||
<syntaxhighlight lang="bash"> | |||
pi=3.14159265 | |||
tshift=0.4 | |||
sfspike n1=256 k1=101 |\ | |||
sfbandpass flo=4 fhi=30 |\ | |||
sffft1 opt=n sym=y |\ | |||
sfmath output="sqrt(input*exp(2*$pi*$tshift*x1*I))*exp(-2*$pi*$tshift*x1*I)" |\ | |||
sffft1 opt=n sym=y inv=y |\ | |||
sfgraph |\ | |||
sfpen | |||
</syntaxhighlight> | |||
==sfpad== | ==sfpad== | ||
| Line 1,329: | Line 1,383: | ||
! colspan="4" style="background:#ffdead;" | Pad a dataset with zeros. | ! colspan="4" style="background:#ffdead;" | Pad a dataset with zeros. | ||
|- | |- | ||
! colspan="4" | sfpad < in.rsf > out.rsf | ! colspan="4" | sfpad < in.rsf > out.rsf beg#=0 end#=0 n#= | ||
|- | |- | ||
| colspan="4" | | | colspan="4" | <br>n#out is equivalent to n#, both of them overwrite end#.<br><br>Other parameters from the command line are passed to the output (similar to sfput). | ||
|- | |||
| ''int '' || '''beg#=0''' || || the number of zeros to add before the beginning of #-th axis | |||
|- | |||
| ''int '' || '''end#=0''' || || the number of zeros to add after the end of #-th axis | |||
|- | |||
| ''int '' || '''n#=''' || || the output length of #-th axis - padding at the end | |||
|} | |} | ||
<tt>sfpad</tt> increases the dimensions of the input dataset by padding | |||
<tt> | |||
the data with zeroes. Here are some simple examples. | the data with zeroes. Here are some simple examples. | ||
<pre> | <pre> | ||
| Line 1,374: | Line 1,433: | ||
! colspan="4" style="background:#ffdead;" | Input parameters into a header. | ! colspan="4" style="background:#ffdead;" | Input parameters into a header. | ||
|- | |- | ||
! colspan="4" | sfput < in.rsf > out.rsf | ! colspan="4" | sfput < in.rsf > out.rsf [parameter=value list] | ||
|} | |} | ||
| Line 1,380: | Line 1,439: | ||
<tt>sfput</tt> is a very simple program. It simply appends parameters | <tt>sfput</tt> is a very simple program. It simply appends parameters | ||
from the command line to the output RSF file. One can achieve similar | from the command line to the output RSF file. One can achieve similar | ||
results | results by editing the file by hand or with standard Unix utilities like | ||
<tt>sed</tt> and <tt>echo</tt>. <tt>sfput</tt> is sometimes more | <tt>sed</tt> and <tt>echo</tt>. <tt>sfput</tt> is sometimes more | ||
convenient because it handles input/output operations similarly to | convenient because it handles input/output operations similarly to | ||
other | other Madagascar programs. | ||
<pre> | <pre> | ||
bash$ sfspike n1=10 > spike.rsf | bash$ sfspike n1=10 > spike.rsf | ||
| Line 1,410: | Line 1,469: | ||
<tt>sfreal</tt> extracts the real part of a complex type dataset. The | <tt>sfreal</tt> extracts the real part of a complex type dataset. The | ||
imaginary part can be extracted with <tt>sfimag</tt>, | imaginary part can be extracted with <tt>sfimag</tt>, and the real | ||
and imaginary part can be combined together with <tt>sfcmplx</tt>. | and imaginary part can be combined together with <tt>sfcmplx</tt>. | ||
Here is a simple example. Let us first create a complex dataset | Here is a simple example. Let us first create a complex dataset | ||
| Line 1,439: | Line 1,498: | ||
! colspan="4" style="background:#ffdead;" | Reverse one or more axes in the data hypercube. | ! colspan="4" style="background:#ffdead;" | Reverse one or more axes in the data hypercube. | ||
|- | |- | ||
! colspan="4" | sfreverse < in.rsf > out.rsf which=-1 verb= | ! colspan="4" | sfreverse < in.rsf > out.rsf which=-1 verb=n memsize=sf_memsize() opt= | ||
|- | |- | ||
| ''int '' || '''memsize=sf_memsize()''' || || Max amount of RAM (in Mb) to be used | | ''int '' || '''memsize=sf_memsize()''' || || Max amount of RAM (in Mb) to be used | ||
| Line 1,598: | Line 1,657: | ||
! 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 the real part and even ones for the 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> | ||
| Line 1,631: | Line 1,693: | ||
! 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 | | 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. | ||
| Line 1,671: | Line 1,736: | ||
10: 0.2 0.4 0.6 0.8 1 | 10: 0.2 0.4 0.6 0.8 1 | ||
</pre> | </pre> | ||
The <tt>rscale=</tt> parameter is synonymous | The <tt>rscale=</tt> parameter is synonymous with <tt>dscale=</tt> except | ||
when it is equal to zero. With <tt>sfscale dscale=0</tt>, the dataset gets | when it is equal to zero. With <tt>sfscale dscale=0</tt>, the dataset gets | ||
multiplied by zero. If using <tt>rscale=0</tt>, the other parameters are | multiplied by zero. If using <tt>rscale=0</tt>, the other parameters are | ||
| Line 1,677: | Line 1,742: | ||
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== | ||
| Line 1,688: | Line 1,747: | ||
! 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. | ||
| Line 1,714: | Line 1,773: | ||
| ''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 | ||
| Line 1,793: | Line 1,853: | ||
10: 0 0 0.6 0.4 0 | 10: 0 0 0.6 0.4 0 | ||
</pre> | </pre> | ||
<tt>sfspike</tt> supplies default dimensions and labels to all | <tt>sfspike</tt> supplies default dimensions and labels to all axes: | ||
<pre> | <pre> | ||
bash$ sfspike n1=5 n2=3 n3=4 > spike.rsf | bash$ sfspike n1=5 n2=3 n3=4 > spike.rsf | ||
| Line 1,904: | Line 1,964: | ||
! 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. | ||
| Line 1,915: | Line 1,975: | ||
|- | |- | ||
| ''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 | ||
| Line 1,965: | Line 2,030: | ||
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 < | 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 | ||
| Line 1,998: | Line 2,063: | ||
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 < | amount of available memory using the <tt>memsize=</tt> parameter or | ||
the < | the <tt>RSFMEMSIZE</tt> environmental variable. | ||
==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 | ! 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 | ||
|- | |- | ||
| '' | | ''largeint'' || '''f#=(0,...)''' || || window start in #-th dimension | ||
|- | |- | ||
| ''int '' || '''j#=(1,...)''' || || jump in #-th dimension | | ''int '' || '''j#=(1,...)''' || || jump in #-th dimension | ||
| Line 2,017: | Line 2,084: | ||
| ''float '' || '''min#=(o1,o2,,...)''' || || minimum in #-th dimension | | ''float '' || '''min#=(o1,o2,,...)''' || || minimum 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 | ||
| Line 2,070: | Line 2,137: | ||
5: 12 | 5: 12 | ||
</pre> | </pre> | ||
Alternatively, <b>sfwindow</b> can | Alternatively, <b>sfwindow</b> can select a window from the minimum and maximum | ||
parameters | parameters. In the following example, we are | ||
creating a dataset with <b>sfspike</b> and then windowing a portion of it | creating a dataset with <b>sfspike</b> and then windowing a portion of it | ||
between 1 and 2 seconds in time and sampled at 8 miliseconds. | between 1 and 2 seconds in time and sampled at 8 miliseconds. | ||
| Line 2,136: | Line 2,203: | ||
| ''float '' || '''maxe=10.''' || || stability constraint | | ''float '' || '''maxe=10.''' || || stability constraint | ||
|} | |} | ||
Sample workflow from [http:// | Sample workflow from [http://www.ahay.org/RSF/book/sep/fkamo/paper_html/ SEP-110, 63-70 (2001)], with the addition of a bandpass for the input: | ||
Create input -- a (t,x,y) common-offset cube: | Create input -- a (t,x,y) common-offset cube: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
sfspike \ | sfspike \ | ||
n1=128 o1=0.4 d1=0.0032 k1=65 label1=t \ | n1=128 o1=0.4 d1=0.0032 k1=65 label1=t \ | ||
| Line 2,145: | Line 2,212: | ||
n3=128 o3=-1.024 d3=0.016 k3=65 label3=y | \ | n3=128 o3=-1.024 d3=0.016 k3=65 label3=y | \ | ||
sfbandpass flo=5 fhi=60 > spikebps.rsf | sfbandpass flo=5 fhi=60 > spikebps.rsf | ||
</ | </syntaxhighlight> | ||
Apply log-stretch FFT: | Apply log-stretch FFT: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
<spikebps.rsf sfstretch rule=L dens=4 |\ | <spikebps.rsf sfstretch rule=L dens=4 |\ | ||
sffft1 |\ | sffft1 |\ | ||
sffft3 axis=2 |\ | sffft3 axis=2 |\ | ||
sffft3 axis=3 > spikefft3.rsf | sffft3 axis=3 > spikefft3.rsf | ||
</ | </syntaxhighlight> | ||
Compute AMO operator for a file of the dimensions of <tt>spikefft3.rsf</tt>. The only information taken from stdin are the n, o, d parameters: | Compute the AMO operator for a file of the dimensions of <tt>spikefft3.rsf</tt>. The only information taken from stdin are the n, o, d parameters: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
<spikefft3.rsf sffkamo h2=2 f2=10 h1=1.8 f1=30 >oper.rsf | <spikefft3.rsf sffkamo h2=2 f2=10 h1=1.8 f1=30 >oper.rsf | ||
</ | </syntaxhighlight> | ||
Apply the operator by multiplication and fft back to (t, mx, my): | Apply the operator by multiplication and fft back to (t, mx, my): | ||
<bash> | <syntaxhighlight lang="bash"> | ||
< spikefft3.rsf sfadd mode=prod oper.rsf |\ | < spikefft3.rsf sfadd mode=prod oper.rsf |\ | ||
sffft3 axis=3 inv=y |\ | sffft3 axis=3 inv=y |\ | ||
| Line 2,167: | Line 2,234: | ||
sffft1 inv=y |\ | sffft1 inv=y |\ | ||
sfstretch rule=L dens=4 inv=y > spikeamo.rsf | sfstretch rule=L dens=4 inv=y > spikeamo.rsf | ||
</ | </syntaxhighlight> | ||
Prepare for 8-bit greyscale visualization: | Prepare for 8-bit greyscale visualization: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
< spikeamo.rsf sfbyte pclip=100 gainpanel=a > spikebyte.rsf | < spikeamo.rsf sfbyte pclip=100 gainpanel=a > spikebyte.rsf | ||
</ | </syntaxhighlight> | ||
Picture from the middle of the impulse response: | Picture from the middle of the impulse response: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
<spikebyte.rsf sfgrey3 frame1=65 frame2=129 frame3=65 \ | <spikebyte.rsf sfgrey3 frame1=65 frame2=129 frame3=65 \ | ||
point1=0.333 title='AMO saddle, no f-k filter' | sfpen & | point1=0.333 title='AMO saddle, no f-k filter' | sfpen & | ||
</ | </syntaxhighlight> | ||
Picture illustrating the artifacts (i.e. need for f-k filter): | Picture illustrating the artifacts (i.e. need for f-k filter): | ||
<bash> | <syntaxhighlight lang="bash"> | ||
< spikebyte.rsf sfgrey3 frame1=65 frame2=97 frame3=97 \ | < spikebyte.rsf sfgrey3 frame1=65 frame2=97 frame3=97 \ | ||
point1=0.333 title='No f-k filter' | sfpen & | point1=0.333 title='No f-k filter' | sfpen & | ||
</ | </syntaxhighlight> | ||
Apply the f-k filter and (in this case) visualize: | Apply the f-k filter and (in this case) visualize: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
< spikeamo.rsf sffft1 |\ | < spikeamo.rsf sffft1 |\ | ||
sffft3 axis=2 |\ | sffft3 axis=2 |\ | ||
| Line 2,198: | Line 2,265: | ||
sfgrey3 frame1=65 frame2=97 frame3=97 point1=0.333 title='With f-k filter' |\ | sfgrey3 frame1=65 frame2=97 frame3=97 point1=0.333 title='With f-k filter' |\ | ||
sfpen & | sfpen & | ||
</ | </syntaxhighlight> | ||
==sfheaderattr== | ==sfheaderattr== | ||
| Line 2,227: | Line 2,294: | ||
For different standard keywords, a minimum, maximum, and mean values | For different standard keywords, a minimum, maximum, and mean values | ||
are reported unless they are identically zero. This quick inspection | are reported unless they are identically zero. This quick inspection | ||
can help | can help identify meaningful keywords in the data. The input | ||
data type must be <tt>int</tt>. | data type must be <tt>int</tt>. | ||
| Line 2,247: | Line 2,314: | ||
<tt>n2</tt> matrix that contains one row made out of mathematical | <tt>n2</tt> matrix that contains one row made out of mathematical | ||
operations on the other rows. <tt>sfheadermath</tt> can identify a row | operations on the other rows. <tt>sfheadermath</tt> can identify a row | ||
by number or by a standard SEGY keyword. The latter is | by number or by a standard SEGY keyword. The latter is helpful in | ||
processing headers extracted from SEGY or SU files. | processing headers extracted from SEGY or SU files. | ||
Here is an example. First, we create an SU file with <tt>suplane</tt> and convert it to RSF using <tt>sfsegyread</tt>. | Here is an example. First, we create an SU file with <tt>suplane</tt> and convert it to RSF using <tt>sfsegyread</tt>. | ||
| Line 2,278: | Line 2,345: | ||
32 elements 128 bytes | 32 elements 128 bytes | ||
</pre> | </pre> | ||
We defined " | We defined "header" as being the row number 1 in the input (note | ||
that numbering starts with 0) and combined it with "offset", which | that numbering starts with 0) and combined it with "offset", which | ||
is a standard SEGY keyword that denotes row number 11 (see the output | is a standard SEGY keyword that denotes row number 11 (see the output | ||
| Line 2,337: | Line 2,404: | ||
The SEG Y format is an [http://en.wikipedia.org/wiki/Open_standard open standard] for the exchange of geophysical data. It is controlled by the non-profit [http://www.seg.org/SEGportalWEBproject/portals/SEG_Online.portal?_nfpb=true&_pageLabel=pg_gen_content&Doc_Url=prod/SEG-Publications/Pub-Yearbook/committees.htm SEG Technical Standards Committee]. There are two versions of this standard: [http://www.seg.org/SEGportalWEBproject/prod/SEG-Publications/Pub-Technical-Standards/Documents/seg_y_rev0.pdf rev0] (1975)<ref>Barry, K.M., Cavers, D.A., and Kneale, C.W. 1975. Recommended standards for digital tape formats. ''Geophysics'', '''40''', no. 02, 344–352.</ref> and [http://www.seg.org/SEGportalWEBproject/prod/SEG-Publications/Pub-Technical-Standards/Documents/seg_y_rev1.pdf rev1] (2002)<ref>Norris, M.W., Faichney, A.K., ''Eds''. 2001. SEG Y rev1 Data Exchange format. Society of Exploration Geophysicists, Tulsa, OK, 45 pp.</ref>. The implementation in <tt>sfsegyread</tt> is a mixture of rev0 (i.e. no checks for Extended Textual Headers) and rev1 ([http://en.wikipedia.org/wiki/IEEE_floating-point_standard IEEE floating point format] allowed for trace data samples). | The SEG Y format is an [http://en.wikipedia.org/wiki/Open_standard open standard] for the exchange of geophysical data. It is controlled by the non-profit [http://www.seg.org/SEGportalWEBproject/portals/SEG_Online.portal?_nfpb=true&_pageLabel=pg_gen_content&Doc_Url=prod/SEG-Publications/Pub-Yearbook/committees.htm SEG Technical Standards Committee]. There are two versions of this standard: [http://www.seg.org/SEGportalWEBproject/prod/SEG-Publications/Pub-Technical-Standards/Documents/seg_y_rev0.pdf rev0] (1975)<ref>Barry, K.M., Cavers, D.A., and Kneale, C.W. 1975. Recommended standards for digital tape formats. ''Geophysics'', '''40''', no. 02, 344–352.</ref> and [http://www.seg.org/SEGportalWEBproject/prod/SEG-Publications/Pub-Technical-Standards/Documents/seg_y_rev1.pdf rev1] (2002)<ref>Norris, M.W., Faichney, A.K., ''Eds''. 2001. SEG Y rev1 Data Exchange format. Society of Exploration Geophysicists, Tulsa, OK, 45 pp.</ref>. The implementation in <tt>sfsegyread</tt> is a mixture of rev0 (i.e. no checks for Extended Textual Headers) and rev1 ([http://en.wikipedia.org/wiki/IEEE_floating-point_standard IEEE floating point format] allowed for trace data samples). | ||
An SEG-Y file, as understood by <tt>sfsegyread</tt>, contains a "Reel Identification Header" (3200 bytes in EBCDIC followed by 400 bytes in a binary encoding), followed by a number of "Trace Blocks." Each "Trace Block" contains a 240-byte "Trace Header" (binary) followed by "Trace Data" -- a sequence of <tt>ns</tt> samples. Binary values in both reel headers and trace headers are two's complement integers, either two bytes or four bytes long. There are no floating-point values defined in the headers. Trace Data samples can have various encodings, either floating point or integer, described further down, but they are all big-endian. To convert from SEG-Y to RSF, <tt>sfsegyread</tt> will strip the tape reel EBCDIC header and convert it to ASCII, will extract the reel binary header without changing it, and will put the trace headers into one RSF file, and the traces themselves on another. | |||
===SEG-Y Trace Headers=== | ===SEG-Y Trace Headers=== | ||
In the SEG-Y standard, only the first 180 bytes of the 240-byte trace header are defined; bytes 181-240 are reserved for non-standard header information, and these locations are increasingly used in modern SEG-Y files and | In the SEG-Y standard, only the first 180 bytes of the 240-byte trace header are defined; bytes 181-240 are reserved for non-standard header information, and these locations are increasingly used in modern SEG-Y files and their variants. The standard provides for a total of 71 4-byte and 2-byte predefined header words. These 71 standard words have defined lengths and byte offsets, and only these words and byte locations are read using <tt>segyread</tt> and output to the RSF header file with the <tt>tfile=</tt> option. The user may remap these predefined keywords to different byte offsets. | ||
===SU File Format=== | ===SU File Format=== | ||
An [http://www.cwp.mines.edu/sututor/node22.html SU file] is nothing more than | An [http://www.cwp.mines.edu/sututor/node22.html SU file] is nothing more than an SEG-Y file without the reel headers and with the Trace Data samples in the native encoding of the CPU the file was created on (Attention -- limited portability!). So, to convert from SU to RSF, <tt>sfsegyread</tt> will just separate headers and traces into two RSF files. | ||
===SEG-Y specific parameters=== | ===SEG-Y specific parameters=== | ||
*<tt>hfile=</tt> specifies the name of the file in which the EBCDIC reel header will be put after conversion to ASCII. If you are certain there is no useful information in it, <tt>hfile=/dev/null</tt> works just fine. If you do not specify anything for this parameter you will get an ASCII file named <tt>header</tt> in the current directory. If you want to quickly preview this header before running <tt>sfsegyread</tt>, use<pre>dd if=input.segy count=40 bs=80 cbs=80 conv=unblock,ascii</pre> | *<tt>hfile=</tt> specifies the name of the file in which the EBCDIC reel header will be put after conversion to ASCII. If you are certain there is no useful information in it, <tt>hfile=/dev/null</tt> works just fine. If you do not specify anything for this parameter, you will get an ASCII file named <tt>header</tt> in the current directory. If you want to quickly preview this header before running <tt>sfsegyread</tt>, use<pre>dd if=input.segy count=40 bs=80 cbs=80 conv=unblock,ascii</pre> | ||
*<tt>bfile=</tt> specifies name of the file in which the binary reel header (the 400- | *<tt>bfile=</tt> specifies the name of the file in which the binary reel header (the 400-byte thing following the 3600-byte EBCDIC) will be put without any conversion. The default name is "binary". Unless you have software that knows how to read exactly this special type of file, it will be completely useless, so do <tt>bfile=/dev/null</tt> | ||
*<tt>format=</tt> specifies the format in which the trace data samples are in the SEG-Y input file. This is read from the binary reel header of the SEG-Y file. Valid values are 1(IBM floating point), 2 (4-byte integer), 3 (2-byte integer) and 5 (IEEE floating point). If the input file is SU, the format will be assumed to be the native <tt>float</tt> format. | *<tt>format=</tt> specifies the format in which the trace data samples are in the SEG-Y input file. This is read from the binary reel header of the SEG-Y file. Valid values are 1(IBM floating point), 2 (4-byte integer), 3 (2-byte integer), and 5 (IEEE floating point). If the input file is SU, the format will be assumed to be the native <tt>float</tt> format. | ||
*<tt>keyname=</tt> specifies the byte offset to remap a header using the trace header key names shown above. For example, if the CDP locations have been placed in bytes 181-184 instead of the standard 21-24, <tt>cdp=180</tt> will remap the trace header to that location. | *<tt>keyname=</tt> specifies the byte offset to remap a header using the trace header key names shown above. For example, if the CDP locations have been placed in bytes 181-184 instead of the standard 21-24, <tt>cdp=180</tt> will remap the trace header to that location. | ||
===SU-specific parameters=== | ===SU-specific parameters=== | ||
*<tt>suxdr=</tt> specifies whether the input file was created with | *<tt>suxdr=</tt> specifies whether the input file was created with an SU package with XDR support enabled. If you have access to the source code of your SU install (try <tt>$CWPROOT/src</tt>), type: <tt>grep 'XDRFLAG =' $CWPROOT/src/Makefile.config</tt> and look at the last uncommented entry. If no value is given for <tt>XDRFLAG</tt>, the package was not compiled with XDR support. | ||
===Common parameters=== | ===Common parameters=== | ||
*<tt>su=</tt> specifies if the input file is SU or SEG-Y. | *<tt>su=</tt> specifies if the input file is SU or SEG-Y. The default is <tt>su=n</tt> (SEG-Y file). | ||
*<tt>read=</tt> specifies what parts of the "Trace Blocks" will be read. It can be <tt>read=d</tt> (only trace data is read), <tt>read=h</tt> (only trace headers are read) or <tt>read=b</tt> (both are read). | |||
*<tt>read=</tt> specifies what parts of the "Trace Blocks" will be read. It can be <tt>read= | |||
*<tt>tfile=</tt> gives the name of the RSF file to which trace headers are written. Obviously, it should be only specified with <tt>read=h</tt> or <tt>read=b</tt>. | *<tt>tfile=</tt> gives the name of the RSF file to which trace headers are written. Obviously, it should be only specified with <tt>read=h</tt> or <tt>read=b</tt>. | ||
*<tt>mask=</tt> is an optional parameter specifying the name of a mask that says which traces will be read. The mask is a 1-D RSF file with integers. The number of samples | *<tt>mask=</tt> is an optional parameter specifying the name of a mask that says which traces will be read. The mask is a 1-D RSF file with integers. The number of mask samples is the same as the number of traces in the unmasked SEG-Y. There should be zeros in the mask in places corresponding to unwanted traces. | ||
*<tt>ns=</tt> specifies the number of samples in a trace. For SEG-Y files, the default is taken from the binary reel header, and for SU files, from the header of the first trace. This parameter is however critical enough that a command line override was given for it. | *<tt>ns=</tt> specifies the number of samples in a trace. For SEG-Y files, the default is taken from the binary reel header, and for SU files, from the header of the first trace. This parameter is, however, critical enough that a command line override was given for it. | ||
*<tt>verbose=</tt> is the verbosity flag. Can be <tt>y</tt> or <tt>n</tt>. | *<tt>verbose=</tt> is the verbosity flag. Can be <tt>y</tt> or <tt>n</tt>. | ||
*<tt>endian=</tt> is a y/n flag (default y), specifying whether to automatically | *<tt>endian=</tt> is a y/n flag (default y), specifying whether to estimate automatically or not if samples in the Trace Data blocks are big-endian or little-endian. Try it if you are in trouble and do not know what else to do; otherwise, let the automatic estimation do its job. | ||
==sfsegywrite== | ==sfsegywrite== | ||
| Line 2,384: | Line 2,450: | ||
| ''bool '' || '''verb=n''' || [y/n] || Verbosity flag | | ''bool '' || '''verb=n''' || [y/n] || Verbosity flag | ||
|} | |} | ||
Please see <tt>sfsegyread</tt> for a complete description of parameter meanings and background issues. Parameters <tt>bfile</tt> and <tt>hfile</tt> should only be given values when the desired file is SEG-Y (default). The | Please see <tt>sfsegyread</tt> for a complete description of parameter meanings and background issues. Parameters <tt>bfile</tt> and <tt>hfile</tt> should only be given values when the desired file is SEG-Y (default). The <tt>tape=</tt> tag specifies the output file. | ||
=Generic programs= | =Generic programs= | ||
Programs in this category are general signal and image processing programs. The source files for these programs can be found under [http://rsf.svn.sourceforge.net/viewvc/rsf/trunk/system/ | Programs in this category are general signal and image processing programs. The source files for these programs can be found under [http://rsf.svn.sourceforge.net/viewvc/rsf/trunk/system/generic/ system/generic] in the Madagascar distribution. | ||
==sfnoise== | ==sfnoise== | ||
{| class="wikitable" align="center" cellspacing="0" border="1" | {| class="wikitable" align="center" cellspacing="0" border="1" | ||
| Line 2,637: | Line 2,703: | ||
|} | |} | ||
Different [ | Different [https://ahay.org/blog/2005/03/28/color-schemes/ color schemes] are available | ||
for sfgrey and sfgrey3. Examples are in the book at [ | for sfgrey and sfgrey3. Examples are in the book at [https://ahay.org/RSF/book/rsf/rsf/sfgrey.html rsf/rsf/sfgrey]. | ||
==sfgrey== | ==sfgrey== | ||
| Line 2,691: | Line 2,757: | ||
|} | |} | ||
Different [ | 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]. | ||
and examples are in the book at [ | |||
==sfplas== | ==sfplas== | ||
| Line 2,830: | Line 2,895: | ||
=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 | <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. | ||
<python> | <syntaxhighlight lang="python"> | ||
from rsf.proj import * | from rsf.proj import * | ||
| Line 2,861: | Line 2,926: | ||
End() | End() | ||
</ | </syntaxhighlight> | ||
=system/generic programs= | =system/generic programs= | ||
| Line 2,967: | Line 3,032: | ||
Short description of the algorithm: | Short description of the algorithm: | ||
# Start from the top (first time slice), pick an initial (source) point, evaluate all other points with the direct traveltime. | # Start from the top (first time slice), pick an initial (source) point, evaluate all other points with the direct traveltime. | ||
# At each grid point at the next level, find the traveltime to points at the previous level, add the traveltimes from the previous level, and select minimum. The | # At each grid point at the next level, find the traveltime to points at the previous level, add the traveltimes from the previous level, and select minimum. The aperture (gate= parameter in sfpick) limits the search radius. | ||
# Repeat step 2 until reaching the bottom. | # Repeat step 2 until reaching the bottom. | ||
# Pick the minimum traveltime at the bottom and track the ray back to the source by following the traveltime gradient direction. | # Pick the minimum traveltime at the bottom and track the ray back to the source by following the traveltime gradient direction. | ||
# Postprocessing (smooth= parameter in sfpick): smooth the picked ray path using shaping regularization. | # Postprocessing (smooth= parameter in sfpick): smooth the picked ray path using shaping regularization. | ||
Many people have discovered and rediscovered the algorithm. The best reference is probably ''V. Meshbey, E. Ragoza, D. Kosloff, U. Egozi, and D. Wexler, 2002, Three-dimensional Travel-time Calculation Based on Fermat's Principle: Pure and Applied Geophysics, v. 159, 1563-1582.'' | |||
=user/ivlad programs= | =user/ivlad programs= | ||
| Line 2,981: | Line 3,046: | ||
! colspan="4" | sfprep4plot inp= out= verb=n h=none w=none unit= ppi= prar=y | ! colspan="4" | sfprep4plot inp= out= verb=n h=none w=none unit= ppi= prar=y | ||
|- | |- | ||
| colspan="4" | Only one of the h and w parameters needs to be specified.<br>If prar=n, no action will be taken on axis for which h/w was not specified<br>If prar=y and only one par (h or w) is specified, the picture will scale<br>along both axes until it is of the specified dimension. | | colspan="4" | Only one of the h and w parameters needs to be specified.<br>If prar=n, no action will be taken on the axis for which h/w was not specified<br>If prar=y and only one par (h or w) is specified, the picture will scale<br>along both axes until it is of the specified dimension. | ||
|- | |- | ||
| ''int '' || '''h=none''' || || output height | | ''int '' || '''h=none''' || || output height | ||
| Line 3,050: | Line 3,115: | ||
|} | |} | ||
A small usage example | A small usage example follows below. First, create an input file: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
$ echo -e '5,6,8,9.2\n11,124,5,0,1' | tee file.csv | $ echo -e '5,6,8,9.2\n11,124,5,0,1' | tee file.csv | ||
5,6,8,9.2 | 5,6,8,9.2 | ||
11,124,5,0,1 | 11,124,5,0,1 | ||
</ | </syntaxhighlight> | ||
You may notice that the number of values in each row is different. | You may notice that the number of values in each row is different. | ||
Run <tt>sfcsv2rsf</tt>. Notice that no options are needed. By default, zeros will be appended to make the rows equal length: | Run <tt>sfcsv2rsf</tt>. Notice that no options are needed. By default, zeros will be appended to make the rows equal in length: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
$ <file.csv sfcsv2rsf > junk.rsf ; sfdisfil < junk.rsf | $ <file.csv sfcsv2rsf > junk.rsf ; sfdisfil < junk.rsf | ||
0: 5 6 8 9.2 0 | 0: 5 6 8 9.2 0 | ||
5: 11 124 5 0 1 | 5: 11 124 5 0 1 | ||
</ | </syntaxhighlight> | ||
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 | 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 transposed on disk: | ||
<syntaxhighlight lang="bash"> | |||
$ sfin junk.rsf | $ sfin junk.rsf | ||
junk.rsf: | junk.rsf: | ||
| Line 3,077: | Line 3,143: | ||
n2=2 d2=1 o2=0 unit2="unknown" | n2=2 d2=1 o2=0 unit2="unknown" | ||
10 elements 40 bytes | 10 elements 40 bytes | ||
</ | </syntaxhighlight> | ||
Depending on your needs, you may want to run the output through <tt>sftransp</tt>. However, if creating an input for <tt>sfmatmult</tt>, this will not be necessary, because <tt>sfmatmult</tt> is made to work with matrices that are displayed with <tt>sfdisfil</tt>, and takes as input a transpose matrix. | |||
Pipes can be used, of course, to skip the creation of intermediary files: | Pipes can be used, of course, to skip the creation of intermediary files: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
$ <file.csv sfcsv2rsf | sfdisfil | $ <file.csv sfcsv2rsf | sfdisfil | ||
0: 5 6 8 9.2 0 | 0: 5 6 8 9.2 0 | ||
5: 11 124 5 0 1 | 5: 11 124 5 0 1 | ||
</ | </syntaxhighlight> | ||
Note that since this program does not need any arguments (just stdin and stdout), | Note that since this program does not need any arguments (just stdin and stdout), it will not display the man page when called with no arguments. In order to consult the automatically generated documentation, you need to pass the option <tt>help=y</tt> . | ||
=user/jennings programs= | =user/jennings programs= | ||
| Line 3,106: | Line 3,172: | ||
This program computes the "theoretical" size in bytes of the data fork of RSF files. The actual space occupied on disk may be different and machine dependent due to disk blocking factors, etc. This theoretical array size should be reproducible. It is also fast because the program only reads the RSF headers files, not the actual data. | This program computes the "theoretical" size in bytes of the data fork of RSF files. The actual space occupied on disk may be different and machine-dependent due to disk blocking factors, etc. This theoretical array size should be reproducible. It is also fast because the program only reads the RSF headers files, not the actual data. | ||
For example, to get the total size of all RSF files in a directory, in human readable format, without listing each file: | For example, to get the total size of all RSF files in a directory, in human-readable format, without listing each file: | ||
<pre> | <pre> | ||
sfsizes files=n human=y *.rsf | sfsizes files=n human=y *.rsf | ||
| Line 3,155: | Line 3,221: | ||
This tool lists Vplot files in "Fig" and "Lock" directories and compares them using sfvplotdiff. | This tool lists Vplot files in the "Fig" and "Lock" directories and compares them using sfvplotdiff. | ||
The Fig directory defaults to ./Fig and the Lock directory defaults to the | The Fig directory defaults to ./Fig and the Lock directory defaults to the | ||
| Line 3,169: | Line 3,235: | ||
if any of these environment variables are not defined. | if any of these environment variables are not defined. | ||
The tool gives a summary count of files that are the same, files that | The tool gives a summary count of files that are the same, files that are different, files in Fig that are missing from Lock, and files in Lock that are missing from Fig. | ||
are different, files in Fig that are missing from Lock, and files in | |||
Lock that are missing from Fig. | |||
The parameters '''list''' (default=all) and '''show''' (default=none) control which files are listed or "flipped" with sfpen. The file listing indicates which files are the same, which are different, and which are missing from Fig or Lock. | The parameters '''list''' (default=all) and '''show''' (default=none) control which files are listed or "flipped" with sfpen. The file listing indicates which files are the same, which are different, and which are missing from Fig or Lock. | ||
| Line 3,186: | Line 3,250: | ||
=user/psava programs= | =user/psava programs= | ||
== | ==sfawefd2d== | ||
{| class="wikitable" align="center" cellspacing="0" border="1" | {| class="wikitable" align="center" cellspacing="0" border="1" | ||
! colspan="4" style="background:#ffdead;" | acoustic time-domain FD modeling | ! colspan="4" style="background:#ffdead;" | acoustic time-domain FD modeling | ||
| Line 3,227: | Line 3,291: | ||
|} | |} | ||
Below, we will demonstrate an example of a model with nx=nz=200 and dx=dz=4m (size: 800x800m). There are two layers: the first is 100x200 samples in (z,x), and the velocity is 1500m/s; the second layer has the same dimension, and the velocity is 3000m/s. The density is set to 1 for the whole grid. A source and a receiver are co-located at x=400 and z=100. The full wavefield for the entire model aperture will be saved every 10th time step. | |||
< | <ol> | ||
<li>Velocity model: | |||
sfspike >Fvel.rsf mag=1500,3000 nsp=2 k1=1,101 l1=100,200 d1=4 d2=4 \ | <syntaxhighlight lang="bash"> | ||
sfspike > Fvel.rsf mag=1500,3000 nsp=2 k1=1,101 l1=100,200 d1=4 d2=4 \ | |||
label1=z label2=x n1=200 n2=200 o1=2 o2=2 unit1=m unit2=m | label1=z label2=x n1=200 n2=200 o1=2 o2=2 unit1=m unit2=m | ||
</syntaxhighlight> | |||
</li> | |||
<li>Density model: | |||
sfspike >Fden.rsf mag=1 nsp=1 k1=1 l1=200 d1=4 d2=4 label1=z \ | <syntaxhighlight lang="bash"> | ||
sfspike > Fden.rsf mag=1 nsp=1 k1=1 l1=200 d1=4 d2=4 label1=z \ | |||
label2=x n1=200 n2=200 o1=2 o2=2 unit1=m unit2=m | label2=x n1=200 n2=200 o1=2 o2=2 unit1=m unit2=m | ||
</syntaxhighlight> | |||
</li> | |||
<li>Source position (x,z): | |||
sfspike n1=2 nsp=2 k1=1,2 mag=400,100 o1=0 o2=0 >Fsou.rsf | <syntaxhighlight lang="bash"> | ||
sfspike n1=2 nsp=2 k1=1,2 mag=400,100 o1=0 o2=0 > Fsou.rsf | |||
</syntaxhighlight> | |||
</li> | |||
<li>Receiver position (x,z): | |||
sfspike n1=2 nsp=2 k1=1,2 mag=400,100 o1=0 o2=0 >Frec.rsf | <syntaxhighlight lang="bash"> | ||
sfspike n1=2 nsp=2 k1=1,2 mag=400,100 o1=0 o2=0 > Frec.rsf | |||
</syntaxhighlight> | |||
</li> | |||
<li>Source wavelet: | |||
<syntaxhighlight lang="bash"> | |||
sfspike nsp=1 n1=2000 d1=0.0005 k1=200 | sfricker1 frequency=20 |\ | sfspike nsp=1 n1=2000 d1=0.0005 k1=200 | sfricker1 frequency=20 |\ | ||
sftransp >Fwav.rsf | sftransp > Fwav.rsf | ||
</syntaxhighlight> | |||
</li> | |||
<li>Creating data at specified receiver + saving full wavefield every 10th step: | |||
sfawefd2d <Fwav.rsf vel=Fvel.rsf sou=Fsou.rsf rec=Frec.rsf wfl=Fwfl.rsf \ | <syntaxhighlight lang="bash"> | ||
den=Fden.rsf >Fdat.rsf verb=y free=y expl=y snap=y dabc=y jdata=1 jsnap=10 | sfawefd2d < Fwav.rsf vel=Fvel.rsf sou=Fsou.rsf rec=Frec.rsf wfl=Fwfl.rsf \ | ||
den=Fden.rsf > Fdat.rsf verb=y free=y expl=y snap=y dabc=y jdata=1 jsnap=10 | |||
echo 'label1=z unit1=m label2=x unit2=m' >> Fwfl.rsf | echo 'label1=z unit1=m label2=x unit2=m' >> Fwfl.rsf | ||
</syntaxhighlight> | |||
</li> | |||
<li>View the wavefield movie: | |||
< Fwfl.rsf sfgrey gainpanel=a pclip=99 color=j scalebar=y | sfpen | <syntaxhighlight lang="bash"> | ||
< Fwfl.rsf sfgrey gainpanel=a pclip=99 color=j scalebar=y | sfpen | |||
</syntaxhighlight> | |||
</li> | |||
<li>View a wavefield snapshot: | |||
<syntaxhighlight lang="bash"> | |||
< Fwfl.rsf sfwindow f3=80 n3=1 |\ | < Fwfl.rsf sfwindow f3=80 n3=1 |\ | ||
sfgrey pclip=99 color=j title='snapshot at t=0.4s' |\ | sfgrey pclip=99 color=j title='snapshot at t=0.4s' |\ | ||
sfpen | sfpen | ||
</syntaxhighlight> | |||
</li> | |||
<li>View the data recorded at the receiver: | |||
<Fdat.rsf sfwindow |\ | <syntaxhighlight lang="bash"> | ||
< Fdat.rsf sfwindow |\ | |||
sfgraph title='Data recorded at receiver' unit2='' label2=amplitude |\ | sfgraph title='Data recorded at receiver' unit2='' label2=amplitude |\ | ||
sfpen | sfpen | ||
</ | </syntaxhighlight> | ||
</li> | |||
</ol> | |||
[[Image:sfawefd_wfld.jpg|frame|center|sfawefd wavefield screenshot]] | [[Image:sfawefd_wfld.jpg|frame|center|sfawefd wavefield screenshot]] | ||
| Line 3,344: | Line 3,435: | ||
|} | |} | ||
This program performs 3-D and 2-D shot-record (a.k.a. shot-profile) migration with an extended Split-Step Fourier (SSF) extrapolator with multiple reference velocities (hence "extended"). It takes as input a shot wavefield (<tt>stdin</tt>), receiver wavefield (<tt>rwf=</tt>) and slowness model (<tt>slo=</tt>). Outputs are an image (<tt>stdout</tt>) and a cube of Common Image Gathers (<tt>cig=</tt>). An important parameter is <tt>nrmax</tt>, the number of reference velocities. Its default value is 1, but | This program performs 3-D and 2-D shot-record (a.k.a. shot-profile) migration with an extended Split-Step Fourier (SSF) extrapolator with multiple reference velocities (hence "extended"). It takes as input a shot wavefield (<tt>stdin</tt>), receiver wavefield (<tt>rwf=</tt>) and slowness model (<tt>slo=</tt>). Outputs are an image (<tt>stdout</tt>) and a cube of Common Image Gathers (<tt>cig=</tt>). An important parameter is <tt>nrmax</tt>, the number of reference velocities. Its default value is 1, but it should be 5 or so for reasonable results. It is also good to specify nonzero taper values (<tt>tmx</tt> and, for 3-D, <tt>tmy</tt> as well). The values of padding parameters <tt>pmx</tt> and <tt>pmy</tt> are split in two by the program, i.e., if your data x-axis is 501-points long, specify pmx=11 to get a value of 512 that will result in fast Fourier Transforms. | ||
The program will also migrate converted-wave data if a file with the S-wave slowness model (<tt>sls=</tt>) is provided. | The program will also migrate converted-wave data if a file with the S-wave slowness model (<tt>sls=</tt>) is provided. | ||
| Line 3,351: | Line 3,442: | ||
===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 [ | 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: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
sfsegyread tape=sigsbee2a_nfs.segy tfile=tdata.rsf hfile=/dev/null bfile=/dev/null > ddata.rsf | sfsegyread tape=sigsbee2a_nfs.segy tfile=tdata.rsf hfile=/dev/null bfile=/dev/null > ddata.rsf | ||
</ | </syntaxhighlight> | ||
Convert trace headers to float (required by <tt>sfheadermath</tt>): | Convert trace headers to float (required by <tt>sfheadermath</tt>): | ||
<bash> | <syntaxhighlight lang="bash"> | ||
< tdata.rsf sfdd type=float > trchdr.rsf | < tdata.rsf sfdd type=float > trchdr.rsf | ||
</ | </syntaxhighlight> | ||
Shot positions: | Shot positions: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
< trchdr.rsf sfheadermath output="fldr + 10925/150" | sfwindow squeeze=y > tsi.rsf | < trchdr.rsf sfheadermath output="fldr + 10925/150" | sfwindow squeeze=y > tsi.rsf | ||
</ | </syntaxhighlight> | ||
Extract offset positions from the trace header files, eliminate length-1 axis, scale, create a header for binning (required by <tt>sfintbin</tt>): | Extract offset positions from the trace header files, eliminate length-1 axis, scale, and create a header for binning (required by <tt>sfintbin</tt>): | ||
<bash> | <syntaxhighlight lang="bash"> | ||
< trchdr.rsf sfheadermath output="offset" |\ | < trchdr.rsf sfheadermath output="offset" |\ | ||
sfwindow squeeze=y |\ | sfwindow squeeze=y |\ | ||
| Line 3,373: | Line 3,464: | ||
sftransp |\ | sftransp |\ | ||
sfdd type=int > tos.rsf | sfdd type=int > tos.rsf | ||
</ | </syntaxhighlight> | ||
Binning and muting: | Binning and muting: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
< ddata.rsf sfintbin head=tos.rsf xkey=0 ykey=1 |\ | < ddata.rsf sfintbin head=tos.rsf xkey=0 ykey=1 |\ | ||
sfput label1=Time unit1=s d2=0.075 o2=0.0 label2=hx d3=0.150 o3=10.925 label3=sx |\ | sfput label1=Time unit1=s d2=0.075 o2=0.0 label2=hx d3=0.150 o3=10.925 label3=sx |\ | ||
sfmutter half=false t0=1.0 v0=6.0 |\ | sfmutter half=false t0=1.0 v0=6.0 |\ | ||
sfput d2=0.02286 o2=0 unit2=km d3=0.04572 o3=3.32994 unit3=km > shots.rsf | sfput d2=0.02286 o2=0 unit2=km d3=0.04572 o3=3.32994 unit3=km > shots.rsf | ||
</ | </syntaxhighlight> | ||
Keeping only 20 shots so that this 1-node job will not take forever, FFT-ing, decimating frequency slices (same as shortening the time axis), and creating y and hy axes of length 1: | Keeping only 20 shots so that this 1-node job will not take forever, FFT-ing, decimating frequency slices (same as shortening the time axis), and creating y and hy axes of length 1: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
< shots.rsf sfwindow n3=20 f3=10 j3=20 |\ | < shots.rsf sfwindow n3=20 f3=10 j3=20 |\ | ||
sffft1 |\ | sffft1 |\ | ||
| Line 3,388: | Line 3,479: | ||
sfspray axis=3 n=1 o=0 d=1 label=hy |\ | sfspray axis=3 n=1 o=0 d=1 label=hy |\ | ||
sfspray axis=5 n=1 o=0 d=1 label=sy > rfft.rsf | sfspray axis=5 n=1 o=0 d=1 label=sy > rfft.rsf | ||
</ | </syntaxhighlight> | ||
The dimensions of the cube thus created are: | The dimensions of the cube thus created are: | ||
<pre> | <pre> | ||
| Line 3,402: | Line 3,493: | ||
</pre> | </pre> | ||
Create the source wavelet (limited to the same frequency band as the data) and Fourier transform it: | Create the source wavelet (limited to the same frequency band as the data) and Fourier transform it: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
sfspike k1=1 n1=1500 d1=0.008 |\ | sfspike k1=1 n1=1500 d1=0.008 |\ | ||
sfbandpass flo=15 fhi=25 |\ | sfbandpass flo=15 fhi=25 |\ | ||
| Line 3,408: | Line 3,499: | ||
sfwindow n1=200 min1=1 j1=3 |\ | sfwindow n1=200 min1=1 j1=3 |\ | ||
sfput label1=freq > sfft.rsf | sfput label1=freq > sfft.rsf | ||
</ | </syntaxhighlight> | ||
This creates a frequency-domain wavelet: | This creates a frequency-domain wavelet: | ||
<pre> | <pre> | ||
| Line 3,418: | Line 3,509: | ||
200 elements 1600 bytes | 200 elements 1600 bytes | ||
</pre> | </pre> | ||
Create "synched" source and receiver wavefields with <tt>srsyn</tt> from wavelet and data frequency slices. | Create "synched" source and receiver wavefields with <tt>srsyn</tt> from wavelet and data frequency slices. The receiver and shot frequency slices are "placed" at the right location and padded with zeros up to the x-axis dimension specified below. | ||
<bash> | <syntaxhighlight lang="bash"> | ||
< rfft.rsf sfsrsyn nx=1067 dx=0.02286 ox=3.05562 wav=sfft.rsf swf=swav.rsf > rwav.rsf | < rfft.rsf sfsrsyn nx=1067 dx=0.02286 ox=3.05562 wav=sfft.rsf swf=swav.rsf > rwav.rsf | ||
</ | </syntaxhighlight> | ||
This creates frequency slices ready for migration for both source and receiver, only axis 1 (frequency) must become axis 3, for both datasets: | This creates frequency slices ready for migration for both source and receiver, only axis 1 (frequency) must become axis 3, for both datasets: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
< swav.rsf sftransp plane=12 | sftransp plane=23 > stra.rsf | < swav.rsf sftransp plane=12 | sftransp plane=23 > stra.rsf | ||
</ | </syntaxhighlight> | ||
<bash> | <syntaxhighlight lang="bash"> | ||
< rwav.rsf sftransp plane=12 | sftransp plane=23 > rtra.rsf | < rwav.rsf sftransp plane=12 | sftransp plane=23 > rtra.rsf | ||
</ | </syntaxhighlight> | ||
This creates a surface receiver wavefield ready for input to migration. Axis 4 is shot number. The values of axis 4 are arbitrary because each shot has been padded with zeros so that it covers the entire velocity model. Therefore the aperture of the downward continuation for each shot will be as large as the survey. | This creates a surface receiver wavefield ready for input to migration. Axis 4 is the shot number. The values of axis 4 are arbitrary because each shot has been padded with zeros so that it covers the entire velocity model. Therefore, the aperture of the downward continuation for each shot will be as large as that of the whole survey. | ||
<pre> | <pre> | ||
sfin trail=n rtra.rsf | sfin trail=n rtra.rsf | ||
| Line 3,441: | Line 3,532: | ||
4268000 elements 34144000 bytes | 4268000 elements 34144000 bytes | ||
</pre> | </pre> | ||
Convert the velocity model from SEG-Y to RSF, decimate, convert from feet to km, transpose, convert to slowness and insert an additional axis: | Convert the velocity model from SEG-Y to RSF, decimate, convert from feet to km, transpose, convert to slowness, and insert an additional axis: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
sfsegyread tape=sigsbee2a_migvel.sgy tfile=/dev/null hfile=/dev/null bfile=/dev/null |\ | sfsegyread tape=sigsbee2a_migvel.sgy tfile=/dev/null hfile=/dev/null bfile=/dev/null |\ | ||
sfput o1=0 d1=0.00762 label1=z unit1=km o2=3.05562 d2=0.01143 label2=x unit2=km |\ | sfput o1=0 d1=0.00762 label1=z unit1=km o2=3.05562 d2=0.01143 label2=x unit2=km |\ | ||
| Line 3,451: | Line 3,542: | ||
sfspray axis=2 n=1 d=1 o=0 |\ | sfspray axis=2 n=1 d=1 o=0 |\ | ||
sfput label2=y > slow.rsf | sfput label2=y > slow.rsf | ||
</ | </syntaxhighlight> | ||
This creates a slowness file ready for input to migration, with an x axis identical to the x axis of the wavefield files: | This creates a slowness file ready for input to migration, with an x-axis identical to the x-axis of the wavefield files: | ||
<pre> | <pre> | ||
$ sfin slow.rsf | $ sfin slow.rsf | ||
| Line 3,463: | Line 3,554: | ||
321167 elements 1284668 bytes | 321167 elements 1284668 bytes | ||
</pre> | </pre> | ||
Finally, the migration command (for a 4-processor machine, hence the <tt>ompnth</tt> value). We choose not to compute any image gathers (<tt>itype=o</tt>), but due to the construction of the program we still have to explicitly assign the <tt>cig</tt> tag, or else | Finally, the migration command (for a 4-processor machine, hence the <tt>ompnth</tt> value). We choose not to compute any image gathers (<tt>itype=o</tt>), but due to the construction of the program we still have to explicitly assign the <tt>cig</tt> tag, or else an RSF file with the name of the tag and no rsf extension will be created: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
< stra.rsf sfsrmig3 nrmax=20 dtmax=5e-05 eps=0.01 verb=y ompnth=4 \ | < stra.rsf sfsrmig3 nrmax=20 dtmax=5e-05 eps=0.01 verb=y ompnth=4 \ | ||
tmx=16 rwf=rtra.rsf slo=slow.rsf itype=o cig=/dev/null > img.rsf | tmx=16 rwf=rtra.rsf slo=slow.rsf itype=o cig=/dev/null > img.rsf | ||
</ | </syntaxhighlight> | ||
The migration of 20 shots takes approximately | The migration of 20 shots takes approximately three hours on a 4-processor machine (1 shot=9 minutes). Without the frequency slice decimation by a factor of 3 and the depth axis decimation by a factor of 4, it would have taken twelve times as much. The resulting image has a y-axis of length 1: | ||
<pre> | <pre> | ||
$ sfin img.rsf trail=n | $ sfin img.rsf trail=n | ||
| Line 3,480: | Line 3,571: | ||
</pre> | </pre> | ||
To properly visualize the image, we need to eliminate the axis of length 1, then transpose the x and z axes to their natural position: | To properly visualize the image, we need to eliminate the axis of length 1, then transpose the x and z axes to their natural position: | ||
<bash> | <syntaxhighlight lang="bash"> | ||
<img.rsf sfwindow squeeze=y | sftransp | sfgrey > img.vpl | <img.rsf sfwindow squeeze=y | sftransp | sfgrey > img.vpl | ||
</ | </syntaxhighlight> | ||
=References= | =References= | ||
<references/> | <references/> | ||
Latest revision as of 00:13, 19 November 2024
This guide introduces some of the most used Madagascar programs and illustrates their usage with examples.
Main programs[edit]
The source files for these programs can be found under system/main in the Madagascar distribution. The "main" programs perform general-purpose operations on RSF hypercubes regardless of the data dimensionality or physical dimensions.
sfadd[edit]
| Add, multiply, or divide RSF datasets. | |||
|---|---|---|---|
| sfadd > out.rsf scale= add= sqrt= abs= log= exp= mode= [< file0.rsf] file1.rsf file2.rsf ... | |||
| The various operations, if selected, occur in the following order: (1) Take absolute value, abs= (2) Add a scalar, add= (3) Take the natural logarithm, log= (4) Take the square root, sqrt= (5) Multiply by a scalar, scale= (6) Compute the base-e exponential, exp= (7) Add, multiply, or divide the data sets, mode= sfadd operates on integer, float, or complex data, but all the input and output files must be of the same data type. An alternative to sfadd is sfmath, which is more versatile, but may be less efficient. | |||
| bools | abs= | If true take absolute value [nin] | |
| floats | add= | Scalar values to add to each dataset [nin] | |
| bools | exp= | If true compute exponential [nin] | |
| bools | log= | If true take logarithm [nin] | |
| string | mode= | 'a' means add (default), 'p' or 'm' means multiply, 'd' means divide | |
| floats | scale= | Scalar values to multiply each dataset with [nin] | |
| bools | sqrt= | If true take square root [nin] | |
sfadd is useful for combining (adding, dividing, or multiplying) several datasets. What if you want to subtract two datasets? Easy. Use the scale parameter as follows:
bash$ sfadd data1.rsf data2.rsf scale=1,-1 > diff.rsf
or
bash$ sfadd < data1.rsf data2.rsf scale=1,-1 > diff.rsf
The same task can be accomplished with the more general sfmath program:
bash$ sfmath one=data1.rsf two=data2.rsf output='one-two' > diff.rsf
or
bash$ sfmath < data1.rsf two=data2.rsf output='input-two' > diff.rsf
In both cases, the size and shape of data1.rsf and data2.rsf hypercubes should be the same, and a warning message is printed out if the axis sampling parameters (such as o1 or d1) in these files are different.
Implementation: system/main/add.c[edit]
The first input file is either in the list or in the standard input.
/* find number of input files */
if (isatty(fileno(stdin))) {
/* no input file in stdin */
nin=0;
} else {
filename[0] = "in";
nin=1;
}Collect input files in the in array from all command-line parameters that don't contain an "=" sign. The total number of input files is nin.
for (i=1; i< argc; i++) { /* collect inputs */
if (NULL != strchr(argv[i],'=')) continue; /* not a file */
filename[nin] = argv[i];
nin++;
}
if (0==nin) sf_error ("no input");
/* nin = no of input files*/A helper function check_compat checks the compatibility of input files.
static void
check_compat (sf_datatype type /* data type */,
size_t nin /* number of files */,
sf_file* in /* input files [nin] */,
int dim /* file dimensionality */,
const int* n /* dimensions [dim] */)
/* Check that the input files are compatible.
Issue error for type mismatch or size mismatch.
Issue warning for grid parameters mismatch. */
{
int ni, id;
size_t i;
float d, di, o, oi;
char key[3];
const float tol=1.e-5; /* tolerance for comparison */
for (i=1; i < nin; i++) {
if (sf_gettype(in[i]) != type)
sf_error ("type mismatch: need %d",type);
for (id=1; id <= dim; id++) {
(void) snprintf(key,3,"n%d",id);
if (!sf_histint(in[i],key,&ni) || ni != n[id-1])
sf_error("%s mismatch: need %d",key,n[id-1]);
(void) snprintf(key,3,"d%d",id);
if (sf_histfloat(in[0],key,&d)) {
if (!sf_histfloat(in[i],key,&di) ||
(fabsf(di-d) > tol*fabsf(d)))
sf_warning("%s mismatch: need %g",key,d);
} else {
d = 1.;
}
(void) snprintf(key,3,"o%d",id);
if (sf_histfloat(in[0],key,&o) &&
(!sf_histfloat(in[i],key,&oi) ||
(fabsf(oi-o) > tol*fabsf(d))))
sf_warning("%s mismatch: need %g",key,o);
}
}
}Finally, we enter the main loop, where the input data are getting read buffer by buffer and combined in the total product depending on the data type.
for (nbuf /= sf_esize(in[0]); nsiz > 0; nsiz -= nbuf) {
if (nbuf > nsiz) nbuf=nsiz;
for (j=0; j < nin; j++) {
collect = (bool) (j != 0);
switch(type) {
case SF_FLOAT:
sf_floatread((float*) bufi,
nbuf,
in[j]);
add_float(collect,
nbuf,
(float*) buf,
(const float*) bufi,
cmode,
scale[j],
add[j],
abs_flag[j],
log_flag[j],
sqrt_flag[j],
exp_flag[j]);
break;The data combination program for floating point numbers is add_float.
static void add_float (bool collect, /* if collect */
size_t nbuf, /* buffer size */
float* buf, /* output [nbuf] */
const float* bufi, /* input [nbuf] */
char cmode, /* operation */
float scale, /* scale factor */
float add, /* add factor */
bool abs_flag, /* if abs */
bool log_flag, /* if log */
bool sqrt_flag, /* if sqrt */
bool exp_flag /* if exp */)
/* Add floating point numbers */
{
size_t j;
float f;
for (j=0; j < nbuf; j++) {
f = bufi[j];
if (abs_flag) f = fabsf(f);
f += add;
if (log_flag) f = logf(f);
if (sqrt_flag) f = sqrtf(f);
if (1. != scale) f *= scale;
if (exp_flag) f = expf(f);
if (collect) {
switch (cmode) {
case 'p': /* product */
case 'm': /* multiply */
buf[j] *= f;
break;
case 'd': /* delete */
if (f != 0.) buf[j] /= f;
break;
default: /* add */
buf[j] += f;
break;
}
} else {
buf[j] = f;
}
}
}sfattr[edit]
| Display dataset attributes. | |||
|---|---|---|---|
| sfattr < in.rsf lval=2 want= | |||
Sample output from "sfspike n1=100 | sfbandpass fhi=60 | sfattr" ******************************************* rms = 0.992354 mean = 0.987576 2-norm = 9.92354 variance = 0.00955481 std dev = 0.0977487 max = 1.12735 at 97 min = 0.151392 at 100 nonzero samples = 100 total samples = 100 ******************************************* rms = sqrt[ sum(data^2) / n ] mean = sum(data) / n norm = sum(abs(data)^lval)^(1/lval) variance = [ sum(data^2) - n*mean^2 ] / [ n-1 ] standard deviation = sqrt [ variance ] | |||
| int | lval=2 | norm option, lval is a non-negative integer, computes the vector lval-norm | |
| string | want= | 'all'(default), 'rms', 'mean', 'norm', 'var', 'std', 'max', 'min', 'nonzero', 'samples', 'short'
| |
sfattr is a useful diagnostic program. It reports certain
statistical values for an RSF dataset: RMS (root-mean-square)
amplitude, mean value, vector norm value, variance, standard deviation,
maximum and minimum values, number of nonzero samples, and the total
number of samples.
If we denote data values as for , then the RMS
value is , the mean
value is , the -norm value
is , the variance is
, and the standard
deviation is the square root of the variance. Using sfattr is a quick way to see the distribution of data values and check it for anomalies.
![{\displaystyle {\frac {1}{n-1}}\,\left[\sum \limits _{i=0}^{n}d_{i}^{2}-{\frac {1}{n}}\left(\sum \limits _{i=0}^{n}d_{i}\right)^{2}\right]}](https://wikimedia.org/api/rest_v1/media/math/render/svg/6c6e744187777d584f3b3aa9e264f8274c8dd450)
The output can be parsed using utilities such as awk, to extract only a numeric value for feeding it as a parameter value into a command line interface. Notice the backticks in the example below:
sfgrey <vel.rsf allpos=y bias=`sfattr <vel.rsf want=min | awk '{print $4}'` | sfpenImplementation: system/main/attr.c[edit]
Computations start by finding the input data (in) size (nsiz) and dimensions (dim).
dim = (size_t) sf_largefiledims (in,n);
for (nsiz=1, i=0; i < dim; i++) {
nsiz *= n[i];
}
In the main loop, we read the input data buffer by buffer.
for (nleft=nsiz; nleft > 0; nleft -= nbuf) {
nbuf = (bufsiz < nleft)? bufsiz: nleft;
switch (type) {
case SF_FLOAT:
sf_floatread((float*) buf,nbuf,in);
break;
case SF_INT:
sf_intread((int*) buf,nbuf,in);
break;
case SF_SHORT:
sf_shortread((short*) buf,nbuf,in);
break;
case SF_COMPLEX:
sf_complexread((sf_complex*) buf,nbuf,in);
break;
case SF_UCHAR:
sf_ucharread((unsigned char*) buf,nbuf,in);
break;
case SF_CHAR:
default:
sf_charread(buf,nbuf,in);
break;
}
The data attributes are accumulated in corresponding double-precision variables.
fsum += f;
fsqr += (double) f*f;
Finally, the attributes are reduced and printed out.
fmean = fsum/nsiz;
if (lval==2) fnorm = sqrt(fsqr);
else if (lval==0) fnorm = nsiz-nzero;
else fnorm = pow(flval,1./lval);
frms = sqrt(fsqr/nsiz);
if (nsiz > 1) fvar = fabs(fsqr-nsiz*fmean*fmean)/(nsiz-1);
else fvar = 0.0;
fstd = sqrt(fvar); if(NULL==want || 0==strcmp(want,"rms"))
printf("rms = %13.6g \n",(float) frms);
if(NULL==want || 0==strcmp(want,"mean"))
printf("mean = %13.6g \n",(float) fmean);
if(NULL==want || 0==strcmp(want,"norm"))
printf("%d-norm value = %13.6g \n",lval,(float) fnorm);
if(NULL==want || 0==strcmp(want,"var"))
printf("variance = %13.6g \n",(float) fvar);
if(NULL==want || 0==strcmp(want,"std"))
printf("standard deviation = %13.6g \n",(float) fstd);sfcat[edit]
| Concatenate datasets. | |||
|---|---|---|---|
| sfcat > out.rsf order= space= axis=3 nspace=(int) (ni/(20*nin) + 1) o= d= [<file0.rsf] file1.rsf file2.rsf ... | |||
| sfmerge inserts additional space between merged data. | |||
| int | axis=3 | Axis being merged | |
| float | d= | axis sampling | |
| int | nspace=(int) (ni/(20*nin) + 1) | if space=y, number of traces to insert | |
| float | o= | axis origin | |
| ints | order= | concatenation order [nin] | |
| bool | space= | [y/n] | Insert additional space.
|
sfcat and sfmerge concatenate two or more files together along a particular axis. It is the same program, only sfcat has the default space=n and sfmerge has the default space=y. Example of sfcat:
bash$ sfspike n1=2 n2=3 > one.rsf
bash$ sfin one.rsf
one.rsf:
in="/tmp/one.rsf@"
esize=4 type=float form=native
n1=2 d1=0.004 o1=0 label1="Time" unit1="s"
n2=3 d2=0.1 o2=0 label2="Distance" unit2="km"
6 elements 24 bytes
bash$ sfcat one.rsf one.rsf axis=1 > two.rsf
bash$ sfin two.rsf
two.rsf:
in="/tmp/two.rsf@"
esize=4 type=float form=native
n1=4 d1=0.004 o1=0 label1="Time" unit1="s"
n2=3 d2=0.1 o2=0 label2="Distance" unit2="km"
12 elements 48 bytes
Example of sfmerge:
bash$ sfmerge one.rsf one.rsf axis=2 > two.rsf
bash$ sfin two.rsf
two.rsf:
in="/tmp/two.rsf@"
esize=4 type=float form=native
n1=2 d1=0.004 o1=0 label1="Time" unit1="s"
n2=7 d2=0.1 o2=0 label2="Distance" unit2="km"
14 elements 56 bytes
In this case, an extra empty trace is inserted between the two merged files. The axes that are not being merged are checked for consistency:
bash$ sfcat one.rsf two.rsf > three.rsf sfcat: n2 mismatch: need 3
Implementation: system/main/cat.c[edit]
The first input file is either in the list or in the standard input.
in = (sf_file*) sf_alloc ((size_t) argc,sizeof(sf_file));
if (!sf_stdin()) { /* no input file in stdin */
nin=0;
} else {
filename[0] = "in";
nin=1;
}Everything on the command line that does not contain a "=" sign is treated as a file name, and the corresponding file object is added to the list.
for (i=1; i< argc; i++) { /* collect inputs */
if (NULL != strchr(argv[i],'='))
continue; /* not a file */
filename[nin] = argv[i];
nin++;
}
if (0==nin) sf_error ("no input");As explained above, if the space= parameter is not set, it is inferred from the program name: sfmerge corresponds to space=y and sfcat corresponds to space=n.
if (!sf_getbool("space",&space)) {
/* Insert additional space.
y is default for sfmerge, n is default for sfcat */
prog = sf_getprog();
if (NULL != strstr (prog, "merge")) {
space = true;
} else if (NULL != strstr (prog, "cat")) {
space = false;
} else {
sf_warning("%s is neither merge nor cat,"
" assume merge",prog);
space = true;
}
}Find the axis for the merging (from the command line axis= argument) and figure out two sizes: n1 for everything after the axis and n2 for everything before the axis.
n1=1;
n2=1;
for (i=1; i <= dim; i++) {
if (i < axis) n1 *= n[i-1];
else if (i > axis) n2 *= n[i-1];
}In the output, the selected axis will get extended.
/* figure out the length of extended axis */
ni = 0;
for (j=0; j < nin; j++) {
ni += naxis[j];
}
if (space) {
if (!sf_getint("nspace",&nspace))
nspace = (int) (ni/(20*nin) + 1);
/* if space=y, number of traces to insert */
ni += nspace*(nin-1);
}
(void) snprintf(key,3,"n%d",axis);
sf_putint(out,key,(int) ni);The rest is simple: loop through the datasets reading and writing the data in buffer-size chunks and adding extra empty chunks if space=y.
for (i2=0; i2 < n2; i2++) {
for (j=0; j < nin; j++) {
for (ni = n1*naxis[j]*esize; ni > 0; ni -= nbuf) {
nbuf = (BUFSIZ < ni)? BUFSIZ: ni;
sf_charread (buf,nbuf,in[j]);
sf_charwrite (buf,nbuf,out);
}
if (!space || j == nin-1) continue;
/* Add spaces */
memset(buf,0,BUFSIZ);
for (ni = n1*nspace*esize; ni > 0; ni -= nbuf) {
nbuf = (BUFSIZ < ni)? BUFSIZ: ni;
sf_charwrite (buf,nbuf,out);
}
}
}sfcdottest[edit]
| Generic dot-product test for complex linear operators with adjoints | |||
|---|---|---|---|
| sfcdottest mod=mod.rsf dat=dat.rsf > pip.rsf | |||
| file | dat= | auxiliary input file name | |
| file | mod= | auxiliary input file name | |
A simple demonstration of the program can be made by taking advantage that the complex-to-complex FFT is a linear operator:
sfspike n1=100 | sfrtoc > spike.rsf
< spike.rsf sffft axis=1 pad=1 > spike2.rsf
sfcdottest sffft mod=spike.rsf dat=spike2.rsf axis=1 pad=1The output should show values identical down to the last decimal:
sfcdottest: L[m]*d=(3.73955,-1.86955) sfcdottest: L'[d]*m=(3.73955,-1.86955)
sfcmplx[edit]
| Create a complex dataset from its real and imaginary parts. | |||
|---|---|---|---|
| sfcmplx < real.rsf > cmplx.rsf real.rsf imag.rsf | |||
| There has to be only two input files specified and no additional parameters. |
sfcmplx simply creates a complex dataset from its real and
imaginary parts. The reverse operation can be accomplished with
sfreal and sfimag.
Example of sfcmplx:
bash$ sfspike n1=2 n2=3 > one.rsf
bash$ sfin one.rsf
one.rsf:
in="/tmp/one.rsf@"
esize=4 type=float form=native
n1=2 d1=0.004 o1=0 label1="Time" unit1="s"
n2=3 d2=0.1 o2=0 label2="Distance" unit2="km"
6 elements 24 bytes
bash$ sfcmplx one.rsf one.rsf > cmplx.rsf
bash$ sfin cmplx.rsf
cmplx.rsf:
in="/tmp/cmplx.rsf@"
esize=8 type=complex form=native
n1=2 d1=0.004 o1=0 label1="Time" unit1="s"
n2=3 d2=0.1 o2=0 label2="Distance" unit2="km"
6 elements 48 bytes
Implementation: system/main/cmplx.c[edit]
The program flow is simple. First, get the names of the input files.
/* the first two non-parameters are real and imag files */
for (i=1; i< argc; i++) {
if (NULL == strchr(argv[i],'=')) {
if (NULL == real) {
real = sf_input (argv[i]);
} else {
imag = sf_input (argv[i]);
break;
}
}
}
if (NULL == imag) {
if (NULL == real) sf_error ("not enough input");
/* if only one input, real is in stdin */
imag = real;
real = sf_input("in");
}The main part of the program reads the real and imaginary parts buffer by buffer and assembles and writes out the complex input.
for (nleft= (size_t) (rsize*resize); nleft > 0; nleft -= nbuf) {
nbuf = (BUFSIZ < nleft)? BUFSIZ: nleft;
sf_charread(rbuf,nbuf,real);
sf_charread(ibuf,nbuf,imag);
for (i=0; i < nbuf; i += resize) {
memcpy(cbuf+2*i, rbuf+i,(size_t) resize);
memcpy(cbuf+2*i+resize,ibuf+i,(size_t) resize);
}
sf_charwrite(cbuf,2*nbuf,cmplx);
}sfconjgrad[edit]
| Generic conjugate-gradient solver for linear inversion | |||
|---|---|---|---|
| sfconjgrad < dat.rsf mod=mod.rsf mwt=mwt.rsf known=known.rsf x0=x0.rsf > to.rsf < from.rsf > out.rsf niter=1 | |||
| string | known= | auxiliary input file name | |
| file | mod= | auxiliary input file name | |
| string | mwt= | auxiliary input file name | |
| int | niter=1 | number of iterations | |
| string | x0= | auxiliary input file name | |
sfconjgrad is a generic program for least-squares linear inversion with the conjugate-gradient method. Suppose you have an executable program <prog> that takes an RSF file from the standard input and produces an RSF file in the standard output. It may take any number of additional parameters but one of them must be adj= that sets the forward (adj=0) or adjoint (adj=1) operations. The program <prog> is typically an RSF program but it could be anything (a script, a multiprocessor MPI program, etc.) as long as it implements a linear operator and its adjoint. There are no restrictions on the data size or shape. You can easily test the adjointness with sfdottest. The sfconjgrad program searches for a vector that minimizes the least-square misfit for the given input data vector .
The pseudocode for sfconjgrad is given at the end of the "Model fitting with least squares" chapter of Imaging Estimation by Example by Jon Claerbout, with the earliest form published in "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 "An introduction to the Conjugate Gradient Method Without the Agonizing Pain" by J.R. Shewchuk, 1994, when the equation (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 sfcconjgrad implements this algorithm for the case when inputs are complex.
Here is an example. The sfhelicon program implements Claerbout's multidimensional helical filtering (Claerbout, 1998[1]). It requires a filter to be specified in addition to the input and output vectors. We create a helical 2-D filter using the Unix echo command.
bash$ echo 1 19 20 n1=3 n=20,20 data_format=ascii_int in=lag.rsf > lag.rsf bash$ echo 1 1 1 a0=-3 n1=3 data_format=ascii_float in=flt.rsf > flt.rsf
Next, we create an example 2-D model and data vector with sfspike.
bash$ sfspike n1=50 n2=50 > vec.rsf
The sfdottest program can perform the dot product test to check that the adjoint mode works correctly.
bash$ sfdottest sfhelicon filt=flt.rsf lag=lag.rsf mod=vec.rsf dat=vec.rsf sfdottest: L[m]*d=5.28394 sfdottest: L'[d]*m=5.28394
Your numbers may be different because sfdottest generates new random input on each run. Next, let us make some random data with sfnoise.
bash$ sfnoise seed=2005 rep=y < vec.rsf > dat.rsf
and try to invert the filtering operation using sfconjgrad:
bash$ sfconjgrad sfhelicon filt=flt.rsf lag=lag.rsf mod=vec.rsf < dat.rsf > mod.rsf niter=10 sfconjgrad: iter 1 of 10 sfconjgrad: grad=3253.65 sfconjgrad: iter 2 of 10 sfconjgrad: grad=289.421 sfconjgrad: iter 3 of 10 sfconjgrad: grad=92.3481 sfconjgrad: iter 4 of 10 sfconjgrad: grad=36.9417 sfconjgrad: iter 5 of 10 sfconjgrad: grad=18.7228 sfconjgrad: iter 6 of 10 sfconjgrad: grad=11.1794 sfconjgrad: iter 7 of 10 sfconjgrad: grad=7.26941 sfconjgrad: iter 8 of 10 sfconjgrad: grad=5.15945 sfconjgrad: iter 9 of 10 sfconjgrad: grad=4.23055 sfconjgrad: iter 10 of 10 sfconjgrad: grad=3.57495
The output shows that, in 10 iterations, the norm of the gradient vector decreases by almost 1000. We can check the residual misfit before
bash$ < dat.rsf sfattr want=norm norm value = 49.7801
and after
bash$ sfhelicon filt=flt.rsf lag=lag.rsf < mod.rsf | sfadd scale=1,-1 dat.rsf | sfattr want=norm norm value = 5.73563
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 sfcconjgrad. A lightweight Python implementation can be found in $PYTHONPATH/rsf/conjgrad.py.
sfcp[edit]
| Copy or move a dataset. | |||
|---|---|---|---|
| sfcp < in.rsf > out.rsf in.rsf out.rsf | |||
| sfcp - copy, sfmv - move. Mimics standard Unix commands. |
The sfcp and sfmv command imitate the Unix
cp and mv commands and serve for copying and moving
RSF files. Example:
bash$ sfspike n1=2 n2=3 > one.rsf
bash$ sfin one.rsf
one.rsf:
in="/tmp/one.rsf@"
esize=4 type=float form=native
n1=2 d1=0.004 o1=0 label1="Time" unit1="s"
n2=3 d2=0.1 o2=0 label2="Distance" unit2="km"
6 elements 24 bytes
bash$ sfcp one.rsf two.rsf
bash$ sfin two.rsf
two.rsf:
in="/tmp/two.rsf@"
esize=4 type=float form=native
n1=2 d1=0.004 o1=0 label1="Time" unit1="s"
n2=3 d2=0.1 o2=0 label2="Distance" unit2="km"
6 elements 24 bytes
Implementation: system/main/cp.c[edit]
First, we look for the two first command-line arguments that don't have the "=" character in them and consider them as the names of the input and the output files.
/* the first two non-parameters are in and out files */
for (i=1; i< argc; i++) {
if (NULL == strchr(argv[i],'=')) {
if (NULL == in) {
infile = argv[i];
in = sf_input (infile);
} else {
out = sf_output (argv[i]);
break;
}
}
}
if (NULL == in || NULL == out)
sf_error ("not enough input");Next, we use library functions sf_cp and sf_rm to do the actual work.
sf_cp(in,out);
if (NULL != strstr (prog,"mv"))
sf_rm(infile,false,false,false);sfcut[edit]
| Zero a portion of the dataset. | |||
|---|---|---|---|
| sfcut < in.rsf > out.rsf verb=n j#=(1,...) d#=(d1,d2,...) f#=(0,...) min#=(o1,o2,,...) n#=(0,...) max#=(o1+(n1-1)*d1,o2+(n1-1)*d2,,...) | |||
Reverse of window. | |||
| float | d#=(d1,d2,...) | sampling in #-th dimension | |
| largeint | f#=(0,...) | window start in #-th dimension | |
| int | j#=(1,...) | jump in #-th dimension | |
| float | max#=(o1+(n1-1)*d1,o2+(n1-1)*d2,,...) | maximum in #-th dimension | |
| float | min#=(o1,o2,,...) | minimum in #-th dimension | |
| int | n#=(0,...) | window size in #-th dimension | |
| bool | verb=n | [y/n] | Verbosity flag |
The sfcut command is related to sfwindow and has the same set of arguments, only instead of extracting the selected window, it fills it with zeroes. The size of the input data is preserved. Examples:
bash$ sfspike n1=5 n2=5 > in.rsf bash$ < in.rsf sfdisfil 0: 1 1 1 1 1 5: 1 1 1 1 1 10: 1 1 1 1 1 15: 1 1 1 1 1 20: 1 1 1 1 1 bash$ < in.rsf sfcut n1=2 f1=1 n2=3 f2=2 | sfdisfil 0: 1 1 1 1 1 5: 1 1 1 1 1 10: 1 0 0 1 1 15: 1 0 0 1 1 20: 1 0 0 1 1 bash$ < in.rsf sfcut j1=2 | sfdisfil 0: 0 1 0 1 0 5: 0 1 0 1 0 10: 0 1 0 1 0 15: 0 1 0 1 0 20: 0 1 0 1 0
sfdd[edit]
| Convert between different formats. | |||
|---|---|---|---|
| sfdd < in.rsf > out.rsf trunc=n line=8 ibm=n form= type= format= | |||
| string | form= | ascii, native, xdr | |
| string | format= | Element format (for conversion to ASCII) | |
| bool | ibm=n | [y/n] | Special case - assume integers actually represent IBM floats |
| int | line=8 | Number of numbers per line (for conversion to ASCII) | |
| bool | trunc=n | [y/n] | Truncate or round to nearest when converting from float to int/short |
| string | type= | int, float, complex, short, long | |
The sfdd program is used to change either the form (ascii,
xdr, native) or the type (complex, float,
int, char) of the input dataset.
In the example below, we create a plain text (ASCII) file with numbers and
then use sfdd to generate an RSF file in xdr form with
complex numbers.
bash$ cat test.txt
1 2 3 4 5 6
bash$ echo n1=6 data_format=ascii_int in=test.txt > test.rsf
bash$ sfin test.rsf
test.rsf:
in="test.txt"
esize=0 type=int form=ascii
n1=6 d1=? o1=?
6 elements
bash$ sfdd < test.rsf form=xdr type=complex > test2.rsf
bash$ sfin test2.rsf
test2.rsf:
in="/tmp/test2.rsf@"
esize=8 type=complex form=xdr
n1=3 d1=? o1=?
3 elements 24 bytes
bash$ sfdisfil < test2.rsf
0: 1, 2i 3, 4i 5, 6i
To learn more about the RSF data format, consult the guide to RSF format.
sfdisfil[edit]
| Print out data values. | |||
|---|---|---|---|
| sfdisfil < in.rsf number=y col=0 format= header= trailer= | |||
Alternatively, use sfdd and convert to ASCII form. | |||
| int | col=0 | Number of columns.
| |
| string | format= | Format for numbers (printf-style).
| |
| string | header= | Optional header string to output before data | |
| bool | number=y | [y/n] | If number the elements |
| string | trailer= | Optional trailer string to output after data | |
The sfdisfil program simply dumps the data contents to the standard
output in a text form. It is used mostly for debugging purposes to examine RSF files quickly. Here is an example:
bash$ sfmath o1=0 d1=2 n1=12 output=x1 > test.rsf bash$ < test.rsf sfdisfil 0: 0 2 4 6 8 5: 10 12 14 16 18 10: 20 22
The output format is easily configurable.
bash$ < test.rsf sfdisfil col=6 number=n format="%5.1f" 0.0 2.0 4.0 6.0 8.0 10.0 12.0 14.0 16.0 18.0 20.0 22.0
Along with sfdd, sfdisfil provides a simple way to convert RSF data to an ASCII form.
sfdottest[edit]
| Generic dot-product test for linear operators with adjoints | |||
|---|---|---|---|
| sfdottest mod=mod.rsf dat=dat.rsf > pip.rsf | |||
| file | dat= | auxiliary input file name | |
| file | mod= | auxiliary input file name | |
sfdottest is a generic dot-product test program for testing linear operators. Suppose there is an executable program <prog> that takes an RSF file from the standard input and produces an RSF file in the standard output. It may take any number of additional parameters but one of them must be adj= that sets the forward (adj=0) or adjoint (adj=1) operations. The program <prog> is typically an RSF program but it could be anything (a script, a multiprocessor MPI program, etc.) as long as it implements a linear operator and its adjoint . The sfdottest program is testing the equality
by using random vectors and . You can invoke it with
bash$ sfdottest <prog> [optional aruments] mod=mod.rsf dat=dat.rsf
where mod.rsf and dat.rsf are RSF files that represent vectors from the model and data spaces. Pay attention to the dimensions and size of these vectors! If the program does not respond for a very long time, the dimension and size of the vectors may be inconsistent with the requirement of the program to be tested. sfdottest does not create any temporary files and has no restrictive limitations on the size of the vectors. Here is an example. We first create a vector with 100 elements using sfspike and then run sfdottest to test the sfcausint program. sfcausint implements a linear operator of causal integration and its adjoint, the anti-causal integration.
bash$ sfspike n1=100 > vec.rsf bash$ sfdottest sfcausint mod=vec.rsf dat=vec.rsf sfdottest: L[m]*d=1410.2 sfdottest: L'[d]*m=1410.2 bash$ sfdottest sfcausint mod=vec.rsf dat=vec.rsf sfdottest: L[m]*d=1165.87 sfdottest: L'[d]*m=1165.87
The numbers are different on subsequent runs because of changing seed in the random number generator. Here is a somewhat more complicated example. The sfhelicon program implements Claerbout's multidimensional helical filtering (Claerbout, 1998[2]). It requires a filter to be specified in addition to the input and output vectors. We create a helical 2-D filter using the Unix echo command.
bash$ echo 1 19 20 n1=3 n=20,20 data_format=ascii_int in=lag.rsf > lag.rsf bash$ echo 1 1 1 a0=-3 n1=3 data_format=ascii_float in=flt.rsf > flt.rsf
Next, we create an example 2-D model and data vector with sfspike.
bash$ sfspike n1=50 n2=50 > vec.rsf
Now the sfdottest program can perform the dot product test.
bash$ sfdottest sfhelicon filt=flt.rsf lag=lag.rsf \ > mod=vec.rsf dat=vec.rsf sfdottest: L[m]*d=8.97375 sfdottest: L'[d]*m=8.97375
Here is the same program tested in the inverse filtering mode:
bash$ sfdottest sfhelicon filt=flt.rsf lag=lag.rsf \ > mod=vec.rsf dat=vec.rsf div=y sfdottest: L[m]*d=15.0222 sfdottest: L'[d]*m=15.0222
sfget[edit]
| Output parameters from the header. | |||
|---|---|---|---|
| sfget parform=y all=n par1 par2 ... | |||
| bool | all=n | [y/n] | If output all values. |
| bool | parform=y | [y/n] | If y, print out parameter=value. If n, print out value. |
The sfget program extracts a parameter value from an RSF file. It is useful mostly for scripting. Here is, for example, a quick calculation of the maximum value on the first axis in an RSF dataset (the output of sfspike) using the standard Unix bc calculator.
bash$ ( sfspike n1=100 | sfget n1 d1 o1; echo "o1+(n1-1)*d1" ) | bc .396
See also sfput.
Implementation: system/main/get.c[edit]
The implementation is trivial. Loop through all command-line parameters that contain the "=" character.
for (i = 1; i < argc; i++) {
key = argv[i];
if (NULL != strchr(key,'=')) continue;Get the parameter value (as a string) and output it as either key=value or value, depending on the parform parameter.
string = sf_histstring(in,key);
if (NULL == string) {
sf_warning("No key %s",key);
} else {
if (parform) printf ("%s=",key);
printf("%s\n",string);
}sfheadercut[edit]
| Zero a portion of a dataset based on a header mask. | |||
|---|---|---|---|
| sfheadercut mask=head.rsf < in.rsf > out.rsf | |||
The input data is a collection of traces n1xn2, mask is an integer array of size n2. | |||
| file | mask= | auxiliary input file name | |
sfheadercut is close to sfheaderwindow but instead of windowing the dataset, it fills the traces specified by the header mask with zeroes. The size of the input data is preserved. Here is an example of using sfheaderwindow for zeroing every other trace in the input file. First, let us create an input file with ten traces:
bash$ sfmath n1=5 n2=10 output=x2+1 > input.rsf bash$ < input.rsf sfdisfil 0: 1 1 1 1 1 5: 2 2 2 2 2 10: 3 3 3 3 3 15: 4 4 4 4 4 20: 5 5 5 5 5 25: 6 6 6 6 6 30: 7 7 7 7 7 35: 8 8 8 8 8 40: 9 9 9 9 9 45: 10 10 10 10 10
Next, we can create a mask with alternating ones and zeros using sfinterleave.
bash$ sfspike n1=5 mag=1 | sfdd type=int > ones.rsf bash$ sfspike n1=5 mag=0 | sfdd type=int > zeros.rsf bash$ sfinterleave axis=1 ones.rsf zeros.rsf > mask.rsf bash$ sfdisfil < mask.rsf 0: 1 0 1 0 1 0 1 0 1 0
Finally, sfheadercut zeros the input traces.
bash$ sfheadercut < input.rsf mask=mask.rsf > output.rsf bash$ sfdisfil < output.rsf 0: 1 1 1 1 1 5: 0 0 0 0 0 10: 3 3 3 3 3 15: 0 0 0 0 0 20: 5 5 5 5 5 25: 0 0 0 0 0 30: 7 7 7 7 7 35: 0 0 0 0 0 40: 9 9 9 9 9 45: 0 0 0 0 0
sfheadersort[edit]
| Sort a dataset according to a header key. | |||
|---|---|---|---|
| sfheadersort < in.rsf > out.rsf head= | |||
| string | head= | header file | |
sfheadersort is used to sort traces in the input file
according to trace header information.
Here is an example of using
sfheadersort for randomly shuffling traces in the input
file. First, let us create an input file with seven traces:
bash$ sfmath n1=5 n2=7 output=x2+1 > input.rsf bash$ < input.rsf sfdisfil 0: 1 1 1 1 1 5: 2 2 2 2 2 10: 3 3 3 3 3 15: 4 4 4 4 4 20: 5 5 5 5 5 25: 6 6 6 6 6 30: 7 7 7 7 7
Next, we can create a random file with seven header values using sfnoise.
bash$ sfspike n1=7 | sfnoise rep=y type=n > random.rsf bash$ < random.rsf sfdisfil 0: 0.05256 -0.2879 0.1487 0.4097 0.1548 5: 0.4501 0.2836
If you reproduce this example, your numbers will most likely be different, because, in the absence of seed= parameter, sfnoise uses a random seed value to generate pseudo-random numbers. Finally, we apply sfheadersort to shuffle the input traces.
bash$ < input.rsf sfheadersort head=random.rsf > output.rsf bash$ < output.rsf sfdisfil 0: 2 2 2 2 2 5: 1 1 1 1 1 10: 3 3 3 3 3 15: 5 5 5 5 5 20: 7 7 7 7 7 25: 4 4 4 4 4 30: 6 6 6 6 6
As expected, the order of traces in the output file corresponds to the order of values in the header. Thanks to the separation between headers and data, the operation of sfheadersort is optimally efficient. It first sorts the headers and only then accesses the data, reading each data trace only once.
sfheaderwindow[edit]
| Window a dataset based on a header mask. | |||
|---|---|---|---|
| sfheaderwindow mask=head.rsf < in.rsf > out.rsf inv=n | |||
The input data is a collection of traces n1xn2, mask is an integer array os size n2, windowed is n1xm2, where m2 is the number of nonzero elements in mask. | |||
| bool | inv=n | [y/n] | inversion flag |
| file | mask= | auxiliary input file name | |
sfheaderwindow is used to window traces in the input file
according to trace header information.
Here is an example of using sfheaderwindow for randomly
selecting part of the traces in the input file. First, let us create
an input file with ten traces:
bash$ sfmath n1=5 n2=10 output=x2+1 > input.rsf bash$ < input.rsf sfdisfil 0: 1 1 1 1 1 5: 2 2 2 2 2 10: 3 3 3 3 3 15: 4 4 4 4 4 20: 5 5 5 5 5 25: 6 6 6 6 6 30: 7 7 7 7 7 35: 8 8 8 8 8 40: 9 9 9 9 9 45: 10 10 10 10 10
Next, we can create a random file with ten header values using sfnoise.
bash$ sfspike n1=10 | sfnoise rep=y type=n > random.rsf bash$ < random.rsf sfdisfil 0: -0.005768 0.02258 -0.04331 -0.4129 -0.3909 5: -0.03582 0.4595 -0.3326 0.498 -0.3517
If you reproduce this example, your numbers will most likely be different, because, in the absence of seed= parameter, sfnoise uses a random seed value to generate pseudo-random numbers. Finally, we apply sfheaderwindow to window the input traces selecting only those for which the header is greater than zero.
bash$ < random.rsf sfmask min=0 > mask.rsf bash$ < mask.rsf sfdisfil 0: 0 1 0 0 0 0 1 0 1 0 bash$ < input.rsf sfheaderwindow mask=mask.rsf > output.rsf bash$ < output.rsf sfdisfil 0: 2 2 2 2 2 5: 7 7 7 7 7 10: 9 9 9 9 9
In this case, only three traces are selected for the output. Thanks to the separation between headers and data, the operation of sfheaderwindow is optimally efficient.
sfin[edit]
| Display basic information about RSF files. | |||
|---|---|---|---|
| sfin info=y check=2. trail=y [<file0.rsf] file1.rsf file2.rsf ... | |||
| n1,n2,... are data dimensions o1,o2,... are axis origins d1,d2,... are axis sampling intervals label1,label2,... are axis labels unit1,unit2,... are axis units | |||
| float | check=2. | Portion of the data (in Mb) to check for zero values. | |
| bool | info=y | [y/n] | If n, only display the name of the data file. |
| bool | trail=y | [y/n] | If n, skip trailing dimensions of one |
sfin is one of the most useful programs for operating with
RSF files. It produces quick information on the file hypercube
dimensions and checks the consistency of the associated data file.
Here is an example. Let us create an RSF file and examine it with sfin.
bash$ sfspike n1=100 n2=20 > spike.rsf
bash$ sfin spike.rsf
spike.rsf:
in="/tmp/spike.rsf@"
esize=4 type=float form=native
n1=100 d1=0.004 o1=0 label1="Time" unit1="s"
n2=20 d2=0.1 o2=0 label2="Distance" unit2="km"
2000 elements 8000 bytes
sfin reports the following information:
- location of the data file (/tmp/spike.rsf\@)
- element size (4 bytes)
- element type (floating point)
- element form (native)
- hypercube dimensions (100 by 20)
- axes scale (0.004 and 0.1)
- axes origin (0 and 0)
- axes labels
- axes units
- total number of elements
- total number of bytes in the data file
Suppose that the file got corrupted by a buggy program and reports incorrect dimensions. The sfin program should be able to catch the discrepancy.
bash$ echo n2=100 >> spike.rsf bash$ sfin spike.rsf > /dev/null sfin: Actually 8000 bytes, 20% of expected.
sfin also checks the first records in the file for zeros.
bash$ sfspike n1=100 n2=100 k2=99 > spike2.rsf bash$ sfin spike2.rsf >/dev/null sfin: The first 32768 bytes are all zeros
The number of bytes to check is adjustable
bash$ sfin spike2.rsf check=0.01 >/dev/null sfin: The first 16384 bytes are all zeros
You can also output only the location of the data file. This is sometimes handy in scripts.
bash$ sfin spike.rsf spike2.rsf info=n /tmp/spike.rsf@ /tmp/spike2.rsf@
An alternative is to use sfget, as follows:
bash$ sfget parform=n in < spike.rsf /tmp/spike.rsf@
To actually eliminate annoying trailing dimensions of length one (not just stop displaying them with trail=n), you may use sed. Example for eliminating axis 6:
sed -i 's/n6=1//g' file.rsfsfinterleave[edit]
| Combine several datasets by interleaving. | |||
|---|---|---|---|
| sfinterleave > out.rsf axis=3 [< file0.rsf] file1.rsf file2.rsf ... | |||
| int | axis=3 | Axis for interleaving | |
sfinterleave combines two or more datasets by interleaving them on one
of the axes. Here is a quick example:
bash$ sfspike n1=5 n2=5 > one.rsf bash$ sfdisfil < one.rsf 0: 1 1 1 1 1 5: 1 1 1 1 1 10: 1 1 1 1 1 15: 1 1 1 1 1 20: 1 1 1 1 1 bash$ sfscale < one.rsf dscale=2 > two.rsf bash$ sfdisfil < two.rsf 0: 2 2 2 2 2 5: 2 2 2 2 2 10: 2 2 2 2 2 15: 2 2 2 2 2 20: 2 2 2 2 2 bash$ sfinterleave one.rsf two.rsf axis=1 | sfdisfil 0: 1 2 1 2 1 5: 2 1 2 1 2 10: 1 2 1 2 1 15: 2 1 2 1 2 20: 1 2 1 2 1 25: 2 1 2 1 2 30: 1 2 1 2 1 35: 2 1 2 1 2 40: 1 2 1 2 1 45: 2 1 2 1 2 bash$ sfinterleave < one.rsf two.rsf axis=2 | sfdisfil 0: 1 1 1 1 1 5: 2 2 2 2 2 10: 1 1 1 1 1 15: 2 2 2 2 2 20: 1 1 1 1 1 25: 2 2 2 2 2 30: 1 1 1 1 1 35: 2 2 2 2 2 40: 1 1 1 1 1 45: 2 2 2 2 2
sfmask[edit]
| Create a mask. | |||
|---|---|---|---|
| sfmask < in.rsf > out.rsf min= max= | |||
Mask is an integer data with ones and zeros. Ones correspond to input values between min and max. The output can be used with sfheaderwindow. | |||
| float | max= | maximum header value | |
| float | min= | minimum header value | |
sfmask creates an integer output of ones and zeros comparing
the values of the input data to specified min= and
max= parameters. It is useful for sfheaderwindow and
in many other applications. Here is a quick example:
bash$ sfmath n1=10 output="sin(x1)" > sin.rsf bash$ < sin.rsf sfdisfil 0: 0 0.8415 0.9093 0.1411 -0.7568 5: -0.9589 -0.2794 0.657 0.9894 0.4121 bash$ < sin.rsf sfmask min=-0.5 max=0.5 | sfdisfil 0: 1 0 0 1 0 0 1 0 0 1
sfmath[edit]
| Mathematical operations on data files. | |||
|---|---|---|---|
| sfmath > out.rsf nostdin=n n#= d#=(1,1,...) o#=(0,0,...) label#= unit#= type= label= unit= output= | |||
Known functions: cos, sin, tan, acos, asin, atan, cosh, sinh, tanh, acosh, asinh, atanh, exp, log, sqrt, abs, erf, erfc, sign (for float data), arg, conj, real, imag (for complex data). sfmath will work on float or complex data, but all the input and output files must be of the same data type. An alternative to sfmath is sfadd, which may be more efficient, but is less versatile. Examples: sfmath x=file1.rsf y=file2.rsf power=file3.rsf output='sin((x+2*y)^power)' > out.rsf sfmath < file1.rsf tau=file2.rsf output='exp(tau*input)' > out.rsf sfmath n1=100 type=complex output="exp(I*x1)" > out.rsf Arguments which are not treated as variables in mathematical expressions: datapath=, type=, out= See also: sfheadermath. | |||
| float | d#=(1,1,...) | sampling on #-th axis | |
| string | label= | data label | |
| string | label#= | label on #-th axis | |
| largeint | n#= | size of #-th axis | |
| bool | nostdin=n | [y/n] | y - ignore stdin |
| float | o#=(0,0,...) | origin on #-th axis | |
| string | output= | Mathematical description of the output | |
| string | type= | output data type [float,complex] | |
| string | unit= | data unit | |
| string | unit#= | unit on #-th axis | |
sfmath is a versatile program for mathematical operations with RSF files. It can operate with several input files with the same dimensions and data type. The data type can be real (floating point) or complex. The following example demonstrates several features of sfmath.
bash$ sfmath n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5 \ output="x2*(8+sin(6*x1+x2/10))" > rad.rsf bash$ < rad.rsf sfrtoc | sfmath output="input*exp(I*x1)" > rose.rsf bash$ < rose.rsf sfgraph title=Rose screenratio=1 wantaxis=n | sfpen
The first line creates a 2-D dataset that consists of 40 traces 629 samples each. The values of the data are computed with the formula "x2*(8+sin(6*x1+x2/10))", where x1 refers to the coordinate on the first axis, and x2 is the coordinate of the second axis. In the second line, we convert the data from real to complex using sfrtoc and produce a complex dataset using formula "input*exp(I*x1)", where input refers to the input file. Finally, we plot the complex data as a collection of parametric curves using sfgraph and display the result using sfpen. The plot appearing on your screen should look similar to the figure.
One possible alternative to the second line above is
bash$ < rad.rsf sfmath output=x1 > ang.rsf bash$ sfmath r=rad.rsf a=ang.rsf output="r*cos(a)" > cos.rsf bash$ sfmath r=rad.rsf a=ang.rsf output="r*sin(a)" > sin.rsf bash$ sfcmplx cos.rsf sin.rsf > rose.rsf
Here we refer to input files by names (r and a) and combine the names in a formula.
Functions can be nested and combined, and variable names, as well as the input keyword, may be combined with the axes keywords x1, x2, etc. Here is an example that shifts a wavelet -0.4s to t=0, computes the frequency-domain complex square root (equivalent to the convolutional square root in time), and shifts the result back to t=0.4s:
pi=3.14159265
tshift=0.4
sfspike n1=256 k1=101 |\
sfbandpass flo=4 fhi=30 |\
sffft1 opt=n sym=y |\
sfmath output="sqrt(input*exp(2*$pi*$tshift*x1*I))*exp(-2*$pi*$tshift*x1*I)" |\
sffft1 opt=n sym=y inv=y |\
sfgraph |\
sfpensfpad[edit]
| Pad a dataset with zeros. | |||
|---|---|---|---|
| sfpad < in.rsf > out.rsf beg#=0 end#=0 n#= | |||
n#out is equivalent to n#, both of them overwrite end#. Other parameters from the command line are passed to the output (similar to sfput). | |||
| int | beg#=0 | the number of zeros to add before the beginning of #-th axis | |
| int | end#=0 | the number of zeros to add after the end of #-th axis | |
| int | n#= | the output length of #-th axis - padding at the end | |
sfpad increases the dimensions of the input dataset by padding the data with zeroes. Here are some simple examples.
bash$ sfspike n1=5 n2=3 > one.rsf bash$ sfdisfil < one.rsf 0: 1 1 1 1 1 5: 1 1 1 1 1 10: 1 1 1 1 1 bash$ < one.rsf sfpad n2=5 | sfdisfil 0: 1 1 1 1 1 5: 1 1 1 1 1 10: 1 1 1 1 1 15: 0 0 0 0 0 20: 0 0 0 0 0 bash$ < one.rsf sfpad beg2=2 | sfdisfil 0: 0 0 0 0 0 5: 0 0 0 0 0 10: 1 1 1 1 1 15: 1 1 1 1 1 20: 1 1 1 1 1 bash$ < one.rsf sfpad beg2=1 end2=1 | sfdisfil 0: 0 0 0 0 0 5: 1 1 1 1 1 10: 1 1 1 1 1 15: 1 1 1 1 1 20: 0 0 0 0 0 bash$ < one.rsf sfwindow n1=3 | sfpad n1=5 n2=5 beg1=1 beg2=1 | sfdisfil 0: 0 0 0 0 0 5: 0 1 1 1 0 10: 0 1 1 1 0 15: 0 1 1 1 0 20: 0 0 0 0 0
You can use sfcat to pad data with values other than zeroes.
sfput[edit]
| Input parameters into a header. | |||
|---|---|---|---|
| sfput < in.rsf > out.rsf [parameter=value list] |
sfput is a very simple program. It simply appends parameters
from the command line to the output RSF file. One can achieve similar
results by editing the file by hand or with standard Unix utilities like
sed and echo. sfput is sometimes more
convenient because it handles input/output operations similarly to
other Madagascar programs.
bash$ sfspike n1=10 > spike.rsf
bash$ sfin spike.rsf
spike.rsf:
in="/tmp/spike.rsf@"
esize=4 type=float form=native
n1=10 d1=0.004 o1=0 label1="Time" unit1="s"
10 elements 40 bytes
bash$ sfput < spike.rsf d1=25 label1=Depth unit1=m > spike2.rsf
bash$ sfin spike2.rsf
spike2.rsf:
in="/tmp/spike2.rsf@"
esize=4 type=float form=native
n1=10 d1=25 o1=0 label1="Depth" unit1="m"
10 elements 40 bytes
sfreal[edit]
| Extract real (sfreal) or imaginary (sfimag) part of a complex dataset. | |||
|---|---|---|---|
| sfreal < cmplx.rsf > real.rsf |
sfreal extracts the real part of a complex type dataset. The
imaginary part can be extracted with sfimag, and the real
and imaginary part can be combined together with sfcmplx.
Here is a simple example. Let us first create a complex dataset
with sfmath
bash$ sfmath n1=10 type=complex output="(2+I)*x1" > cmplx.rsf bash$ fdisfil < cmplx.rsf 0: 0, 0i 2, 1i 4, 2i 3: 6, 3i 8, 4i 10, 5i 6: 12, 6i 14, 7i 16, 8i 9: 18, 9i
Extracting the real part with sfreal:
bash$ sfreal < cmplx.rsf | sfdisfil 0: 0 2 4 6 8 5: 10 12 14 16 18
Extracting the imaginary part with sfimag:
bash$ sfimag < cmplx.rsf | sfdisfil 0: 0 1 2 3 4 5: 5 6 7 8 9
sfreverse[edit]
| Reverse one or more axes in the data hypercube. | |||
|---|---|---|---|
| sfreverse < in.rsf > out.rsf which=-1 verb=n memsize=sf_memsize() opt= | |||
| int | memsize=sf_memsize() | Max amount of RAM (in Mb) to be used | |
| string | opt= | If y, change o and d parameters on the reversed axis;
| |
| bool | verb=n | [y/n] | Verbosity flag |
| int | which=-1 | Which axis to reverse.
| |
Here is an example of using sfreverse. First, let us create a 2-D dataset.
bash$ sfmath n1=5 d1=1 n2=3 d2=1 output=x1+x2 > test.rsf bash$ < test.rsf sfdisfil 0: 0 1 2 3 4 5: 1 2 3 4 5 10: 2 3 4 5 6
Reversing the first axis:
bash$ < test.rsf sfreverse which=1 | sfdisfil 0: 4 3 2 1 0 5: 5 4 3 2 1 10: 6 5 4 3 2
Reversing the second axis:
bash$ < test.rsf sfreverse which=2 | sfdisfil 0: 2 3 4 5 6 5: 1 2 3 4 5 10: 0 1 2 3 4
Reversing both the first and the second axis:
bash$ < test.rsf sfreverse which=3 | sfdisfil 0: 2 3 4 5 6 5: 1 2 3 4 5 10: 0 1 2 3 4
As you can see, the which= parameter controls the axes that are being reversed by encoding them into one number. When an axis is reversed, what happens with its axis origin and sampling parameters? This behavior is controlled by opt=. In our example,
bash$ < test.rsf sfget n1 o1 d1 n1=5 o1=0 d1=1 bash$ < test.rsf sfreverse which=1 | sfget o1 d1 o1=4 d1=-1
The default behavior (equivalent to opt=y) puts the origin o1 at the end of the axis and reverses the sampling parameter d1. Using opt=n preserves the sampling but reverses the origin.
bash$ < test.rsf sfreverse which=1 opt=n | sfget o1 d1 o1=-4 d1=1
Using opt=i preserves both the sampling and the origin while reversing the axis.
bash$ < test.rsf sfreverse which=1 opt=i | sfget o1 d1 o1=0 d1=1
One of the three possible behaviors may be desirable depending on the application.
sfrm[edit]
| Remove RSF files together with their data. | |||
|---|---|---|---|
| sfrm file1.rsf [file2.rsf ...] [-i] [-v] [-f] | |||
| Mimics the standard Unix rm command. See also: sfmv, sfcp. |
sfrm is a program for removing RSF files. Its arguments mimic the arguments of the standard Unix rm utility: -v for verbosity, -i for interactive inquiry, -f for force removal of suspicious files. Unlike the Unix rm, sfrm removes both the RSF header files and the binary files that the headers point to. Example:
bash$ sfspike n1=10 > spike.rsf datapath=./ bash$ sfget in < spike.rsf in=./spike.rsf@ bash$ ls spike* spike.rsf spike.rsf@ bash$ sfrm -v spike.rsf sfrm: sf_rm: Removing header spike.rsf sfrm: sf_rm: Removing data ./spike.rsf@ bash$ ls spike* ls: No match.
sfrotate[edit]
| Rotate a portion of one or more axes in the data hypercube. | |||
|---|---|---|---|
| sfrotate < in.rsf > out.rsf verb=n memsize=sf_memsize() rot#=(0,0,...) | |||
| int | memsize=sf_memsize() | Max amount of RAM (in Mb) to be used | |
| int | rot#=(0,0,...) | length of #-th axis that is moved to the end | |
| bool | verb=n | [y/n] | Verbosity flag |
sfrotate modifies the input dataset by splitting it into parts and putting the parts back in a different order. Here is a quick example.
bash$ sfmath n1=5 d1=1 n2=3 d2=1 output=x1+x2 > test.rsf bash$ < test.rsf sfdisfil 0: 0 1 2 3 4 5: 1 2 3 4 5 10: 2 3 4 5 6
Rotating the first axis by putting the last two columns in front:
bash$ < test.rsf sfrotate rot1=2 | sfdisfil 0: 3 4 0 1 2 5: 4 5 1 2 3 10: 5 6 2 3 4
Rotating the second axis by putting the last row in front:
bash$ < test.rsf sfrotate rot2=1 | sfdisfil 0: 2 3 4 5 6 5: 0 1 2 3 4 10: 1 2 3 4 5
Rotating both the first and the second axis:
bash$ < test.rsf sfrotate rot1=3 rot2=1 | sfdisfil 0: 4 5 6 2 3 5: 2 3 4 0 1 10: 3 4 5 1 2
The transformation is shown schematically in Figure~(fig:rotate).
sfrtoc[edit]
| Convert real data to complex (by adding zero imaginary part). | |||
|---|---|---|---|
| sfrtoc < real.rsf > cmplx.rsf pair=n | |||
See also: sfcmplx | |||
| bool | pair=n | [y/n] | y - use odd elements for the real part and even ones for the imaginary part |
The input to sfrtoc can be any type=float dataset:
bash$ sfspike n1=10 n2=20 n3=30 >real.rsf
bash$ sfin real.rsf
real.rsf:
in="/var/tmp/real.rsf@"
esize=4 type=float form=native
n1=10 d1=0.004 o1=0 label1="Time" unit1="s"
n2=20 d2=0.1 o2=0 label2="Distance" unit2="km"
n3=30 d3=0.1 o3=0 label3="Distance" unit3="km"
6000 elements 24000 bytes
The output dataset will have type=complex, and its binary will be twice the size of the input:
bash$ <real.rsf sfrtoc >complex.rsf
bash$ sfin complex.rsf
complex.rsf:
in="/var/tmp/complex.rsf@"
esize=8 type=complex form=native
n1=10 d1=0.004 o1=0 label1="Time" unit1="s"
n2=20 d2=0.1 o2=0 label2="Distance" unit2="km"
n3=30 d3=0.1 o3=0 label3="Distance" unit3="km"
6000 elements 48000 bytes
sfscale[edit]
| Scale data. | |||
|---|---|---|---|
| sfscale < in.rsf > out.rsf axis=0 rscale=0. pclip=100. dscale=1. | |||
To scale by a constant factor, you can also use sfmath. | |||
| 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 | pclip=100. | data clip percentile | |
| float | rscale=0. | Scale by this factor. | |
sfscale scales the input dataset by a factor. Here are some simple examples. First, let us create a test dataset.
bash$ sfmath n1=5 n2=3 o1=1 o2=1 output="x1*x2" > test.rsf bash$ < test.rsf sfdisfil 0: 1 2 3 4 5 5: 2 4 6 8 10 10: 3 6 9 12 15
Scale every data point by 2:
bash$ < test.rsf sfscale dscale=2 | sfdisfil 0: 2 4 6 8 10 5: 4 8 12 16 20 10: 6 12 18 24 30
Divide every trace by its maximum value:
bash$ < test.rsf sfscale axis=1 | sfdisfil 0: 0.2 0.4 0.6 0.8 1 5: 0.2 0.4 0.6 0.8 1 10: 0.2 0.4 0.6 0.8 1
Divide by the maximum value in the whole 2-D dataset:
bash$ < test.rsf sfscale axis=2 | sfdisfil 0: 0.06667 0.1333 0.2 0.2667 0.3333 5: 0.1333 0.2667 0.4 0.5333 0.6667 10: 0.2 0.4 0.6 0.8 1
The rscale= parameter is synonymous with dscale= except when it is equal to zero. With sfscale dscale=0, the dataset gets multiplied by zero. If using rscale=0, the other parameters are used to define scaling. Thus, sfscale rscale=0 axis=1 is equivalent to sfscale axis=1, and sfscale rscale=0 is equivalent to sfscale dscale=1.
sfspike[edit]
| Generate simple data: spikes, boxes, planes, constants. | |||
|---|---|---|---|
| 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= | |||
Spike positioning is given in samples and starts with 1. | |||
| float | d#=[0.004,0.1,0.1,...] | sampling on #-th axis | |
| ints | k#=[0,...] | spike starting position [nsp] | |
| ints | l#=[k1,k2,...] | spike ending position [nsp] | |
| string | label#=[Time,Distance,Distance,...] | label on #-th axis | |
| floats | mag= | spike magnitudes [nsp] | |
| int | n#= | size of #-th axis | |
| int | nsp=1 | Number of spikes | |
| float | o#=[0,0,...] | origin on #-th axis | |
| floats | p#=[0,...] | spike inclination (in samples) [nsp] | |
| string | title= | title for plots | |
| string | unit#=[s,km,km,...] | unit on #-th axis | |
sfspike takes no input and generates an output with
"spikes". It is an easy way to create data. Here is an example:
bash$ sfspike n1=5 n2=3 k1=4 k2=1 | sfdisfil 0: 0 0 0 1 0 5: 0 0 0 0 0 10: 0 0 0 0 0
The spike location is specified by parameters k1=4 and k2=1. Note that the locations are numbered starting from 1. If one of the parameters is omitted or given the value of zero, the spike in the corresponding direction becomes a plane:
bash$ sfspike n1=5 n2=3 k1=4 | sfdisfil 0: 0 0 0 1 0 5: 0 0 0 1 0 10: 0 0 0 1 0
If no spike parameters are given, the whole dataset is filled with ones:
bash$ sfspike n1=5 n2=3 | sfdisfil 0: 1 1 1 1 1 5: 1 1 1 1 1 10: 1 1 1 1 1
To create several spikes, use the nsp= parameter and give a comma-separated list of values to k#= arguments:
bash$ sfspike n1=5 n2=3 nsp=3 k1=1,3,4 k2=1,2,3 | sfdisfil 0: 1 0 0 0 0 5: 0 0 1 0 0 10: 0 0 0 1 0
If the number of values in the list is smaller than nsp, the last value gets repeated, and the spikes add on top of each other, creating larger amplitudes:
bash$ sfspike n1=5 n2=3 nsp=3 k1=1,3 k2=1,2 | sfdisfil 0: 1 0 0 0 0 5: 0 0 2 0 0 10: 0 0 0 0 0
The magnitude of the spikes can be controlled explicitly with the mag= parameter:
bash$ sfspike n1=5 n2=3 nsp=3 k1=1,3,4 k2=1,2,3 mag=1,4,2 | sfdisfil 0: 1 0 0 0 0 5: 0 0 4 0 0 10: 0 0 0 2 0
You can create boxes instead of spikes by using l#= parameters:
bash$ sfspike n1=5 n2=3 k1=2 l1=4 k2=2 mag=8 | sfdisfil 0: 0 0 0 0 0 5: 0 8 8 8 0 10: 0 0 0 0 0
In this case, k1=2 specifies the box start, and l1=4 specifies the box end. Finally, multi-dimensional planes can be given an inclination by using p#= parameters:
bash$ sfspike n1=5 n2=3 k1=2 p2=1 | sfdisfil 0: 0 1 0 0 0 5: 0 0 1 0 0 10: 0 0 0 1 0
Note that sfspike interprets the p#= parameters in stepout from sample to sample, not in terms of axes units (i.e. s/m).
More than one p parameter can be specified. In this case, a (hyper) plane will be created.
When the inclination value is not integer, simple linear interpolation is used:
bash$ sfspike n1=5 n2=3 k1=2 p2=0.7 | sfdisfil 0: 0 1 0 0 0 5: 0 0.3 0.7 0 0 10: 0 0 0.6 0.4 0
sfspike supplies default dimensions and labels to all axes:
bash$ sfspike n1=5 n2=3 n3=4 > spike.rsf
bash$ sfin spike.rsf
spike.rsf:
in="/var/tmp/spike.rsf@"
esize=4 type=float form=native
n1=5 d1=0.004 o1=0 label1="Time" unit1="s"
n2=3 d2=0.1 o2=0 label2="Distance" unit2="km"
n3=4 d3=0.1 o3=0 label3="Distance" unit3="km"
60 elements 240 bytes
As you can see, the first axis is assumed to be time, with sampling of seconds. All other axes are assumed to be distance, with sampling of kilometers. All these parameters can be changed on the command line.
bash$ sfspike n1=5 n2=3 n3=4 label3=Offset unit3=ft d3=20 > spike.rsf
bash$ sfin spike.rsf
spike.rsf:
in="/var/tmp/spike.rsf@"
esize=4 type=float form=native
n1=5 d1=0.004 o1=0 label1="Time" unit1="s"
n2=3 d2=0.1 o2=0 label2="Distance" unit2="km"
n3=4 d3=20 o3=0 label3="Offset" unit3="ft"
60 elements 240 bytes
sfspray[edit]
| Extend a dataset by duplicating in the specified axis dimension. | |||
|---|---|---|---|
| sfspray < in.rsf > out.rsf axis=2 n= d= o= label= unit= | |||
| This operation is adjoint to sfstack. | |||
| int | axis=2 | which axis to spray | |
| float | d= | Sampling of the newly created dimension | |
| string | label= | Label of the newly created dimension | |
| int | n= | Size of the newly created dimension | |
| float | o= | Origin of the newly created dimension | |
| string | unit= | Units of the newly created dimension | |
sfspray extends the input hypercube by replicating the data in one of the dimensions. The output dataset acquires one additional dimension. Here is an example: Start with a 2-D dataset
bash$ sfmath n1=5 n2=2 output=x1+x2 > test.rsf
bash$ sfin test.rsf
test.rsf:
in="/var/tmp/test.rsf@"
esize=4 type=float form=native
n1=5 d1=1 o1=0
n2=2 d2=1 o2=0
10 elements 40 bytes
bash$ < test.rsf sfdisfil
0: 0 1 2 3 4
5: 1 2 3 4 5
Extend the data in the second dimension
bash$ < test.rsf sfspray axis=2 n=3 > test2.rsf
bash$ sfin test2.rsf
test2.rsf:
in="/var/tmp/test2.rsf@"
esize=4 type=float form=native
n1=5 d1=1 o1=0
n2=3 d2=1 o2=0
n3=2 d3=1 o3=0
30 elements 120 bytes
bash$ < test2.rsf sfdisfil
0: 0 1 2 3 4
5: 0 1 2 3 4
10: 0 1 2 3 4
15: 1 2 3 4 5
20: 1 2 3 4 5
25: 1 2 3 4 5
The output is three-dimensional, with traces from the original data duplicated along the second axis. Extend the data in the third dimension
bash$ < test.rsf sfspray axis=3 n=2 > test3.rsf
bash$ sfin test3.rsf
test3.rsf:
in="/var/tmp/test3.rsf@"
esize=4 type=float form=native
n1=5 d1=1 o1=0
n2=2 d2=1 o2=0
n3=2 d3=? o3=?
20 elements 80 bytes
bash$ < test3.rsf sfdisfil
0: 0 1 2 3 4
5: 1 2 3 4 5
10: 0 1 2 3 4
15: 1 2 3 4 5
The output is also three-dimensional, with the original data replicated along the third axis.
sfstack[edit]
| Stack a dataset over one of the dimensions. | |||
|---|---|---|---|
| sfstack < in.rsf > out.rsf scale= axis=2 rms=n norm=y min=n max=n prod=n | |||
This operation is adjoint to sfspray. | |||
| 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 | min=n | [y/n] | If y, find minimum instead of stack. Ignores rms and norm. |
| 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. |
| floats | scale= | optionally scale before stacking [n2] | |
While sfspray adds a dimension to a hypercube, sfstack effectively removes one of the dimensions by stacking over it. Here are some examples:
bash$ sfmath n1=5 n2=3 output=x1+x2 > test.rsf bash$ < test.rsf sfdisfil 0: 0 1 2 3 4 5: 1 2 3 4 5 10: 2 3 4 5 6 bash$ < test.rsf sfstack axis=2 | sfdisfil 0: 1.5 2 3 4 5 bash$ < test.rsf sfstack axis=1 | sfdisfil 0: 2.5 3 4
Why is the first value not 1 (in the first case) or 2 (in the second case)? By default, sfstack normalizes the stack by the fold (the number of non-zero entries). To avoid normalization, use norm=n, as follows:
bash$ < test.rsf sfstack norm=n | sfdisfil 0: 3 6 9 12 15
sfstack can also compute root-mean-square values as well as minimum and maximum values.
bash$ < test.rsf sfstack rms=y | sfdisfil 0: 1.581 2.16 3.109 4.082 5.066 bash$ < test.rsf sfstack min=y | sfdisfil 0: 0 1 2 3 4 bash$ < test.rsf sfstack axis=1 max=y | sfdisfil 0: 4 5 6
sftransp[edit]
| Transpose two axes in a dataset. | |||
|---|---|---|---|
| sftransp < in.rsf > out.rsf memsize=sf_memsize() plane= | |||
If you get a "Cannot allocate memory" error, give the program a memsize=1 command-line parameter to force out-of-core operation. | |||
| int | memsize=sf_memsize() | Max amount of RAM (in Mb) to be used | |
| int | plane= | Two-digit number with axes to transpose. The default is 12 | |
The sftransp program transposes the input hypercube exchanging the two axes specified by the plane= parameter.
bash$ sfspike n1=10 n2=20 n3=30 > orig123.rsf
bash$ sfin orig123.rsf
orig123.rsf:
in="/var/tmp/orig123.rsf@"
esize=4 type=float form=native
n1=10 d1=0.004 o1=0 label1="Time" unit1="s"
n2=20 d2=0.1 o2=0 label2="Distance" unit2="km"
n3=30 d3=0.1 o3=0 label3="Distance" unit3="km"
6000 elements 24000 bytes
bash$ <orig123.rsf sftransp plane=23 >out132.rsf
bash$ sfin out132.rsf
out132.rsf:
in="/var/tmp/out132.rsf@"
esize=4 type=float form=native
n1=10 d1=0.004 o1=0 label1="Time" unit1="s"
n2=30 d2=0.1 o2=0 label2="Distance" unit2="km"
n3=20 d3=0.1 o3=0 label3="Distance" unit3="km"
6000 elements 24000 bytes
bash$ <orig123.rsf sftransp plane=13 >out321.rsf
bash$ sfin out321.rsf
out321.rsf:
in="/var/tmp/out132.rsf@"
esize=4 type=float form=native
n1=30 d1=0.1 o1=0 label1="Distance" unit1="km"
n2=20 d2=0.1 o2=0 label2="Distance" unit2="km"
n3=10 d3=0.004 o3=0 label3="Time" unit3="s"
6000 elements 24000 bytes
sftransp tries to fit the dataset in memory to transpose it there but, if not enough memory is available, it performs a slower transpose out of core using disk operations. You can control the amount of available memory using the memsize= parameter or the RSFMEMSIZE environmental variable.
sfwindow[edit]
| Window a portion of a dataset. | |||
|---|---|---|---|
| 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,,...) | |||
Other parameters from the command line are passed to the output (similar to sfput). | |||
| float | d#=(d1,d2,...) | sampling in #-th dimension | |
| largeint | f#=(0,...) | window start in #-th dimension | |
| int | j#=(1,...) | jump in #-th dimension | |
| float | max#=(o1+(n1-1)*d1,o2+(n1-1)*d2,,...) | maximum in #-th dimension | |
| float | min#=(o1,o2,,...) | minimum 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 | verb=n | [y/n] | Verbosity flag |
sfwindow is used to window a portion of the dataset. Here is
a quick example: Start by creating some data.
bash$ sfmath n1=5 n2=3 o1=1 o2=1 output="x1*x2" > test.rsf bash$ < test.rsf sfdisfil 0: 1 2 3 4 5 5: 2 4 6 8 10 10: 3 6 9 12 15
Now window the first two rows:
bash$ < test.rsf sfwindow n2=2 | sfdisfil 0: 1 2 3 4 5 5: 2 4 6 8 10
Window the first three columns:
bash$ < test.rsf sfwindow n1=3 | sfdisfil 0: 1 2 3 2 4 5: 6 3 6 9
Window the middle row:
bash$ < test.rsf sfwindow f2=1 n2=1 | sfdisfil 0: 2 4 6 8 10
You can interpret the f# and n# parameters as meaning "skip that many rows/columns" and "select that many rows/columns" correspondingly. Window the middle point in the dataset:
bash$ < test.rsf sfwindow f1=2 n1=1 f2=1 n2=1 | sfdisfil 0: 6
Window every other column:
bash$ < test.rsf sfwindow j1=2 | sfdisfil 0: 1 3 5 2 6 5: 10 3 9 15
Window every third column:
bash$ < test.rsf sfwindow j1=3 | sfdisfil 0: 1 4 2 8 3 5: 12
Alternatively, sfwindow can select a window from the minimum and maximum parameters. In the following example, we are creating a dataset with sfspike and then windowing a portion of it between 1 and 2 seconds in time and sampled at 8 miliseconds.
bash$ sfspike n1=1000 n2=10 > spike.rsf
bash$ sfin spike.rsf
spike.rsf:
in="/var/tmp/spike.rsf@"
esize=4 type=float form=native
n1=1000 d1=0.004 o1=0 label1="Time" unit1="s"
n2=10 d2=0.1 o2=0 label2="Distance" unit2="km"
10000 elements 40000 bytes
bash$ < spike.rsf sfwindow min1=1 max1=2 d1=0.008 > window.rsf
bash$ sfin window.rsf
window.rsf:
in="/var/tmp/window.rsf@"
esize=4 type=float form=native
n1=126 d1=0.008 o1=1 label1="Time" unit1="s"
n2=10 d2=0.1 o2=0 label2="Distance" unit2="km"
1260 elements 5040 bytes
By default, sfwindow "squeezes" the hypercube dimensions that are equal to one toward the end of the dataset. Here is an example of taking a time slice:
bash$ < spike.rsf sfwindow n1=1 min1=1 > slice.rsf
bash$ sfin slice.rsf
slice.rsf:
in="/var/tmp/slice.rsf@"
esize=4 type=float form=native
n1=10 d1=0.1 o1=0 label1="Distance" unit1="km"
n2=1 d2=0.004 o2=1 label2="Time" unit2="s"
10 elements 40 bytes
You can change this behavior by specifying squeeze=n.
bash$ < spike.rsf sfwindow n1=1 min1=1 squeeze=n > slice.rsf
bash$ sfin slice.rsf
slice.rsf:
in="/var/tmp/slice.rsf@"
esize=4 type=float form=native
n1=1 d1=0.004 o1=1 label1="Time" unit1="s"
n2=10 d2=0.1 o2=0 label2="Distance" unit2="km"
10 elements 40 bytes
Seismic programs[edit]
Programs in this category are specific for operations on seismic data. The source files for these programs can be found under system/seismic in the Madagascar distribution.
sffkamo[edit]
| Computes Azimuth Move-Out (AMO) operator in the f-k log-stretch domain | |||
|---|---|---|---|
| sffkamo < in.rsf > out.rsf h1= h2= f1= f2= maxe=10. | |||
| float | f1= | input azimuth in degrees | |
| float | f2= | output azimuth in degrees | |
| float | h1= | input offset | |
| float | h2= | output offset | |
| float | maxe=10. | stability constraint | |
Sample workflow from SEP-110, 63-70 (2001), with the addition of a bandpass for the input:
Create input -- a (t,x,y) common-offset cube:
sfspike \
n1=128 o1=0.4 d1=0.0032 k1=65 label1=t \
n2=256 o2=-1.536 d2=0.012 k2=129 label2=x \
n3=128 o3=-1.024 d3=0.016 k3=65 label3=y | \
sfbandpass flo=5 fhi=60 > spikebps.rsfApply log-stretch FFT:
<spikebps.rsf sfstretch rule=L dens=4 |\
sffft1 |\
sffft3 axis=2 |\
sffft3 axis=3 > spikefft3.rsfCompute the AMO operator for a file of the dimensions of spikefft3.rsf. The only information taken from stdin are the n, o, d parameters:
<spikefft3.rsf sffkamo h2=2 f2=10 h1=1.8 f1=30 >oper.rsfApply the operator by multiplication and fft back to (t, mx, my):
< spikefft3.rsf sfadd mode=prod oper.rsf |\
sffft3 axis=3 inv=y |\
sffft3 axis=2 inv=y |\
sffft1 inv=y |\
sfstretch rule=L dens=4 inv=y > spikeamo.rsfPrepare for 8-bit greyscale visualization:
< spikeamo.rsf sfbyte pclip=100 gainpanel=a > spikebyte.rsfPicture from the middle of the impulse response:
<spikebyte.rsf sfgrey3 frame1=65 frame2=129 frame3=65 \
point1=0.333 title='AMO saddle, no f-k filter' | sfpen &Picture illustrating the artifacts (i.e. need for f-k filter):
< spikebyte.rsf sfgrey3 frame1=65 frame2=97 frame3=97 \
point1=0.333 title='No f-k filter' | sfpen &Apply the f-k filter and (in this case) visualize:
< spikeamo.rsf sffft1 |\
sffft3 axis=2 |\
sffft3 axis=3 |\
sfdipfilter v1=-2.5 v2=-1.5 v3=1.5 v4=2.5 taper=2 pass=0 dim=3 |\
sffft3 axis=3 inv=y |\
sffft3 axis=2 inv=y |\
sffft1 inv=y |\
sfbyte pclip=100 gainpanel=a |\
sfgrey3 frame1=65 frame2=97 frame3=97 point1=0.333 title='With f-k filter' |\
sfpen &sfheaderattr[edit]
| Integer header attributes. | |||
|---|---|---|---|
| sfheaderattr < head.rsf | |||
Only nonzero values are reported. |
The sfheaderattr examines the contents of a trace header file, typically generated by sfsegyread. In the example below, we examine trace headers in the output of suplane, a program from Seismic Unix.
bash$ suplane > plane.su bash$ sfsegyread tape=plane.su su=y tfile=tfile.rsf > plane.rsf bash$ sfheaderattr < tfile.rsf ******************************************* 71 headers, 32 traces key[0]="tracl" min[0]=1 max[31]=32 mean=16.5 key[1]="tracr" min[0]=1 max[31]=32 mean=16.5 key[11]="offset" min[0]=400 max[31]=400 mean=400 key[38]="ns" min[0]=64 max[31]=64 mean=64 key[39]="dt" min[0]=4000 max[31]=4000 mean=4000 *******************************************
For different standard keywords, a minimum, maximum, and mean values are reported unless they are identically zero. This quick inspection can help identify meaningful keywords in the data. The input data type must be int.
sfheadermath[edit]
| Mathematical operations, possibly on header keys. | |||
|---|---|---|---|
| sfheadermath < in.rsf > out.rsf memsize=sf_memsize() output= | |||
Known functions: cos, sin, tan, acos, asin, atan, cosh, sinh, tanh, acosh, asinh, atanh, exp, log, sqrt, abs See also sfmath. An addition operation can be performed by sfstack. | |||
| int | memsize=sf_memsize() | Max amount of RAM (in Mb) to be used | |
| string | output= | Describes the output in a mathematical notation. | |
sfheadermath is a versatile program for mathematical operations on rows of the input file. If the input file is an n1 by n2 matrix, the output will be a 1 by n2 matrix that contains one row made out of mathematical operations on the other rows. sfheadermath can identify a row by number or by a standard SEGY keyword. The latter is helpful in processing headers extracted from SEGY or SU files. Here is an example. First, we create an SU file with suplane and convert it to RSF using sfsegyread.
bash$ suplane > plane.su bash$ sfsegyread tape=plane.su su=y tfile=tfile.rsf > plane.rsf
The trace header information is saved in tfile.rsf. It contains 71 headers for 32 traces in integer format.
bash$ sfin tfile.rsf
tfile.rsf:
in="/tmp/tfile.rsf@"
esize=4 type=int form=native
n1=71 d1=? o1=?
n2=32 d2=? o2=?
2272 elements 9088 bytes
Next, we will convert tfile.rsf to a floating-point format and run sfheadermath to create a new header.
bash$ < tfile.rsf sfdd type=float | \
sfheadermath myheader=1 output="sqrt(myheader+(2+10*offset^2))" > new.rsf
bash$ sfin new.rsf
new.rsf:
in="/tmp/new.rsf@"
esize=4 type=float form=native
n1=1 d1=? o1=?
n2=32 d2=? o2=?
32 elements 128 bytes
We defined "header" as being the row number 1 in the input (note that numbering starts with 0) and combined it with "offset", which is a standard SEGY keyword that denotes row number 11 (see the output of sfheaderattr above.) A variety of mathematical expressions can be defined in the output= string. The expression processing engine is shared with sfmath.
sfsegyheader[edit]
| Make a trace header file for segywrite. | |||
|---|---|---|---|
| sfsegyheader < in.rsf > out.rsf n1= d1= | |||
Use the output for tfile= argument in segywrite. | |||
| float | d1= | trace sampling | |
| int | n1= | number of samples in a trace | |
sfsegyread[edit]
| Convert a SEG-Y or SU dataset to RSF. | |||
|---|---|---|---|
| sfsegyread mask=msk.rsf > out.rsf tfile=hdr.rsf verb=n su= suxdr=n endian=y format=segyformat (bhead) ns=segyns (bhead) tape= read= hfile= bfile= | |||
Data headers and trace headers are separated from the data. "suread" is equivalent to "segyread su=y" SEGY key names: tracl: trace sequence number within line 0 tracr: trace sequence number within reel 4 fldr: field record number 8 tracf: trace number within field record 12 ep: energy source point number 16 cdp: CDP ensemble number 20 cdpt: trace number within CDP ensemble 24 trid: trace identification code: 1 = seismic data 2 = dead 3 = dummy 4 = time break 5 = uphole 6 = sweep 7 = timing 8 = water break 9---, N = optional use (N = 32,767) 28 nvs: number of vertically summed traces 30 nhs: number of horizontally summed traces 32 duse: data use: 1 = production 2 = test 34 offset: distance from source point to receiver group (negative if opposite to direction in which the line was shot) 36 gelev: receiver group elevation from sea level (above sea level is positive) 40 selev: source elevation from sea level (above sea level is positive) 44 sdepth: source depth (positive) 48 gdel: datum elevation at receiver group 52 sdel: datum elevation at source 56 swdep: water depth at source 60 gwdep: water depth at receiver group 64 scalel: scale factor for previous 7 entries with value plus or minus 10 to the power 0, 1, 2, 3, or 4 (if positive, multiply, if negative divide) 68 scalco: scale factor for next 4 entries with value plus or minus 10 to the power 0, 1, 2, 3, or 4 (if positive, multiply, if negative divide) 70 sx: X source coordinate 72 sy: Y source coordinate 76 gx: X group coordinate 80 gy: Y group coordinate 84 counit: coordinate units code: for previous four entries 1 = length (meters or feet) 2 = seconds of arc (in this case, the X values are unsigned longitude and the Y values are latitude, a positive value designates the number of seconds east of Greenwich or north of the equator 88 wevel: weathering velocity 90 swevel: subweathering velocity 92 sut: uphole time at source 94 gut: uphole time at receiver group 96 sstat: source static correction 98 gstat: group static correction 100 tstat: total static applied 102 laga: lag time A, time in ms between end of 240- byte trace identification header and time break, positive if time break occurs after end of header, time break is defined as the initiation pulse which maybe recorded on an auxiliary trace or as otherwise specified by the recording system 104 lagb: lag time B, time in ms between the time break and the initiation time of the energy source, may be positive or negative 106 delrt: delay recording time, time in ms between initiation time of energy source and time when recording of data samples begins (for deep water work if recording does not start at zero time) 108 muts: mute time--start 110 mute: mute time--end 112 ns: number of samples in this trace 114 dt: sample interval, in micro-seconds 116 gain: gain type of field instruments code: 1 = fixed 2 = binary 3 = floating point 4 ---- N = optional use 118 igc: instrument gain constant 120 igi: instrument early or initial gain 122 corr: correlated: 1 = no 2 = yes 124 sfs: sweep frequency at start 126 sfe: sweep frequency at end 128 slen: sweep length in ms 130 styp: sweep type code: 1 = linear 2 = cos-squared 3 = other 132 stas: sweep trace length at start in ms 134 stae: sweep trace length at end in ms 136 tatyp: taper type: 1=linear, 2=cos^2, 3=other 138 afilf: alias filter frequency if used 140 afils: alias filter slope 142 nofilf: notch filter frequency if used 144 nofils: notch filter slope 146 lcf: low cut frequency if used 148 hcf: high cut frequncy if used 150 lcs: low cut slope 152 hcs: high cut slope 154 year: year data recorded 156 day: day of year 158 hour: hour of day (24 hour clock) 160 minute: minute of hour 162 sec: second of minute 164 timbas: time basis code: 1 = local 2 = GMT 3 = other 166 trwf: trace weighting factor, defined as 1/2^N volts for the least sigificant bit 168 grnors: geophone group number of roll switch position one 170 grnofr: geophone group number of trace one within original field record 172 grnlof: geophone group number of last trace within original field record 174 gaps: gap size (total number of groups dropped) 176 otrav: overtravel taper code: 1 = down (or behind) 2 = up (or ahead) 178 cdpx: X coordinate of CDP 180 cdpy: Y coordinate of CDP 184 iline: in-line number 188 xline: cross-line number 192 shnum: shotpoint number 196 shsca: shotpoint scalar 200 tval: trace value meas. 202 tconst4: transduction const 204 tconst2: transduction const 208 tunits: transduction units 210 device: device identifier 212 tscalar: time scalar 214 stype: source type 216 sendir: source energy dir. 218 unknown: unknown 222 smeas4: source measurement 224 smeas2: source measurement 228 smeasu: source measurement unit 230 unass1: unassigned 232 unass2: unassigned 236 | |||
| string | bfile= | output binary data header file | |
| bool | endian=y | [y/n] | Whether to automatically estimate endianness or not |
| int | format=segyformat (bhead) | [1,2,3,5] | Data format. The default is taken from binary header.
|
| string | hfile= | output text data header file | |
| string | mask= | optional header mask for reading only selected traces (auxiliary input file name) | |
| int | ns=segyns (bhead) | Number of samples. The default is taken from binary header | |
| string | read= | what to read: h - header, d - data, b - both (default) | |
| bool | su= | [y/n] | y if input is SU, n if input is SEGY |
| bool | suxdr=n | [y/n] | y, SU has XDR support |
| string | tape= | input data | |
| string | tfile= | output trace header file (auxiliary output file name) | |
| bool | verb=n | [y/n] | Verbosity flag |
The SEG Y format is an open standard for the exchange of geophysical data. It is controlled by the non-profit SEG Technical Standards Committee. There are two versions of this standard: rev0 (1975)[3] and rev1 (2002)[4]. The implementation in sfsegyread is a mixture of rev0 (i.e. no checks for Extended Textual Headers) and rev1 (IEEE floating point format allowed for trace data samples).
An SEG-Y file, as understood by sfsegyread, contains a "Reel Identification Header" (3200 bytes in EBCDIC followed by 400 bytes in a binary encoding), followed by a number of "Trace Blocks." Each "Trace Block" contains a 240-byte "Trace Header" (binary) followed by "Trace Data" -- a sequence of ns samples. Binary values in both reel headers and trace headers are two's complement integers, either two bytes or four bytes long. There are no floating-point values defined in the headers. Trace Data samples can have various encodings, either floating point or integer, described further down, but they are all big-endian. To convert from SEG-Y to RSF, sfsegyread will strip the tape reel EBCDIC header and convert it to ASCII, will extract the reel binary header without changing it, and will put the trace headers into one RSF file, and the traces themselves on another.
SEG-Y Trace Headers[edit]
In the SEG-Y standard, only the first 180 bytes of the 240-byte trace header are defined; bytes 181-240 are reserved for non-standard header information, and these locations are increasingly used in modern SEG-Y files and their variants. The standard provides for a total of 71 4-byte and 2-byte predefined header words. These 71 standard words have defined lengths and byte offsets, and only these words and byte locations are read using segyread and output to the RSF header file with the tfile= option. The user may remap these predefined keywords to different byte offsets.
SU File Format[edit]
An SU file is nothing more than an SEG-Y file without the reel headers and with the Trace Data samples in the native encoding of the CPU the file was created on (Attention -- limited portability!). So, to convert from SU to RSF, sfsegyread will just separate headers and traces into two RSF files.
SEG-Y specific parameters[edit]
- hfile= specifies the name of the file in which the EBCDIC reel header will be put after conversion to ASCII. If you are certain there is no useful information in it, hfile=/dev/null works just fine. If you do not specify anything for this parameter, you will get an ASCII file named header in the current directory. If you want to quickly preview this header before running sfsegyread, use
dd if=input.segy count=40 bs=80 cbs=80 conv=unblock,ascii
- bfile= specifies the name of the file in which the binary reel header (the 400-byte thing following the 3600-byte EBCDIC) will be put without any conversion. The default name is "binary". Unless you have software that knows how to read exactly this special type of file, it will be completely useless, so do bfile=/dev/null
- format= specifies the format in which the trace data samples are in the SEG-Y input file. This is read from the binary reel header of the SEG-Y file. Valid values are 1(IBM floating point), 2 (4-byte integer), 3 (2-byte integer), and 5 (IEEE floating point). If the input file is SU, the format will be assumed to be the native float format.
- keyname= specifies the byte offset to remap a header using the trace header key names shown above. For example, if the CDP locations have been placed in bytes 181-184 instead of the standard 21-24, cdp=180 will remap the trace header to that location.
SU-specific parameters[edit]
- suxdr= specifies whether the input file was created with an SU package with XDR support enabled. If you have access to the source code of your SU install (try $CWPROOT/src), type: grep 'XDRFLAG =' $CWPROOT/src/Makefile.config and look at the last uncommented entry. If no value is given for XDRFLAG, the package was not compiled with XDR support.
Common parameters[edit]
- su= specifies if the input file is SU or SEG-Y. The default is su=n (SEG-Y file).
- read= specifies what parts of the "Trace Blocks" will be read. It can be read=d (only trace data is read), read=h (only trace headers are read) or read=b (both are read).
- tfile= gives the name of the RSF file to which trace headers are written. Obviously, it should be only specified with read=h or read=b.
- mask= is an optional parameter specifying the name of a mask that says which traces will be read. The mask is a 1-D RSF file with integers. The number of mask samples is the same as the number of traces in the unmasked SEG-Y. There should be zeros in the mask in places corresponding to unwanted traces.
- ns= specifies the number of samples in a trace. For SEG-Y files, the default is taken from the binary reel header, and for SU files, from the header of the first trace. This parameter is, however, critical enough that a command line override was given for it.
- verbose= is the verbosity flag. Can be y or n.
- endian= is a y/n flag (default y), specifying whether to estimate automatically or not if samples in the Trace Data blocks are big-endian or little-endian. Try it if you are in trouble and do not know what else to do; otherwise, let the automatic estimation do its job.
sfsegywrite[edit]
| Convert an RSF dataset to SEGY or SU. | |||
|---|---|---|---|
| sfsegywrite < in.rsf tfile=hdr.rsf verb=false su=false endian=sf_endian() tape= hfile= bfile= | |||
Merges trace headers with data. | |||
| string | bfile= | input binary data header file | |
| bool | endian=sf_endian() | [y/n] | big/little endian flag. The default is estimated automatically |
| string | hfile= | input text data header file | |
| bool | su=n | [y/n] | y if output is SU, n if output is SEGY |
| string | tape= | ||
| bool | verb=n | [y/n] | Verbosity flag |
Please see sfsegyread for a complete description of parameter meanings and background issues. Parameters bfile and hfile should only be given values when the desired file is SEG-Y (default). The tape= tag specifies the output file.
Generic programs[edit]
Programs in this category are general signal and image processing programs. The source files for these programs can be found under system/generic in the Madagascar distribution.
sfnoise[edit]
| Add random noise to the data. | |||
|---|---|---|---|
| sfnoise < in.rsf > out.rsf seed=time(NULL) type=y var= range= mean=0 rep=n | |||
| float | mean=0 | noise mean | |
| float | range= | noise range (default=1) | |
| bool | rep=n | [y/n] | if y, replace data with noise |
| int | seed=time(NULL) | random seed | |
| bool | type=y | [y/n] | noise distribution, y: normal, n: uniform |
| float | var= | noise variance | |
See the Program of the Month blog entry.
Plotting programs (stable)[edit]
The source files for these programs can be found under plot/main in the Madagascar distribution.
sfbox[edit]
| Draw a balloon-style label. | |||
|---|---|---|---|
| sfbox lab_color=VP_WHITE lab_fat=0 pscale=1. pointer=y reverse=n lat=0. long=90. angle=0. x0=0. y0=0. scale0=1. xt=2. yt=0. x_oval=0. y_oval=0. boxit=y length= scalet= size=.25 label= > out.vpl | |||
| float | angle=0. | longitude of floating label in 3-D | |
| bool | boxit=y | [y/n] | if y, create a box around text |
| int | lab_color=VP_WHITE | label color | |
| int | lab_fat=0 | label fatness | |
| string | label= | text for label | |
| float | lat=0. | ||
| float | length= | normalization for xt and yt | |
| float | long=90. | latitude and longitude of viewpoint in 3-D | |
| bool | pointer=y | [y/n] | if y, create arrow pointer |
| float | pscale=1. | scale factor for width of pointer | |
| bool | reverse=n | [y/n] | |
| float | scale0=1. | scale factor for x0 and y0 | |
| float | scalet= | ||
| float | size=.25 | text height in inches | |
| float | x0=0. | ||
| float | x_oval=0. | ||
| float | xt=2. | ||
| float | y0=0. | position of the pointer tip | |
| float | y_oval=0. | size of the oval around pointer | |
| float | yt=0. | relative position of text | |
sfcontour[edit]
| Contour plot. | |||
|---|---|---|---|
| sfcontour < in.rsf c= min1=o1 min2=o2 max1=o1+(n1-1)*d1 max2=o2+(n2-1)*d2 nc=50 dc= c0= transp=y minval= maxval= allpos=y barlabel= > plot.vpl | |||
| Run "sfdoc stdplot" for more parameters. | |||
| bool | allpos=y | [y/n] | contour positive values only |
| string | barlabel= | ||
| floats | c= | [nc] | |
| float | c0= | first contour | |
| float | dc= | contour increment | |
| float | max1=o1+(n1-1)*d1 | ||
| float | max2=o2+(n2-1)*d2 | data window to plot | |
| float | maxval= | maximum value for scalebar (default is the data maximum) | |
| float | min1=o1 | ||
| float | min2=o2 | ||
| float | minval= | minimum value for scalebar (default is the data minimum) | |
| int | nc=50 | number of contours | |
| bool | transp=y | [y/n] | if y, transpose the axes |
sfdots[edit]
| Plot signal with lollipops. | |||
|---|---|---|---|
| sfdots < in.rsf labels= dots=(n1 <= 130)? 1: 0 seemean=(bool) (n2 <= 30) strings=(bool) (n1 <= 400) connect=1 corners= silk=n gaineach=y labelsz=8 yreverse=n constsep=n seedead=n transp=n xxscale=1. yyscale=1. clip=-1. overlap=0.9 screenratio=VP_SCREEN_RATIO screenht=VP_STANDARD_HEIGHT screenwd=screenhigh / screenratio radius=dd1/3 label1= unit1= title= > plot.vpl | |||
| float | clip=-1. | data clip | |
| int | connect=1 | connection type: 1 - diagonal, 2 - bar, 4 - only for non-zero data | |
| bool | constsep=n | [y/n] | if y, use constant trace separation |
| int | corners= | number of polygon corners (default is 6) | |
| int | dots=(n1 <= 130)? 1: 0 | type of dots: 1 - baloon, 0 - no dots, 2 - only for non-zero data | |
| bool | gaineach=y | [y/n] | if y, gain each trace independently |
| string | label1= | ||
| strings | labels= | trace labels [n2] | |
| int | labelsz=8 | label size | |
| float | overlap=0.9 | trace overlap | |
| float | radius=dd1/3 | dot radius | |
| float | screenht=VP_STANDARD_HEIGHT | screen height | |
| float | screenratio=VP_SCREEN_RATIO | screen aspect ratio | |
| float | screenwd=screenhigh / screenratio | screen width | |
| bool | seedead=n | [y/n] | if y, show zero traces |
| bool | seemean=(bool) (n2 <= 30) | [y/n] | if y, draw axis lines |
| bool | silk=n | [y/n] | if y, silky plot |
| bool | strings=(bool) (n1 <= 400) | [y/n] | if y, draw strings |
| string | title= | ||
| bool | transp=n | [y/n] | if y, transpose the axis |
| string | unit1= | ||
| float | xxscale=1. | x scaling | |
| bool | yreverse=n | [y/n] | if y, reverse y axis |
| float | yyscale=1. | y scaling | |
sfgraph3[edit]
| Generate 3-D cube plot for surfaces. | |||
|---|---|---|---|
| sfgraph3 < in.rsf orient=1 min= max= point1=0.5 point2=0.5 frame1=0.5*(min+max) frame2=n1-1 frame3=0 movie=0 dframe=1 n1pix=n1/point1+n3/(1.-point1) n2pix=n2/point2+n3/(1.-point2) flat=y > plot.vpl | |||
| float | dframe=1 | frame increment in a movie | |
| bool | flat=y | [y/n] | if n, display perspective view |
| float | frame1=0.5*(min+max) | ||
| int | frame2=n1-1 | ||
| int | frame3=0 | frame numbers for cube faces | |
| float | max= | maximum function value | |
| float | min= | minimum function value | |
| int | movie=0 | 0: no movie, 1: movie over axis 1, 2: axis 2, 3: axis 3 | |
| int | n1pix=n1/point1+n3/(1.-point1) | number of vertical pixels | |
| int | n2pix=n2/point2+n3/(1.-point2) | number of horizontal pixels | |
| int | orient=1 | function orientation | |
| float | point1=0.5 | fraction of the vertical axis for front face | |
| float | point2=0.5 | fraction of the horizontal axis for front face | |
sfgraph[edit]
| Graph plot. | |||
|---|---|---|---|
| sfgraph < in.rsf symbolsz= pclip=100. transp=n symbol= > plot.vpl | |||
| Run "sfdoc stdplot" for more parameters. | |||
| float | pclip=100. | clip percentile | |
| string | symbol= | if set, plot with symbols instead of lines | |
| floats | symbolsz= | symbol size (default is 2) [n2] | |
| bool | transp=n | [y/n] | if y, transpose the axes |
sfgrey3[edit]
| Generate 3-D cube plot. | |||
|---|---|---|---|
| sfgrey3 < in.rsf point1=0.5 point2=0.5 frame1=0 frame2=n2-1 frame3=0 movie=0 dframe=1 n1pix=n1/point1+n3/(1.-point1) n2pix=n2/point2+n3/(1.-point2) flat=y scalebar=n minval= maxval= barreverse=n nreserve=8 bar= color= > plot.vpl | |||
| Requires an "unsigned char" input (the output of sfbyte). | |||
| string | bar= | file for scalebar data | |
| bool | barreverse=n | [y/n] | if y, go from small to large on the bar scale |
| string | color= | color scheme (default is i) | |
| int | dframe=1 | frame increment in a movie | |
| bool | flat=y | [y/n] | if n, display perspective view |
| int | frame1=0 | ||
| int | frame2=n2-1 | ||
| int | frame3=0 | frame numbers for cube faces | |
| float | maxval= | maximum value for scalebar (default is the data maximum) | |
| float | minval= | minimum value for scalebar (default is the data minimum) | |
| int | movie=0 | 0: no movie, 1: movie over axis 1, 2: axis 2, 3: axis 3 | |
| int | n1pix=n1/point1+n3/(1.-point1) | number of vertical pixels | |
| int | n2pix=n2/point2+n3/(1.-point2) | number of horizontal pixels | |
| int | nreserve=8 | reserved colors | |
| float | point1=0.5 | fraction of the vertical axis for front face | |
| float | point2=0.5 | fraction of the horizontal axis for front face | |
| bool | scalebar=n | [y/n] | if y, draw scalebar |
Different color schemes are available for sfgrey and sfgrey3. Examples are in the book at rsf/rsf/sfgrey.
sfgrey[edit]
| Generate raster plot. | |||
|---|---|---|---|
| sfgrey < in.rsf > out.rsf bar=bar.rsf transp=y yreverse=y xreverse=n gpow= phalf= clip= pclip= gainstep=0.5+n1/256. allpos=n bias=0. polarity=n verb=n scalebar=n minval= maxval= barreverse=n wantframenum=(bool) (n3 > 1) nreserve=8 gainpanel= bar= color= > (plot.vpl | char.rsf) | |||
| Can input char values. If called "byte", outputs char values. Run "sfdoc stdplot" for more parameters. | |||
| bool | allpos=n | [y/n] | if y, assume positive data |
| string | bar= | file for scalebar data | |
| bool | barreverse=n | [y/n] | if y, go from small to large on the bar scale |
| float | bias=0. | subtract bias from data | |
| float | clip= | ||
| string | color= | color scheme (default is i) | |
| string | gainpanel= | gain reference: 'a' for all, 'e' for each, or number | |
| int | gainstep=0.5+n1/256. | subsampling for gpow and clip estimation | |
| float | gpow= | ||
| float | maxval= | maximum value for scalebar (default is the data maximum) | |
| float | minval= | minimum value for scalebar (default is the data minimum) | |
| int | nreserve=8 | reserved colors | |
| float | pclip= | data clip percentile (default is 99) | |
| float | phalf= | percentage for estimating gpow | |
| bool | polarity=n | [y/n] | if y, reverse polarity (white is high by default) |
| bool | scalebar=n | [y/n] | |
| bool | transp=y | [y/n] | if y, transpose the display axes |
| bool | verb=n | [y/n] | verbosity flag |
| bool | wantframenum=(bool) (n3 > 1) | [y/n] | if y, display third axis position in the corner |
| bool | xreverse=n | [y/n] | if y, reverse the horizontal axis |
| bool | yreverse=y | [y/n] | if y, reverse the vertical axis |
Different color schemes are available, and examples are in the book at rsf/rsf/sfgrey.
sfplas[edit]
| Plot Assembler - convert ascii to vplot. | |||
|---|---|---|---|
| sfplas |
sfpldb[edit]
| Plot Debugger - convert vplot to ascii. | |||
|---|---|---|---|
| sfpldb |
sfplotrays[edit]
| Plot rays. | |||
|---|---|---|---|
| sfplotrays frame=frame.rsf nt=n1*n2 jr=1 frame= < rays.rsf > plot.vpl | |||
| Run "sfdoc stdplot" for more parameters. | |||
| string | frame= | ||
| int | jr=1 | skip rays | |
| int | nt=n1*n2 | maximum ray length | |
sfthplot[edit]
| Hidden-line surface plot. | |||
|---|---|---|---|
| sfthplot < in.rsf uflag=y dflag=y alpha=45. titlsz=9 axissz=6 plotfat=0 titlefat=2 axisfat=2 plotcolup=VP_YELLOW plotcoldn=VP_RED axis=y axis1=y axis2=y axis3=y clip=0. pclip=100. gainstep=0.5+nx/256. bias=0. dclip=1. norm=y xc=1.5 zc=3 ratio=5. zmax= zmin= sz=6. label#= unit#= tpow=0 epow=0 gpow=1 title= > plot.vpl | |||
| float | alpha=45. | alpha| < 89 | |
| bool | axis=y | [y/n] | |
| bool | axis1=y | [y/n] | |
| bool | axis2=y | [y/n] | |
| bool | axis3=y | [y/n] | plot axis |
| int | axisfat=2 | axes fatness | |
| int | axissz=6 | axes size | |
| float | bias=0. | subtract bias from data | |
| float | clip=0. | data clip | |
| float | dclip=1. | change the clip: clip *= dclip | |
| bool | dflag=y | [y/n] | if y, plot down side of the surface |
| float | epow=0 | exponential gain | |
| int | gainstep=0.5+nx/256. | subsampling for gpow and clip estimation | |
| float | gpow=1 | power gain | |
| string | label#= | label on #-th axis | |
| bool | norm=y | [y/n] | normalize by the clip |
| float | pclip=100. | data clip percentile | |
| int | plotcoldn=VP_RED | color of the lower side | |
| int | plotcolup=VP_YELLOW | color of the upper side | |
| int | plotfat=0 | line fatness | |
| float | ratio=5. | plot adjustment | |
| float | sz=6. | vertical scale | |
| string | title= | ||
| int | titlefat=2 | title fatness | |
| int | titlsz=9 | title size | |
| string | tpow=0 | time power gain | |
| bool | uflag=y | [y/n] | if y, plot upper side of the surface |
| string | unit#= | unit on #-th axis | |
| float | xc=1.5 | ||
| float | zc=3 | lower left corner of the plot | |
| float | zmax= | ||
| float | zmin= | ||
sfwiggle[edit]
| Plot data with wiggly traces. | |||
|---|---|---|---|
| sfwiggle < in.rsf xpos=xpos.rsf xmax= xmin= poly=n fatp=1 xmask=1 ymask=1 pclip=98. zplot=0.75 clip=0. seemean=n verb=n transp=n yreverse=n xreverse=n xpos= > plot.vpl | |||
| Run "sfdoc stdplot" for more parameters. | |||
| float | clip=0. | data clip (estimated from pclip by default | |
| int | fatp=1 | ||
| float | pclip=98. | clip percentile | |
| bool | poly=n | [y/n] | |
| bool | seemean=n | [y/n] | if y, plot mean lines of traces |
| bool | transp=n | [y/n] | if y, transpose the axes |
| bool | verb=n | [y/n] | verbosity flag |
| int | xmask=1 | ||
| float | xmax= | maximum trace position (if using xpos) | |
| float | xmin= | minimum trace position (if using xpos) | |
| string | xpos= | optional header file with trace positions | |
| bool | xreverse=n | [y/n] | if y, reverse the horizontal axis |
| int | ymask=1 | ||
| bool | yreverse=n | [y/n] | if y, reverse the vertical axis |
| float | zplot=0.75 | ||
Plotting programs (development)[edit]
sfplsurf[edit]
sfplsurf utilizes PLplot's surface rendering capabilities. Output is dumped to stdout in VPLOT format, so it can easily be used like sfgrey or other plotting programs. It also supports animation, if n3 > 1 in the input file. A SConstruct usage example can be found below. A movie of the output is available as well.
from rsf.proj import *
# x & y dimensions
o1=-2
o2=-2
n1=41
n2=41
d1=0.1
d2=0.1
# z dimension
o3=-1
n3=21
d3=0.1
Flow('membrane',None,
'''
math o1=%g o2=%g n1=%d n2=%d d1=%g d2=%g
o3=%g n3=%d d3=%g
output="x3*cos(x1*x1+x2*x2)*exp(-0.1*(x1*x1+x2*x2))"
''' % (o1,o2,n1,n2,d1,d2,o3,n3,d3))
Result('membrane',
'''
plsurf title="Membrane" mesh=n color=j
minval=%g maxval=%g
''' % (o3,o3 + d3*(n3-1)))
End()system/generic programs[edit]
sfremap1[edit]
| 1-D ENO interpolation. | |||
|---|---|---|---|
| sfremap1 < in.rsf > out.rsf pattern=pattern.rsf n1=n1 d1=d1 o1=o1 order=3 | |||
| float | d1=d1 | Output sampling | |
| int | n1=n1 | Number of output samples | |
| float | o1=o1 | Output origin | |
| int | order=3 | Interpolation order | |
| string | pattern= | auxiliary input file name | |
To give an example of usage, we will create an input for sfremap1 with:
sfmath n1=11 n2=11 d1=1 d2=1 o1=-5 o2=-5 output="x1*x1+x2*x2" > inp2remap1.rsf
Let us interpolate the data across both dimensions, then display it:
< inp2remap1.rsf sfremap1 n1=1001 d1=0.01 | sftransp | \ sfremap1 n1=1001 d1=0.01 | sftransp | sfgrey allpos=y | sfpen
The comparison with the uninterpolated data ( < inp2remap1.rsf sfgrey allpos=y | sfpen ) is quite telling.
system/seismic programs[edit]
sfstretch[edit]
| Stretch of the time axis. | |||
|---|---|---|---|
| sfstretch < in.rsf > out.rsf datum=dat.rsf inv=n dens=1 v0= half=y delay= tdelay= hdelay= nout=dens*n1 extend=4 mute=0 maxstr=0 rule= | |||
| file | datum= | auxiliary input file name | |
| float | delay= | time delay for rule=lmo | |
| int | dens=1 | axis stretching factor | |
| int | extend=4 | trace extension | |
| bool | half=y | [y/n] | if y, the second axis is half-offset instead of full offset |
| float | hdelay= | offset delay for rule=rad | |
| bool | inv=n | [y/n] | if y, do inverse stretching |
| float | maxstr=0 | maximum stretch | |
| int | mute=0 | tapering size | |
| int | nout=dens*n1 | output axis length (if inv=n) | |
| string | rule= | Stretch rule:
| |
| float | tdelay= | time delay for rule=rad | |
| float | v0= | moveout velocity | |
sfstretch rule=d (aka sfdatstretch) can be used to apply statics. Here is a synthetic example, courtesy of Alessandro Frigeri:
# generate a dataset with 'flat' signals sfmath n1=200 n2=100 output="sin(0.5*x1)" type=float > scan.rsf # generate a sinusoidal elevation correction sfmath n1=100 output="3*sin(x1)" type=float > statics.rsf # apply statics, producing a 'wavy' output. sfstretch < scan.rsf > out.rsf datum=statics.rsf rule=d
user/fomels programs[edit]
sfpick[edit]
| Automatic picking from semblance-like panels. | |||
|---|---|---|---|
| sfpick < scn.rsf > pik.rsf vel0=o2 niter=100 an=1. gate=3 smooth=y rect#=(1,1,...) rect1=1 rect2=1 ... | |||
| rectN defines the size of the smoothing stencil in N-th dimension. Theory in Appendix B of: S. Fomel, 2009, Velocity analysis using AB semblance: Geophysical Prospecting, v. 57, 311-321. Reproducible version in RSFSRC/book/jsg/avo | |||
| float | an=1. | axes anisotropy | |
| int | gate=3 | picking gate | |
| int | niter=100 | number of iterations | |
| int | rect#=(1,1,...) | smoothing radius on #-th axis | |
| bool | smooth=y | [y/n] | if apply smoothing |
| float | vel0=o2 | surface velocity | |
Short description of the algorithm:
- Start from the top (first time slice), pick an initial (source) point, evaluate all other points with the direct traveltime.
- At each grid point at the next level, find the traveltime to points at the previous level, add the traveltimes from the previous level, and select minimum. The aperture (gate= parameter in sfpick) limits the search radius.
- Repeat step 2 until reaching the bottom.
- Pick the minimum traveltime at the bottom and track the ray back to the source by following the traveltime gradient direction.
- Postprocessing (smooth= parameter in sfpick): smooth the picked ray path using shaping regularization.
Many people have discovered and rediscovered the algorithm. The best reference is probably V. Meshbey, E. Ragoza, D. Kosloff, U. Egozi, and D. Wexler, 2002, Three-dimensional Travel-time Calculation Based on Fermat's Principle: Pure and Applied Geophysics, v. 159, 1563-1582.
user/ivlad programs[edit]
sfprep4plot[edit]
| Resamples a 2-D dataset to the desired picture resolution, with antialias | |||
|---|---|---|---|
| sfprep4plot inp= out= verb=n h=none w=none unit= ppi= prar=y | |||
| Only one of the h and w parameters needs to be specified. If prar=n, no action will be taken on the axis for which h/w was not specified If prar=y and only one par (h or w) is specified, the picture will scale along both axes until it is of the specified dimension. | |||
| int | h=none | output height | |
| string | inp= | input file | |
| string | out= | output file | |
| int | ppi= | output resolution (px/in). Necessary when unit!=px | |
| bool | prar=y | [y/n] | if y, PReserve Aspect Ratio of input |
| string | unit= | unit of h and w. Can be: px(default), mm, cm, in | |
| bool | verb=n | [y/n] | if y, print system commands, outputs |
| int | w=none | output width | |
For a figure that does not need the aspect ratio preserved, and needs to fill a 1280x1024 projector display:
sfprep4plot inp=file1.rsf out=file2.rsf w=1280 h=1024 prar=n
For a print figure that has to fit in a 6x8in box at a resolution of 250 dpi, preserving the aspect ratio:
sfprep4plot inp=file1.rsf out=file2.rsf w=6 h=8 unit=in ppi=250
A comparison of images before and after the application of sfprep4plot, courtesy of Joachim Mispel, is shown below:
sfcsv2rsf[edit]
| Convert a delimited-text ASCII file to RSF binary floating point or int. | |||
|---|---|---|---|
| sfcsv2rsf help=n delimiter=, dtype=float verb=n debug=n trunc=n o1=0. o2=0. d1=1. d2=1. unit1=unknown unit2=unknown label1=unknown label2=unknown | |||
| Zeros will be added if number of elements is not the same in each row. n1 and n2 are computed automatically. For consistency with sfdisfil and sfmatmult, output is C-style order (row-first), i.e. rows in input file become dimension-1 columns in output. Output encoding is native. | |||
| float | d1=1. | ||
| float | d2=1. | ||
| bool | debug=n | [y/n] | Extra verbosity for debugging |
| string | delimiter=, | Separator between values in input file | |
| string | dtype=float | Input type | |
| bool | help=n | [y/n] | |
| string | label1=unknown | ||
| string | label2=unknown | ||
| float | o1=0. | ||
| float | o2=0. | ||
| bool | trunc=n | [y/n] | Truncate or add zeros if nr elems in rows differs |
| string | unit1=unknown | ||
| string | unit2=unknown | ||
| bool | verb=n | [y/n] | Whether to echo n1, n2, infill/truncation |
A small usage example follows below. First, create an input file:
$ echo -e '5,6,8,9.2\n11,124,5,0,1' | tee file.csv
5,6,8,9.2
11,124,5,0,1You may notice that the number of values in each row is different.
Run sfcsv2rsf. Notice that no options are needed. By default, zeros will be appended to make the rows equal in length:
$ <file.csv sfcsv2rsf > junk.rsf ; sfdisfil < junk.rsf
0: 5 6 8 9.2 0
5: 11 124 5 0 1Notice that sfdisfil displays in column order (i.e. matrix is transposed if the number of rows is right). The dimensions of the file are transposed on disk:
$ sfin junk.rsf
junk.rsf:
in="/data/path/junk.rsf@"
esize=4 type=float form=native
n1=5 d1=1 o1=0 unit1="unknown"
n2=2 d2=1 o2=0 unit2="unknown"
10 elements 40 bytesDepending on your needs, you may want to run the output through sftransp. However, if creating an input for sfmatmult, this will not be necessary, because sfmatmult is made to work with matrices that are displayed with sfdisfil, and takes as input a transpose matrix.
Pipes can be used, of course, to skip the creation of intermediary files:
$ <file.csv sfcsv2rsf | sfdisfil
0: 5 6 8 9.2 0
5: 11 124 5 0 1Note that since this program does not need any arguments (just stdin and stdout), it will not display the man page when called with no arguments. In order to consult the automatically generated documentation, you need to pass the option help=y .
user/jennings programs[edit]
sfsizes[edit]
| Display the size of RSF files. | |||
|---|---|---|---|
| sfsizes files=y human=n file1.rsf file2.rsf ... | |||
| Prints the element size, number of elements, and number of bytes for a list of RSF files. Non-RSF files are ignored. | |||
| bool | files=y | [y/n] | If y, print size of each file. If n, print only total. |
| bool | human=n | [y/n] | If y, print human-readable file size. If n, print byte count. |
This program computes the "theoretical" size in bytes of the data fork of RSF files. The actual space occupied on disk may be different and machine-dependent due to disk blocking factors, etc. This theoretical array size should be reproducible. It is also fast because the program only reads the RSF headers files, not the actual data.
For example, to get the total size of all RSF files in a directory, in human-readable format, without listing each file:
sfsizes files=n human=y *.rsf
This will also work because sfsizes simply skips any non-RSF file:
sfsizes files=n human=y *
sffiglist[edit]
| Compare Vplot files in Fig and Lock directories | |||
|---|---|---|---|
| sffiglist figdir= lockdir= list= show= | |||
|
Parameter figdir is path to Fig directory, default is ./Fig.
| |||
| string | figdir= | fig directory, default = ./Fig | |
| string | list= | how much to list [none,diff,miss,all], default = all | |
| string | lockdir= | lock directory, default = lock counterpart of figdir | |
| string | show= | how much to show [none,diff,miss,all], default = none | |
This tool lists Vplot files in the "Fig" and "Lock" directories and compares them using sfvplotdiff.
The Fig directory defaults to ./Fig and the Lock directory defaults to the corresponding directory where "scons lock" puts things, but either default can be overridden with the user parameters figdir and lockdir so that, for example, files in two different Fig directories can be compared.
The default for the Lock directory has some logic to look in $RSFFIGS when Fig is in $RSFSRC/book, or to look in $RSFALTFIGS when Fig is not in $RSFSRC/book because I like to keep two different Lock directories: one for stuff in book and another for my own stuff that is not in book. However, I tried to make the code default to reasonable things if any of these environment variables are not defined.
The tool gives a summary count of files that are the same, files that are different, files in Fig that are missing from Lock, and files in Lock that are missing from Fig.
The parameters list (default=all) and show (default=none) control which files are listed or "flipped" with sfpen. The file listing indicates which files are the same, which are different, and which are missing from Fig or Lock.
For example, to list all the Vplot files in Fig and Lock:
sffiglist list=all
To list all Vplot files and flip only files that are different:
sffiglist list=all show=diff
user/psava programs[edit]
sfawefd2d[edit]
| acoustic time-domain FD modeling | |||
|---|---|---|---|
| sfawefd < Fwav.rsf vel=Fvel.rsf sou=Fsou.rsf rec=Frec.rsf wfl=Fwfl.rsf > Fdat.rsf den=Fden.rsf ompchunk=1 ompnth=0 verb=n snap=n free=n expl=n jdata=1 jsnap=nt nq1=sf_n(a1) nq2=sf_n(a2) oq1=sf_o(a1) oq2=sf_o(a2) | |||
| file | den= | auxiliary input file name | |
| bool | expl=n | [y/n] | "exploding reflector" |
| bool | free=n | [y/n] | free surface flag |
| int | jdata=1 | ||
| int | jsnap=nt | save wavefield every *jsnap* time steps | |
| int | nq1=sf_n(a1) | ||
| int | nq2=sf_n(a2) | ||
| int | ompchunk=1 | OpenMP data chunk size | |
| int | ompnth=0 | OpenMP available threads | |
| float | oq1=sf_o(a1) | ||
| float | oq2=sf_o(a2) | ||
| file | rec= | auxiliary input file name | |
| bool | snap=n | [y/n] | wavefield snapshots flag |
| file | sou= | auxiliary input file name | |
| file | vel= | auxiliary input file name | |
| bool | verb=n | [y/n] | verbosity flag |
| file | wfl= | auxiliary output file name | |
Below, we will demonstrate an example of a model with nx=nz=200 and dx=dz=4m (size: 800x800m). There are two layers: the first is 100x200 samples in (z,x), and the velocity is 1500m/s; the second layer has the same dimension, and the velocity is 3000m/s. The density is set to 1 for the whole grid. A source and a receiver are co-located at x=400 and z=100. The full wavefield for the entire model aperture will be saved every 10th time step.
- Velocity model:
sfspike > Fvel.rsf mag=1500,3000 nsp=2 k1=1,101 l1=100,200 d1=4 d2=4 \ label1=z label2=x n1=200 n2=200 o1=2 o2=2 unit1=m unit2=m
- Density model:
sfspike > Fden.rsf mag=1 nsp=1 k1=1 l1=200 d1=4 d2=4 label1=z \ label2=x n1=200 n2=200 o1=2 o2=2 unit1=m unit2=m
- Source position (x,z):
sfspike n1=2 nsp=2 k1=1,2 mag=400,100 o1=0 o2=0 > Fsou.rsf
- Receiver position (x,z):
sfspike n1=2 nsp=2 k1=1,2 mag=400,100 o1=0 o2=0 > Frec.rsf
- Source wavelet:
sfspike nsp=1 n1=2000 d1=0.0005 k1=200 | sfricker1 frequency=20 |\ sftransp > Fwav.rsf
- Creating data at specified receiver + saving full wavefield every 10th step:
sfawefd2d < Fwav.rsf vel=Fvel.rsf sou=Fsou.rsf rec=Frec.rsf wfl=Fwfl.rsf \ den=Fden.rsf > Fdat.rsf verb=y free=y expl=y snap=y dabc=y jdata=1 jsnap=10 echo 'label1=z unit1=m label2=x unit2=m' >> Fwfl.rsf
- View the wavefield movie:
< Fwfl.rsf sfgrey gainpanel=a pclip=99 color=j scalebar=y | sfpen
- View a wavefield snapshot:
< Fwfl.rsf sfwindow f3=80 n3=1 |\ sfgrey pclip=99 color=j title='snapshot at t=0.4s' |\ sfpen
- View the data recorded at the receiver:
< Fdat.rsf sfwindow |\ sfgraph title='Data recorded at receiver' unit2='' label2=amplitude |\ sfpen
Attention: time steps that are too large can result in numerical instability.
sfsrmig3[edit]
| 3-D S/R migration with extended SSF | |||
|---|---|---|---|
| sfsrmig3 slo=Fs_s.rsf sls=Fs_r.rsf < Fw_s.rsf rwf=Fw_r.rsf > Fi.rsf cig=Fc.rsf ompchunk=1 ompnth=0 verb=y eps=0.01 twoway=n nrmax=1 dtmax=0.004 pmx=0 pmy=0 tmx=0 tmy=0 vpvs=1. hsym=n nht=1 oht=0 dht=0.1 nht=1 oht=0 dht=0.1 hsym=n nhh=1 ohh=0 dhh=0.1 nha=180 oha=0 dha=2.0 nhb=180 ohb=0 dhb=2.0 itype= | |||
| file | cig= | auxiliary output file name | |
| float | dha=2.0 | ||
| float | dhb=2.0 | ||
| float | dhh=0.1 | ||
| float | dht=0.1 | ||
| float | dtmax=0.004 | max time error | |
| float | eps=0.01 | stability parameter | |
| bool | hsym=n | [y/n] | |
| string | itype= | imaging condition type
| |
| int | nha=180 | ||
| int | nhb=180 | ||
| int | nhh=1 | ||
| int | nht=1 | ||
| int | nrmax=1 | max number of refs | |
| float | oha=0 | ||
| float | ohb=0 | ||
| float | ohh=0 | ||
| float | oht=0 | ||
| int | ompchunk=1 | OpenMP data chunk size | |
| int | ompnth=0 | OpenMP available threads | |
| int | pmx=0 | padding on x | |
| int | pmy=0 | padding on y | |
| file | rwf= | auxiliary input file name | |
| file | slo= | auxiliary input file name | |
| string | sls= | auxiliary input file name | |
| int | tmx=0 | taper on x | |
| int | tmy=0 | taper on y | |
| bool | twoway=n | [y/n] | two-way traveltime |
| bool | verb=y | [y/n] | verbosity flag |
| float | vpvs=1. | Vp/Vs ratio | |
This program performs 3-D and 2-D shot-record (a.k.a. shot-profile) migration with an extended Split-Step Fourier (SSF) extrapolator with multiple reference velocities (hence "extended"). It takes as input a shot wavefield (stdin), receiver wavefield (rwf=) and slowness model (slo=). Outputs are an image (stdout) and a cube of Common Image Gathers (cig=). An important parameter is nrmax, the number of reference velocities. Its default value is 1, but it should be 5 or so for reasonable results. It is also good to specify nonzero taper values (tmx and, for 3-D, tmy as well). The values of padding parameters pmx and pmy are split in two by the program, i.e., if your data x-axis is 501-points long, specify pmx=11 to get a value of 512 that will result in fast Fourier Transforms.
The program will also migrate converted-wave data if a file with the S-wave slowness model (sls=) is provided.
The vpvs parameter is only used when itype=h. Do not specify a vpvs value unless you know really well what you are doing.
Usage example[edit]
The commands below, slightly modified from RSFSRC/book/data/sigsbee/ptest, show how to prepare the Sigsbee 2A data and velocity for migration.
Convert input data (shots) from SEG-Y to RSF:
sfsegyread tape=sigsbee2a_nfs.segy tfile=tdata.rsf hfile=/dev/null bfile=/dev/null > ddata.rsfConvert trace headers to float (required by sfheadermath):
< tdata.rsf sfdd type=float > trchdr.rsfShot positions:
< trchdr.rsf sfheadermath output="fldr + 10925/150" | sfwindow squeeze=y > tsi.rsfExtract offset positions from the trace header files, eliminate length-1 axis, scale, and create a header for binning (required by sfintbin):
< trchdr.rsf sfheadermath output="offset" |\
sfwindow squeeze=y |\
sfmath output="input/75" |\
sfcat axis=2 space=n tsi.rsf |\
sftransp |\
sfdd type=int > tos.rsfBinning and muting:
< ddata.rsf sfintbin head=tos.rsf xkey=0 ykey=1 |\
sfput label1=Time unit1=s d2=0.075 o2=0.0 label2=hx d3=0.150 o3=10.925 label3=sx |\
sfmutter half=false t0=1.0 v0=6.0 |\
sfput d2=0.02286 o2=0 unit2=km d3=0.04572 o3=3.32994 unit3=km > shots.rsfKeeping only 20 shots so that this 1-node job will not take forever, FFT-ing, decimating frequency slices (same as shortening the time axis), and creating y and hy axes of length 1:
< shots.rsf sfwindow n3=20 f3=10 j3=20 |\
sffft1 |\
sfwindow n1=200 min1=1 j1=3 |\
sfspray axis=3 n=1 o=0 d=1 label=hy |\
sfspray axis=5 n=1 o=0 d=1 label=sy > rfft.rsfThe dimensions of the cube thus created are:
$ sfin rfft.rsf trail=n
rfft.rsf:
in="/var/tmp/rfft.rsf@"
esize=8 type=complex form=native
n1=200 d1=0.25 o1=1 label1="Frequency" unit1="Hz"
n2=348 d2=0.02286 o2=0 label2="hx" unit2="km"
n3=1 d3=1 o3=0 label3="hy" unit3="km"
n4=20 d4=0.9144 o4=3.78714 label4="sx" unit4="km"
1392000 elements 11136000 bytes
Create the source wavelet (limited to the same frequency band as the data) and Fourier transform it:
sfspike k1=1 n1=1500 d1=0.008 |\
sfbandpass flo=15 fhi=25 |\
sffft1 |\
sfwindow n1=200 min1=1 j1=3 |\
sfput label1=freq > sfft.rsfThis creates a frequency-domain wavelet:
$ sfin sfft.rsf
sfft.rsf:
in="/var/tmp/sfft.rsf@"
esize=8 type=complex form=native
n1=200 d1=0.25 o1=1 label1="freq" unit1="Hz"
200 elements 1600 bytes
Create "synched" source and receiver wavefields with srsyn from wavelet and data frequency slices. The receiver and shot frequency slices are "placed" at the right location and padded with zeros up to the x-axis dimension specified below.
< rfft.rsf sfsrsyn nx=1067 dx=0.02286 ox=3.05562 wav=sfft.rsf swf=swav.rsf > rwav.rsfThis creates frequency slices ready for migration for both source and receiver, only axis 1 (frequency) must become axis 3, for both datasets:
< swav.rsf sftransp plane=12 | sftransp plane=23 > stra.rsf< rwav.rsf sftransp plane=12 | sftransp plane=23 > rtra.rsfThis creates a surface receiver wavefield ready for input to migration. Axis 4 is the shot number. The values of axis 4 are arbitrary because each shot has been padded with zeros so that it covers the entire velocity model. Therefore, the aperture of the downward continuation for each shot will be as large as that of the whole survey.
sfin trail=n rtra.rsf
rtra.rsf:
in="/var/tmp/rtra.rsf@"
esize=8 type=complex form=native
n1=1067 d1=0.02286 o1=3.05562 label1="x" unit1="km"
n2=1 d2=1 o2=0 label2="y" unit2="km"
n3=200 d3=0.25 o3=1 label3="w" unit3="Hz"
n4=20 d4=1 o4=0 label4="e" unit4="km"
4268000 elements 34144000 bytes
Convert the velocity model from SEG-Y to RSF, decimate, convert from feet to km, transpose, convert to slowness, and insert an additional axis:
sfsegyread tape=sigsbee2a_migvel.sgy tfile=/dev/null hfile=/dev/null bfile=/dev/null |\
sfput o1=0 d1=0.00762 label1=z unit1=km o2=3.05562 d2=0.01143 label2=x unit2=km |\
sfwindow j1=4 j2=2 |\
sfscale rscale=0.0003048 |\
sftransp |\
sfmath output="1/input" |\
sfspray axis=2 n=1 d=1 o=0 |\
sfput label2=y > slow.rsfThis creates a slowness file ready for input to migration, with an x-axis identical to the x-axis of the wavefield files:
$ sfin slow.rsf
slow.rsf:
in="/var/tmp/slow.rsf@"
esize=4 type=float form=native
n1=1067 d1=0.02286 o1=3.05562 label1="x" unit1="km"
n2=1 d2=1 o2=0 label2="y" unit2="km"
n3=301 d3=0.03048 o3=0 label3="z" unit3="km"
321167 elements 1284668 bytes
Finally, the migration command (for a 4-processor machine, hence the ompnth value). We choose not to compute any image gathers (itype=o), but due to the construction of the program we still have to explicitly assign the cig tag, or else an RSF file with the name of the tag and no rsf extension will be created:
< stra.rsf sfsrmig3 nrmax=20 dtmax=5e-05 eps=0.01 verb=y ompnth=4 \
tmx=16 rwf=rtra.rsf slo=slow.rsf itype=o cig=/dev/null > img.rsfThe migration of 20 shots takes approximately three hours on a 4-processor machine (1 shot=9 minutes). Without the frequency slice decimation by a factor of 3 and the depth axis decimation by a factor of 4, it would have taken twelve times as much. The resulting image has a y-axis of length 1:
$ sfin img.rsf trail=n
img.rsf:
in="/var/tmp/img.rsf@"
esize=4 type=float form=native
n1=1067 d1=0.02286 o1=3.05562 label1="x" unit1="km"
n2=1 d2=1 o2=0 label2="y" unit2="km"
n3=301 d3=0.03048 o3=0 label3="z" unit3="km"
321167 elements 1284668 bytes
To properly visualize the image, we need to eliminate the axis of length 1, then transpose the x and z axes to their natural position:
<img.rsf sfwindow squeeze=y | sftransp | sfgrey > img.vplReferences[edit]
- ↑ Claerbout, J., 1998, Multidimensional recursive filters via a helix: Geophysics, 63, 1532--1541.
- ↑ Claerbout, J., 1998, Multidimensional recursive filters via a helix: Geophysics, 63, 1532--1541.
- ↑ Barry, K.M., Cavers, D.A., and Kneale, C.W. 1975. Recommended standards for digital tape formats. Geophysics, 40, no. 02, 344–352.
- ↑ Norris, M.W., Faichney, A.K., Eds. 2001. SEG Y rev1 Data Exchange format. Society of Exploration Geophysicists, Tulsa, OK, 45 pp.