gmtconvert

Convert, paste, or extract columns from data tables

Synopsis

gmt convert [ table ] [ -A ] [ -C[+lmin][+umax][+i]] [ -D[template[+oorig]] ] [ -E[f|l|m|Mstride] ] [ -F[c|n|p|v][a|f|s|r|refpoint] ] [ -I[tsr] ] [ -L ] [ -Ncol[+a|d] ] [ -Q[~]selection] [ -S[~]“search string” | -S[~]/regexp/[i] ] [ -T[h][d[[~]selection]] ] [ -V[level] ] [ -W[+n] ] [ -aflags ] [ -bbinary ] [ -d[+ccol]nodata ] [ -eregexp ] [ -fflags ] [ -ggaps ] [ -hheaders ] [ -iflags ] [ -oflags ] [ -qflags ] [ -sflags ] [ -wflags ] [ -:[i|o] ] [ --PAR=value ]

Note: No space is allowed between the option flag and the associated arguments.

Description

convert reads its standard input [or input files] and writes out the desired information to standard output. It can do a combination of nine tasks: (1) convert between binary and ASCII data tables, (2) paste corresponding records from multiple files horizontally into a single file, (3) extract a subset of the available columns, (4) only extract segments whose header record matches a text pattern search, (5) only list segment headers and no data records, (6) extract first and/or last data record for each segment, (7) reverse the order of items on output, (8) output only ranges of segment numbers, and (9) output only segments whose record count matches criteria. Input (and hence output) may have multiple sub-headers, and ASCII tables may have regular headers as well.

Required Arguments

table

One or more ASCII (or binary, see -bi[ncols][type]) data table file(s) holding a number of data columns. If no tables are given then we read from standard input.

Optional Arguments

-A

The records from the input files should be pasted horizontally, not appended vertically [Default]. All files must have the same number of segments and number of rows per segment. Note for binary input, all the files you want to paste must have the same number of columns (as set with -bi); ASCII tables can have different number of columns.

-C[+lmin][+umax][+i]

Only output segments whose number of records matches your given criteria: Append +lmin to ensure all segment must have at least min records to be written to output [0], and append +umax to ensure all segments must have at most max records to be written [inf]. You may append +i to invert the selection, i.e., only segments with record counts outside the given range will be output.

-D[template[+oorig]]

For multiple segment data, dump each segment to a separate output file [Default writes a multiple segment file to stdout]. Append a format template for the individual file names; this template must contain a C format specifier that can format an integer argument (the running segment number across all tables); this is usually %d but could be %08d which gives leading zeros, etc. [Default is gmtconvert_segment_%d.{txt|bin}, depending on -bo]. Append +oorig to start the numbering from orig instead of zero. Alternatively, give a template with two C format specifiers and we will supply the table number and the segment number within the table to build the file name. Append +otorig/sorig to start the numbering of tables from torig and numbering of segments within a table from sorig instead of zero. The +o modifier will be stripped off before the template is used.

-E[f|l|m|Mstride]

Only extract the first and last record for each segment of interest [Default extracts all records]. Optionally, append f or l to only extract the first or last record of each segment, respectively. Alternatively, append mstride to extract every stride records; use M to also include the last record.

-F[c|n|p|v][a|f|s|r|refpoint]

Alter the way points are connected (by specifying a scheme) and data are grouped (by specifying a method). Append one of four line connection schemes: c: Form continuous line segments for each group [Default]. p: Form line segments from a reference point reset for each group. n: Form networks of line segments between all points in each group. v: Form vector line segments suitable for plot -Sv+s. Optionally, append the one of four segmentation methods to define the group: a: Ignore all segment headers, i.e., let all points belong to a single group, and set group reference point to the very first point of the first file. f: Consider all data in each file to be a single separate group and reset the group reference point to the first point of each group. s: Segment headers are honored so each segment is a group; the group reference point is reset to the first point of each incoming segment [Default]. r: Same as s, but the group reference point is reset after each record to the previous point (this method is only available with the -Fp scheme). Instead of the codes a|f|s|r you may append the coordinates of a refpoint which will serve as a fixed external reference point for all groups.

-I[tsr]

Invert the order of items, i.e., output the items in reverse order, starting with the last and ending up with the first item [Default keeps original order]. Append up to three items that should be reversed: t will reverse the order of tables, s will reverse the order of segments within each table, and r will reverse the order of records within each segment [Default].

-L

Only output a listing of all segment header records and no data records (requires ASCII data).

-Ncol[+a|d]

Numerically sort each segment based on values in column col. The data records will be sorted such that the chosen column will fall into ascending order [+a, which is Default]. Append +d to sort into descending order instead. The -N option can be combined with any other ordering scheme except -F (segmentation) and is applied at the end.

-Q[~]selection

Only write segments whose number is included in selection and skip all others. Cannot be used with -S. The selection syntax is range[,range,…] where each range of items is either a single segment number or a range with stepped increments given via start[:step:]:stop (step is optional and defaults to 1). A leading ~ will invert the selection and write all segments but the ones listed. Instead of a list of ranges, use +ffile to supply a file list with one range per line.

-S[~]“search string” or -S[~]/regexp/[i]

Only output those segments whose header record contains the specified text string. To reverse the search, i.e., to output segments whose headers do not contain the specified pattern, use -S~. Should your pattern happen to start with ~ you need to escape this character with a backslash [Default output all segments]. Cannot be used with -Q. For matching segments based on aspatial values (via OGR/GMT format), give the search string as varname=value and we will compare value against the value of varname for each segment. Note: If the features are polygons then a match of a particular polygon perimeter also means that any associated polygon holes will also be matched. For matching segment headers against extended regular expressions enclose the expression in slashes. Append i for case-insensitive matching. For a list of such patterns, give +ffile with one pattern per line. To give a single pattern starting with +f, escape it with a backslash.

-T[h][d[[~]selection]]

Suppress the writing of certain records on output. Append h to suppress segment headers [Default], and/or d to suppress duplicate data records. Use -Thd to suppress both types of records. By default, all columns must be identical across the two records to skip the record. ALternatively, append a column selection to only use those columns in the comparisons instead. The selection syntax is range[,range,…] where each range of items is either a single column number or a range with stepped increments given via start[:step:]:stop (step is optional and defaults to 1). A leading ~ will invert the selection and select all columns but the ones listed. To add the trailing text to the comparison as well, add the column t to the list. If no numerical columns are specified, just t, then we only consider trailing text.

-V[level]

Select verbosity level [w]. (See full description) (See cookbook information).

-W[+n]

Attempt to convert each word in the trailing text to a number and append such values to the numerical output columns. Text that cannot be converted (because they are not numbers) will appear as NaNs. Use modifier +n to exclude the columns with NaNs. Note: These columns are identified based on the first input record only.

-a[[col=]name[,…]] (more …)

Set aspatial column associations col=name.

-birecord[+b|l] (more …)

Select native binary format for primary table input.

-borecord[+b|l] (more …)

Select native binary format for table output. [Default is same as input].

-d[i|o][+ccol]nodata (more …)

Replace input columns that equal nodata with NaN and do the reverse on output.

-e[~]“pattern” | -e[~]/regexp/[i] (more …)

Only accept data records that match the given pattern.

-f[i|o]colinfo (more …)

Specify data types of input and/or output columns.

-gx|y|z|d|X|Y|Dgap[u][+a][+ccol][+n|p] (more …)

Determine data gaps and line breaks.

-h[i|o][n][+c][+d][+msegheader][+rremark][+ttitle] (more …)

Skip or produce header record(s).

-icols[+l][+ddivisor][+sscale|d|k][+ooffset][,…][,t[word]] (more …)

Select input columns and transformations (0 is first column, t is trailing text, append word to read one word only).

-ocols[,…][,t[word]] (more …)

Select output columns (0 is first column; t is trailing text, append word to write one word only).

-q[i|o][~]rows|limits[+ccol][+a|f|s] (more …)

Select input or output rows or data limit(s) [all].

-s[cols][+a][+r] (more …)

Set handling of NaN records for output.

-wy|a|w|d|h|m|s|cperiod[/phase][+ccol] (more …)

Convert an input coordinate to a cyclical coordinate.

-:[i|o] (more …)

Swap 1st and 2nd column on input and/or output.

-^ or just -

Print a short message about the syntax of the command, then exit (NOTE: on Windows just use -).

-+ or just +

Print an extensive usage (help) message, including the explanation of any module-specific option (but not the GMT common options), then exit.

-? or no arguments

Print a complete usage (help) message, including the explanation of all options, then exit.

--PAR=value

Temporarily override a GMT default setting; repeatable. See gmt.conf for parameters.

ASCII Format Precision

The ASCII output formats of numerical data are controlled by parameters in your gmt.conf file. Longitude and latitude are formatted according to FORMAT_GEO_OUT, absolute time is under the control of FORMAT_DATE_OUT and FORMAT_CLOCK_OUT, whereas general floating point values are formatted according to FORMAT_FLOAT_OUT. Be aware that the format in effect can lead to loss of precision in ASCII output, which can lead to various problems downstream. If you find the output is not written with enough precision, consider switching to binary output (-bo if available) or specify more decimals using the FORMAT_FLOAT_OUT setting.

Examples

Note: Below are some examples of valid syntax for this module. The examples that use remote files (file names starting with @) can be cut and pasted into your terminal for testing. Other commands requiring input files are just dummy examples of the types of uses that are common but cannot be run verbatim as written.

To convert the binary file test.b (single precision) with 4 columns to ASCII:

gmt convert test.b -bi4f > test.dat

To convert the multiple segment ASCII table test.txt to a double precision binary file:

gmt convert test.txt -bo > test.b

You have an ASCII table with 6 columns and you want to plot column 5 versus column 0. Try:

gmt convert table.txt -o5,0 | gmt plot ...

If the file instead is the binary file results.b which has 9 single-precision values per record, we extract the last column and columns 4-6 and write ASCII with the command:

gmt convert results.b -o8,4-6 -bi9s | gmt plot ...

You want to plot the 2nd column of a 2-column file left.txt versus the first column of a file right.txt:

gmt convert left.txt right.txt -A -o1,2 | gmt plot ...

To extract all segments in the file big_file.txt whose headers contain the string “RIDGE AXIS”, try:

gmt convert big_file.txt -S"RIDGE AXIS" > subset.txt

To invert the selection of segments whose headers begin with “profile ” followed by an integer number and any letter between “g” and “l”, try:

gmt convert -S~"/^profile [0-9]+[g-l]$/"

To reverse the order of segments in a file without reversing the order of records within each segment, try:

gmt convert lots_of_segments.txt -Is > last_segment_first.txt

To extract segments 20 to 40 in steps of 2, plus segment 0 in a file, try:

gmt convert lots_of_segments.txt -Q0,20:2:40 > my_segments.txt

To extract the attribute ELEVATION from an ogr gmt file like this:

# @VGMT1.0 @GPOINT
...
# @NELEVATION|DISPX|DISPY
# @Tdouble|double|double
# FEATURE_DATA
# @D4.945000|-106500.00000000|-32700.00000000
-9.36890245902635 39.367156766570389

do:

gmt convert file.gmt -a2=ELEVATION > xyz.dat

or just:

gmt convert file.gmt -aELEVATION > xyz.dat

To connect all points in the file sensors.txt with the specified origin at 23.5/19, try:

gmt convert sensors.txt -F23.5/19 > lines.txt

To write all segments in the two files A.txt and B.txt to individual files named profile_005000.txt, profile_005001.txt, etc., where we reset the origin of the sequential numbering from 0 to 5000, try:

gmt convert A.txt B.txt -Dprofile_%6.6d.txt+o5000

To only read rows 100-200 and 500-600 from file junk.txt, try:

gmt convert junk.txt -q100-200,500-600 > subset.txt

To get all rows except those bad ones between rows 1000-2000, try:

gmt convert junk.txt -q~1000-2000 > good.txt

See Also

gmt, gmtinfo, gmtselect