1FITS(3) User Contributed Perl Documentation FITS(3)
2
6 PDL::IO::FITS -- Simple FITS support for PDL
7
9 use PDL;
10 use PDL::IO::FITS;
11 $a = rfits('foo.fits'); # read a FITS file
13 $a->wfits('bar.fits'); # write a FITS file
14
16 This module provides basic FITS support for PDL, in the sense of read‐
17 ing and writing whole FITS files. (For more complex operations, such
18 as prefiltering rows out of tables or performing operations on the FITS
19 file in-place on disk), you can use the Astro::FITS::CFITSIO module
20 that is available on CPAN.
21 Basic FITS image files are supported, along with BINTABLE and IMAGE
23 extensions. ASCII Table support is planned, as are the HEASARC
24 bintable extensions that are recommended in the 1999 FITS standard.
25 Table support is based on hashes and named columns, rather than the
27 less convenient (but slightly more congruent) technique of perl lists
28 of numbered columns.
29 The principle interface routines are "rfits" and "wfits", for reading
31 and writing respectively. FITS headers are returned as perl hashes or
32 (if the module is present) Astro::FITS::Header objects that are tied to
33 perl hashes. Astro::FITS::Header objects provide convenient access
34 through the tied hash interface, but also allow you to control the card
35 structure in more detail using a separate method interface; see the
36 Astro::FITS::Header documentation for details.
37
39 Copyright (C) Karl Glazebrook, Craig DeForest, and Doug Burke,
40 1997-2004. There is no warranty. You are allowed to redistribute
41 and/or modify this software under certain conditions. For details, see
42 the file COPYING in the PDL distribution. If this file is separated
43 from the PDL distribution, the copyright notice should be pasted into
44 in this file.
45
47 rfits()
48 Simple piddle FITS reader.
50 $pdl = rfits('file.fits'); # Read a simple FITS image
52 Suffix magic:
54 $pdl = rfits('file.fits.gz'); # Read a file with gunzip(1)
56 $pdl = rfits('file.fits.Z'); # Read a file with uncompress(1)
57 $pdl = rfits('file.fits[2]'); # Read 2nd extension
59 $pdl = rfits('file.fits.gz[3]'); # Read 3rd extension
60 @pdls = rfits('file.fits'); # Read primary data and extensions
61 $hdr = rfits('file.fits',{data=>0}); # Options hash changes behavior
63 In list context, "rfits" reads the primary image and all possible
65 extensions, returning them in the same order that they occurred in the
66 file. In scalar context, the default is to read the primary HDU. One
67 can read other HDU's by using the [n] syntax, the second one is [1].
68 Currently recognized extensions are IMAGE and BINTABLE. (See the
69 addendum on EXTENSIONS for details).
70 "rfits" accepts several options that may be passed in as a hash ref if
72 desired:
73 bscale (default=1)
75 Determines whether the data are linearly scaled using the
76 BSCALE/BZERO keywords in the FITS header. To read in the exact data
77 values in the file, set this to 0.
78 data (default=1)
80 Determines whether to read the data, or just the header. If you set
81 this to 0, you will get back the FITS header rather than the data
82 themselves. (Note that the header is normally returned as the "hdr"
83 field of the returned PDL; this causes it to be returned as a hash
84 ref directly.)
85 hdrcpy (default=0)
87 Determines whether the hdrcpy flag is set in the returned PDL. Set‐
88 ting the flag will cause an explicit deep copy of the header when‐
89 ever you use the returned PDL in an arithmetic or slicing operation.
90 That is useful in many circumstances but also causes a hit in speed.
91 FITS image headers are stored in the output PDL and can be retrieved
93 with hdr or gethdr. The hdrcpy flag of the PDL is set so that the
94 header is copied to derived piddles by default. (This is inefficient
95 if you are planning to do lots of small operations on the data; clear
96 the flag with "->hcpy(0)" or via the options hash if that's the case.)
97 The header is a hash whose keys are the keywords in the FITS header.
99 If you have the "Astro::FITS::Header" module installed, the header is
100 actually a tied hash to a FITS header object, which can give you more
101 control over card order, comment fields, and variable types. (see
102 Astro::FITS::Header for details).
103 The header keywords are converted to uppercase per the FITS standard.
105 Access is case-insensitive on the perl side, provided that
106 Astro::FITS::Header is installed.
107 If Astro::FITS::Header is not installed, then a built-in legacy parser
109 is used to generate the header hash. Keyword-associated comments in
110 the headers are stored under the hash key "<keyword>_COMMENT>". All
111 HISTORY cards in the header are collected into a single multiline
112 string stored in the "HISTORY" key. All COMMENT cards are similarly
113 collected under the "COMMENT" key.
114 BSCALE/BZERO
116 If the BSCALE and/or BZERO keywords are set, they are applied to the
118 image before it is returned. The returned PDL is promoted as necessary
119 to contain the multiplied values, and the BSCALE and BZERO keywords are
120 deleted from the header for clarity. If you don't want this type of
121 processing, set 'bscale=>0' in the options hash.
122 EXTENSIONS
124 Sometimes a FITS file contains only extensions and a stub header in the
126 first header/data unit ("primary HDU"). In scalar context, you nor‐
127 mally only get back the primary HDU -- but in this special case, you
128 get back the first extension HDU. You can force a read of the primary
129 HDU by adding a '[0]' suffix to the file name.
130 BINTABLE EXTENSIONS
132 Binary tables are handled. Currently only the following PDL datatypes
134 are supported: byte, short, ushort, long, float, and double. At present
135 ushort() data is written as a long rather than as a short with
136 TSCAL/ZERO; this may change.
137 The return value for a binary table is a hash ref containing the names
139 of the columns in the table (in UPPER CASE as per the FITS standard).
140 Each element of the hash contains a PDL (for numerical values) or a
141 perl list (for string values). The PDL's 0th dimension runs across
142 rows; the 1st dimension runs across the repeat index within the row
143 (for rows with more than one value).
144 Thus, if your table contains a column named "FOO" with type "5D", the
146 expression
147 $a->{FOO}->((2))
149 returns a 5-element double-precision PDL containing the values of FOO
151 from the third row of the table.
152 The header of the table itself is parsed as with a normal FITS HDU, and
154 is returned in the element 'hdr' of the returned hash. You can use
155 that to preserve the original column order or access the table at a low
156 level, if you like.
157 Scaling and zero-point adjustment are performed as with BSCALE/BZERO:
159 the appropriate keywords are deleted from the as-returned header. To
160 avoid this behavior, set 'bscale=>0' in the options hash.
161 As appropriate, TSCAL/ZERO and TUNIT are copied into each column-PDL's
163 header as BSCALE/BZERO and BUNIT.
164 The main hash also contains the element 'tbl', which is set to 'binary'
166 to distinguish it from an ASCII table.
167 Because different columns in the table might have identical names in a
169 FITS file, the binary table reader practices collision avoidance. If
170 you have multiple columns named "FOO", then the first one encountered
171 (numerically) gets the name "FOO", the next one gets "FOO_1", and the
172 next "FOO_2", etc. The appropriate TTYPEn fields in the header are
173 changed to match the renamed column fields.
174 Columns with no name are assigned the name "COL_<n>", where <n> starts
176 at 1 and increments for each no-name column found.
177 If a FITS file contains the "BLANK" keyword (and has "BITPIX > 0"), the
179 piddle will have its bad flag set, and those elements which equal the
180 "BLANK" value will be set bad. For "BITPIX < 0", any NaN's are con‐
181 verted to bad (if necessary).
182 rfitshdr()
184 Read only the header of a FITS file or an extension within it.
186 This is syntactic sugar for the "data=>0" option to rfits.
188 See rfits for details on header handling. rfitshdr() runs the same
190 code to read the header, but returns it rather than reading in a data
191 structure as well.
192 wfits()
194 Simple PDL FITS writer
196 wfits $pdl, 'filename.fits', [$BITPIX];
198 wfits $hash, 'filename.fits', [$OPTIONS];
199 $pdl->wfits('foo.fits',-32);
200 Suffix magic:
202 # Automatically compress through pipe to gzip
204 wfits $pdl, 'filename.fits.gz';
205 # Automatically compress through pipe to compress
206 wfits $pdl, 'filename.fits.Z';
207 * Ordinary (PDL) data handling:
209 If the first argument is a PDL, then the PDL is written out as an
210 ordinary FITS file with a single Header/Data Unit of data.
211 $BITPIX is then optional and coerces the output data type according
213 to the standard FITS convention for the BITPIX field (with positive
214 values representing integer types and negative values representing
215 floating-point types).
216 If $pdl has a FITS header attached to it (actually, any hash that
218 contains a "SIMPLE=>T" keyword), then that FITS header is written
219 out to the file. The image dimension tags are adjusted to the
220 actual dataset. If there's a mismatch between the dimensions of the
221 data and the dimensions in the FITS header, then the header gets
222 corrected and a warning is printed.
223 * Table handling:
225 If you feed in a hash ref instead of a PDL, then the hash ref is
226 written out as a binary table extension. The hash ref keys are
227 treated as column names, and their values are treated as the data to
228 be put in each column.
229 For numeric information, the hash values should contain PDLs. The
231 0th dim of the PDL runs across rows, and higher dims are written as
232 multi-value entries in the table (e.g. a 7x5 PDL will yield a single
233 named column with 7 rows and 5 numerical entries per row, in a
234 binary table). ASCII tables only allow one entry per column in each
235 row, so if you plan to write an ASCII table then all of the values
236 of $hash should have at most one dim.
237 All of the column dims must agree in the threading sense. That is to
239 say, the 0th dimension of all of the values of $hash should be the
240 same (indicating that all columns have the same number of rows). As
241 an exception, if the 0th dim of any of the values is 1, or if that
242 value is a PDL scalar (with 0 dims), then that value is "threaded"
243 over -- copied into all rows.
244 Data dimensions higher than 2 are not possible in ordinary FITS
246 tables, so dims higher than 1 are clumped. (e.g. a 7x5x3 PDL will
247 yield a single named column with 7 rows and 15 numerical entries per
248 row). If $PDL::Verbose is set, this condition causes a warning mes‐
249 sage to be printed. [There is a multidim extension that is not yet
250 implemented but should be].
251 Non-PDL Perl scalars are treated as strings, even if they contain
253 numerical values. For example, a list ref containing 7 values is
254 treated as 7 rows containing one string each. There is no such
255 thing as a multi-string column in FITS tables, so any nonscalar val‐
256 ues in the list are stringified before being written. For example,
257 if you pass in a perl list of 7 PDLs, each PDL will be stringified
258 before being written, just as if you printed it to the screen. This
259 is probably not what you want -- you should use glue to connect the
260 separate PDLs into a single one. (e.g.
261 "$a->glue(1,$b,$c)->mv(1,0)")
262 The column names are case-insensitive, but by convention the keys of
264 $hash should normally be ALL CAPS, containing only digits, capital
265 letters, hyphens, and underscores. If you include other characters,
266 then case is smashed to ALL CAPS, whitespace is converted to under‐
267 scores, and unrecognized characters are ignored -- so if you include
268 the key "Au Purity (%)", it will be written to the file as a column
269 that is named "AU_PURITY". Since this is not guaranteed to produce
270 unique column names, subsequent columns by the same name are disam‐
271 biguated by the addition of numbers.
272 Two special keys, 'hdr' and 'tbl', can contain meta-information
274 about the type of table you want to write. You may override them by
275 including an $OPTIONS hash with a 'hdr' and/or 'tbl' key.
276 The 'tbl' key, if it exists, must contain either 'ASCII' or 'binary'
278 (case-insensitive), indicating whether to write an ascii or binary
279 table. The default is binary. [ASCII table writing is planned but
280 does not yet exist].
281 You can specify the format of the table quite specifically with the
283 'hdr' key or option field. If it exists, then the 'hdr' key should
284 contain fields appropriate to the table extension being used. Any
285 field information that you don't specify will be filled in automati‐
286 cally, so (for example) you can specify that a particular column
287 name goes in a particular position, but allow "wfits" to arrange the
288 other columns in the usual alphabetical order into any unused slots
289 that you leave behind. The "TFORMn", "TFIELDS", "PCOUNT", "GCOUNT",
290 "NAXIS", and "NAXISn" keywords are ignored: their values are calcu‐
291 lated based on the hash that you supply. Any other fields are
292 passed into the final FITS header verbatim.
293 As an example, the following
295 $a = long(1,2,4);
297 $b = double(1,2,4);
298 wfits { 'COLA'=>$a, 'COLB'=>$b }, "table1.fits";
299 will create a binary FITS table called table1.fits which contains
301 two columns called "COLA" and "COLB". The order of the columns is
302 controlled by setting the "TTYPEn" keywords in the header array, so
303 $h = { 'TTYPE1'=>'Y', 'TTYPE2'=>'X' };
305 wfits { 'X'=>$a, 'Y'=>$b, hdr=>$h }, "table2.fits";
306 creates table2.fits where the first column is called "Y" and the
308 second column is "X".
309 * multi-value handling
311 If you feed in a perl list rather than a PDL or a hash, then each
312 element is written out as a separate HDU in the FITS file. Each
313 element of the list must be a PDL or a hash. [This is not imple‐
314 mented yet but should be soon!]
315 * DEVEL NOTES
317 ASCII tables are not yet handled but should be.
318 Binary tables currently only handle one vector (up to 1-D array) per
320 table entry; the standard allows more, and should be fully imple‐
321 mented. This means that PDL::Complex piddles currently can not be
322 written to disk.
323 Handling multidim arrays implies that perl multidim lists should
325 also be handled.
326 For integer types (ie "BITPIX > 0"), the "BLANK" keyword is set to the
328 bad value. For floating-point types, the bad value is converted to NaN
329 (if necessary) before writing.
330 fits_field_cmp
332 fits_field_cmp
334 Sorting comparison routine that makes proper sense of the digits at the
336 end of some FITS header fields. Sort your hash keys using
337 "fits_field_cmp" and you will get (e.g.) your "TTYPE" fields in the
338 correct order even if there are 140 of them.
339 This is a standard kludgey perl comparison sub -- it uses the magical
341 $a and $b variables, rather than normal argument passing.
342 _rows()
344 Return the number of rows in a variable for table entry
346 You feed in a PDL or a list ref, and you get back the 0th dimension.
348 _prep_table()
350 Accept a hash ref containing a table, and return a header describing
352 the table and a string to be written out as the table, or barf.
353 You can indicate whether the table should be binary or ascii. The
355 default is binary; it can be overridden by the "tbl" field of the hash
356 (if present) or by parameter.
357perl v5.8.8 2006-08-19 FITS(3)