1FITS(3) User Contributed Perl Documentation FITS(3)
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6 PDL::IO::FITS -- Simple FITS support for PDL
7
9 use PDL;
10 use PDL::IO::FITS;
11 $x = rfits('foo.fits'); # read a FITS file
13 $x->wfits('bar.fits'); # write a FITS file
14
16 This module provides basic FITS support for PDL, in the sense of
17 reading and writing whole FITS files. (For more complex operations,
18 such as prefiltering rows out of tables or performing operations on the
19 FITS file in-place on disk), you can use the Astro::FITS::CFITSIO
20 module 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 1997-2010. 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 ndarray FITS reader.
49 $pdl = rfits('file.fits'); # Read a simple FITS image
51 Suffix magic:
53 $pdl = rfits('file.fits.gz'); # Read a file with gunzip(1)
55 $pdl = rfits('file.fits.Z'); # Read a file with uncompress(1)
56 $pdl = rfits('file.fits[2]'); # Read 2nd extension
58 $pdl = rfits('file.fits.gz[3]'); # Read 3rd extension
59 @pdls = rfits('file.fits'); # Read primary data and extensions
60 Tilde expansion:
62 #expand leading ~ to home directory (using glob())
64 $pdl = rfits '~/filename.fits';
65 $hdr = rfits('file.fits',{data=>0}); # Options hash changes behavior
67 In list context, "rfits" reads the primary image and all possible
69 extensions, returning them in the same order that they occurred in the
70 file -- except that, by default, the primary HDU is skipped if it
71 contains no data. In scalar context, the default is to read the first
72 HDU that contains data. One can read other HDU's by using the [n]
73 syntax. Using the [0] syntax forces a read of the first HDU,
74 regardless of whether it contains data or no. Currently recognized
75 extensions are IMAGE and BINTABLE. (See the addendum on EXTENSIONS for
76 details).
77 "rfits" accepts several options that may be passed in as a hash ref if
79 desired:
80 bscale (default=1)
82 Determines whether the data are linearly scaled using the
83 BSCALE/BZERO keywords in the FITS header. To read in the exact data
84 values in the file, set this to 0.
85 data (default=1)
87 Determines whether to read the data, or just the header. If you set
88 this to 0, you will get back the FITS header rather than the data
89 themselves. (Note that the header is normally returned as the "hdr"
90 field of the returned PDL; this causes it to be returned as a hash
91 ref directly.)
92 hdrcpy (default=0)
94 Determines whether the hdrcpy flag is set in the returned PDL.
95 Setting the flag will cause an explicit deep copy of the header
96 whenever you use the returned PDL in an arithmetic or slicing
97 operation. That is useful in many circumstances but also causes a
98 hit in speed. When two or more PDLs with hdrcpy set are used in an
99 expression, the result gets the header of the first PDL in the
100 expression. See hdrcpy for an example.
101 expand (default=1)
103 Determines whether auto-expansion of tile-compressed images should
104 happen. Tile-compressed images are transmitted as binary tables
105 with particular fields ("ZIMAGE") set. Leaving this alone does what
106 you want most of the time, unpacking such images transparently and
107 returning the data and header as if they were part of a normal IMAGE
108 extension. Setting "expand" to 0 delivers the binary table, rather
109 than unpacking it into an image.
110 afh (default=1)
112 By default rfits uses Astro::FITS::Header tied-hash objects to
113 contain the FITS header information. This permits explicit control
114 over FITS card information, and conforms well with the FITS
115 specification. But Astro::FITS::Header objects are about 40-60x
116 more memory intensive than comparable perl hashes, and also use ~10x
117 more CPU to manage. For jobs where header processing performance is
118 important (e.g. reading just the headers of 1,000 FITS files), set
119 afh to 0 to use the legacy parser and get a large boost in speed.
120 FITS image headers are stored in the output PDL and can be retrieved
122 with hdr or gethdr. The hdrcpy flag of the PDL is set so that the
123 header is copied to derived ndarrays by default. (This is inefficient
124 if you are planning to do lots of small operations on the data; clear
125 the flag with "->hcpy(0)" or via the options hash if that's the case.)
126 The header is a hash whose keys are the keywords in the FITS header.
128 If you have the "Astro::FITS::Header" module installed, the header is
129 actually a tied hash to a FITS header object, which can give you more
130 control over card order, comment fields, and variable types. (see
131 Astro::FITS::Header for details).
132 The header keywords are converted to uppercase per the FITS standard.
134 Access is case-insensitive on the perl side, provided that
135 Astro::FITS::Header is installed.
136 If Astro::FITS::Header is not installed, then a built-in legacy parser
138 is used to generate the header hash. Keyword-associated comments in
139 the headers are stored under the hash key "<keyword>_COMMENT>". All
140 HISTORY cards in the header are collected into a single multiline
141 string stored in the "HISTORY" key. All COMMENT cards are similarly
142 collected under the "COMMENT" key.
143 BSCALE/BZERO
145 If the BSCALE and/or BZERO keywords are set, they are applied to the
147 image before it is returned. The returned PDL is promoted as necessary
148 to contain the multiplied values, and the BSCALE and BZERO keywords are
149 deleted from the header for clarity. If you don't want this type of
150 processing, set 'bscale=>0' in the options hash.
151 EXTENSIONS
153 Sometimes a FITS file contains only extensions and a stub header in the
155 first header/data unit ("primary HDU"). In scalar context, you
156 normally only get back the primary HDU -- but in this special case, you
157 get back the first extension HDU. You can force a read of the primary
158 HDU by adding a '[0]' suffix to the file name.
159 BINTABLE EXTENSIONS
161 Binary tables are handled. Currently only the following PDL datatypes
163 are supported: byte, short, ushort, long, float, and double. At present
164 ushort() data is written as a long rather than as a short with
165 TSCAL/ZERO; this may change.
166 The return value for a binary table is a hash ref containing the names
168 of the columns in the table (in UPPER CASE as per the FITS standard).
169 Each element of the hash contains a PDL (for numerical values) or a
170 perl list (for string values). The PDL's 0th dimension runs across
171 rows; the 1st dimension runs across the repeat index within the row
172 (for rows with more than one value). (Note that this is different from
173 standard threading order - but it allows Least Surprise to work when
174 adding more complicated objects such as collections of numbers (via the
175 repeat count) or variable length arrays.)
176 Thus, if your table contains a column named "FOO" with type "5D", the
178 expression
179 $x->{FOO}->((2))
181 returns a 5-element double-precision PDL containing the values of FOO
183 from the third row of the table.
184 The header of the table itself is parsed as with a normal FITS HDU, and
186 is returned in the element 'hdr' of the returned hash. You can use
187 that to preserve the original column order or access the table at a low
188 level, if you like.
189 Scaling and zero-point adjustment are performed as with BSCALE/BZERO:
191 the appropriate keywords are deleted from the as-returned header. To
192 avoid this behavior, set 'bscale=>0' in the options hash.
193 As appropriate, TSCAL/ZERO and TUNIT are copied into each column-PDL's
195 header as BSCALE/BZERO and BUNIT.
196 The main hash also contains the element 'tbl', which is set to 'binary'
198 to distinguish it from an ASCII table.
199 Because different columns in the table might have identical names in a
201 FITS file, the binary table reader practices collision avoidance. If
202 you have multiple columns named "FOO", then the first one encountered
203 (numerically) gets the name "FOO", the next one gets "FOO_1", and the
204 next "FOO_2", etc. The appropriate TTYPEn fields in the header are
205 changed to match the renamed column fields.
206 Columns with no name are assigned the name "COL_<n>", where <n> starts
208 at 1 and increments for each no-name column found.
209 Variable-length arrays are supported for reading. They are unpacked
211 into PDLs that appear exactly the same as the output for fixed-length
212 rows, except that each row is padded to the maximum length given in the
213 extra characters -- e.g. a row with TFORM of 1PB(300) will yield an
214 NAXIS2x300 output field in the final hash. The padding uses the TNULn
215 keyword for the column, or 0 if TNULn is not present. The output hash
216 also gets an additional field, "len_<name>", that contains the number
217 of elements in each table row.
218 TILE-COMPRESSED IMAGES
220 CFITSIO and several large projects (including NASA's Solar Dynamics
222 Observatory) now support an unofficial extension to FITS that stores
223 images as a collection of individually compressed tiles within a
224 BINTABLE extension. These images are automagically uncompressed by
225 default, and delivered as if they were normal image files. You can
226 override this behavior by supplying the "expand" key in the options
227 hash.
228 Currently, only Rice compression is supported, though there is a
230 framework in place for adding other compression schemes.
231 BAD VALUE HANDLING
233 If a FITS file contains the "BLANK" keyword (and has "BITPIX > 0"), the
235 ndarray will have its bad flag set, and those elements which equal the
236 "BLANK" value will be set bad. For "BITPIX < 0", any NaN's are
237 converted to bad (if necessary).
238 rfitshdr()
240 Read only the header of a FITS file or an extension within it.
241 This is syntactic sugar for the "data=>0" option to rfits.
243 See rfits for details on header handling. rfitshdr() runs the same
245 code to read the header, but returns it rather than reading in a data
246 structure as well.
247 wfits()
249 Simple PDL FITS writer
250 wfits $pdl, 'filename.fits', [$BITPIX], [$COMPRESSION_OPTIONS];
252 wfits $hash, 'filename.fits', [$OPTIONS];
253 $pdl->wfits('foo.fits',-32);
254 Suffix magic:
256 # Automatically compress through pipe to gzip
258 wfits $pdl, 'filename.fits.gz';
259 # Automatically compress through pipe to compress
260 wfits $pdl, 'filename.fits.Z';
261 Tilde expansion:
263 #expand leading ~ to home directory (using glob())
265 wfits $pdl, '~/filename.fits';
266 • Ordinary (PDL) data handling:
268 If the first argument is a PDL, then the PDL is written out as an
270 ordinary FITS file with a single Header/Data Unit of data.
271 $BITPIX is then optional and coerces the output data type according
273 to the standard FITS convention for the BITPIX field (with positive
274 values representing integer types and negative values representing
275 floating-point types).
276 If $pdl has a FITS header attached to it (actually, any hash that
278 contains a "SIMPLE=>T" keyword), then that FITS header is written
279 out to the file. The image dimension tags are adjusted to the
280 actual dataset. If there's a mismatch between the dimensions of the
281 data and the dimensions in the FITS header, then the header gets
282 corrected and a warning is printed.
283 If $pdl is a slice of another PDL with a FITS header already present
285 (and header copying enabled), then you must be careful. "wfits"
286 will remove any extraneous "NAXISn" keywords (per the FITS
287 standard), and also remove the other keywords associated with that
288 axis: "CTYPEn", "CRPIXn", "CRVALn", "CDELTn", and "CROTAn". This
289 may cause confusion if the slice is NOT out of the last dimension:
290 "wfits($x(:,(0),:),'file.fits');" and you would be best off
291 adjusting the header yourself before calling "wfits".
292 You can tile-compress images according to the CFITSIO extension to
294 the FITS standard, by adding an option hash to the arguments:
295 compress
297 CURRENTLY UNIMPLEMENTED. Below describes the envisioned usage.
298 This can be either unity, in which case Rice compression is used,
300 or a (case-insensitive) string matching the CFITSIO compression
301 type names. Currently supported compression algorithms are:
302 • RICE_1 - linear Rice compression
304 This uses limited-symbol-length Rice compression, which works
306 well on low entropy image data (where most pixels differ from
307 their neighbors by much less than the dynamic range of the
308 image).
309 tilesize (default "[-1,1]")
311 This specifies the dimension of the compression tiles, in pixels.
312 You can hand in a PDL, a scalar, or an array ref. If you specify
313 fewer dimensions than exist in the image, the last dim is
314 repeated - so "32" yields 32x32 pixel tiles in a 2-D image. A
315 dim of -1 in any dimension duplicates the image size, so the
316 default "[-1,1]" causes compression along individual rows.
317 tilesize (RICE_1 only; default 32)
319 For RICE_1, BLOCKSIZE indicates the number of pixel samples to
320 use for each compression block within the compression algorithm.
321 The blocksize is independent of the tile dimensions. For RICE
322 compression the pixels from each tile are arranged in normal
323 pixel order (early dims fastest) and compressed as a linear
324 stream.
325 • Table handling:
327 If you feed in a hash ref instead of a PDL, then the hash ref is
329 written out as a binary table extension. The hash ref keys are
330 treated as column names, and their values are treated as the data to
331 be put in each column.
332 For numeric information, the hash values should contain PDLs. The
334 0th dim of the PDL runs across rows, and higher dims are written as
335 multi-value entries in the table (e.g. a 7x5 PDL will yield a single
336 named column with 7 rows and 5 numerical entries per row, in a
337 binary table). Note that this is slightly different from the usual
338 concept of threading, in which dimension 1 runs across rows.
339 ASCII tables only allow one entry per column in each row, so if you
341 plan to write an ASCII table then all of the values of $hash should
342 have at most one dim.
343 All of the columns' 0 dims must agree in the threading sense. That
345 is to say, the 0th dimension of all of the values of $hash should be
346 the same (indicating that all columns have the same number of rows).
347 As an exception, if the 0th dim of any of the values is 1, or if
348 that value is a PDL scalar (with 0 dims), then that value is
349 "threaded" over -- copied into all rows.
350 Data dimensions higher than 2 are preserved in binary tables, via
352 the TDIMn field (e.g. a 7x5x3 PDL is stored internally as seven rows
353 with 15 numerical entries per row, and reconstituted as a 7x5x3 PDL
354 on read).
355 Non-PDL Perl scalars are treated as strings, even if they contain
357 numerical values. For example, a list ref containing 7 values is
358 treated as 7 rows containing one string each. There is no such
359 thing as a multi-string column in FITS tables, so any nonscalar
360 values in the list are stringified before being written. For
361 example, if you pass in a perl list of 7 PDLs, each PDL will be
362 stringified before being written, just as if you printed it to the
363 screen. This is probably not what you want -- you should use "glue"
364 to connect the separate PDLs into a single one. (e.g.
365 "$x->glue(1,$y,$c)->mv(1,0)")
366 The column names are case-insensitive, but by convention the keys of
368 $hash should normally be ALL CAPS, containing only digits, capital
369 letters, hyphens, and underscores. If you include other characters,
370 then case is smashed to ALL CAPS, whitespace is converted to
371 underscores, and unrecognized characters are ignored -- so if you
372 include the key "Au Purity (%)", it will be written to the file as a
373 column that is named "AU_PURITY". Since this is not guaranteed to
374 produce unique column names, subsequent columns by the same name are
375 disambiguated by the addition of numbers.
376 You can specify the use of variable-length rows in the output,
378 saving space in the file. To specify variable length rows for a
379 column named "FOO", you can include a separate key "len_FOO" in the
380 hash to be written. The key's value should be a PDL containing the
381 number of actual samples in each row. The result is a FITS P-type
382 variable length column that, upon read with "rfits()", will restore
383 to a field named FOO and a corresponding field named "len_FOO".
384 Invalid data in the final PDL consist of a padding value (which
385 defaults to 0 but which you may set by including a TNULL field in
386 the hdr specificaion). Variable length arrays must be 2-D PDLs,
387 with the variable length in the 1 dimension.
388 Two further special keys, 'hdr' and 'tbl', can contain meta-
390 information about the type of table you want to write. You may
391 override them by including an $OPTIONS hash with a 'hdr' and/or
392 'tbl' key.
393 The 'tbl' key, if it exists, must contain either 'ASCII' or 'binary'
395 (case-insensitive), indicating whether to write an ascii or binary
396 table. The default is binary. [ASCII table writing is planned but
397 does not yet exist].
398 You can specify the format of the table quite specifically with the
400 'hdr' key or option field. If it exists, then the 'hdr' key should
401 contain fields appropriate to the table extension being used. Any
402 field information that you don't specify will be filled in
403 automatically, so (for example) you can specify that a particular
404 column name goes in a particular position, but allow "wfits" to
405 arrange the other columns in the usual alphabetical order into any
406 unused slots that you leave behind. The "TFORMn", "TFIELDS",
407 "PCOUNT", "GCOUNT", "NAXIS", and "NAXISn" keywords are ignored:
408 their values are calculated based on the hash that you supply. Any
409 other fields are passed into the final FITS header verbatim.
410 As an example, the following
412 $x = long(1,2,4);
414 $y = double(1,2,4);
415 wfits { 'COLA'=>$x, 'COLB'=>$y }, "table1.fits";
416 will create a binary FITS table called table1.fits which contains
418 two columns called "COLA" and "COLB". The order of the columns is
419 controlled by setting the "TTYPEn" keywords in the header array, so
420 $h = { 'TTYPE1'=>'Y', 'TTYPE2'=>'X' };
422 wfits { 'X'=>$x, 'Y'=>$y, hdr=>$h }, "table2.fits";
423 creates table2.fits where the first column is called "Y" and the
425 second column is "X".
426 • multi-value handling
428 If you feed in a perl list rather than a PDL or a hash, then each
430 element is written out as a separate HDU in the FITS file. Each
431 element of the list must be a PDL or a hash. [This is not
432 implemented yet but should be soon!]
433 • DEVEL NOTES
435 ASCII tables are not yet handled but should be.
437 Binary tables currently only handle one vector (up to 1-D array) per
439 table entry; the standard allows more, and should be fully
440 implemented.
441 Handling multidim arrays implies that perl multidim lists should
443 also be handled.
444 For integer types (ie "BITPIX > 0"), the "BLANK" keyword is set to the
446 bad value. For floating-point types, the bad value is converted to NaN
447 (if necessary) before writing.
448 fits_field_cmp
450 fits_field_cmp
451 Sorting comparison routine that makes proper sense of the digits at the
453 end of some FITS header fields. Sort your hash keys using
454 "fits_field_cmp" and you will get (e.g.) your "TTYPE" fields in the
455 correct order even if there are 140 of them.
456 This is a standard kludgey perl comparison sub -- it uses the magical
458 $a and $b variables, rather than normal argument passing.
459 _rows()
461 Return the number of rows in a variable for table entry
462 You feed in a PDL or a list ref, and you get back the 0th dimension.
464 _prep_table()
466 Accept a hash ref containing a table, and return a header describing
467 the table and a string to be written out as the table, or barf.
468 You can indicate whether the table should be binary or ascii. The
470 default is binary; it can be overridden by the "tbl" field of the hash
471 (if present) or by parameter.
472perl v5.34.0 2021-08-16 FITS(3)