1FlexRaw(3)            User Contributed Perl Documentation           FlexRaw(3)
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4

NAME

6       PDL::IO::FlexRaw -- A flexible binary I/O format for PerlDL
7

SYNOPSIS

9           use PDL;
10           use PDL::IO::FlexRaw;
11
12           # To obtain the header for reading (if multiple files use the
13           # same header, for example):
14           #
15           $hdr = PDL::IO::FlexRaw::_read_flexhdr("filename.hdr")
16
17           ($x,$y,...) = readflex("filename" [, $hdr])
18           ($x,$y,...) = mapflex("filename" [, $hdr] [, $opts])
19
20           $hdr = writeflex($file, $pdl1, $pdl2,...)
21           writeflexhdr($file, $hdr)
22
23           # if $PDL::IO::FlexRaw::writeflexhdr is true and
24           #    $file is a filename, writeflexhdr() is called automatically
25           #
26           $hdr = writeflex($file, $pdl1, $pdl2,...)  # need $hdr for something
27           writeflex($file, $pdl1, $pdl2,...)         # ..if $hdr not needed
28

DESCRIPTION

30       FlexRaw is a generic method for the input and output of `raw' data
31       arrays.  In particular, it is designed to read output from FORTRAN 77
32       UNFORMATTED files and the low-level C write function, even if the files
33       are compressed or gzipped.  As in FastRaw, the data file is
34       supplemented by a header file (although this can be replaced by the
35       optional $hdr argument).  More information can be included in the
36       header file than for FastRaw -- the description can be extended to
37       several data objects within a single input file.
38
39       For example, to read the output of a FORTRAN program
40
41           real*4 a(4,600,600)
42           open (8,file='banana',status='new',form='unformatted')
43           write (8) a
44           close (8)
45
46       the header file (`banana.hdr') could look like
47
48           # FlexRaw file header
49           # Header word for F77 form=unformatted
50           Byte 1 4
51           # Data
52           Float 3            # this is ignored
53                    4 600 600
54           Byte 1 4           As is this, as we've got all dims
55
56       The data can then be input using
57
58           $a = (readflex('banana'))[1];
59
60       The format of the hdr file is an extension of that used by FastRaw.
61       Comment lines (starting with #) are allowed, as are descriptive names
62       (as elsewhere: byte, short, ushort, long, float, double) for the data
63       types -- note that case is ignored by FlexRaw.  After the type, one
64       integer specifies the number of dimensions of the data `chunk', and
65       subsequent integers the size of each dimension.  So the specifier above
66       (`Float 3 4 600 600') describes our FORTRAN array.  A scalar can be
67       described as `float 0' (or `float 1 1', or `float 2 1 1', etc.).
68
69       When all the dimensions are read -- or a # appears after whitespace --
70       the rest of the current input line is ignored, unless badvalues are
71       being read or written.  In that case, the next token will be the string
72       "badvalue" followed by the bad value used, if needed.
73
74       What about the extra 4 bytes at the head and tail, which we just threw
75       away?  These are added by FORTRAN (at least on Suns, Alphas and Linux),
76       and specify the number of bytes written by each WRITE -- the same
77       number is put at the start and the end of each chunk of data.  You may
78       need to know all this in some cases.  In general, FlexRaw tries to
79       handle it itself, if you simply add a line saying `f77' to the header
80       file, before any data specifiers:
81
82           # FlexRaw file header for F77 form=unformatted
83           F77
84           # Data
85           Float 3
86           4 600 600
87
88       -- the redundancy in FORTRAN data files even allows FlexRaw to
89       automatically deal with files written on other machines which use back-
90       to-front byte ordering.  This won't always work -- it's a 1 in 4
91       billion chance it won't, even if you regularly read 4Gb files!  Also,
92       it currently doesn't work for compressed files, so you can say `swap'
93       (again before any data specifiers) to make certain the byte order is
94       swapped.
95
96       The optional $hdr argument allows the use of an anonymous array to give
97       header information, rather than using a .hdr file.  For example,
98
99           $header = [
100               {Type => 'f77'},
101               {Type => 'float', NDims => 3, Dims => [ 4,600,600 ] }
102           ];
103           @a = readflex('banana',$header);
104
105       reads our example file again.  As a special case, when NDims is 1, Dims
106       may be given as a scalar.
107
108       Within PDL, readflex and writeflex can be used to write several pdls to
109       a single file -- e.g.
110
111           use PDL;
112           use PDL::IO::FlexRaw;
113
114           @pdls = ($pdl1, $pdl2, ...);
115           $hdr = writeflex("fname",@pdls);
116           @pdl2 = readflex("fname",$hdr);
117
118           writeflexhdr("fname",$hdr);  # not needed if $PDL::IO::FlexRaw::writeflexhdr is set
119           @pdl3 = readflex("fname");
120
121       -- "writeflex" produces the data file and returns the file header as an
122       anonymous hash, which can be written to a .hdr file using
123       "writeflexhdr".
124
125       If the package variable $PDL::IO::FlexRaw::writeflexhdr is true, and
126       the "writeflex" call was with a filename and not a handle,
127       "writeflexhdr" will be called automatically (as done by "writefraw".
128
129       The reading of compressed data is switched on automatically if the
130       filename requested ends in .gz or .Z, or if the originally specified
131       filename does not exist, but one of these compressed forms does.
132
133       If "writeflex" and "readflex" are given a reference to a file handle as
134       a first parameter instead of a filename, then the data is read or
135       written to the open filehandle.  This gives an easy way to read an
136       arbitrary slice in a big data volume, as in the following example:
137
138           use PDL;
139           use PDL::IO::FastRaw;
140
141           open(DATA, "raw3d.dat");
142           binmode(DATA);
143
144           # assume we know the data size from an external source
145           ($width, $height, $data_size) = (256,256, 4);
146
147           my $slice_num = 64;   # slice to look at
148           # Seek to slice
149           seek(DATA, $width*$height*$data_size * $slice_num, 0);
150           $pdl = readflex \*DATA, [{Dims=>[$width, $height], Type=>'long'}];
151
152       WARNING: In later versions of perl (5.8 and up) you must be sure that
153       your file is in "raw" mode (see the perlfunc man page entry for
154       "binmode", for details).  Both readflex and writeflex automagically
155       switch the file to raw mode for you -- but in code like the snipped
156       above, you could end up seeking the wrong byte if you forget to make
157       the binmode() call.
158
159       "mapflex" memory maps, rather than reads, the data files.  Its
160       interface is similar to "readflex".  Extra options specify if the data
161       is to be loaded `ReadOnly', if the data file is to be `Creat'-ed anew
162       on the basis of the header information or `Trunc'-ated to the length of
163       the data read.  The extra speed of access brings with it some
164       limitations: "mapflex" won't read compressed data, auto-detect f77
165       files, or read f77 files written by more than a single unformatted
166       write statement.  More seriously, data alignment constraints mean that
167       "mapflex" cannot read some files, depending on the requirements of the
168       host OS (it may also vary depending on the setting of the `uac' flag on
169       any given machine).  You may have run into similar problems with common
170       blocks in FORTRAN.
171
172       For instance, floating point numbers may have to align on 4 byte
173       boundaries -- if the data file consists of 3 bytes then a float, it
174       cannot be read.  "mapflex" will warn about this problem when it occurs,
175       and return the PDLs mapped before the problem arose.  This can be dealt
176       with either by reorganizing the data file (large types first helps, as
177       a rule-of-thumb), or more simply by using "readflex".
178

BUGS

180       The test on two dimensional byte arrays fail using g77 2.7.2, but not
181       Sun f77.  I hope this isn't my problem!
182
183       Assumes gzip is on the PATH.
184
185       Can't auto-swap compressed files, because it can't seek on them.
186
187       The header format may not agree with that used elsewhere.
188
189       Should it handle handles?
190
191       Mapflex should warn and fallback to reading on SEGV?  Would have to
192       make sure that the data was written back after it was `destroyed'.
193

FUNCTIONS

195   readflex
196       Read a binary file with flexible format specification
197
198           Usage:
199
200           ($x,$y,...) = readflex("filename" [, $hdr])
201           ($x,$y,...) = readflex(FILEHANDLE [, $hdr])
202
203   writeflex
204       Write a binary file with flexible format specification
205
206           Usage:
207
208           $hdr = writeflex($file, $pdl1, $pdl2,...) # or
209           $hdr = writeflex(FILEHANDLE, $pdl1, $pdl2,...)
210           # now you must call writeflexhdr()
211           writeflexhdr($file, $hdr)
212
213       or
214
215           $PDL::IO::FlexRaw::writeflexhdr = 1;  # set so we don't have to call writeflexhdr
216
217           $hdr = writeflex($file, $pdl1, $pdl2,...)  # remember, $file must be filename
218           writeflex($file, $pdl1, $pdl2,...)         # remember, $file must be filename
219
220   writeflexhdr
221       Write the header file corresponding to a previous writeflex call
222
223           Usage:
224
225           writeflexhdr($file, $hdr)
226
227           $file or "filename" is the filename used in a previous writeflex
228           If $file is actually a "filename" then writeflexhdr() will be
229           called automatically if $PDL::IO::FlexRaw::writeflexhdr is true.
230           If writeflex() was to a FILEHANDLE, you will need to call
231           writeflexhdr() yourself since the filename cannot be determined
232           (at least easily).
233
234   mapflex
235       Memory map a binary file with flexible format specification
236
237           Usage:
238
239           ($x,$y,...) = mapflex("filename" [, $hdr] [, $opts])
240
241           All of these options default to false unless set true:
242
243           ReadOnly - Data should be readonly
244           Creat    - Create file if it doesn't exist
245           Trunc    - File should be truncated to a length that conforms
246                      with the header
247
248   _read_flexhdr
249       Read a FlexRaw header file and return a header structure.
250
251           Usage:
252
253           $hdr = PDL::IO::FlexRaw::_read_flexhdr($file)
254
255       Note that "_read_flexhdr" is supposed to be an internal function.  It
256       was not originally documented and it is not tested.  However, there
257       appeared to be no other method for obtaining a header structure from a
258       file, so I figured I would write a small bit of documentation on it.
259

Bad Value Support

261       As of PDL-2.4.8, PDL::IO::FlexRaw has support for reading and writing
262       pdls with bad values in them.
263
264       On "writeflex", a piddle argument with "$pdl->badflag == 1" will have
265       the keyword/token "badvalue" added to the header file after the
266       dimension list and an additional token with the bad value for that pdl
267       if "$pdl->badvalue != $pdl->orig_badvalue".
268
269       On "readflex", a pdl with the "badvalue" token in the header will
270       automatically have its badflag set and its badvalue as well if it is
271       not the standard default for that type.
272
273       The new badvalue support required some additions to the header
274       structure.  However, the interface is still being finalized.  For
275       reference the current $hdr looks like this:
276
277           $hdr = {
278                    Type => 'byte',    # data type
279                    NDims => 2,        # number of dimensions
280                    Dims => [640,480], # dims
281                    BadFlag => 1,      # is set/set badflag
282                    BadValue => undef, # undef==default
283                  };
284
285           $badpdl = readflex('badpdl', [$hdr]);
286
287       If you use bad values and try the new PDL::IO::FlexRaw bad value
288       support, please let us know via the perldl mailing list.  Suggestions
289       and feedback are also welcome.
290

AUTHOR

292       Copyright (C) Robin Williams <rjrw@ast.leeds.ac.uk> 1997.  All rights
293       reserved. There is no warranty. You are allowed to redistribute this
294       software / documentation under certain conditions. For details, see the
295       file COPYING in the PDL distribution. If this file is separated from
296       the PDL distribution, the copyright notice should be included in the
297       file.
298
299       Documentation contributions copyright (C) David Mertens, 2010.
300
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303perl v5.28.1                      2018-05-05                        FlexRaw(3)
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