1 |
greg |
2.1 |
#ifndef lint |
2 |
greg |
2.3 |
static const char RCSid[] = "$Id: rcollate.c,v 2.2 2013/09/05 18:30:58 greg Exp $"; |
3 |
greg |
2.1 |
#endif |
4 |
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/* |
5 |
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* Utility to re-order records in a binary or ASCII data file (matrix) |
6 |
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*/ |
7 |
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8 |
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#include <stdlib.h> |
9 |
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#include <unistd.h> |
10 |
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#include <string.h> |
11 |
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#include <ctype.h> |
12 |
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#include "platform.h" |
13 |
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#include "rtio.h" |
14 |
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#include "resolu.h" |
15 |
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#ifndef _WIN32 |
16 |
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#include <sys/mman.h> |
17 |
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#endif |
18 |
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19 |
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#ifdef getc_unlocked /* avoid horrendous overhead of flockfile */ |
20 |
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#undef getc |
21 |
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#undef putc |
22 |
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#define getc getc_unlocked |
23 |
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#define putc putc_unlocked |
24 |
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#endif |
25 |
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26 |
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typedef struct { |
27 |
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void *base; /* pointer to base memory */ |
28 |
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size_t len; /* allocated memory length */ |
29 |
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int mapped; /* memory-mapped file? */ |
30 |
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} MEMLOAD; /* file loaded/mapped into memory */ |
31 |
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32 |
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typedef struct { |
33 |
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int nw_rec; /* number of words per record */ |
34 |
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int nrecs; /* number of records we found */ |
35 |
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char *rec[1]; /* record array (extends struct) */ |
36 |
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} RECINDEX; |
37 |
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38 |
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/* free loaded file */ |
39 |
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static void |
40 |
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free_load(MEMLOAD *mp) |
41 |
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{ |
42 |
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if (mp == NULL || (mp->base == NULL) | (mp->len <= 0)) |
43 |
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return; |
44 |
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#ifdef MAP_FILE |
45 |
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if (mp->mapped) |
46 |
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munmap(mp->base, mp->len); |
47 |
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else |
48 |
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#endif |
49 |
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free(mp->base); |
50 |
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mp->base = NULL; |
51 |
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mp->len = 0; |
52 |
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} |
53 |
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54 |
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/* load a file into memory */ |
55 |
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static int |
56 |
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load_file(MEMLOAD *mp, FILE *fp) |
57 |
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{ |
58 |
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int fd; |
59 |
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off_t skip, flen; |
60 |
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61 |
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if (mp == NULL) |
62 |
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return(-1); |
63 |
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mp->base = NULL; |
64 |
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mp->len = 0; |
65 |
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mp->mapped = 0; |
66 |
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if (fp == NULL) |
67 |
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return(-1); |
68 |
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fd = fileno(fp); |
69 |
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skip = ftello(fp); |
70 |
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flen = lseek(fd, 0, SEEK_END); |
71 |
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if (flen <= skip) |
72 |
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return((int)(flen - skip)); |
73 |
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mp->len = (size_t)(flen - skip); |
74 |
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#ifdef MAP_FILE |
75 |
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if (mp->len > 1L<<20) { /* map file if > 1 MByte */ |
76 |
greg |
2.2 |
mp->base = mmap(NULL, mp->len, PROT_READ, MAP_PRIVATE, fd, skip); |
77 |
greg |
2.1 |
if (mp->base != MAP_FAILED) { |
78 |
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mp->mapped = 1; |
79 |
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return(1); /* mmap() success */ |
80 |
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} |
81 |
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mp->base = NULL; /* fall back to reading it in... */ |
82 |
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} |
83 |
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#endif |
84 |
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if (lseek(fd, skip, SEEK_SET) != skip || |
85 |
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(mp->base = malloc(mp->len)) == NULL) { |
86 |
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mp->len = 0; |
87 |
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return(-1); |
88 |
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} |
89 |
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if (read(fd, (char *)mp->base, mp->len) != mp->len) { |
90 |
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free_load(mp); |
91 |
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return(-1); |
92 |
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} |
93 |
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return(1); |
94 |
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} |
95 |
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96 |
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/* load memory from an input stream, starting from current position */ |
97 |
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static int |
98 |
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load_stream(MEMLOAD *mp, FILE *fp) |
99 |
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{ |
100 |
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char buf[8192]; |
101 |
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size_t nr; |
102 |
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103 |
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if (mp == NULL) |
104 |
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return(-1); |
105 |
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mp->base = NULL; |
106 |
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mp->len = 0; |
107 |
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mp->mapped = 0; |
108 |
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if (fp == NULL) |
109 |
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return(-1); |
110 |
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while ((nr = fread(buf, 1, sizeof(buf), fp)) > 0) { |
111 |
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if (!mp->len) |
112 |
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mp->base = malloc(nr); |
113 |
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else |
114 |
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mp->base = realloc(mp->base, mp->len+nr); |
115 |
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if (mp->base == NULL) |
116 |
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return(-1); |
117 |
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memcpy((char *)mp->base + mp->len, buf, nr); |
118 |
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mp->len += nr; |
119 |
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} |
120 |
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if (ferror(fp)) { |
121 |
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free_load(mp); |
122 |
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return(-1); |
123 |
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} |
124 |
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return(mp->len > 0); |
125 |
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} |
126 |
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127 |
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/* free a record index */ |
128 |
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#define free_records(rp) free(rp) |
129 |
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130 |
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/* compute record index */ |
131 |
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static RECINDEX * |
132 |
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index_records(const MEMLOAD *mp, int nw_rec) |
133 |
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{ |
134 |
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RECINDEX *rp; |
135 |
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char *cp, *mend; |
136 |
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int n; |
137 |
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138 |
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if (mp == NULL || (mp->base == NULL) | (mp->len <= 0)) |
139 |
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return(NULL); |
140 |
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if (nw_rec <= 0) |
141 |
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return(NULL); |
142 |
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rp = (RECINDEX *)malloc(sizeof(RECINDEX) + mp->len/(2*nw_rec)*sizeof(char *)); |
143 |
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if (rp == NULL) |
144 |
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return(NULL); |
145 |
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rp->nw_rec = nw_rec; |
146 |
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rp->nrecs = 0; |
147 |
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cp = (char *)mp->base; |
148 |
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mend = cp + mp->len; |
149 |
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for ( ; ; ) { /* whitespace-separated words */ |
150 |
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while (cp < mend && !*cp | isspace(*cp)) |
151 |
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++cp; |
152 |
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if (cp >= mend) |
153 |
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break; |
154 |
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rp->rec[rp->nrecs++] = cp; /* point to first non-white */ |
155 |
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n = rp->nw_rec; |
156 |
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while (++cp < mend) /* find end of record */ |
157 |
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if (!*cp | isspace(*cp)) { |
158 |
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if (--n <= 0) |
159 |
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break; /* got requisite # words */ |
160 |
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do { /* else find next word */ |
161 |
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if (*cp == '\n') { |
162 |
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fprintf(stderr, |
163 |
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"Unexpected EOL in record!\n"); |
164 |
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free_records(rp); |
165 |
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return(NULL); |
166 |
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} |
167 |
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if (++cp >= mend) |
168 |
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break; |
169 |
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} while (!*cp | isspace(*cp)); |
170 |
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} |
171 |
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} |
172 |
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rp->rec[rp->nrecs] = mend; /* reallocate to save space */ |
173 |
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rp = (RECINDEX *)realloc(rp, |
174 |
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sizeof(RECINDEX) + rp->nrecs*sizeof(char *)); |
175 |
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return(rp); |
176 |
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} |
177 |
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178 |
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/* count number of columns based on first EOL */ |
179 |
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static int |
180 |
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count_columns(const RECINDEX *rp) |
181 |
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{ |
182 |
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char *cp = rp->rec[0]; |
183 |
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char *mend = rp->rec[rp->nrecs]; |
184 |
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int i; |
185 |
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186 |
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while (*cp != '\n') |
187 |
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if (++cp >= mend) |
188 |
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return(0); |
189 |
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for (i = 0; i < rp->nrecs; i++) |
190 |
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if (rp->rec[i] >= cp) |
191 |
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break; |
192 |
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return(i); |
193 |
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} |
194 |
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195 |
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/* copy nth record from index to stdout */ |
196 |
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static int |
197 |
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print_record(const RECINDEX *rp, int n) |
198 |
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{ |
199 |
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int words2go = rp->nw_rec; |
200 |
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char *scp; |
201 |
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202 |
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if ((n < 0) | (n >= rp->nrecs)) |
203 |
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return(0); |
204 |
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scp = rp->rec[n]; |
205 |
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do { |
206 |
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putc(*scp++, stdout); |
207 |
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if (!*scp | isspace(*scp)) { |
208 |
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if (--words2go <= 0) |
209 |
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break; |
210 |
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putc(' ', stdout); /* single space btwn. words */ |
211 |
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do |
212 |
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if (++scp >= rp->rec[n+1]) |
213 |
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break; |
214 |
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while (!*scp | isspace(*scp)); |
215 |
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} |
216 |
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} while (scp < rp->rec[n+1]); |
217 |
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/* caller adds record sep. */ |
218 |
|
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return(1); |
219 |
|
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} |
220 |
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221 |
|
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/* copy a stream to stdout */ |
222 |
|
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static int |
223 |
|
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output_stream(FILE *fp) |
224 |
|
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{ |
225 |
|
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char buf[8192]; |
226 |
|
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ssize_t n; |
227 |
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|
228 |
|
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if (fp == NULL) |
229 |
|
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return(0); |
230 |
|
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fflush(stdout); /* assumes nothing in input buffer */ |
231 |
|
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while ((n = read(fileno(fp), buf, sizeof(buf))) > 0) |
232 |
|
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if (write(fileno(stdout), buf, n) != n) |
233 |
|
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return(0); |
234 |
|
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return(n >= 0); |
235 |
|
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} |
236 |
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|
237 |
|
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/* get next word from stream, leaving stream on EOL or start of next word */ |
238 |
|
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static char * |
239 |
|
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fget_word(char buf[256], FILE *fp) |
240 |
|
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{ |
241 |
|
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int c; |
242 |
|
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char *cp; |
243 |
|
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/* skip nul's and white space */ |
244 |
|
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while (!(c = getc(fp)) || isspace(c)) |
245 |
|
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; |
246 |
|
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if (c == EOF) |
247 |
|
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return(NULL); |
248 |
|
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cp = buf; |
249 |
|
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do |
250 |
|
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*cp++ = c; |
251 |
|
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while ((c = getc(fp)) != EOF && !isspace(c) && cp < buf+255); |
252 |
|
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*cp = '\0'; |
253 |
|
|
while (isspace(c) & (c != '\n')) |
254 |
|
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c = getc(fp); |
255 |
|
|
if (c != EOF) |
256 |
|
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ungetc(c, fp); |
257 |
|
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return(buf); |
258 |
|
|
} |
259 |
|
|
|
260 |
|
|
char *fmtid = "ascii"; /* format id */ |
261 |
|
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int record_width = 3; /* words/record (<0 binary) */ |
262 |
|
|
int ni_columns = 0; /* number of input columns */ |
263 |
|
|
int ni_rows = 0; /* number of input rows */ |
264 |
|
|
int no_columns = 0; /* number of output columns */ |
265 |
|
|
int no_rows = 0; /* number of output rows */ |
266 |
|
|
|
267 |
|
|
/* output transposed ASCII or binary data from memory */ |
268 |
|
|
static int |
269 |
|
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do_transpose(const MEMLOAD *mp) |
270 |
|
|
{ |
271 |
|
|
static const char tabEOL[2] = {'\t','\n'}; |
272 |
|
|
RECINDEX *rp = NULL; |
273 |
|
|
long nrecords; |
274 |
|
|
int i, j; |
275 |
|
|
/* get # records (& index) */ |
276 |
|
|
if (record_width > 0) { |
277 |
|
|
if ((rp = index_records(mp, record_width)) == NULL) |
278 |
|
|
return(0); |
279 |
|
|
if (ni_columns <= 0) |
280 |
|
|
ni_columns = count_columns(rp); |
281 |
|
|
nrecords = rp->nrecs; |
282 |
greg |
2.3 |
} else if ((ni_rows > 0) & (ni_columns > 0)) { |
283 |
greg |
2.1 |
nrecords = ni_rows*ni_columns; |
284 |
greg |
2.3 |
if (nrecords > mp->len / -record_width) { |
285 |
|
|
fprintf(stderr, |
286 |
|
|
"Input too small for specified size and type\n"); |
287 |
|
|
return(0); |
288 |
|
|
} |
289 |
|
|
} else |
290 |
greg |
2.1 |
nrecords = mp->len / -record_width; |
291 |
|
|
/* check sizes */ |
292 |
|
|
if (ni_rows <= 0) |
293 |
|
|
ni_rows = no_columns; |
294 |
|
|
if (ni_columns <= 0) |
295 |
|
|
ni_columns = no_rows; |
296 |
|
|
if ((ni_rows <= 0) & (ni_columns > 0)) |
297 |
|
|
ni_rows = nrecords/ni_columns; |
298 |
|
|
if ((ni_columns <= 0) & (ni_rows > 0)) |
299 |
|
|
ni_columns = nrecords/ni_rows; |
300 |
|
|
if (nrecords != ni_rows*ni_columns) |
301 |
|
|
goto badspec; |
302 |
|
|
if (no_columns <= 0) |
303 |
|
|
no_columns = ni_rows; |
304 |
|
|
if (no_rows <= 0) |
305 |
|
|
no_rows = ni_columns; |
306 |
|
|
if ((no_rows != ni_columns) | (no_columns != ni_rows)) |
307 |
|
|
goto badspec; |
308 |
|
|
/* transpose records */ |
309 |
|
|
for (i = 0; i < no_rows; i++) { |
310 |
|
|
for (j = 0; j < no_columns; j++) |
311 |
|
|
if (rp != NULL) { /* ASCII output */ |
312 |
|
|
print_record(rp, j*ni_columns + i); |
313 |
|
|
putc(tabEOL[j >= no_columns-1], stdout); |
314 |
|
|
} else { /* binary output */ |
315 |
|
|
fwrite((char *)mp->base + |
316 |
|
|
-record_width*(j*ni_columns + i), |
317 |
|
|
-record_width, 1, stdout); |
318 |
|
|
} |
319 |
|
|
if (ferror(stdout)) { |
320 |
|
|
fprintf(stderr, "Error writing to stdout\n"); |
321 |
|
|
return(0); |
322 |
|
|
} |
323 |
|
|
} |
324 |
|
|
if (rp != NULL) |
325 |
|
|
free_records(rp); |
326 |
|
|
return(1); |
327 |
|
|
badspec: |
328 |
|
|
fprintf(stderr, "Bad transpose specification -- check dimension(s)\n"); |
329 |
|
|
return(0); |
330 |
|
|
} |
331 |
|
|
|
332 |
|
|
/* resize ASCII stream input by ignoring EOLs between records */ |
333 |
|
|
static int |
334 |
|
|
do_resize(FILE *fp) |
335 |
|
|
{ |
336 |
|
|
long records2go = ni_rows*ni_columns; |
337 |
|
|
int columns2go = no_columns; |
338 |
|
|
char word[256]; |
339 |
|
|
/* sanity checks */ |
340 |
|
|
if (record_width <= 0) { |
341 |
|
|
fprintf(stderr, "Bad call to do_resize (record_width = %d)\n", |
342 |
|
|
record_width); |
343 |
|
|
return(0); |
344 |
|
|
} |
345 |
|
|
if (no_columns <= 0) { |
346 |
|
|
fprintf(stderr, "Missing -oc specification\n"); |
347 |
|
|
return(0); |
348 |
|
|
} |
349 |
|
|
if ((records2go <= 0) & (no_rows > 0)) |
350 |
|
|
records2go = no_rows*no_columns; |
351 |
|
|
else if (no_rows*no_columns != records2go) { |
352 |
|
|
fprintf(stderr, |
353 |
|
|
"Input and output data sizes disagree (%dx%d != %dx%d)\n", |
354 |
|
|
ni_rows, ni_columns, no_rows, no_columns); |
355 |
|
|
return(0); |
356 |
|
|
} |
357 |
|
|
do { /* reshape records */ |
358 |
|
|
int n; |
359 |
|
|
|
360 |
|
|
for (n = record_width; n--; ) { |
361 |
|
|
if (fget_word(word, fp) == NULL) { |
362 |
|
|
if (records2go > 0 || n < record_width-1) |
363 |
|
|
break; |
364 |
|
|
goto done; /* normal EOD */ |
365 |
|
|
} |
366 |
|
|
fputs(word, stdout); |
367 |
|
|
if (n) { /* mid-record? */ |
368 |
|
|
int c = getc(fp); |
369 |
|
|
if ((c == '\n') | (c == EOF)) |
370 |
|
|
break; |
371 |
|
|
ungetc(c, fp); |
372 |
|
|
putc(' ', stdout); |
373 |
|
|
} |
374 |
|
|
} |
375 |
|
|
if (n >= 0) { |
376 |
|
|
fprintf(stderr, "Incomplete record / unexpected EOF\n"); |
377 |
|
|
return(0); |
378 |
|
|
} |
379 |
|
|
if (--columns2go <= 0) { /* time to end output row? */ |
380 |
|
|
putc('\n', stdout); |
381 |
|
|
columns2go = no_columns; |
382 |
|
|
} else /* else separate records */ |
383 |
|
|
putc('\t', stdout); |
384 |
|
|
} while (--records2go); /* expected EOD? */ |
385 |
|
|
done: |
386 |
|
|
if (columns2go != no_columns) |
387 |
|
|
fprintf(stderr, "Warning -- incomplete final row\n"); |
388 |
|
|
if (fget_word(word, fp) != NULL) |
389 |
|
|
fprintf(stderr, "Warning -- data beyond expected EOF\n"); |
390 |
|
|
return(1); |
391 |
|
|
} |
392 |
|
|
|
393 |
|
|
/* process a header line and copy to stdout */ |
394 |
|
|
static int |
395 |
|
|
headline(char *s, void *p) |
396 |
|
|
{ |
397 |
|
|
char fmt[32]; |
398 |
|
|
|
399 |
|
|
if (formatval(fmt, s)) { |
400 |
|
|
if (!strcmp(fmt, fmtid)) |
401 |
|
|
return(0); |
402 |
|
|
fprintf(stderr, "Input format '%s' != '%s'\n", fmt, fmtid); |
403 |
|
|
return(-1); |
404 |
|
|
} |
405 |
|
|
fputs(s, stdout); /* copy header info. */ |
406 |
|
|
return(0); |
407 |
|
|
} |
408 |
|
|
|
409 |
|
|
/* main routine for converting rows/columns in data file */ |
410 |
|
|
int |
411 |
|
|
main(int argc, char *argv[]) |
412 |
|
|
{ |
413 |
|
|
int do_header = 1; /* header i/o? */ |
414 |
|
|
int transpose = 0; /* transpose rows & cols? */ |
415 |
|
|
int i; |
416 |
|
|
|
417 |
|
|
for (i = 1; i < argc && argv[i][0] == '-'; i++) |
418 |
|
|
switch (argv[i][1]) { |
419 |
|
|
case 'i': /* input */ |
420 |
|
|
if (argv[i][2] == 'c') /* columns */ |
421 |
|
|
ni_columns = atoi(argv[++i]); |
422 |
|
|
else if (argv[i][2] == 'r') |
423 |
|
|
ni_rows = atoi(argv[++i]); |
424 |
|
|
else |
425 |
|
|
goto userr; |
426 |
|
|
break; |
427 |
|
|
case 'o': /* output */ |
428 |
|
|
if (argv[i][2] == 'c') /* columns */ |
429 |
|
|
no_columns = atoi(argv[++i]); |
430 |
|
|
else if (argv[i][2] == 'r') |
431 |
|
|
no_rows = atoi(argv[++i]); |
432 |
|
|
else |
433 |
|
|
goto userr; |
434 |
|
|
break; |
435 |
|
|
case 'h': /* header on/off */ |
436 |
|
|
do_header = !do_header; |
437 |
|
|
break; |
438 |
|
|
case 't': /* transpose on/off */ |
439 |
|
|
transpose = !transpose; |
440 |
|
|
break; |
441 |
|
|
case 'f': /* format */ |
442 |
|
|
switch (argv[i][2]) { |
443 |
|
|
case 'a': /* ASCII */ |
444 |
|
|
case 'A': |
445 |
|
|
fmtid = "ascii"; |
446 |
|
|
record_width = 1; |
447 |
|
|
break; |
448 |
|
|
case 'f': /* float */ |
449 |
|
|
case 'F': |
450 |
|
|
fmtid = "float"; |
451 |
|
|
record_width = -(int)sizeof(float); |
452 |
|
|
break; |
453 |
|
|
case 'd': /* double */ |
454 |
|
|
case 'D': |
455 |
|
|
fmtid = "double"; |
456 |
|
|
record_width = -(int)sizeof(double); |
457 |
|
|
break; |
458 |
|
|
case 'b': /* binary (bytes) */ |
459 |
|
|
case 'B': |
460 |
|
|
fmtid = "byte"; |
461 |
|
|
record_width = -1; |
462 |
|
|
break; |
463 |
|
|
default: |
464 |
|
|
goto userr; |
465 |
|
|
} |
466 |
|
|
if (argv[i][3]) { |
467 |
|
|
if (!isdigit(argv[i][3])) |
468 |
|
|
goto userr; |
469 |
|
|
record_width *= atoi(argv[i]+3); |
470 |
|
|
} |
471 |
|
|
break; |
472 |
|
|
default: |
473 |
|
|
goto userr; |
474 |
|
|
} |
475 |
|
|
if (!record_width) |
476 |
|
|
goto userr; |
477 |
|
|
if (i < argc-1) /* arg count OK? */ |
478 |
|
|
goto userr; |
479 |
|
|
/* open input file? */ |
480 |
|
|
if (i == argc-1 && freopen(argv[i], "r", stdin) == NULL) { |
481 |
|
|
fprintf(stderr, "%s: cannot open for reading\n", argv[i]); |
482 |
|
|
return(1); |
483 |
|
|
} |
484 |
|
|
if (record_width < 0) { |
485 |
|
|
SET_FILE_BINARY(stdin); |
486 |
|
|
SET_FILE_BINARY(stdout); |
487 |
|
|
} |
488 |
|
|
/* check for no-op */ |
489 |
|
|
if (!transpose && (record_width < 0 || |
490 |
|
|
(no_columns == ni_columns) & (no_rows == ni_rows))) { |
491 |
|
|
fprintf(stderr, "%s: no-op -- copying input verbatim\n", |
492 |
|
|
argv[0]); |
493 |
|
|
if (!output_stream(stdin)) |
494 |
|
|
return(1); |
495 |
|
|
return(0); |
496 |
|
|
} |
497 |
|
|
if (do_header) { /* read/write header */ |
498 |
|
|
if (getheader(stdin, &headline, NULL) < 0) |
499 |
|
|
return(1); |
500 |
|
|
printargs(argc, argv, stdout); |
501 |
|
|
fputformat(fmtid, stdout); |
502 |
|
|
fputc('\n', stdout); /* finish new header */ |
503 |
|
|
} |
504 |
|
|
if (transpose) { /* transposing rows & columns? */ |
505 |
|
|
MEMLOAD myMem; /* need to load into memory */ |
506 |
|
|
if (i == argc-1) { |
507 |
|
|
if (load_file(&myMem, stdin) <= 0) { |
508 |
|
|
fprintf(stderr, "%s: error loading file into memory\n", |
509 |
|
|
argv[i]); |
510 |
|
|
return(1); |
511 |
|
|
} |
512 |
|
|
} else if (load_stream(&myMem, stdin) <= 0) { |
513 |
|
|
fprintf(stderr, "%s: error loading stdin into memory\n", |
514 |
|
|
argv[0]); |
515 |
|
|
return(1); |
516 |
|
|
} |
517 |
|
|
if (!do_transpose(&myMem)) |
518 |
|
|
return(1); |
519 |
|
|
/* free_load(&myMem); */ |
520 |
|
|
} else if (!do_resize(stdin)) /* just reshaping input */ |
521 |
|
|
return(1); |
522 |
|
|
return(0); |
523 |
|
|
userr: |
524 |
|
|
fprintf(stderr, |
525 |
|
|
"Usage: %s [-h][-f[afdb][N]][-t][-ic in_col][-ir in_row][-oc out_col][-or out_row] [input.dat]\n", |
526 |
|
|
argv[0]); |
527 |
|
|
return(1); |
528 |
|
|
} |