1 /*****************************************************************************
2 Major portions of this software are copyrighted by the Medical College
3 of Wisconsin, 1994-2000, and are released under the Gnu General Public
4 License, Version 2. See the file README.Copyright for details.
5 ******************************************************************************/
6
7 #include "mrilib.h"
8 #include "thd.h"
9
10 /*=============================================================================*/
11 /*** Adapted from THD_get_many_timeseries() for *.1D files ***/
12
13 /*** Read all *.csv and *.tsv files from a list of directories ***/
14
THD_get_many_tcsv(THD_string_array * dlist)15 NI_ELARR * THD_get_many_tcsv( THD_string_array *dlist )
16 {
17 int id , ii , ndir ;
18 NI_ELARR *outar=NULL, *tmpar=NULL ;
19 char *epath , *eee ;
20 char efake[] = "./" ;
21 THD_string_array *qlist ; /* 02 Feb 2002 */
22
23 ENTRY("THD_get_many_tcsv") ;
24
25 /*----- sanity check and initialize -----*/
26
27 epath = my_getenv( "AFNI_TSPATH" ) ;
28 if( epath == NULL ) epath = my_getenv( "AFNI_TS_PATH" ) ;
29 if( epath == NULL ) epath = efake ;
30
31 ndir = (dlist != NULL) ? dlist->num : 0 ;
32
33 if( ndir == 0 && epath == NULL ) RETURN( outar ) ;
34
35 INIT_ELARR( outar ) ; /* output array */
36 INIT_SARR( qlist ) ; /* list of directories */
37
38 /*----- for each input directory, find all *.1D files -----*/
39
40 for( id=0 ; id < ndir ; id++ ){
41
42 if( THD_forbidden_directory(dlist->ar[id]) ) continue ;
43
44 ADDTO_SARR(qlist,dlist->ar[id]) ; /* save this name for later use */
45
46 tmpar = THD_get_all_tcsv( dlist->ar[id] ) ; /* read files from */
47 if( tmpar == NULL ) continue ; /* this directory */
48
49 for( ii=0 ; ii < tmpar->num ; ii++ ) /* move data to output array */
50 ADDTO_ELARR( outar , tmpar->elarr[ii] ) ;
51
52 FREE_ELARR(tmpar) ; /* don't need this no more */
53 }
54
55 /*----- also do directories in environment path, if any -----*/
56
57 if( epath != NULL ){
58 int epos = 0 , ll = strlen(epath) ;
59 char *elocal ;
60 char ename[THD_MAX_NAME] ;
61
62 /* copy path list into local memory */
63
64 elocal = (char *) malloc( sizeof(char) * (ll+2) ) ;
65 if( elocal == NULL ){
66 fprintf(stderr,
67 "\n*** THD_get_many_tcsv malloc failure - is memory full? ***\n");
68 EXIT(1) ;
69 }
70 strcpy( elocal , epath ) ; elocal[ll] = ' ' ; elocal[ll+1] = '\0' ;
71
72 /* replace colons with blanks */
73
74 for( ii=0 ; ii < ll ; ii++ )
75 if( elocal[ii] == ':' ) elocal[ii] = ' ' ;
76
77 /* extract blank delimited strings,
78 use as directory names to get timeseries files */
79
80 do{
81 ii = sscanf( elocal+epos , "%s%n" , ename , &id ) ;
82 if( ii < 1 ) break ; /* no read --> end of work */
83 epos += id ; /* epos = char after last one scanned */
84
85 ii = strlen(ename) ; /* make sure name has */
86 if( ename[ii-1] != '/' ){ /* a trailing '/' on it */
87 ename[ii] = '/' ; ename[ii+1] = '\0' ;
88 }
89
90 if( !THD_is_directory(ename) ) continue ; /* 21 May 2002 - rcr */
91 if( THD_forbidden_directory(ename) ) continue ; /* 18 Sep 2020 */
92
93 /* 02 Feb 2002: check if scanned this directory before */
94
95 for( ii=0 ; ii < qlist->num ; ii++ )
96 if( THD_equiv_files(qlist->ar[ii],ename) ) break ;
97 if( ii < qlist->num ) continue ; /* skip to end of do loop */
98 ADDTO_SARR(qlist,ename) ;
99
100 tmpar = THD_get_all_tcsv( ename ) ; /* read all files from this directory */
101 if( tmpar != NULL ){
102 for( ii=0 ; ii < tmpar->num ; ii++ ) /* move data to output array */
103 ADDTO_ELARR( outar , tmpar->elarr[ii] ) ;
104
105 FREE_ELARR(tmpar) ; /* don't need this no more */
106 }
107 } while( epos < ll ) ; /* scan until 'epos' is after end of epath */
108
109 free(elocal) ;
110 }
111
112 if( ELARR_COUNT(outar) == 0 ) DESTROY_ELARR(outar) ;
113
114 DESTROY_SARR(qlist) ;
115 RETURN( outar ) ;
116 }
117
118 /*---------------------------------------------------*/
119 /* Read all *.tsv and *.csv files from directory */
120 /*---------------------------------------------------*/
121
THD_get_all_tcsv(char * dname)122 NI_ELARR * THD_get_all_tcsv( char *dname )
123 {
124 int ir , ii ;
125 char *fname , * tname ;
126 float *far ;
127 char *cmd , *flist ;
128 NI_str_array *qsar=NULL ;
129 NI_element *outim , *flim=NULL ;
130 NI_ELARR *outar ;
131
132 unsigned long max_fsize ; /* 20 Jul 2004: max 1D file size to load */
133
134 ENTRY("THD_get_all_tcsv") ;
135
136 max_fsize = (unsigned long) AFNI_numenv( "AFNI_MAX_1DSIZE" ) ;
137 if( max_fsize == 0 ) max_fsize = 123*1024 ;
138 if( max_fsize == 1 ) RETURN(NULL) ;
139
140 /*----- sanity check and initialize -----*/
141
142 if( dname == NULL || strlen(dname) == 0 ) RETURN(NULL) ;
143
144 /*----- find all *.csv and *.tsv files -----*/
145
146 ii = strlen(dname) ;
147 cmd = (char *) malloc(sizeof(char)*3*(ii+64)) ;
148 sprintf( cmd , "find %s -maxdepth 4 -type f -name '*.[ctCT][sS][vV]'" , dname ) ;
149
150 flist = THD_suck_pipe( cmd ) ;
151 free(cmd) ;
152 if( flist == NULL || strlen(flist) < 4 ){
153 if( flist != NULL ) free(flist) ;
154 RETURN(NULL) ;
155 }
156
157 /* break output into discrete strings */
158
159 qsar = NI_decode_string_list( flist , ";" ) ;
160 if( qsar == NULL || qsar->num == 0 ){ /* should never happen */
161 free(flist) ; RETURN(NULL) ;
162 }
163
164 INIT_ELARR( outar ) ;
165
166 /* try to read each file */
167
168 for( ir=0 ; ir < qsar->num ; ir++ ){
169 fname = qsar->str[ir] ; if( fname == NULL ) continue ;
170
171 /* too big? */
172 if( THD_filesize(fname) > max_fsize ) continue ;
173
174 if( STRING_HAS_SUFFIX_CASE(fname,".csv") ){ /* .csv */
175 flim = THD_read_csv( fname ) ;
176 } else if( STRING_HAS_SUFFIX_CASE(fname,".tsv") ){ /* .tsv */
177 flim = THD_read_tsv( fname ) ;
178 } else {
179 flim = NULL ;
180 }
181
182 /* if it worked, and it's OK, add it to the output */
183
184 if( flim != NULL && NI_element_type(flim) == NI_ELEMENT_TYPE ){
185 if( flim->vec_num <= 0 || flim->vec_len <= 0 ){
186 NI_free_element(flim) ; flim = NULL ; /* nothing inside?! */
187 } else {
188 tname = THD_trailname(fname,1) ;
189 flim->filename = strdup(tname) ;
190 ADDTO_ELARR( outar , flim ) ;
191 }
192 } else {
193 NI_free_element(flim) ; flim = NULL ; /* should not happen */
194 }
195 }
196
197 /* return to the caller */
198
199 NI_delete_str_array(qsar) ;
200 if( ELARR_COUNT(outar) == 0 ) DESTROY_ELARR(outar) ;
201 RETURN(outar) ;
202 }
203