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Functions
sifio.c File Reference

Functions for reading and writing SIF format files. More...

#include "libtpcimgio.h"

Go to the source code of this file.

Functions

int sifRead (char *filename, SIF *data)
int sifWrite (SIF *data, char *filename)
void sifPrint (SIF *data)

Detailed Description

Functions for reading and writing SIF format files.

Author
Vesa Oikonen, Jarkko Johansson, Harri Merisaari

Definition in file sifio.c.

Function Documentation

◆ sifPrint()

void sifPrint ( SIF * data)

Prints to stdout the contents of SIF data structure.

See also
sifWrite, sifRead
Parameters
dataPointer to SIF structure.

Definition at line 234 of file sifio.c.

237 {
238 char buf[32];
239
240 if(!ctime_r_int((time_t*)&data->scantime, buf))
241 strcpy(buf, "1900-01-01 00:00:00");
242 printf("Scan time: %s\n", buf);
243 printf("Isotope: %s\n", data->isotope_name);
244 printf("Frame start end Prompts Randoms Trues Weight\n");
245 for(int i=0; i<data->frameNr; i++) {
246 printf(" %03d %6.1f %6.1f %10.0f %10.0f %10.0f %8.6f\n", i+1,
247 data->x1[i], data->x2[i], data->prompts[i], data->randoms[i],
248 data->trues[i], data->weights[i]);
249 }
250 return;
251}
ctime_r_int
char * ctime_r_int(const time_t *t, char *buf)
Convert calendard time t into a null-terminated string of the form YYYY-MM-DD hh:mm:ss,...
Definition datetime.c:110
SIF::x1
double * x1
Definition libtpcimgio.h:1457
SIF::prompts
double * prompts
Definition libtpcimgio.h:1461
SIF::frameNr
int frameNr
Definition libtpcimgio.h:1447
SIF::x2
double * x2
Definition libtpcimgio.h:1459
SIF::scantime
time_t scantime
Definition libtpcimgio.h:1445
SIF::isotope_name
char isotope_name[8]
Definition libtpcimgio.h:1455
SIF::weights
double * weights
Definition libtpcimgio.h:1467
SIF::randoms
double * randoms
Definition libtpcimgio.h:1463
SIF::trues
double * trues
Definition libtpcimgio.h:1465

Referenced by imgSetWeights(), and sifAllocateWithIMG().

◆ sifRead()

int sifRead ( char * filename,
SIF * data )

Reads SIF file contents to the specified data structure.

Weights are set to 1.

Returns
Returns 0 if ok, 1 invalid input, 2 failed to open file, 3 failed to allocate memory, 4 header parsing error, 5 wrong file type, 6 failed to allocate memory, 8 parse error, 9 wrong data format
See also
sifInit, sifEmpty, sifWrite, sifExistentCounts, textfileReadLines
Parameters
filenameSIF file name to be read.
dataPointer to initiated SIF structure; any existing contents will be deleted.

Definition at line 21 of file sifio.c.

26 {
27 int i, n, frameNr, yy, mm, dd, h, m, s;
28 int ret;
29 struct tm *st;
30 time_t timet;
31
32
33 if(SIF_TEST) printf("sifRead(%s, *sif)\n", filename);
34 if(filename==NULL || data==NULL) return(1);
35 /* Empty data */
36 sifEmpty(data);
37
38 /* Read the lines of the SIF */
39 STR_TOKEN_LIST tlst; str_token_list_init(&tlst);
40 //printf("reading lines\n");
41 ret=textfileReadLines(filename, &tlst);
42 if(ret>2) {strcpy(siferrmsg, "cannot read file"); return(5);}
43 else if(ret>0) {strcpy(siferrmsg, "cannot open file"); return(2);}
44 if(0) {
45 printf("lineNr:=%d\n", tlst.token_nr);
46 for(int i=0; i<tlst.token_nr; i++) printf("token[%d] := '%s'\n", i, tlst.tok[i]);
47 }
48
49 /* Remove any comment or empty lines */
50 //printf("removing any comment lines\n");
51 i=tlst.token_nr-1;
52 while(i>=0 && tlst.token_nr>0) {
53 //printf("i=%d line='%s'\n", i, tlst.tok[i]);
54 if(strnlen(tlst.tok[i], 2)<1 || asciiCommentLine(tlst.tok[i], NULL)) {
55 //printf("-> remove\n");
56 str_token_list_del(&tlst, 1+i);
57 }
58 i--;
59 }
60 if(tlst.token_nr<1) {
61 str_token_list_empty(&tlst);
62 strcpy(siferrmsg, "wrong format"); return(4);
63 }
64 if(0) {
65 printf("lineNr:=%d\n", tlst.token_nr);
66 for(int i=0; i<tlst.token_nr; i++)
67 printf("token[%d] := '%s'\n", i, tlst.tok[i]);
68 }
69
70 /* Read the title line */
71 if(SIF_TEST) printf("SIF title := '%s'\n", tlst.tok[0]);
72 n=sscanf(tlst.tok[0], "%d/%d/%d %d:%d:%d %d %d %d %255s %7s",
73 &dd, &mm, &yy, &h, &m, &s, &frameNr, &data->colNr, &data->version,
74 data->studynr, data->isotope_name);
75 //printf("tok_n := %d\n", n);
76 if(n<9 || frameNr<1 || data->colNr<2 || data->version!=1) {
77 if(SIF_TEST) printf("invalid SIF title line\n");
78 strcpy(siferrmsg, "wrong filetype");
79 str_token_list_empty(&tlst);
80 return(4);
81 }
82 timet=time(NULL); st=gmtime(&timet);
83 if(st!=NULL) {
84 st->tm_mday=dd; st->tm_mon=mm-1; st->tm_year=yy-1900;
85 st->tm_hour=h; st->tm_min=m; st->tm_sec=s; st->tm_isdst=-1;
86 data->scantime=timegm(st); if(data->scantime==-1) data->scantime=0;
87 } else {
88 data->scantime=0;
89 }
90 //printf("frameNr := %d\n", frameNr);
91
92 /* Allocate memory for SIF data */
93 if(sifSetmem(data, frameNr)) {
94 str_token_list_empty(&tlst);
95 strcpy(siferrmsg, "cannot allocate SIF"); return(6);
96 }
97
98 /* Read data lines into SIF */
99 i=0;
100 while(i<data->frameNr && i<tlst.token_nr-1) {
101 //printf("i := %d\n", i);
102 data->prompts[i]=data->randoms[i]=0.0;
103 n=sscanf(tlst.tok[1+i], "%lf %lf %lf %lf", &data->x1[i], &data->x2[i],
104 &data->prompts[i], &data->randoms[i]);
105 //printf("n := %d\n", n);
106 //if(n<data->colNr || data->x2[i]<data->x1[i]) {
107 if(n<2) {
108 strcpy(siferrmsg, "wrong data format");
109 str_token_list_empty(&tlst);
110 sifEmpty(data);
111 return(9);
112 }
113 if(data->x2[i]<data->x1[i]) {
114 strcpy(siferrmsg, "invalid time frames");
115 str_token_list_empty(&tlst);
116 sifEmpty(data);
117 return(9);
118 }
119 i++;
120 }
121 str_token_list_empty(&tlst);
122 if(i!=data->frameNr) {
123 strcpy(siferrmsg, "wrong data format");
124 sifEmpty(data);
125 return(9);
126 }
127
128
129 /* Calculate trues */
130 if(data->colNr>=4) for(i=0; i<data->frameNr; i++)
131 data->trues[i]=data->prompts[i]-data->randoms[i];
132 /* Set weights to 1.0 */
133 for(i=0; i<data->frameNr; i++) data->weights[i]=1.0;
134
135 return(0);
136}
timegm
time_t timegm(struct tm *tm)
Inverse of gmtime, converting struct tm to time_t.
Definition datetime.c:69
SIF_TEST
int SIF_TEST
Definition sif.c:6
sifSetmem
int sifSetmem(SIF *data, int frameNr)
Definition sif.c:56
sifEmpty
void sifEmpty(SIF *data)
Definition sif.c:33
siferrmsg
char siferrmsg[128]
Definition sif.c:7
str_token_list_empty
void str_token_list_empty(STR_TOKEN_LIST *lst)
Definition readfile.c:26
str_token_list_del
int str_token_list_del(STR_TOKEN_LIST *lst, int item)
Definition readfile.c:70
textfileReadLines
int textfileReadLines(const char *filename, STR_TOKEN_LIST *lst)
Definition readfile.c:136
str_token_list_init
void str_token_list_init(STR_TOKEN_LIST *lst)
Definition readfile.c:13
strnlen
size_t strnlen(const char *s, size_t n)
Definition strext.c:181
asciiCommentLine
int asciiCommentLine(const char *line, int *cont)
Definition readfile.c:246
SIF::version
int version
Definition libtpcimgio.h:1451
SIF::studynr
char studynr[MAX_STUDYNR_LEN+1]
Definition libtpcimgio.h:1453
SIF::colNr
int colNr
Definition libtpcimgio.h:1449
STR_TOKEN_LIST
Definition libtpcmisc.h:387
STR_TOKEN_LIST::tok
char ** tok
Definition libtpcmisc.h:393
STR_TOKEN_LIST::token_nr
int token_nr
Definition libtpcmisc.h:389

Referenced by imgReadAnalyze(), imgReadAnalyzeFrame(), imgReadAnalyzeHeader(), imgReadModelingData(), imgReadNiftiFrame(), imgReadNiftiHeader(), imgWriteAnalyze(), and imgWriteNifti().

◆ sifWrite()

int sifWrite ( SIF * data,
char * filename )

Write SIF data to a standard SIF file, emptying files old contents.

Returns
Returns 0 if successful, 1 invalid input, 2 failed to open file, 3 failed to write into file.
See also
sifInit, sifEmpty, sifRead, sifPrint, sifWeight
Parameters
dataPointer to SIF structure containing data to be written in file.
filenameFile name for SIF; Set to 'stdout' to print the contents on console. File is overwritten without backup.

Definition at line 145 of file sifio.c.

151 {
152 int i, n, req_decimals=0;
153 char buf[1024];
154 struct tm tm; //*st;
155
156
157 if(SIF_TEST) printf("sifWrite(*sif, %s)\n", filename);
158 /* Check data */
159 if(data->frameNr<1) {strcpy(siferrmsg, "no data to save"); return 1;}
160
161 /* Set file pointer */
162 FILE *fp;
163 int intofile;
164 if(strcasecmp(filename, "STDOUT")==0) {
165 fp=stdout; intofile=0;
166 } else {
167 /* Open file */
168 fp=fopen(filename, "w");
169 if(fp==NULL) {strcpy(siferrmsg, "cannot open file"); return 2;}
170 intofile=1;
171 }
172
173 /* Write title line */
174 if(!gmtime_r((time_t*)&data->scantime, &tm) || !strftime(buf, 1024, "%d/%m/%Y %H:%M:%S", &tm))
175 strcpy(buf, "1/1/1900 00:00:00");
176 n=fprintf(fp, "%s %d %d %d", buf, data->frameNr, data->colNr, data->version);
177 if(SIF_TEST) printf("%s %d %d %d\n", buf, data->frameNr, data->colNr, data->version);
178 if(n<7) {
179 strcpy(siferrmsg, "cannot write file"); if(intofile) fclose(fp);
180 return 2;
181 }
182 if(strlen(data->studynr)!=0 || strlen(data->isotope_name)!=0) {
183 /* Write also study number and isotope */
184 if(strlen(data->studynr)==0) fprintf(fp, " ."); else fprintf(fp, " %s", data->studynr);
185 if(strlen(data->isotope_name)>0) fprintf(fp, " %s", data->isotope_name);
186 }
187 fprintf(fp, "\n");
188
189 /* Check if frame times need to printed with decimals */
190 for(i=1, req_decimals=0; i<data->frameNr; i++) {
191 if(round(data->x1[i])==round(data->x1[i-1])) {req_decimals=1; break;}
192 if(round(data->x2[i])==round(data->x2[i-1])) {req_decimals=1; break;}
193 }
194
195 /* Write data lines */
196 for(i=0; i<data->frameNr; i++) {
197 if(req_decimals==0) n=fprintf(fp, "%.0f %.0f", data->x1[i], data->x2[i]);
198 else n=fprintf(fp, "%.1f %.1f", data->x1[i], data->x2[i]);
199 if(n<3) {
200 strcpy(siferrmsg, "cannot write file"); if(intofile) fclose(fp);
201 return 3;
202 }
203 if(data->colNr<=2) {n=fprintf(fp, "\n"); continue;}
204 n=fprintf(fp, " %.0f %.0f", data->prompts[i], data->randoms[i]);
205 if(n<1) {
206 strcpy(siferrmsg, "cannot write file"); if(intofile) fclose(fp);
207 return 3;
208 }
209 if(data->colNr<5) {n=fprintf(fp, "\n"); continue;}
210 n=fprintf(fp, " %.0f", data->trues[i]);
211 if(n<1) {
212 strcpy(siferrmsg, "cannot write file"); if(intofile) fclose(fp);
213 return 3;
214 }
215 if(data->colNr<6) {n=fprintf(fp, "\n"); continue;}
216 n=fprintf(fp, " %.5f\n", data->weights[i]);
217 if(n<1) {
218 strcpy(siferrmsg, "cannot write file"); if(intofile) fclose(fp);
219 return 3;
220 }
221 }
222
223 /* Close file */
224 if(intofile) fclose(fp);
225
226 return 0;
227}
gmtime_r
struct tm * gmtime_r(const time_t *t, struct tm *tm)
Convert time_t to GMT struct tm.
Definition datetime.c:22

Referenced by imgWriteAnalyze(), and imgWriteNifti().

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