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abssio.c
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1
9/*****************************************************************************/
10#include "tpcclibConfig.h"
11/*****************************************************************************/
12#include <stdio.h>
13#include <stdlib.h>
14#include <math.h>
15#include <time.h>
16#include <string.h>
17/*****************************************************************************/
18//#include "tpcextensions.h"
19//#include "tpctac.h"
20/*****************************************************************************/
21#include "tpcabss.h"
22/*****************************************************************************/
23
24/*****************************************************************************/
30ABSS_DEVICE abssIdFromFName(
32 const char *fname
33) {
34 if(fname==NULL || strnlen(fname, 10)<5) return(ABSS_UNKNOWN);
35 /* Get pointer to the extension, starting with the dot */
36 char *cptr=filenameGetExtension(fname);
37 if(cptr==NULL) return(ABSS_UNKNOWN);
38 if(strcasecmp(cptr, ".lis")==0) return(ABSS_SCANDITRONICS);
39 if(strcasecmp(cptr, ".bld")==0) return(ABSS_GEMS);
40 if(strcasecmp(cptr, ".alg")==0) return(ABSS_ALLOGG_OLD);
41 if(strcasecmp(cptr, ".txt")==0) return(ABSS_ALLOGG);
42 return(ABSS_UNKNOWN);
43}
44/*****************************************************************************/
45
46/*****************************************************************************/
53int abssWrite(
56 TAC *d,
58 FILE *fp,
60 TPCSTATUS *status
61) {
62 int verbose=0; if(status!=NULL) verbose=status->verbose;
63 if(verbose>0) {printf("%s()\n", __func__); fflush(stdout);}
64 if(fp==NULL) {
65 statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_CANNOT_WRITE);
66 return TPCERROR_CANNOT_WRITE;
67 }
68 if(d==NULL || d->sampleNr<1 || d->tacNr<1) {
69 statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_NO_DATA);
70 return TPCERROR_NO_DATA;
71 }
72
73 char buf[1024];
74 int ret=TPCERROR_OK;
75
76 if(d->format==TAC_FORMAT_ABSS_GEMS) {
77
78 ret=TPCERROR_OK;
79
80 /* Write the header */
81 int ii;
82 d->h.space_before_eq=0; d->h.space_after_eq=1; /* Set no space before ':' */
83 ii=iftFindKey(&d->h, "Protocol", 0);
84 if(ii>=0) ret=iftWriteItem(&d->h, ii, fp, status);
85 if(ret!=TPCERROR_OK) {
86 statusSet(status, __func__, __FILE__, __LINE__, ret); return(ret);
87 }
88
89 if(tacGetHeaderStudynr(&d->h, buf, NULL)!=TPCERROR_OK) {
90 ii=iftFindKey(&d->h, "Patient", 0);
91 if(ii>=0) strlcpy(buf, d->h.item[ii].value, 256); else strcpy(buf, "");
92 }
93 fprintf(fp, "# Patient: %s\n", buf);
94
95 if(tacGetHeaderIsotope(&d->h, buf, NULL)==TPCERROR_OK) {
96 double hl=isotopeHalflife(isotopeIdentify(buf));
97 if(!isnan(hl)) sprintf(buf, "%f", hl); else strcpy(buf, "");
98 } else {
99 ii=iftFindKey(&d->h, "Isotope half-life", 0);
100 if(ii>=0) strlcpy(buf, d->h.item[ii].value, 256); else strcpy(buf, "");
101 }
102 fprintf(fp, "# Isotope half-life: %s\n", buf);
103
104 fprintf(fp, "# Start Interv 1st detector pair");
105 fprintf(fp, " 2nd detector pair AUX\n");
106 fprintf(fp, "# time time coinc singl1 singl2");
107 fprintf(fp, " coinc singl1 singl2 counts\n");
108
109 ii=iftFindKey(&d->h, "sampler_start_time", 0);
110 if(ii>=0) {
111 fprintf(fp, "# %s\n", d->h.item[ii].value);
112 } else if(tacGetHeaderScanstarttime(&d->h, buf, NULL)==TPCERROR_OK) {
113 fprintf(fp, "# %s\n", buf);
114 }
115
116
117 /* Write the sample data */
118 double sod=0.0; /* Time from start of the day */
119 if(tacGetHeaderScanstarttime(&d->h, buf, NULL)==TPCERROR_OK) {
120 struct tm tmsod;
121 if(!strDateTimeRead(buf, &tmsod))
122 sod=3600.*tmsod.tm_hour+60.*tmsod.tm_min+tmsod.tm_sec;
123 }
124 int i, j;
125 for(i=0; i<d->sampleNr; i++) {
126 fprintf(fp, "%9.1f %9.1f %9.1f", sod+d->x1[i], d->x1[i], d->x2[i]-d->x1[i]);
127 for(j=0; j<7; j++) {
128 if(j<d->tacNr) fprintf(fp, " %7.0f", d->c[j].y[i]);
129 else fprintf(fp, " %7.0f", 0.0);
130 }
131 if(fprintf(fp, "\n")<1) {ret=TPCERROR_CANNOT_WRITE; break;}
132 }
133 if(ret!=TPCERROR_OK) {
134 statusSet(status, __func__, __FILE__, __LINE__, ret); return(ret);
135 }
136
137 statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
138 return(TPCERROR_OK);
139 }
140
141
142 if(d->format==TAC_FORMAT_ABSS_SCANDITRONICS) {
143
144 ret=TPCERROR_OK;
145
146 /* Write the header */
147 fprintf(fp, "# Scanditronics Automated Blood Measurement System\n");
148 int ii;
149 d->h.space_before_eq=0; d->h.space_after_eq=1; /* Set no space before ':' */
150 ii=iftFindKey(&d->h, "Protocol", 0);
151 if(ii>=0) ret=iftWriteItem(&d->h, ii, fp, status);
152 if(ret!=TPCERROR_OK) {
153 statusSet(status, __func__, __FILE__, __LINE__, ret); return(ret);
154 }
155
156 fprintf(fp, "# Start Interv 1st detector pair");
157 fprintf(fp, " 2nd detector pair AUX\n");
158 fprintf(fp, "# time time coinc singl1 singl2");
159 fprintf(fp, " coinc singl1 singl2 counts\n");
160
161 ii=iftFindKey(&d->h, "sampler_start_time", 0);
162 if(ii>=0) {
163 fprintf(fp, "# %s\n", d->h.item[ii].value);
164 } else if(tacGetHeaderScanstarttime(&d->h, buf, NULL)==TPCERROR_OK) {
165 fprintf(fp, "# %s\n", buf);
166 }
167
168
169 /* Write the sample data */
170 time_t t=0.0;
171 if(tacGetHeaderScanstarttime(&d->h, buf, NULL)==TPCERROR_OK) {
172 //printf("scanstarttime=%s\n", buf);
173 struct tm tmsod;
174 if(!strDateTimeRead(buf, &tmsod)) t=mktime(&tmsod);
175 }
176 int i, j;
177 for(i=0; i<d->sampleNr; i++) {
178 fprintf(fp, "%13.1f %9.1f %9.1f",
179 d->x1[i]+(unsigned long int)t, d->x1[i], d->x2[i]-d->x1[i]);
180 for(j=0; j<7; j++) {
181 if(j<d->tacNr) fprintf(fp, " %7.0f", d->c[j].y[i]);
182 else fprintf(fp, " %7.0f", 0.0);
183 }
184 if(fprintf(fp, "\n")<1) {ret=TPCERROR_CANNOT_WRITE; break;}
185 }
186 if(ret!=TPCERROR_OK) {
187 statusSet(status, __func__, __FILE__, __LINE__, ret); return(ret);
188 }
189
190 statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
191 return(TPCERROR_OK);
192 }
193
194
195 if(d->format==TAC_FORMAT_ABSS_ALLOGG_OLD) {
196
197 ret=TPCERROR_OK;
198
199 if(d->tacNr<2) {
200 statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_NO_DATA);
201 return(TPCERROR_NO_DATA);
202 }
203
204 /* Write the header */
205 fprintf(fp, "# Allogg1\n");
206 int ii;
207 d->h.space_before_eq=0; d->h.space_after_eq=1; /* Set no space before ':' */
208
209 ii=iftFindKey(&d->h, "Protocol", 0);
210 if(ii>=0) ret=iftWriteItem(&d->h, ii, fp, status);
211 if(ret!=TPCERROR_OK) {
212 statusSet(status, __func__, __FILE__, __LINE__, ret); return(ret);
213 }
214
215 ii=iftFindKey(&d->h, "Discriminators", 0);
216 if(ii>=0) ret=iftWriteItem(&d->h, ii, fp, status);
217 if(ret!=TPCERROR_OK) {
218 statusSet(status, __func__, __FILE__, __LINE__, ret); return(ret);
219 }
220
221 if(tacGetHeaderScanstarttime(&d->h, buf, NULL)==TPCERROR_OK) {
222 fprintf(fp, "# %s\n", buf);
223 }
224
225 ii=iftSearchKey(&d->h, "Background", 0);
226 if(ii>=0) ret=iftWriteItem(&d->h, ii, fp, status);
227 if(ret!=TPCERROR_OK) {
228 statusSet(status, __func__, __FILE__, __LINE__, ret); return(ret);
229 }
230
231 /* Start time in format HHMMSS */
232 if(tacGetHeaderScanstarttime(&d->h, buf, NULL)==TPCERROR_OK) {
233 fprintf(fp, "\n%2.2s%2.2s%2.2s\n", buf+11, buf+14, buf+17);
234 } else {
235 fprintf(fp, "\n000000\n");
236 }
237
238 /* Write the sample data */
239 for(int i=0; i<d->sampleNr; i++) {
240 if(fprintf(fp, "%6.1f %5.0f %5.0f\n",
241 d->x2[i], d->c[0].y[i], d->c[1].y[i]) < 10)
242 {
243 ret=TPCERROR_CANNOT_WRITE; break;
244 }
245 }
246 if(ret!=TPCERROR_OK) {
247 statusSet(status, __func__, __FILE__, __LINE__, ret); return(ret);
248 }
249
250 statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
251 return(TPCERROR_OK);
252 }
253
254
255 if(d->format==TAC_FORMAT_ABSS_ALLOGG) {
256
257 if(d->tacNr<2) {
258 statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_NO_DATA);
259 return(TPCERROR_NO_DATA);
260 }
261
262 int ii;
263 //d->h.space_before_eq=0; d->h.space_after_eq=1; /* Set no space before ':' */
264 ret=TPCERROR_OK;
265
266 /* Write the background */
267 ii=iftSearchKey(&d->h, "background counts", 0);
268 if(ii>=0 &&
269 fprintf(fp, "%s :\t%s\n", d->h.item[ii].key, d->h.item[ii].value)<10)
270 {
271 statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_CANNOT_WRITE);
272 return TPCERROR_CANNOT_WRITE;
273 }
274
275 /* Write the header */
276 fprintf(fp, "//Heading\n");
277
278 ii=iftFindKey(&d->h, "System ID", 0);
279 if(ii>=0) fprintf(fp, "%s:\t%s\n", d->h.item[ii].key, d->h.item[ii].value);
280 ii=iftFindKey(&d->h, "User name", 0);
281 if(ii>=0) fprintf(fp, "%s:\t%s\n", d->h.item[ii].key, d->h.item[ii].value);
282 ii=iftFindKey(&d->h, "Run number", 0);
283 if(ii>=0) fprintf(fp, "%s:\t%s\n", d->h.item[ii].key, d->h.item[ii].value);
284 ii=iftFindKey(&d->h, "Patient ID", 0);
285 if(ii>=0) fprintf(fp, "%s:\t%s\n", d->h.item[ii].key, d->h.item[ii].value);
286 ii=iftFindKey(&d->h, "HalfTime", 0);
287 if(ii>=0) fprintf(fp, "%s:\t%s\n", d->h.item[ii].key, d->h.item[ii].value);
288 ii=iftFindKey(&d->h, "Tube length", 0);
289 if(ii>=0) fprintf(fp, "%s:\t%s\n", d->h.item[ii].key, d->h.item[ii].value);
290 ii=iftFindKey(&d->h, "Pump speed", 0);
291 if(ii>=0) fprintf(fp, "%s:\t%s\n", d->h.item[ii].key, d->h.item[ii].value);
292 ii=iftFindKey(&d->h, "DeadTimeSingles", 0);
293 if(ii>=0) fprintf(fp, "%s:\t%s\n", d->h.item[ii].key, d->h.item[ii].value);
294 ii=iftFindKey(&d->h, "DeadTimeCoincidents", 0);
295 if(ii>=0) fprintf(fp, "%s:\t%s\n", d->h.item[ii].key, d->h.item[ii].value);
296 ii=iftFindKey(&d->h, "DiscriminatorSingles", 0);
297 if(ii>=0) fprintf(fp, "%s:\t%s\n", d->h.item[ii].key, d->h.item[ii].value);
298 ii=iftFindKey(&d->h, "DiscriminatorCoincidents", 0);
299 if(ii>=0) fprintf(fp, "%s:\t%s\n", d->h.item[ii].key, d->h.item[ii].value);
300 ii=iftFindKey(&d->h, "EffectivitySingles", 0);
301 if(ii>=0) fprintf(fp, "%s:\t%s\n", d->h.item[ii].key, d->h.item[ii].value);
302 ii=iftFindKey(&d->h, "EffectivityCoincidents", 0);
303 if(ii>=0) fprintf(fp, "%s:\t%s\n", d->h.item[ii].key, d->h.item[ii].value);
304
305 /* Write the data */
306 if(fprintf(fp, "//Data\n")<6) {
307 statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_CANNOT_WRITE);
308 return TPCERROR_CANNOT_WRITE;
309 }
310 fprintf(fp, "Absolute time\t");
311 fprintf(fp, "Time after start [s]\t");
312 fprintf(fp, "Singles [cnt]\t");
313 fprintf(fp, "Coincidents [cnt]\t");
314 fprintf(fp, "Singles count rate [kBq/ml]\t");
315 fprintf(fp, "Coincidents count rate [kBq/ml]\t");
316 fprintf(fp, "Singles count rate DTC [kBq/ml]\t");
317 fprintf(fp, "Coincidents count rate DTC [kBq/ml]\t");
318 fprintf(fp, "Singles DTC&decay [kBq/ml]\t");
319 fprintf(fp, "Coincidents DTC&decay [kBq/ml]\n");
320 struct tm tmtod;
321 if(tacGetHeaderScanstarttime(&d->h, buf, NULL)==TPCERROR_OK) {
322 //printf("scanstarttime=%s\n", buf);
323 strDateTimeRead(buf, &tmtod);
324 }
325 int i, j;
326 for(i=0; i<d->sampleNr; i++) {
327 if(i>0) tmAdd(d->x1[i]-d->x1[i-1], &tmtod);
328 if(strftime(buf, 32, "%Y-%m-%d %H:%M:%S", &tmtod)==0)
329 strcpy(buf, "1970-01-01 00:00:00");
330 fprintf(fp, "%s\t%.1f\t%.0f\t%.0f",
331 buf, d->x1[i], d->c[0].y[i], d->c[1].y[i]);
332 for(j=2; j<8; j++) {
333 if(j<d->tacNr) fprintf(fp, "\t%.12f", d->c[j].y[i]);
334 else fprintf(fp, "\t%f", 0.0);
335 }
336 if(fprintf(fp, "\n")<1) {ret=TPCERROR_CANNOT_WRITE; break;}
337 }
338 if(ret!=TPCERROR_OK) {
339 statusSet(status, __func__, __FILE__, __LINE__, ret); return(ret);
340 }
341
342 statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
343 return(TPCERROR_OK);
344 }
345
346
347 statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_UNSUPPORTED);
348 return(TPCERROR_UNSUPPORTED);
349}
350/*****************************************************************************/
351
352/*****************************************************************************/
abssWrite
int abssWrite(TAC *d, FILE *fp, TPCSTATUS *status)
Definition abssio.c:53
abssIdFromFName
ABSS_DEVICE abssIdFromFName(const char *fname)
Definition abssio.c:30
strDateTimeRead
int strDateTimeRead(const char *str, struct tm *date)
Definition datetime.c:350
tmAdd
void tmAdd(int s, struct tm *d)
Definition datetime.c:500
filenameGetExtension
char * filenameGetExtension(const char *s)
Get the last extension of a file name.
Definition filename.c:178
iftSearchKey
int iftSearchKey(IFT *ift, const char *s, int start_index)
Definition iftfind.c:86
iftFindKey
int iftFindKey(IFT *ift, const char *key, int start_index)
Definition iftfind.c:30
iftWriteItem
int iftWriteItem(IFT *ift, int item, FILE *fp, TPCSTATUS *status)
Definition iftio.c:25
isotopeHalflife
double isotopeHalflife(int isotope_code)
Definition isotope.c:62
isotopeIdentify
int isotopeIdentify(const char *isotope)
Definition isotope.c:145
statusSet
void statusSet(TPCSTATUS *s, const char *func, const char *srcfile, int srcline, tpcerror error)
Definition statusmsg.c:142
strnlen
size_t strnlen(const char *s, size_t n)
Definition stringext.c:566
strlcpy
size_t strlcpy(char *dst, const char *src, size_t dstsize)
Definition stringext.c:632
IFT_ITEM::value
char * value
Definition tpcift.h:37
IFT_ITEM::key
char * key
Definition tpcift.h:32
IFT::item
IFT_ITEM * item
Definition tpcift.h:57
IFT::space_after_eq
int space_after_eq
Definition tpcift.h:55
IFT::space_before_eq
int space_before_eq
Definition tpcift.h:53
TACC::y
double * y
Definition tpctac.h:75
TAC
Definition tpctac.h:87
TAC::format
tacformat format
Definition tpctac.h:93
TAC::sampleNr
int sampleNr
Definition tpctac.h:89
TAC::h
IFT h
Optional (but often useful) header information.
Definition tpctac.h:141
TAC::c
TACC * c
Definition tpctac.h:117
TAC::x2
double * x2
Definition tpctac.h:101
TAC::x1
double * x1
Definition tpctac.h:99
TAC::tacNr
int tacNr
Definition tpctac.h:91
TPCSTATUS::verbose
int verbose
Verbose level, used by statusPrint() etc.
Definition tpcextensions.h:242
tacGetHeaderScanstarttime
int tacGetHeaderScanstarttime(IFT *h, char *s, TPCSTATUS *status)
Definition tacift.c:372
tacGetHeaderStudynr
int tacGetHeaderStudynr(IFT *h, char *s, TPCSTATUS *status)
Definition tacift.c:26
tacGetHeaderIsotope
int tacGetHeaderIsotope(IFT *h, char *s, TPCSTATUS *status)
Definition tacift.c:290
tpcabss.h
Header file for libtpcabss.
ABSS_DEVICE
ABSS_DEVICE
Definition tpcabss.h:30
TPCERROR_UNSUPPORTED
@ TPCERROR_UNSUPPORTED
Unsupported file type.
Definition tpcextensions.h:202
TPCERROR_OK
@ TPCERROR_OK
No error.
Definition tpcextensions.h:191
TPCERROR_NO_DATA
@ TPCERROR_NO_DATA
File contains no data.
Definition tpcextensions.h:203
TPCERROR_CANNOT_WRITE
@ TPCERROR_CANNOT_WRITE
Cannot write file.
Definition tpcextensions.h:199
TAC_FORMAT_ABSS_ALLOGG
@ TAC_FORMAT_ABSS_ALLOGG
ALLOGG ABSS data; reading supported.
Definition tpctac.h:56
TAC_FORMAT_ABSS_GEMS
@ TAC_FORMAT_ABSS_GEMS
GEMS ABSS data; reading supported.
Definition tpctac.h:54
TAC_FORMAT_ABSS_ALLOGG_OLD
@ TAC_FORMAT_ABSS_ALLOGG_OLD
ALLOGG ABSS data (old format); reading supported.
Definition tpctac.h:55
TAC_FORMAT_ABSS_SCANDITRONICS
@ TAC_FORMAT_ABSS_SCANDITRONICS
Scanditronics ABSS data; reading supported.
Definition tpctac.h:53
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