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efixplnr.c File Reference

Set plane, frame, gate and/or bed numbers in ECAT files to continuous sequence. More...

Go to the source code of this file.

Functions

int ecat63CopyFile (ECAT63_mainheader *mh, MATRIXLIST *ml, FILE *fp, char *resfile)
int ecat7CopyFile (ECAT7_mainheader *mh, ECAT7_MATRIXLIST *ml, FILE *fp, char *resfile)
int ecatFixMatrixlist (char *ecatfile, int do_planes, int do_frames, int do_gates, int do_beds, int verbose)

Detailed Description

Set plane, frame, gate and/or bed numbers in ECAT files to continuous sequence.

Copyright
(c) Turku PET Centre
Author
Vesa Oikonen
Test
Add tests.

Definition in file efixplnr.c.

Function Documentation

◆ ecat63CopyFile()

int ecat63CopyFile ( ECAT63_mainheader * mh,
MATRIXLIST * ml,
FILE * fp,
char * resfile )

Create a new ECAT 6.3 file with name outfile, containing data from existing file (file pointer given), with given mainheader and matrixlist.

Returns
errstatus, which is STATUS_OK (0) when call was successful, and >0 in case of an error.
Parameters
mhPointer to mainheader which is appropriate for both input and output data
mlPointer to matrixlist which is appropriate for both input and output data
fpFile pointer to input file opened in binary mode
resfileFilename for output file

Definition at line 69 of file efixplnr.c.

78 {
79 FILE *fp2=NULL;
80 int m, blkNr, nxtblk, bi;
81 char buf[MatBLKSIZE];
82
83
84 if(mh==NULL || ml==NULL || fp==NULL || resfile==NULL) return STATUS_FAULT;
85 /* Open output file */
86 fp2=ecat63Create(resfile, mh); if(fp2==NULL) return STATUS_NOWRITEPERM;
87 /* Copy the matrices */
88 for(m=0; m<ml->matrixNr; m++) if(ml->matdir[m].matstat==1) {
89 blkNr=1+ml->matdir[m].endblk-ml->matdir[m].strtblk;
90 /* Get block number for matrix header and data */
91 nxtblk=ecat63Matenter(fp2, ml->matdir[m].matnum, blkNr-1);
92 if(nxtblk<1) {fclose(fp2); remove(resfile); return STATUS_INVALIDMATLIST;}
93 /* Copy each block */
94 for(bi=ml->matdir[m].strtblk; bi<=ml->matdir[m].endblk; bi++) {
95 /* Read block */
96 fseek(fp, (bi-1)*MatBLKSIZE, SEEK_SET);
97 if(ftell(fp)!=(bi-1)*MatBLKSIZE) {
98 fclose(fp2); remove(resfile); return STATUS_NOMATRIX;}
99 if(fread(buf, MatBLKSIZE, 1, fp)<1) {
100 fclose(fp2); remove(resfile); return STATUS_NOMATRIX;}
101 /* Write block */
102 fseek(fp2, (nxtblk-1)*MatBLKSIZE, SEEK_SET);
103 if(ftell(fp2)!=(nxtblk-1)*MatBLKSIZE) {
104 fclose(fp2); remove(resfile); return STATUS_INVALIDMATLIST;}
105 if(fwrite(buf, 1, MatBLKSIZE, fp2)<1) {
106 fclose(fp2); remove(resfile); return STATUS_DISKFULL;}
107 nxtblk++;
108 }
109 }
110 fclose(fp2);
111 return STATUS_OK;
112}
ecat63Matenter
int ecat63Matenter(FILE *fp, int matnum, int blkNr)
Definition ecat63ml.c:159
ecat63Create
FILE * ecat63Create(const char *fname, ECAT63_mainheader *h)
Definition ecat63w.c:365
MatBLKSIZE
#define MatBLKSIZE
Definition libtpcimgio.h:210
MATRIXLIST::matdir
MatDir * matdir
Definition libtpcimgio.h:984
MatDir::matstat
int matstat
Definition libtpcimgio.h:974
MatDir::endblk
int endblk
Definition libtpcimgio.h:972
MatDir::matnum
int matnum
Definition libtpcimgio.h:968
MatDir::strtblk
int strtblk
Definition libtpcimgio.h:970

Referenced by ecatFixMatrixlist().

◆ ecat7CopyFile()

int ecat7CopyFile ( ECAT7_mainheader * mh,
ECAT7_MATRIXLIST * ml,
FILE * fp,
char * resfile )

Create a new ECAT 7 file with name outfile, containing data from existing file (file pointer given), with given mainheader and matrixlist.

Returns
errstatus, which is STATUS_OK (0) when call was successful, and >0 in case of an error.
Parameters
mhPointer to mainheader which is appropriate for both input and output data
mlPointer to matrixlist which is appropriate for both input and output data
fpFile pointer to input file opened in binary mode
resfileFilename for output file

Definition at line 121 of file efixplnr.c.

130 {
131 FILE *fp2=NULL;
132 int m, blkNr, nxtblk, bi;
133 char buf[MatBLKSIZE];
134
135
136 if(mh==NULL || ml==NULL || fp==NULL || resfile==NULL) return STATUS_FAULT;
137 /* Open output file */
138 fp2=ecat7Create(resfile, mh); if(fp2==NULL) return STATUS_NOWRITEPERM;
139 /* Copy the matrices */
140 for(m=0; m<ml->matrixNr; m++) if(ml->matdir[m].status==1) {
141 blkNr=1+ml->matdir[m].endblk-ml->matdir[m].strtblk;
142 /* Get block number for matrix header and data */
143 nxtblk=ecat7EnterMatrix(fp2, ml->matdir[m].id, blkNr-1);
144 if(nxtblk<1) {fclose(fp2); remove(resfile); return STATUS_INVALIDMATLIST;}
145 /* Copy each block */
146 for(bi=ml->matdir[m].strtblk; bi<=ml->matdir[m].endblk; bi++) {
147 /* Read block */
148 fseek(fp, (bi-1)*MatBLKSIZE, SEEK_SET);
149 if(ftell(fp)!=(bi-1)*MatBLKSIZE) {
150 fclose(fp2); remove(resfile); return STATUS_NOMATRIX;}
151 if(fread(buf, MatBLKSIZE, 1, fp)<1) {
152 fclose(fp2); remove(resfile); return STATUS_NOMATRIX;}
153 /* Write block */
154 fseek(fp2, (nxtblk-1)*MatBLKSIZE, SEEK_SET);
155 if(ftell(fp2)!=(nxtblk-1)*MatBLKSIZE) {
156 fclose(fp2); remove(resfile); return STATUS_INVALIDMATLIST;}
157 if(fwrite(buf, 1, MatBLKSIZE, fp2)<1) {
158 fclose(fp2); remove(resfile); return STATUS_DISKFULL;}
159 nxtblk++;
160 }
161 }
162 fclose(fp2);
163 return STATUS_OK;
164}
ecat7EnterMatrix
int ecat7EnterMatrix(FILE *fp, int matrix_id, int block_nr)
Definition ecat7ml.c:147
ecat7Create
FILE * ecat7Create(const char *fname, ECAT7_mainheader *h)
Definition ecat7w.c:567
ECAT7_MATRIXLIST::matdir
ECAT7_MatDir * matdir
Definition libtpcimgio.h:908
ECAT7_MATRIXLIST::matrixNr
int matrixNr
Definition libtpcimgio.h:904
ECAT7_MatDir::id
int id
Definition libtpcimgio.h:892
ECAT7_MatDir::strtblk
int strtblk
Definition libtpcimgio.h:894
ECAT7_MatDir::endblk
int endblk
Definition libtpcimgio.h:896
ECAT7_MatDir::status
int status
Definition libtpcimgio.h:898

Referenced by ecatFixMatrixlist().

◆ ecatFixMatrixlist()

int ecatFixMatrixlist ( char * ecatfile,
int do_planes,
int do_frames,
int do_gates,
int do_beds,
int verbose )

Set plane, frame, gate and/or bed numbers in ECAT files to continuous sequence.

Returns
Returns 0 when successful.
Parameters
ecatfilePointer to ECAT filename
do_planesDo or do not fix plane numbers (1/0)
do_framesDo or do not fix frame numbers (1/0)
do_gatesDo or do not fix gate numbers (1/0)
do_bedsDo or do not fix bed numbers (1/0)
verboseVerbose level; set to <=0 to print nothing in stdout

Definition at line 172 of file efixplnr.c.

185 {
186 int ret;
187 int ecat_format=0; // 6 or 7
188 char outfile[FILENAME_MAX];
189 FILE *fp=NULL;
190 ECAT7_mainheader ecat7_main_header;
191 ECAT63_mainheader ecat63_main_header;
192 ECAT7_MATRIXLIST ml7;
193 MATRIXLIST ml6;
194
195
196 /*
197 * Open the file
198 */
199 if(verbose>1) printf(" opening %s in binary format\n", ecatfile);
200 if((fp=fopen(ecatfile, "rb")) == NULL) {
201 fprintf(stderr, "Error: cannot read file %s\n", ecatfile);
202 return(2);
203 }
204
205 /*
206 * Determine the file format (ECAT 6 or 7)
207 * Read mainheader
208 */
209 if(verbose>2) printf(" reading main header\n");
210 ecat_format=0;
211 /* Try to read ECAT 7.x main header */
212 ret=ecat7ReadMainheader(fp, &ecat7_main_header);
213 if(ret) {
214 fprintf(stderr, "Error: unsupported file format %s\n", ecatfile);
215 fclose(fp); return(3);
216 }
217 /* If header could be read, check for magic number */
218 if(strncmp(ecat7_main_header.magic_number, ECAT7V_MAGICNR, 7)==0) {
219 ecat_format=7;
220 } else { // maybe this is ECAT 6.3
221 ret=ecat63ReadMainheader(fp, &ecat63_main_header);
222 if(ret==0) ecat_format=6;
223 }
224 if(verbose>2) printf(" ecat_format := %d\n", ecat_format);
225
226 /*
227 * Read matrixlist
228 */
229 if(verbose>1) printf(" reading matrix list\n");
230 ecat7InitMatlist(&ml7);
231 ecat63InitMatlist(&ml6);
232 if(ecat_format==7) {
233 ret=ecat7ReadMatlist(fp, &ml7, verbose-1);
234 if(ret==0 && (ml7.matrixNr<1 || ecat7CheckMatlist(&ml7))) ret=99;
235 } else if(ecat_format==6) {
236 ret=ecat63ReadMatlist(fp, &ml6, verbose-1);
237 if(ret==0 && (ml6.matrixNr<1 || ecat63CheckMatlist(&ml6))) ret=99;
238 } else {
239 fprintf(stderr, "Error: unsupported file format %s\n", ecatfile);
240 fclose(fp); return(3);
241 }
242 if(ret) {
243 fprintf(stderr, "Error %d: invalid matrix list.\n", ret);
244 fclose(fp); return(4);
245 }
246
247 /*
248 * Fix matrixlist
249 */
250 if(verbose>1) printf(" fixing matrix list\n");
251 if(ecat_format==6) {
252 if(verbose>2) ecat63PrintMatlist(&ml6); // print original matrixlist
253 ecat63GatherMatlist(&ml6, do_planes, do_frames, do_gates, do_beds);
254 if(verbose>2) ecat63PrintMatlist(&ml6); // print fixed matrixlist
255 } else {
256 if(verbose>2) ecat7PrintMatlist(&ml7); // print original matrixlist
257 ecat7GatherMatlist(&ml7, do_planes, do_frames, do_gates, do_beds);
258 if(verbose>2) ecat7PrintMatlist(&ml7); // print fixed matrixlist
259 }
260
261 /*
262 * Replace ECAT data with new matrixlist:
263 * Write data with new matrix list in temp file
264 * Delete original file
265 * Rename temp file to original filename
266 */
267 if(verbose>1) printf(" writing fixed data in temporary file\n");
268 /* Make tempfile name */
269 strcpy(outfile, ecatfile); strcat(outfile, "_efixplnr");
270 if(verbose>3) printf(" tempfile := %s\n", outfile);
271 if(ecat_format==6) {
272 /* Update num_* in mainheader */
273 ecat63GetNums(&ml6,
274 &ecat63_main_header.num_planes, // strict 2D format
275 &ecat63_main_header.num_frames,
276 &ecat63_main_header.num_gates,
277 &ecat63_main_header.num_bed_pos);
278 ret=ecat63CopyFile(&ecat63_main_header, &ml6, fp, outfile);
279 } else {
280 /* Update num_* in mainheader */
281 ecat7GetNums(&ml7, &ecat7_main_header, fp,
282 &ecat7_main_header.num_planes,
283 &ecat7_main_header.num_frames,
284 &ecat7_main_header.num_gates,
285 &ecat7_main_header.num_bed_pos);
286 ret=ecat7CopyFile(&ecat7_main_header, &ml7, fp, outfile);
287 }
288 fclose(fp);
289 if(ret) {fprintf(stderr, "Error: %s\n", imgStatus(ret)); return(11);}
290 /* Remove input file */
291 if(verbose>1) printf(" removing %s\n", ecatfile);
292 ret=remove(ecatfile); if(ret) {
293 fprintf(stderr, "Error: cannot overwrite file %s\n", ecatfile);
294 return(13);
295 }
296 /* Rename temp file to input name */
297 if(verbose>1) printf(" renaming %s to %s\n", outfile, ecatfile);
298 ret=rename(outfile, ecatfile); if(ret) {
299 fprintf(stderr, "Error: could not rename %s to %s\n", outfile, ecatfile);
300 return(15);
301 }
302
303 return(0);
304}
ecat63ReadMatlist
int ecat63ReadMatlist(FILE *fp, MATRIXLIST *ml, int verbose)
Definition ecat63ml.c:46
ecat63InitMatlist
void ecat63InitMatlist(MATRIXLIST *mlist)
Definition ecat63ml.c:20
ecat63GatherMatlist
int ecat63GatherMatlist(MATRIXLIST *ml, short int do_planes, short int do_frames, short int do_gates, short int do_beds)
Definition ecat63ml.c:510
ecat63GetNums
int ecat63GetNums(MATRIXLIST *ml, short int *num_planes, short int *num_frames, short int *num_gates, short int *num_bed_pos)
Definition ecat63ml.c:450
ecat63PrintMatlist
void ecat63PrintMatlist(MATRIXLIST *ml)
Definition ecat63ml.c:130
ecat63CheckMatlist
int ecat63CheckMatlist(MATRIXLIST *ml)
Definition ecat63ml.c:324
ecat63ReadMainheader
int ecat63ReadMainheader(FILE *fp, ECAT63_mainheader *h)
Definition ecat63r.c:25
ecat7InitMatlist
void ecat7InitMatlist(ECAT7_MATRIXLIST *mlist)
Definition ecat7ml.c:15
ecat7GetNums
int ecat7GetNums(ECAT7_MATRIXLIST *ml, ECAT7_mainheader *mh, FILE *fp, short int *num_planes, short int *num_frames, short int *num_gates, short int *num_bed_pos)
Definition ecat7ml.c:452
ecat7ReadMatlist
int ecat7ReadMatlist(FILE *fp, ECAT7_MATRIXLIST *ml, int verbose)
Definition ecat7ml.c:41
ecat7GatherMatlist
int ecat7GatherMatlist(ECAT7_MATRIXLIST *ml, short int do_planes, short int do_frames, short int do_gates, short int do_beds)
Definition ecat7ml.c:535
ecat7PrintMatlist
void ecat7PrintMatlist(ECAT7_MATRIXLIST *ml)
Definition ecat7ml.c:112
ecat7CheckMatlist
int ecat7CheckMatlist(ECAT7_MATRIXLIST *ml)
Definition ecat7ml.c:329
ecat7ReadMainheader
int ecat7ReadMainheader(FILE *fp, ECAT7_mainheader *h)
Definition ecat7r.c:15
ecat7CopyFile
int ecat7CopyFile(ECAT7_mainheader *mh, ECAT7_MATRIXLIST *ml, FILE *fp, char *resfile)
Definition efixplnr.c:121
ecat63CopyFile
int ecat63CopyFile(ECAT63_mainheader *mh, MATRIXLIST *ml, FILE *fp, char *resfile)
Definition efixplnr.c:69
imgStatus
char * imgStatus(int status_index)
Definition img.c:330
ECAT63_mainheader
Definition libtpcimgio.h:1002
ECAT63_mainheader::num_bed_pos
short int num_bed_pos
Definition libtpcimgio.h:1107
ECAT63_mainheader::num_gates
short int num_gates
Definition libtpcimgio.h:1104
ECAT63_mainheader::num_planes
short int num_planes
Definition libtpcimgio.h:1098
ECAT63_mainheader::num_frames
short int num_frames
Definition libtpcimgio.h:1101
ECAT7_MATRIXLIST
Definition libtpcimgio.h:902
ECAT7_mainheader
Definition libtpcimgio.h:300
ECAT7_mainheader::num_frames
short int num_frames
Definition libtpcimgio.h:387
ECAT7_mainheader::magic_number
char magic_number[14]
Definition libtpcimgio.h:302
ECAT7_mainheader::num_gates
short int num_gates
Definition libtpcimgio.h:389
ECAT7_mainheader::num_planes
short int num_planes
Definition libtpcimgio.h:385
ECAT7_mainheader::num_bed_pos
short int num_bed_pos
Definition libtpcimgio.h:391
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