Skip to content

ENH: code review of recent nifti_image_conflicted_names PR #11

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
seanm wants to merge 1 commit into
base: master
Choose a base branch
from
Open

ENH: code review of recent nifti_image_conflicted_names PR #11

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
134 changes: 67 additions & 67 deletions nifti2/nifti2_io.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3748,7 +3748,7 @@ char * nifti_findhdrname(const char* fname)
if (nifti_fileexists(gzname)) {
fprintf(stderr,"Image Exception : Multiple possible filenames detected for basename (*.nii, *.nii.gz): %s\n", basename);
free(gzname);
exit(134);
return NULL;
}
free(gzname);
return hdrname;
Expand Down Expand Up @@ -5966,8 +5966,8 @@ nifti_image *nifti_image_read( const char *hname , int read_data )

#ifdef REJECT_COMPLEX
if ((nim->datatype == DT_COMPLEX64) || (nim->datatype == DT_COMPLEX128) || (nim->datatype == DT_COMPLEX256)) {
fprintf(stderr,"Image Exception Unsupported datatype (COMPLEX64): use fslcomplex to manipulate: %s\n", hname);
exit(13);
fprintf(stderr,"Image Exception Unsupported datatype (COMPLEX): use fslcomplex to manipulate: %s\n", hname);
return NULL;
}
#endif

Expand Down Expand Up @@ -7839,68 +7839,68 @@ znzFile nifti_image_write_hdr_img2(nifti_image *nim, int write_opts,

#ifdef PIGZ
#ifdef HAVE_ZLIB
int doPigz2(nifti_image *nim, struct nifti_2_header nhdr, const nifti_brick_list * NBL) {
FILE *pigzPipe;
char command[768];
strcpy(command, "pigz" );
strcat(command, " -n -f > \"");
strcat(command, nim->fname);
strcat(command, "\"");
#ifdef _MSC_VER
if (( pigzPipe = _popen(command, "w")) == NULL)
return -1;
#else
if (( pigzPipe = popen(command, "w")) == NULL)
return -1;
#endif
znzFile fp;
fp = (znzFile) calloc(1,sizeof(struct znzptr));
fp->zfptr = NULL;
fp->withz = 0;
fp->nzfptr = pigzPipe;
fwrite(&nhdr, sizeof(nhdr), 1, pigzPipe);
if( nim->nifti_type != NIFTI_FTYPE_ANALYZE )
nifti_write_extensions(fp,nim);
nifti_write_all_data(fp,nim,NBL);
#ifdef _MSC_VER
_pclose(pigzPipe);
#else
pclose(pigzPipe);
#endif
free(fp);
return 0;
}

int doPigz(nifti_image *nim, struct nifti_1_header nhdr, const nifti_brick_list * NBL) {
FILE *pigzPipe;
char command[768];
strcpy(command, "pigz" );
strcat(command, " -n -f > \"");
strcat(command, nim->fname);
strcat(command, "\"");
#ifdef _MSC_VER
if (( pigzPipe = _popen(command, "w")) == NULL)
return -1;
#else
if (( pigzPipe = popen(command, "w")) == NULL)
return -1;
#endif
znzFile fp;
fp = (znzFile) calloc(1,sizeof(struct znzptr));
fp->zfptr = NULL;
fp->withz = 0;
fp->nzfptr = pigzPipe;
fwrite(&nhdr, sizeof(nhdr), 1, pigzPipe);
if( nim->nifti_type != NIFTI_FTYPE_ANALYZE )
nifti_write_extensions(fp,nim);
nifti_write_all_data(fp,nim,NBL);
#ifdef _MSC_VER
_pclose(pigzPipe);
#else
pclose(pigzPipe);
#endif
free(fp);
return 0;
static int doPigz2(nifti_image * nim, const nifti_2_header * nhdr, const nifti_brick_list * NBL) {
FILE *pigzPipe;
char command[4096];
strcpy(command, "pigz" );
strcat(command, " -n -f > \"");
strcat(command, nim->fname);
strcat(command, "\"");
#ifdef _MSC_VER
if (( pigzPipe = _popen(command, "w")) == NULL)
return -1;
#else
if (( pigzPipe = popen(command, "w")) == NULL)
return -1;
#endif
znzFile fp;
fp = (znzFile) calloc(1, sizeof(struct znzptr));
fp->zfptr = NULL;
fp->withz = 0;
fp->nzfptr = pigzPipe;
fwrite(nhdr, sizeof(*nhdr), 1, pigzPipe);
if ( nim->nifti_type != NIFTI_FTYPE_ANALYZE )
nifti_write_extensions(fp, nim);
nifti_write_all_data(fp, nim, NBL);
#ifdef _MSC_VER
_pclose(pigzPipe);
#else
pclose(pigzPipe);
#endif
free(fp);
return 0;
}

static int doPigz(nifti_image * nim, const nifti_1_header * nhdr, const nifti_brick_list * NBL) {
FILE *pigzPipe;
char command[4096];
strcpy(command, "pigz" );
strcat(command, " -n -f > \"");
strcat(command, nim->fname);
strcat(command, "\"");
#ifdef _MSC_VER
if (( pigzPipe = _popen(command, "w")) == NULL)
return -1;
#else
if (( pigzPipe = popen(command, "w")) == NULL)
return -1;
#endif
znzFile fp;
fp = (znzFile) calloc(1, sizeof(struct znzptr));
fp->zfptr = NULL;
fp->withz = 0;
fp->nzfptr = pigzPipe;
fwrite(nhdr, sizeof(*nhdr), 1, pigzPipe);
if ( nim->nifti_type != NIFTI_FTYPE_ANALYZE )
nifti_write_extensions(fp, nim);
nifti_write_all_data(fp, nim, NBL);
#ifdef _MSC_VER
_pclose(pigzPipe);
#else
pclose(pigzPipe);
#endif
free(fp);
return 0;
}
#endif //HAVE_ZLIB
#endif //PIGZ
Expand Down Expand Up @@ -8023,10 +8023,10 @@ static int nifti_image_write_engine(nifti_image *nim, int write_opts,
char pigzKey[5] = "PIGZ";
if ((value != NULL) && (strstr(value,pigzKey))) {
if( nver == 2 ) {
if (doPigz2(nim, n2hdr, NBL) == 0)
if (doPigz2(nim, &n2hdr, NBL) == 0)
return 0;
} else {
if (doPigz(nim, n1hdr, NBL) == 0) //success writing with pigz
if (doPigz(nim, &n1hdr, NBL) == 0) //success writing with pigz
return 0;
}
}
Expand Down
98 changes: 33 additions & 65 deletions niftilib/nifti1_io.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2810,7 +2810,7 @@ char * nifti_findhdrname(const char* fname)
if (nifti_fileexists(gzname)) {
fprintf(stderr,"Image Exception : Multiple possible filenames detected for basename (*.nii, *.nii.gz): %s\n", basename);
free(gzname);
exit(134);
return NULL;
}
free(gzname);
return hdrname;
Expand Down Expand Up @@ -4276,7 +4276,7 @@ nifti_image *nifti_image_read( const char *hname , int read_data )

#ifdef REJECT_COMPLEX
if ((nim->datatype == DT_COMPLEX64) || (nim->datatype == DT_COMPLEX128) || (nim->datatype == DT_COMPLEX256)) {
fprintf(stderr,"Image Exception Unsupported datatype (COMPLEX64): use fslcomplex to manipulate: %s\n", hname);
fprintf(stderr,"Image Exception Unsupported datatype (COMPLEX): use fslcomplex to manipulate: %s\n", hname);
exit(13);
}
#endif
Expand Down Expand Up @@ -5756,68 +5756,36 @@ znzFile nifti_image_write_hdr_img2(nifti_image *nim, int write_opts,

#ifdef PIGZ
#ifdef HAVE_ZLIB
int doPigz2(nifti_image *nim, struct nifti_1_header nhdr, const nifti_brick_list * NBL) {
FILE *pigzPipe;
char command[768];
strcpy(command, "pigz" );
strcat(command, " -n -f > \"");
strcat(command, nim->fname);
strcat(command, "\"");
#ifdef _MSC_VER
if (( pigzPipe = _popen(command, "w")) == NULL)
return -1;
#else
if (( pigzPipe = popen(command, "w")) == NULL)
return -1;
#endif
znzFile fp;
fp = (znzFile) calloc(1,sizeof(struct znzptr));
fp->zfptr = NULL;
fp->withz = 0;
fp->nzfptr = pigzPipe;
fwrite(&nhdr, sizeof(nhdr), 1, pigzPipe);
if( nim->nifti_type != NIFTI_FTYPE_ANALYZE )
nifti_write_extensions(fp,nim);
nifti_write_all_data(fp,nim,NBL);
#ifdef _MSC_VER
_pclose(pigzPipe);
#else
pclose(pigzPipe);
#endif
free(fp);
return 0;
}

int doPigz(nifti_image *nim, struct nifti_1_header nhdr, const nifti_brick_list * NBL) {
FILE *pigzPipe;
char command[768];
strcpy(command, "pigz" );
strcat(command, " -n -f > \"");
strcat(command, nim->fname);
strcat(command, "\"");
#ifdef _MSC_VER
if (( pigzPipe = _popen(command, "w")) == NULL)
return -1;
#else
if (( pigzPipe = popen(command, "w")) == NULL)
return -1;
#endif
znzFile fp;
fp = (znzFile) calloc(1,sizeof(struct znzptr));
fp->zfptr = NULL;
fp->withz = 0;
fp->nzfptr = pigzPipe;
fwrite(&nhdr, sizeof(nhdr), 1, pigzPipe);
if( nim->nifti_type != NIFTI_FTYPE_ANALYZE )
nifti_write_extensions(fp,nim);
nifti_write_all_data(fp,nim,NBL);
#ifdef _MSC_VER
_pclose(pigzPipe);
#else
pclose(pigzPipe);
#endif
free(fp);
return 0;
static int doPigz(nifti_image * nim, const nifti_1_header * nhdr, const nifti_brick_list * NBL) {
FILE *pigzPipe;
char command[4096];
strcpy(command, "pigz" );
strcat(command, " -n -f > \"");
strcat(command, nim->fname);
strcat(command, "\"");
#ifdef _MSC_VER
if (( pigzPipe = _popen(command, "w")) == NULL)
return -1;
#else
if (( pigzPipe = popen(command, "w")) == NULL)
return -1;
#endif
znzFile fp;
fp = (znzFile) calloc(1, sizeof(struct znzptr));
fp->zfptr = NULL;
fp->withz = 0;
fp->nzfptr = pigzPipe;
fwrite(nhdr, sizeof(*nhdr), 1, pigzPipe);
if ( nim->nifti_type != NIFTI_FTYPE_ANALYZE )
nifti_write_extensions(fp,nim);
nifti_write_all_data(fp,nim,NBL);
#ifdef _MSC_VER
_pclose(pigzPipe);
#else
pclose(pigzPipe);
#endif
free(fp);
return 0;
}
#endif //HAVE_ZLIB
#endif //PIGZ
Expand Down Expand Up @@ -5919,7 +5887,7 @@ static int nifti_image_write_engine(nifti_image *nim, int write_opts,
//export AFNI_COMPRESSOR=PIGZ
char pigzKey[5] = "PIGZ";
if ((value != NULL) && (strstr(value,pigzKey))) {
if (doPigz(nim, nhdr, NBL) == 0) //success writing with pigz
if (doPigz(nim, &nhdr, NBL) == 0) //success writing with pigz
return 0;
}
}
Expand Down