/*
** read several rows of data from a file
*/
void
VReadObjectData (FILE *fp,int object_id,VImage *image)
{
static VImageInfo imageInfo;
static VAttrList list=NULL;
fseek(fp,0L,SEEK_SET);
if (! ReadHeader (fp)) VError("error reading header");
if (! (list = ReadAttrList (fp)))
VError("error reading attr list");
if (! VGetImageInfo(fp,list,object_id,&imageInfo))
VError(" error reading image info");
if (imageInfo.nbands != VImageNBands((*image)))
VError("incorrect number of bands");
if (imageInfo.nrows != VImageNRows((*image)))
VError("incorrect number of rows");
if (imageInfo.ncolumns != VImageNColumns((*image)))
VError("incorrect number of columns");
if (imageInfo.repn != VPixelRepn((*image)))
VError("incorrect pixel representation");
if (! VReadBlockData (fp,&imageInfo,0,imageInfo.nrows,image))
VError(" error reading data");
}
VAttrList VReadFile (FILE *f, VReadFileFilterProc *filter)
{
VAttrList list;
long offset;
int i;
/* Ensure that the correct FIL_Vista data file header is there: */
if (! ReadHeader (f))
return NULL;
/* Read all attributes in the file: */
if (! (list = ReadAttrList (f)))
return NULL;
/* Swallow the delimiter and read the binary data following it: */
offset = 0;
if (! ReadDelimiter (f) || ! ReadData (f, list, filter, &offset)) {
VDestroyAttrList (list);
return NULL;
}
/* Now we should be at the end of the file: */
i = fgetc (f);
if (i != EOF) {
ungetc (i, f);
VWarning ("VReadFile: File continues beyond expected EOF");
}
return list;
}
EXPORT_VISTA VistaIOAttrList VistaIOReadFile (FILE * f, VistaIOReadFileFilterProc * filter)
{
VistaIOAttrList list;
int i;
ReadStringBuf sbuf = {0,0};
#ifdef SupportUbcIff
/* If the first byte of the file is "I", it looks like a UBC IFF file: */
{
i = fgetc (f);
ungetc (i, f);
if (i == 'I') {
VistaIOImage image = VistaIOReadUbcIff (f);
if (!image)
return FALSE;
list = VistaIOCreateAttrList ();
VistaIOSetAttr (list, "image", NULL, VistaIOImageRepn, image);
return list;
}
}
#endif
/* Ensure that the correct Vista data file header is there: */
if (!ReadHeader (f))
return NULL;
list = ReadAttrList (f, &sbuf);
if (sbuf.max_len)
VistaIOFree(sbuf.buf);
/* Read all attributes in the file: */
if (!list)
return NULL;
/* Swallow the delimiter and read the binary data following it: */
offset = 0;
if (!ReadDelimiter (f) || !ReadData (f, list, filter)) {
VistaIODestroyAttrList (list);
return NULL;
}
/* Now we should be at the end of the file: */
i = fgetc (f);
if (i != EOF) {
ungetc (i, f);
VistaIOWarning ("VistaIOReadFile: File continues beyond expected EOF");
}
return list;
}
VAttrList
GetListInfo(VString in_filename, ListInfo *linfo) {
VAttrList list = NULL;
VAttrListPosn posn;
FILE *in_file = NULL;
VString str, voxel = NULL;
VRepnKind repn = VShortRepn;
int ntimesteps, nrows, ncols;
int id, j, itr, found, nobject, nbands;
VImageInfo *imageInfo = NULL;
in_file = VOpenInputFile(in_filename, TRUE);
if(!in_file)
VError("error opening file %s", in_filename);
if(! ReadHeader(in_file))
VError("error reading header");
if(!(list = ReadAttrList(in_file)))
VError("error reading attr list");
j = 0;
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
j++;
}
imageInfo = (VImageInfo *) VMalloc(sizeof(VImageInfo) * (j + 1));
itr = ntimesteps = nrows = ncols = 0;
nobject = nbands = found = id = 0;
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
str = VGetAttrName(&posn);
if(strncmp(str, "history", 7) == 0) {
nobject++;
continue;
}
VImageInfoIni(&imageInfo[nbands]);
if(! VGetImageInfo(in_file, list, nobject, &imageInfo[nbands]))
VError(" error reading image info");
linfo->ntimesteps = linfo->nrows = linfo->ncols = 0;
if(imageInfo[nbands].repn == VShortRepn) {
found = 1;
repn = imageInfo[nbands].repn;
if(imageInfo[nbands].nbands > ntimesteps)
ntimesteps = imageInfo[nbands].nbands;
if(imageInfo[nbands].nrows > nrows)
nrows = imageInfo[nbands].nrows;
if(imageInfo[nbands].ncolumns > ncols)
ncols = imageInfo[nbands].ncolumns;
if(voxel == NULL)
voxel = imageInfo[nbands].voxel;
/* check if slice contains non-zero data */
linfo->zero[nbands] = 1;
if(imageInfo[nbands].nrows < 2)
linfo->zero[nbands] = 0;
linfo->info[id] = imageInfo[nbands];
itr = imageInfo[nbands].repetition_time;
id++;
nbands++;
}
nobject++;
}
fclose(in_file);
if(!found)
VError(" couldn't find functional data");
linfo->ntimesteps = ntimesteps;
linfo->nrows = nrows;
linfo->ncols = ncols;
linfo->nslices = id;
linfo->itr = itr;
linfo->repn = repn;
linfo->voxel = voxel;
linfo->filename = VNewString(in_filename);
return list;
}
static VAttrList ReadAttrList (FILE *f)
{
VAttrList sublist, list = VCreateAttrList ();
VAttrRec *a;
int ch = 0;
size_t name_size;
VBundle b;
char buf[2], *str, name_buf[VMaxAttrNameLength + 1];
/* Swallow a { marking the start of the attribute list: */
if (fscanf (f, " %1s", buf) != 1 || buf[0] != '{') {
VWarning ("VReadFile: Missing {");
goto Fail;
}
/* For each attribute up to the next "}": */
while (fscanf (f, " %[^}: \t\n]", name_buf) == 1) {
name_size = strlen (name_buf);
/* Read a : and the first character of the attribute's value: */
if (fscanf (f, " %1s", buf) != 1 || buf[0] != ':' ||
fscanf (f, " %1s", buf) != 1) {
VWarning ("VReadFile: Invalid %s attribute", name_buf);
goto Fail;
}
/* The first character of the value tells us whether its an attribute
list, quoted string, or unquoted string: */
if (buf[0] == '{') {
/* The attribute value is another list of attributes: */
ungetc ('{', f);
if (! (sublist = ReadAttrList (f)))
goto Fail;
a = VMalloc (sizeof (VAttrRec) + name_size);
a->value = sublist;
a->repn = VAttrListRepn;
} else {
/* The value doesn't start with '{' -- parse a word or string: */
if (! (str = ReadString (f, buf[0], name_buf)))
goto Fail;
while ((ch = fgetc (f)) && (ch == ' ' || ch == '\t')) ;
ungetc (ch, f);
/* If the word is followed by an '{'... */
if (ch == '{') {
/* ...then it's a typed value -- the word is it's type name
and the { is the start of it's attribute list value. */
b = VCreateBundle (str, NULL, 0, NULL);
if (! (sublist = ReadAttrList (f))) {
VFree (b);
goto Fail;
}
b->list = sublist;
a = VMalloc (sizeof (VAttrRec) + name_size);
a->repn = VBundleRepn;
a->value = b;
} else {
/* ...otherwise store it as a simple string value: */
a = VMalloc (sizeof (VAttrRec) + name_size + strlen (str) + 1);
a->repn = VStringRepn;
a->value = a->name + name_size + 1;
strcpy (a->value, str);
}
VFree(str);
}
/* Copy the attribute's name into the newly allocated node: */
strcpy (a->name, name_buf);
/* Place the new node on the end of the growing attribute list: */
a->next = NULL;
a->prev = list->prev;
if (a->prev) a->prev->next = a;
else list->next = a;
list->prev = a;
}
/* Swallow the terminating "}": */
if (fscanf (f, " %1s", buf) != 1 || buf[0] != '}') {
VWarning ("VReadFile: Missing }");
Fail: VDestroyAttrList (list);
return NULL;
}
return list;
}
VBoolean
VGetImageInfo(FILE *fp,VAttrList list,int object_id,VImageInfo *imageInfo)
{
VBoolean data_found,length_found,found;
VAttrListPosn posn, subposn;
VBundle b;
int nobj=0;
VLong xdata=0;
VLong x=0;
VLong lx=0;
VDouble lf=0;
VString str;
/* if attr list not there, read it from disk */
if (list == NULL) {
fseek(fp,0L,SEEK_SET);
if (! ReadHeader (fp)) return FALSE;
if (! (list = ReadAttrList (fp))) return FALSE;
}
nobj=0;
for (VFirstAttr (list, & posn); VAttrExists (& posn); VNextAttr (& posn)) {
nobj++;
if (nobj-1 != object_id) continue;
if (!VGetAttrValue (& posn, NULL, VBundleRepn, & b))
VWarning("could not read bundle");
/* get image dimensions */
if (VLookupAttr (b->list, "nbands", & subposn)) {
if (! VGetAttrValue (& subposn, NULL, VLongRepn, &x)) {
VWarning ("VReadFile: "
"%s attribute's nbands attribute incorrect",
VGetAttrName (& posn));
return FALSE;
}
imageInfo->nbands = x;
VDeleteAttr (& subposn);
}
else {
imageInfo->nbands = 1;
/* VWarning(" attribute's nbands attribute not found"); */
}
if (VLookupAttr (b->list, VNRowsAttr, & subposn)) {
if (! VGetAttrValue (& subposn, NULL, VLongRepn, &x)) {
VWarning ("VReadFile: "
"%s attribute's nrows attribute incorrect",
VGetAttrName (& posn));
return FALSE;
}
imageInfo->nrows = x;
VDeleteAttr (& subposn);
}
else
VWarning(" attribute's nrows attribute not found");
if (VLookupAttr (b->list, VNColumnsAttr, & subposn)) {
if (! VGetAttrValue (& subposn, NULL, VLongRepn, &x)) {
VWarning ("VReadFile: "
"%s attribute's ncolumns attribute incorrect",
VGetAttrName (& posn));
return FALSE;
}
imageInfo->ncolumns = x;
VDeleteAttr (& subposn);
}
else
VWarning(" attribute's ncolumns attribute not found");
/* get compression info */
imageInfo->ori_nbands = 0;
if (VLookupAttr (b->list, "ori_nbands", & subposn)) {
if (! VGetAttrValue (& subposn, NULL, VLongRepn, &x)) {
VWarning ("VReadFile: "
"%s attribute's ori_nbands attribute incorrect",
VGetAttrName (& posn));
return FALSE;
}
imageInfo->ori_nbands = x;
VDeleteAttr (& subposn);
}
imageInfo->ori_nrows = 0;
if (VLookupAttr (b->list, "ori_nrows", & subposn)) {
if (! VGetAttrValue (& subposn, NULL, VLongRepn, &x)) {
VWarning ("VReadFile: "
"%s attribute's ori_nrows attribute incorrect",
VGetAttrName (& posn));
return FALSE;
}
imageInfo->ori_nrows = x;
VDeleteAttr (& subposn);
}
imageInfo->ori_ncolumns = 0;
if (VLookupAttr (b->list, "ori_ncolumns", & subposn)) {
if (! VGetAttrValue (& subposn, NULL, VLongRepn, &x)) {
VWarning ("VReadFile: "
"%s attribute's ori_ncolumns attribute incorrect",
VGetAttrName (& posn));
return FALSE;
}
imageInfo->ori_ncolumns = x;
VDeleteAttr (& subposn);
}
imageInfo->left_margin = 0;
if (VLookupAttr (b->list, "left_margin", & subposn)) {
if (! VGetAttrValue (& subposn, NULL, VLongRepn, &x)) {
VWarning ("VReadFile: "
"%s attribute's left_margin attribute incorrect",
VGetAttrName (& posn));
return FALSE;
}
imageInfo->left_margin = x;
VDeleteAttr (& subposn);
}
imageInfo->top_margin = 0;
if (VLookupAttr (b->list, "top_margin", & subposn)) {
if (! VGetAttrValue (& subposn, NULL, VLongRepn, &x)) {
VWarning ("VReadFile: "
"%s attribute's top_margin attribute incorrect",
VGetAttrName (& posn));
return FALSE;
}
imageInfo->top_margin = x;
VDeleteAttr (& subposn);
}
/* Extract any data and length attributes in the object's value: */
if (data_found = VLookupAttr (b->list, VDataAttr, & subposn)) {
if (! VGetAttrValue (& subposn, NULL, VLongRepn, &xdata)) {
VWarning ("VReadFile: "
"%s attribute's data attribute incorrect",
VGetAttrName (& posn));
return FALSE;
}
imageInfo->data = (size_t)xdata;
VDeleteAttr (& subposn);
}
else
VWarning(" attribute's data attribute not found");
if (length_found = VLookupAttr (b->list, VLengthAttr, & subposn)) {
if (! VGetAttrValue (& subposn, NULL, VLongRepn, &x)) {
VWarning ("VReadFile: "
"%s attribute's length attribute incorrect",
VGetAttrName (& posn));
return FALSE;
}
imageInfo->length = x;
VDeleteAttr (& subposn);
}
/* None or both must be present: */
if (data_found ^ length_found) {
VWarning ("VReadFile: %s attribute has %s but not %s",
VGetAttrName (& posn),
data_found ? "data" : "length",
data_found ? "length" : "data");
return FALSE;
}
/* get pixel repn */
if (found = VLookupAttr (b->list,VRepnAttr, & subposn)) {
if (! VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
VWarning ("VReadFile: "
"%s attribute's repn attribute incorrect",
VGetAttrName (& posn));
return FALSE;
}
if (strncmp(str,"bit",3) == 0) {
imageInfo->repn = VBitRepn;
imageInfo->pixelSize = sizeof(VBit);
}
else if (strncmp(str,"ubyte",5) == 0) {
imageInfo->repn = VUByteRepn;
imageInfo->pixelSize = sizeof(VUByte);
}
else if (strncmp(str,"sbyte",5) == 0) {
imageInfo->repn = VSByteRepn;
imageInfo->pixelSize = sizeof(VSByte);
}
else if (strncmp(str,"short",5) == 0) {
imageInfo->repn = VShortRepn;
imageInfo->pixelSize = sizeof(VShort);
}
else if (strncmp(str,"long",4) == 0) {
imageInfo->repn = VLongRepn;
imageInfo->pixelSize = sizeof(VLong);
}
else if (strncmp(str,"float",5) == 0) {
imageInfo->repn = VFloatRepn;
imageInfo->pixelSize = sizeof(VFloat);
}
else if (strncmp(str,"double",6) == 0) {
imageInfo->repn = VDoubleRepn;
imageInfo->pixelSize = sizeof(VDouble);
}
else
return FALSE;
/* get fmri specifics */
if (found = VLookupAttr (b->list,"patient", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->patient,0,STRLEN);
strncpy(imageInfo->patient,str,strlen(str));
}
}
if (found = VLookupAttr (b->list,"modality", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->modality,0,STRLEN);
strncpy(imageInfo->modality,str,strlen(str));
}
}
if (found = VLookupAttr (b->list,"angle", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->angle,0,STRLEN);
strncpy(imageInfo->angle,str,strlen(str));
}
}
if (found = VLookupAttr (b->list,"voxel", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->voxel,0,STRLEN);
strncpy(imageInfo->voxel,str,strlen(str));
}
}
if (found = VLookupAttr (b->list,"name", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->name,0,STRLEN);
strncpy(imageInfo->name,str,strlen(str));
}
}
if (found = VLookupAttr (b->list,"fixpoint", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->fixpoint,0,STRLEN);
strncpy(imageInfo->fixpoint,str,strlen(str));
}
}
if (found = VLookupAttr (b->list,"ca", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->ca,0,STRLEN);
strncpy(imageInfo->ca,str,strlen(str));
}
}
if (found = VLookupAttr (b->list,"cp", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->cp,0,STRLEN);
strncpy(imageInfo->cp,str,strlen(str));
}
}
if (found = VLookupAttr (b->list,"location", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->location,0,STRLEN);
strncpy(imageInfo->location,str,strlen(str));
}
}
if (found = VLookupAttr (b->list,"orientation", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->orientation,0,STRLEN);
strncpy(imageInfo->orientation,str,strlen(str));
}
}
if (found = VLookupAttr (b->list,"talairach", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->talairach,0,STRLEN);
strncpy(imageInfo->talairach,str,strlen(str));
}
}
if (found = VLookupAttr (b->list,"MPIL_vista_0", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->MPIL_vista_0,0,STRLEN);
strncpy(imageInfo->MPIL_vista_0,str,strlen(str));
sscanf(str," repetition_time=%ld ",&lx);
imageInfo->repetition_time = lx;
}
}
if (found = VLookupAttr (b->list,"extent", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->extent,0,STRLEN);
strncpy(imageInfo->extent,str,strlen(str));
}
}
if (found = VLookupAttr (b->list,"spPH", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VLongRepn, &lx)) {
imageInfo->spPH = lx;
}
}
if (found = VLookupAttr (b->list,"spPG", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VLongRepn, &lx)) {
imageInfo->spPG = lx;
}
}
if (found = VLookupAttr (b->list,"subjects", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VLongRepn, &lx)) {
imageInfo->subjects = lx;
}
}
if (found = VLookupAttr (b->list,"ntimesteps", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VLongRepn, &lx)) {
imageInfo->ntimesteps = lx;
}
}
if (found = VLookupAttr (b->list,"df", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VDoubleRepn, &lf)) {
imageInfo->df = lf;
}
}
if (found = VLookupAttr (b->list,"norm_mean", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VDoubleRepn, &lf)) {
imageInfo->norm_mean = lf;
}
}
if (found = VLookupAttr (b->list,"norm_sig", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VDoubleRepn, &lf)) {
imageInfo->norm_sig = lf;
}
}
if (found = VLookupAttr (b->list,"repetition_time", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VLongRepn, &lx)) {
imageInfo->repetition_time = lx;
}
}
/* new, 28.3.2013 */
if (found = VLookupAttr (b->list,"indexOrigin", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->indexOrigin,0,STRLEN);
strncpy(imageInfo->indexOrigin,str,strlen(str));
}
}
if (found = VLookupAttr (b->list,"columnVec", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->columnVec,0,STRLEN);
strncpy(imageInfo->columnVec,str,strlen(str));
}
}
if (found = VLookupAttr (b->list,"rowVec", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->rowVec,0,STRLEN);
strncpy(imageInfo->rowVec,str,strlen(str));
}
}
if (found = VLookupAttr (b->list,"sliceVec", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->sliceVec,0,STRLEN);
strncpy(imageInfo->sliceVec,str,strlen(str));
}
}
if (found = VLookupAttr (b->list,"FOV", & subposn)) {
if (VGetAttrValue (& subposn, NULL, VStringRepn, &str)) {
memset(imageInfo->FOV,0,STRLEN);
strncpy(imageInfo->FOV,str,strlen(str));
}
}
}
}
x = VGetHeaderLength(fp);
imageInfo->offsetHdr = x;
/* fprintf(stderr," info: %d %d %d\n",imageInfo->nbands,imageInfo->nrows,imageInfo->ncolumns); */
return TRUE;
}
int main(int argc, char *argv[]) {
/* command line arguments */
static VString out_filename;
static VArgVector in_files;
static VString trans_filename = "";
static VBoolean in_found, out_found;
static VShort minval = 0;
static VBoolean compress = TRUE;
static VFloat resolution = 3;
static VOptionDescRec options[] = {
{ "in", VStringRepn, 0, & in_files, & in_found, NULL, "Input file" },
{ "out", VStringRepn, 1, & out_filename, & out_found, NULL, "Output file" },
{
"trans", VStringRepn, 1, &trans_filename, VRequiredOpt, NULL,
"File containing transformation matrix"
},
{
"resolution", VFloatRepn, 1, &resolution, VOptionalOpt, NULL,
"Output voxel resolution in mm"
},
{
"minval", VShortRepn, 1, &minval, VOptionalOpt, NULL,
"Signal threshold"
},
{
"compress", VBooleanRepn, 1, &compress, VOptionalOpt, NULL,
"Whether to compress empty slices"
}
};
VStringConst in_filename;
FILE *in_file, *out_file, *fp;
VAttrList list, list1, out_list;
VAttrListPosn posn;
VImage trans = NULL;
VImage *dst_image;
VImageInfo *imageInfo;
int nobject = 0, ntimesteps = 0, nbands = 0, nrows = 0, ncols = 0;
VString ca, cp, extent, str;
int found = 0;
int j, dest_nbands;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vfunctrans V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/* Parse command line arguments: */
if(! VParseCommand(VNumber(options), options, & argc, argv) ||
! VIdentifyFiles(VNumber(options), options, "in", & argc, argv, 0) ||
! VIdentifyFiles(VNumber(options), options, "out", & argc, argv, -1))
goto Usage;
if(argc > 1) {
VReportBadArgs(argc, argv);
Usage:
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(EXIT_FAILURE);
}
if(resolution <= 0)
VError(" 'resolution' must be an integer > 0");
/*
** Read the transformation matrix:
*/
fp = VOpenInputFile(trans_filename, TRUE);
list1 = VReadFile(fp, NULL);
if(! list1)
VError("Error reading image");
fclose(fp);
for(VFirstAttr(list1, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
if(strncmp(VGetAttrName(&posn), "transform", 9) != 0)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & trans);
break;
}
if(trans == NULL)
VError("transformation matrix not found");
/*
** check attributes
*/
if(VGetAttr(VImageAttrList(trans), "ca", NULL,
VStringRepn, (VPointer) & ca) != VAttrFound)
VError(" attribute 'ca' missing in transformation matrix ");
if(VGetAttr(VImageAttrList(trans), "cp", NULL,
VStringRepn, (VPointer) & cp) != VAttrFound)
VError(" attribute 'cp' missing in transformation matrix ");
if(VGetAttr(VImageAttrList(trans), "extent", NULL,
VStringRepn, (VPointer) & extent) != VAttrFound)
VError(" attribute 'extent' missing in transformation matrix ");
/*
** open in-file
*/
if(in_files.number < 1 || in_files.number > 1)
VError(" incorrect number of input files: %d", in_files.number);
in_filename = ((VStringConst *) in_files.vector)[0];
if(strcmp(in_filename, "-") == 0)
in_file = stdin;
else {
in_file = fopen((char *)in_filename, "r");
if(! in_file)
VError("Failed to open input file %s", in_filename);
}
/*
** read file info
*/
if(! ReadHeader(in_file))
VError("error reading header");
if(!(list = ReadAttrList(in_file)))
VError("error reading attr list");
j = 0;
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
j++;
}
imageInfo = (VImageInfo *) VMalloc(sizeof(VImageInfo) * (j + 1));
nobject = nbands = found = 0;
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
str = VGetAttrName(&posn);
if(strncmp(str, "history", 7) == 0) {
nobject++;
continue;
}
VImageInfoIni(&imageInfo[nbands]);
if(! VGetImageInfo(in_file, list, nobject, &imageInfo[nbands]))
VError(" error reading image info");
if(imageInfo[nbands].repn == VShortRepn) {
found = 1;
nrows = imageInfo[nbands].nrows;
ncols = imageInfo[nbands].ncolumns;
ntimesteps = imageInfo[nbands].nbands;
nbands++;
}
nobject++;
}
fclose(in_file);
if(!found)
VError(" couldn't find functional data");
/*
** process each time step
*/
dst_image = VFunctrans(in_filename, imageInfo, nbands, trans, resolution,
ntimesteps, minval, compress, &dest_nbands);
/*
** output
*/
out_list = VCreateAttrList();
VHistory(VNumber(options), options, prg_name, &list, &out_list);
for(j = 0; j < dest_nbands; j++) {
VAppendAttr(out_list, "image", NULL, VImageRepn, dst_image[j]);
}
/* Open and write the output file: */
if(strcmp(out_filename, "-") == 0)
out_file = stdout;
else {
out_file = fopen(out_filename, "w");
if(! out_file)
VError("Failed to open output file %s", out_filename);
}
if(!VWriteFile(out_file, out_list) || fclose(out_file))
VSystemError("error writing output file");
fprintf(stderr, "\n%s: done.\n", argv[0]);
return (EXIT_SUCCESS);
}
static VistaIOAttrList ReadAttrList (FILE * f, ReadStringBuf *sbuf)
{
VistaIOAttrList sublist, list = VistaIOCreateAttrList ();
VistaIOAttrRec *a;
int ch = 0;
size_t name_size;
VistaIOBundle b;
char buf[2], *str, name_buf[VistaIOMaxAttrNameLength + 1];
/* Swallow a { marking the start of the attribute list: */
if (fscanf (f, " %1s", buf) != 1 || buf[0] != '{') {
VistaIOWarning ("VistaIOReadFile: Missing {");
goto Fail;
}
/* For each attribute up to the next "}": */
while (fscanf (f, " %255[^}: \t\n]", name_buf) == 1) {
name_size = strlen (name_buf);
/* Covertiy does not detect that strlen(name_buf) <= 255 */
/* Read a : */
if (fscanf (f, " %1s", buf) != 1 || buf[0] != ':') {
VistaIOWarning ("VistaIOReadFile: Invalid %s attribute", name_buf);
goto Fail;
}
do {
ch = fgetc(f);
} while (ch == ' ');
/* File terminated early? */
if (ch == EOF)
goto Fail;
buf[0] = (char)ch;
/* The first character of the value tells us whether its an attribute
list, quoted string, or unquoted string: */
if (buf[0] == '{') {
/* The attribute value is another list of attributes: */
ungetc ('{', f);
if (!(sublist = ReadAttrList (f, sbuf)))
goto Fail;
a = VistaIOMalloc (sizeof (VistaIOAttrRec) + name_size);
a->value = sublist;
a->repn = VistaIOAttrListRepn;
} else if (buf[0] != '}' && buf[0] != '\n') {/* non-empty attr */
/* The value doesn't start with '{' -- parse a word or string: */
if (!(str = ReadString (f, buf[0], name_buf, sbuf)))
goto Fail;
while ((ch = fgetc (f)) && (ch == ' ' || ch == '\t'));
ungetc (ch, f);
/* If the word is followed by an '{'... */
if (ch == '{') {
/* ...then it's a typed value -- the word is it's type name
and the { is the start of it's attribute list value. */
b = VistaIOCreateBundle (str, NULL, 0, NULL);
if (!(sublist = ReadAttrList (f, sbuf))) {
VistaIOFree (b);
goto Fail;
}
b->list = sublist;
a = VistaIOMalloc (sizeof (VistaIOAttrRec) + name_size);
a->repn = VistaIOBundleRepn;
a->value = b;
} else {
/* ...otherwise store it as a simple string value: */
/*coverity[INTEGER_OVERFLOW] name_size is at most 255 (line 309)*/
a = VistaIOMalloc (sizeof (VistaIOAttrRec) + name_size +
strlen (str) + 1);
a->repn = VistaIOStringRepn;
a->value = a->name + name_size + 1;
strcpy (a->value, str);
}
}else{
ungetc (buf[0], f);
a = VistaIOMalloc (sizeof (VistaIOAttrRec) + name_size +
strlen ("") + 1);
a->repn = VistaIOStringRepn;
a->value = a->name + name_size + 1;
strcpy (a->value, "");
}
/* Copy the attribute's name into the newly allocated node: */
strcpy (a->name, name_buf);
/* Place the new node on the end of the growing attribute list: */
a->next = NULL;
if ((a->prev = list->prev))
a->prev->next = a;
else
list->next = a;
list->prev = a;
}
/* Swallow the terminating "}": */
if (fscanf (f, " %1s", buf) != 1 || buf[0] != '}') {
VistaIOWarning ("VistaIOReadFile: Missing }");
Fail:
VistaIODestroyAttrList (list);
return NULL;
}
return list;
}
