void ReadField (VString Name, VImage& X, VImage& Y, VImage& Z, VAttrList& history_list)
{
FILE* file; /* input file */
VAttrList list; /* attribute list */
VAttrListPosn pos; /* position in list */
/* initialize results */
X = Y = Z = NULL;
/* open file */
file = fopen (Name, "r");
if (!file)
{
VError ("Failed to open input file '%s'", Name);
return;
}
/* read file */
list = VReadFile (file, NULL);
if (!list)
{
VError ("Failed to read input file '%s'", Name);
fclose (file);
return;
}
/* Read History */
history_list = VCopyAttrList(VReadHistory(&list));
/* extract field images */
if (VLookupAttr (list, "X", &pos))
{
VGetAttrValue (&pos, NULL, VImageRepn, &X);
VSetAttrValue (&pos, NULL, VImageRepn, NULL);
}
else VError ("Input file '%s' does not contain an image 'X'", Name);
if (VLookupAttr (list, "Y", &pos))
{
VGetAttrValue (&pos, NULL, VImageRepn, &Y);
VSetAttrValue (&pos, NULL, VImageRepn, NULL);
}
else VError ("Input file '%s' does not contain an image 'Y'", Name);
if (VLookupAttr (list, "Z", &pos))
{
VGetAttrValue (&pos, NULL, VImageRepn, &Z);
VSetAttrValue (&pos, NULL, VImageRepn, NULL);
}
else VError ("Input file '%s' does not contain an image 'Z'", Name);
/* clean-up*/
VDestroyAttrList (list);
fclose (file);
} /* ReadField */
VBoolean VExtractAttr (VAttrList list, VStringConst name,
VDictEntry *dict, VRepnKind repn, VPointer value,
VBooleanPromoted required)
{
VAttrListPosn posn;
/* If the attribute is in the list... */
if (VLookupAttr (list, name, & posn)) {
if (value) {
/* Get its value: */
if (! VGetAttrValue (& posn, dict, repn, value)) {
VWarning ("VExtractAttr: %s attribute has bad value", name);
return FALSE;
}
/* Clone or hide the value if we're about to delete it: */
if (repn == VStringRepn)
* (VString *) value = VNewString (* (VString *) value);
}
/* Remove it from the list: */
VDeleteAttr (& posn);
return TRUE;
}
/* Otherwise complain if the attribute was a required one: */
if (required)
VWarning ("VExtractAttr: %s attribute missing", name);
return ! required;
}
VGetAttrResult VGetAttr (VAttrList list, VStringConst name,
VDictEntry *dict, VRepnKind repn, VPointer value)
{
VAttrListPosn posn;
/* Look up the attribute name in the list: */
if (! VLookupAttr (list, name, & posn))
return VAttrMissing;
/* Get its value in the specified representation: */
return VGetAttrValue (& posn, dict, repn, value) ?
VAttrFound : VAttrBadValue;
}
void VSetAttr (VAttrList list, VStringConst name,
VDictEntry *dict, VRepnKind repn, ...)
{
va_list args;
VAttrListPosn posn;
VAttrRec *a;
/* Locate any existing attribute of the specified name: */
va_start (args, repn);
if (VLookupAttr (list, name, & posn))
SetAttr (& posn, dict, repn, & args);
else {
/* None exists -- append a new attribute of that name: */
a = NewAttr (name, dict, repn, & args);
a->next = NULL;
if (a->prev = list->prev)
a->prev->next = a;
else list->next = a;
list->prev = a;
}
va_end (args);
}
static VBoolean ReadData (FILE *f, VAttrList list, VReadFileFilterProc *filter, long *offset)
{
VAttrListPosn posn, subposn;
VAttrList sublist;
VBundle b;
VRepnKind repn;
VBoolean read_data, data_found, length_found;
VLong data, length;
VTypeMethods *methods;
VPointer value;
for (VFirstAttr (list, & posn); VAttrExists (& posn); VNextAttr (& posn)) {
switch (VGetAttrRepn (& posn)) {
case VAttrListRepn:
/* Recurse on nested attribute list: */
VGetAttrValue (& posn, NULL, VAttrListRepn, & sublist);
if (! ReadData (f, sublist, filter, offset))
return FALSE;
break;
case VBundleRepn:
VGetAttrValue (& posn, NULL, VBundleRepn, & b);
repn = VLookupType (b->type_name);
/* If a filter routine was supplied, ask it whether to bother
with the binary data: */
read_data = ! filter || (*filter) (b, repn);
/* Extract any data and length attributes in the object's value: */
data_found = VLookupAttr (b->list, VDataAttr, & subposn);
if (data_found) {
if (! VGetAttrValue (& subposn, NULL, VLongRepn, & data)) {
VWarning ("VReadFile: "
"%s attribute's data attribute incorrect",
VGetAttrName (& posn));
return FALSE;
}
VDeleteAttr (& subposn);
}
length_found = VLookupAttr (b->list, VLengthAttr, & subposn);
if (length_found) {
if (! VGetAttrValue (& subposn, NULL, VLongRepn, & length)) {
VWarning ("VReadFile: "
"%s attribute's length attribute incorrect",
VGetAttrName (& posn));
return FALSE;
}
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;
}
/* Read the binary data associated with the object: */
if (data_found) {
if (data < *offset) {
VWarning ("VReadFile: "
"%s attribute's data attribute incorrect",
VGetAttrName (& posn));
return FALSE;
}
if (! read_data)
data += length;
/* To seek forward to the start of the data block we first
try fseek. That will fail on a pipe, in which case we
seek by reading. */
if (data != *offset &&
fseek (f, (long) data - *offset, SEEK_CUR) == -1 &&
errno == ESPIPE &&
! MySeek (f, data - *offset)) {
VSystemWarning ("VReadFile: Seek within file failed");
return FALSE;
}
if (read_data) {
b->data = VMalloc (b->length = length);
if (fread (b->data, 1, length, f) != length) {
VWarning ("VReadFile: Read from stream failed");
return FALSE;
}
*offset = data + length;
} else
/* bug: read error occured when bundle was not read
by a filter function. FK 24/03/98 */
*offset = data;
}
/* Recurse to read binary data for sublist attributes: */
if (! ReadData (f, b->list, filter, offset))
return FALSE;
/* If the object's type is registered and has a decode method,
invoke it to decode the binary data: */
if (read_data && repn != VUnknownRepn &&
(methods = VRepnMethods (repn)) && methods->decode) {
if (! (value = (methods->decode) (VGetAttrName (& posn), b)))
return FALSE;
/* Replace the old typed value with the newly decoded one: */
VSetAttrValue (& posn, NULL, repn, value);
VDestroyBundle (b);
}
break;
default:
break;
}
}
return TRUE;
}
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;
}
