static VAttrList VGraphEncodeAttrMethod (VPointer value, size_t *lengthp)
{
VGraph graph = value;
VAttrList list;
size_t len, nadj;
int i, slong, sfloat, spriv, nnodes;
VNode n;
VAdjacency adj;
/* Compute the file space needed for the Graph's binary data: */
len = 0;
slong = VRepnPrecision (VLongRepn) / 8;
sfloat = VRepnPrecision (VFloatRepn) / 8;
spriv = graph->nfields * VRepnPrecision (graph->node_repn) / 8;
nnodes = 0;
for (i = 1; i <= graph->size; i++) {
n = VGraphGetNode(graph, i); if (n == 0) continue;
++nnodes;
/* Count the number of adjacencies : */
for (adj = n->base.head, nadj = 0; adj; adj = adj->next) nadj++;
/* each node contains:
* an index and the number of adjacencies
* the private data area
* the list of adjacencies
* optionally reserve space for weights
*/
len += 2 * slong + nadj * slong + spriv;
if (graph->useWeights) len += (nadj+1) * sfloat;
};
*lengthp = len;
assert(nnodes == graph->nnodes); /* for debugging */
graph->nnodes = nnodes; /* just to be safe for now... */
/* Temporarily prepend several attributes to the graph's list: */
if ((list = VGraphAttrList (graph)) == NULL)
list = VGraphAttrList (graph) = VCreateAttrList ();
VPrependAttr (list, VRepnAttr, VNumericRepnDict,
VLongRepn, (VLong) graph->node_repn);
VPrependAttr (list, VNNodeFieldsAttr, NULL, VLongRepn,
(VLong) graph->nfields);
VPrependAttr (list, VNGraphSizeAttr, NULL, VLongRepn,
(VLong) graph->size);
VPrependAttr (list, VNNodeWeightsAttr, NULL, VLongRepn,
(VLong) graph->useWeights);
return list;
}
VBoolean VWriteObjects (FILE *file, VRepnKind repn, VAttrList attributes,
int nobjects, VPointer objects[])
{
VAttrList list;
VAttrListPosn posn;
int i;
VBoolean result;
/* Create an attribute list if none was supplied: */
list = attributes ? attributes : VCreateAttrList ();
/* Prepend to the attribute list an attribute for each object: */
for (i = nobjects - 1; i >= 0; i--)
VPrependAttr (list, VRepnName (repn), NULL, repn, objects[i]);
/* Write the attribute list: */
result = VWriteFile (file, list);
/* Remove the attributes just prepended: */
VFirstAttr (list, & posn);
for (i = 0; i < nobjects; i++)
VDeleteAttr (& posn);
if (list != attributes)
VDestroyAttrList (list);
return result;
}
static VAttrList VImageEncodeAttrMethod (VPointer value, size_t *lengthp)
{
VImage image = value;
VAttrList list;
size_t length;
#define OptionallyPrepend(value, name) \
if (value != 1) \
VPrependAttr (list, name, NULL, VLongRepn, (VLong) value)
/* Temporarily prepend several attributes to the image's attribute list: */
if ((list = VImageAttrList (image)) == NULL)
list = VImageAttrList (image) = VCreateAttrList ();
VPrependAttr (list, VRepnAttr, VNumericRepnDict,
VLongRepn, (VLong) VPixelRepn (image));
VPrependAttr (list, VNColumnsAttr, NULL,
VLongRepn, (VLong) VImageNColumns (image));
VPrependAttr (list, VNRowsAttr, NULL,
VLongRepn, (VLong) VImageNRows (image));
OptionallyPrepend (VImageNComponents (image), VNComponentsAttr);
OptionallyPrepend (VImageNColors (image), VNColorsAttr);
OptionallyPrepend (VImageNViewpoints (image), VNViewpointsAttr);
OptionallyPrepend (VImageNFrames (image), VNFramesAttr);
OptionallyPrepend (VImageNBands (image), VNBandsAttr);
/* Compute the file space needed for the image's binary data: */
length = VImageNPixels (image);
if (VPixelRepn (image) == VBitRepn)
length = (length + 7) / 8;
else length *= VPixelPrecision (image) / 8;
*lengthp = length;
return list;
#undef OptionallyPrepend
}
VBoolean WriteImages (VString Name, VAttrList Images, VAttrList& history_list)
{
FILE* file; /* output file */
VAttrList list; /* attribute list */
VAttrListPosn pos; /* position in list */
VImage image; /* image in list */
VBoolean success; /* success flag */
char history[]="history";
/* open file */
file = fopen (Name, "w");
if (!file)
{
VError ("Failed to open output file '%s'", Name);
return FALSE;
}
/* create list */
list = VCreateAttrList();
/* insert images */
for (VFirstAttr (Images, &pos); VAttrExists (&pos); VNextAttr (&pos))
{
VGetAttrValue (&pos, NULL, VImageRepn, &image);
VAppendAttr (list, VGetAttrName (&pos), NULL, VImageRepn, image);
}
/* Prepend history */
VPrependAttr(list, history ,NULL,VAttrListRepn,history_list);
/* write file */
success = VWriteFile (file, list);
if (!success) VError ("Failed to write output file '%s'", Name);
/* remove images */
for (VFirstAttr (list, &pos); VAttrExists (&pos); VNextAttr (&pos))
if (VGetAttrRepn (&pos) == VImageRepn)
VSetAttrValue (&pos, NULL, VImageRepn, NULL);
/* clean-up*/
VDestroyAttrList (list);
fclose (file);
return success;
} /* WriteImages */
int
main(int argc, char *argv[]) {
static VArgVector in_files;
static VString out_filename;
static VString filename;
static VShort minval = 0;
static VFloat fwhm = 4.0;
static VOptionDescRec options[] = {
{"in", VStringRepn, 0, & in_files, VRequiredOpt, NULL, "Input files" },
{"out", VStringRepn, 1, & out_filename, VRequiredOpt, NULL, "Output file" },
{"design", VStringRepn, 1, (VPointer) &filename, VRequiredOpt, NULL, "Design file"},
{
"fwhm", VFloatRepn, 1, (VPointer) &fwhm, VOptionalOpt, NULL,
"FWHM of temporal Gaussian filter in seconds"
},
{"minval", VShortRepn, 1, (VPointer) &minval, VOptionalOpt, NULL, "Signal threshold"}
};
FILE *fp = NULL, *f = NULL;
VStringConst in_filename;
VString ifilename;
VAttrList list = NULL, list1 = NULL;
VAttrList out_list = NULL, history_list = NULL;
VAttrListPosn posn;
VImage design = NULL;
ListInfo *linfo;
VLong itr = 0;
VFloat sigma = 0, tr = 0;
int i, n, nimages;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vcolorglm V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/*
** parse command line
*/
if(! VParseCommand(VNumber(options), options, & argc, argv)) {
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(EXIT_FAILURE);
}
if(argc > 1) {
VReportBadArgs(argc, argv);
exit(EXIT_FAILURE);
}
/*
** read design matrix
*/
fp = VOpenInputFile(filename, TRUE);
list1 = VReadFile(fp, NULL);
if(! list1)
VError("Error reading design file");
fclose(fp);
n = 0;
for(VFirstAttr(list1, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & design);
if(VPixelRepn(design) != VFloatRepn /* && VPixelRepn(design) != VDoubleRepn */)
continue;
n++;
break;
}
if(n == 0)
VError(" design matrix not found ");
/*
** get pre-coloring info
*/
if(VGetAttr(VImageAttrList(design), "repetition_time", NULL, VLongRepn, &itr) != VAttrFound)
VError(" TR info missing in header");
tr = (float) itr / 1000.0;
sigma = 0;
if(tr > 0.001 && fwhm > 0.001) {
fprintf(stderr, " TR: %.3f seconds\n", tr);
sigma = fwhm / 2.35482;
sigma /= tr;
if(sigma < 0.1) {
VWarning(" 'fwhm/sigma' too small (%.3f / %.3f), will be set to zero", fwhm, sigma);
sigma = 0;
}
}
/*
** Read each input file
*/
nimages = in_files.number;
linfo = (ListInfo *) VMalloc(sizeof(ListInfo) * nimages);
for(i = 0; i < nimages; i++) {
in_filename = ((VStringConst *) in_files.vector)[i];
ifilename = VNewString(in_filename);
fprintf(stderr, " file: %s\n", ifilename);
list = GetListInfo(ifilename, &linfo[i]);
/* Create history */
if(i == 0) {
history_list = VReadHistory(&list);
if(history_list == NULL)
history_list = VCreateAttrList();
VPrependHistory(VNumber(options), options, prg_name, &history_list);
}
}
/*
** GLM
*/
out_list = VRegression(linfo, nimages, minval, design, sigma, itr);
/*
** Output:
*/
VPrependAttr(out_list, "history", NULL, VAttrListRepn, history_list);
f = VOpenOutputFile(out_filename, TRUE);
if(!f)
VError(" error opening outout file %s", out_filename);
if(! VWriteFile(f, out_list))
exit(1);
fprintf(stderr, "%s: done.\n", argv[0]);
return 0;
}
static VBoolean WriteAttr (FILE *f, VAttrListPosn *posn, int indent, VList *data_list, long *offset)
{
int i;
char *str;
VRepnKind repn;
VAttrList sublist;
VBundle b;
DataBlock *db;
VTypeMethods *methods;
size_t length;
VPointer value;
VBoolean result;
VAttrListPosn subposn;
/* Indent by the specified amount: */
for (i = 0; i < indent; i++)
FailTest (fputc ('\t', f));
indent++;
/* Output the attribute's name: */
FailTest (fprintf (f, "%s: ", VGetAttrName (posn)));
/* Ouput its value: */
switch (repn = VGetAttrRepn (posn)) {
case VAttrListRepn:
VGetAttrValue (posn, NULL, VAttrListRepn, (VPointer) & sublist);
result = WriteAttrList (f, sublist, indent, data_list, offset);
break;
case VBundleRepn:
VGetAttrValue (posn, NULL, VBundleRepn, (VBundle) & b);
if (! WriteString (f, b->type_name))
return FALSE;
FailTest (fputc (' ', f));
/* If it's a typed value with binary data... */
if (b->length > 0) {
/* Include "data" and "length" attributes in its attribute list: */
VPrependAttr (b->list, VLengthAttr, NULL, VLongRepn,
(VLong) b->length);
VPrependAttr (b->list, VDataAttr, NULL, VLongRepn,
(VLong) *offset);
/* Add it to the queue of binary data blocks to be written: */
*offset += b->length;
db = VNew (DataBlock);
db->posn = *posn;
db->list = b->list;
db->length = b->length;
VListAppend (*data_list, db);
}
/* Write the typed value's attribute list: */
result = WriteAttrList (f, b->list, indent, data_list, offset);
/* Remove the "data" and "length" attributes added earlier: */
if (b->length > 0) {
VFirstAttr (b->list, & subposn);
VDeleteAttr (& subposn);
VDeleteAttr (& subposn);
}
break;
case VStringRepn:
VGetAttrValue (posn, NULL, VStringRepn, (VPointer) & str);
result = WriteString (f, str);
break;
default:
if (! (methods = VRepnMethods (repn)) ||
! methods->encode_attr || ! methods->encode_data) {
VWarning ("VWriteFile: "
"%s attribute has unwriteable representation: %s",
VGetAttrName (posn), VRepnName (repn));
return FALSE;
}
/* Write the type name: */
if (! WriteString (f, VRepnName (repn)))
return FALSE;
FailTest (fputc (' ', f));
/* Invoke the object type's encode_attr method to obtain an
attribute list: */
VGetAttrValue (posn, NULL, repn, & value);
sublist = (methods->encode_attr) (value, & length);
/* If binary data is indicated... */
if (length > 0) {
/* Include "data" and "length" attributes in the attr list: */
VPrependAttr (sublist, VLengthAttr, NULL, VLongRepn,
(VLong) length);
VPrependAttr (sublist, VDataAttr, NULL, VLongRepn,
(VLong) *offset);
*offset += length;
}
/* Add the object to the queue of binary data blocks to be written: */
db = VNew (DataBlock);
db->posn = *posn;
db->list = sublist;
db->length = length;
VListAppend (*data_list, db);
/* Write the typed value's attribute list: */
result = WriteAttrList (f, sublist, indent, data_list, offset);
/* Remove the "data" and "length" attributes added earlier: */
if (length > 0) {
VFirstAttr (sublist, & subposn);
VDeleteAttr (& subposn);
VDeleteAttr (& subposn);
}
}
/* Output a trailing newline: */
if (result)
FailTest (fputc ('\n', f));
return result;
Fail:
VWarning ("VWriteFile: Write to stream failed");
return FALSE;
}
