Cardinal
Urm__SwapRGMCallbackDesc (RGMCallbackDescPtr callb_desc,
RGMWidgetRecordPtr widget_rec)
{
Cardinal ndx; /* inner loop index */
RGMResourceDescPtr res_desc; /* resource description literal */
char err_msg[300];
swapbytes( callb_desc->validation );
swapbytes( callb_desc->count );
swapbytes( callb_desc->annex );
swapbytes( callb_desc->unres_ref_count );
for (ndx=0 ; ndx < callb_desc->count ; ndx++)
{
#ifdef WORD64
swap4bytes( callb_desc->item[ndx].cb_item.routine );
swap4bytes( callb_desc->item[ndx].cb_item.rep_type );
#else
swap2bytes( callb_desc->item[ndx].cb_item.routine );
swap2bytes( callb_desc->item[ndx].cb_item.rep_type );
#endif
switch (callb_desc->item[ndx].cb_item.rep_type)
{
case MrmRtypeInteger:
case MrmRtypeBoolean:
swapbytes( callb_desc->item[ndx].cb_item.datum.ival );
break;
case MrmRtypeSingleFloat:
swapbytes( callb_desc->item[ndx].cb_item.datum.ival );
_MrmOSIEEEFloatToHost((float *)
&(callb_desc->item[ndx].cb_item.datum.ival));
case MrmRtypeNull:
break;
case MrmRtypeResource:
swapbytes( callb_desc->item[ndx].cb_item.datum.offset );
res_desc = (RGMResourceDesc *)
((char *)widget_rec + callb_desc->item[ndx].cb_item.datum.offset);
Urm__SwapRGMResourceDesc( res_desc );
/* flag this resource as needing further byte swapping */
res_desc->cvt_type |= MrmResourceUnswapped;
break;
default:
swapbytes( callb_desc->item[ndx].cb_item.datum.offset );
sprintf(err_msg, _MrmMMsg_0021,
callb_desc->item[ndx].cb_item.rep_type, ndx);
return Urm__UT_Error ("Urm__SwapRGMCallbackDesc",
err_msg, NULL, NULL, MrmFAILURE) ;
break;
}
}
return MrmSUCCESS;
}
void zaio_endian_(uint32_t aa[], uint32_t *nn) {
uint32_t ii;
for( ii=0; ii<*nn; ii++ ) {
aa[ii] = swap4bytes ( aa[ii] );
}
return;
}
Cardinal
Urm__SwapRGMResourceDesc (RGMResourceDescPtr res_desc)
{
IDBridDesc *idb_rid_ptr;
swapbytes( res_desc->size );
swapbytes( res_desc->annex1 );
if ( res_desc->type == URMrRID )
{
idb_rid_ptr = (IDBridDesc *)&(res_desc->key.id);
#ifdef WORD64
swap4bytes( idb_rid_ptr->internal_id.map_rec );
swap4bytes( idb_rid_ptr->internal_id.res_index );
#else
swap2bytes( idb_rid_ptr->internal_id.map_rec );
swap2bytes( idb_rid_ptr->internal_id.res_index );
#endif
}
return MrmSUCCESS;
}
char *readTiff3DFile2Buffer ( void *fhandler, unsigned char *img, unsigned int img_width, unsigned int img_height, unsigned int first, unsigned int last, int b_swap ) {
uint32 rps;
uint16 spp, bpp, photo, comp, planar_config;
int check, StripsPerImage,LastStripSize;
TIFF *input = (TIFF *) fhandler;
check=TIFFGetField(input, TIFFTAG_ROWSPERSTRIP, &rps);
if (!check)
{
return ((char *) "Image length of undefined.");
}
//rps=600;
check=TIFFGetField(input, TIFFTAG_BITSPERSAMPLE, &bpp);
if (!check)
{
return ((char *) "Undefined bits per sample.");
}
check=TIFFGetField(input, TIFFTAG_SAMPLESPERPIXEL, &spp);
if (!check)
{
return ((char *) "Undefined samples per pixel.");
}
check=TIFFGetField(input, TIFFTAG_PHOTOMETRIC, &photo);
if (!check)
{
return ((char *) "Cannot determine photometric interpretation.");
}
check=TIFFGetField(input, TIFFTAG_COMPRESSION, &comp);
if (!check)
{
return ((char *) "Cannot determine compression technique.");
}
check=TIFFGetField(input, TIFFTAG_PLANARCONFIG, &planar_config);
if (!check)
{
return ((char *) "Cannot determine planar configuration.");
}
StripsPerImage = (img_height + rps - 1) / rps;
LastStripSize = img_height % rps;
if (LastStripSize==0)
LastStripSize=rps;
check=TIFFSetDirectory(input, first);
if (!check)
{
return ((char *) "Cannot open the requested first strip.");
}
unsigned char *buf = img;
int page=0;
do{
for (int i=0; i < StripsPerImage-1; i++){
if (comp==1) {
TIFFReadRawStrip(input, i, buf, spp * rps * img_width * (bpp/8));
buf = buf + spp * rps * img_width * (bpp/8);
}
else{
TIFFReadEncodedStrip(input, i, buf, spp * rps * img_width * (bpp/8));
buf = buf + spp * rps * img_width * (bpp/8);
}
}
if (comp==1) {
TIFFReadRawStrip(input, StripsPerImage-1, buf, spp * LastStripSize * img_width * (bpp/8));
}
else{
TIFFReadEncodedStrip(input, StripsPerImage-1, buf, spp * LastStripSize * img_width * (bpp/8));
}
buf = buf + spp * LastStripSize * img_width * (bpp/8);
page++;
}while ( page < static_cast<int>(last-first+1) && TIFFReadDirectory(input));//while (TIFFReadDirectory(input));
// input file is assumedo ti be already open and it is provided as an handler; the file should be closed by caller
//TIFFClose(input);
if ( page < static_cast<int>(last-first+1) ){
return ((char *) "Cannot read all the pages.");
}
// swap the data bytes if necessary
if (b_swap)
{
int i;
size_t total = img_width * img_height * spp * (last-first+1);
if (bpp/8 == 2)
{
for (i=0;i<total; i++)
{
swap2bytes((void *)(img+2*i));
}
}
else if (bpp/8 == 4)
{
for (i=0;i<total; i++)
{
swap4bytes((void *)(img+4*i));
}
}
}
return (char *) 0;
}
int loadRaw2Stack(char * filename, unsigned char ** img, long ** sz, int datatype) //this is the function of 4-byte raw format.
{
/* This function reads 2-4D image stack from raw data generated by the program "saveStack2Raw.m". */
/* The input parameters img, sz, and datatype should be empty, especially the pointers "img" and "sz". */
int berror = 0;
FILE * fid = fopen(filename, "rb");
if (!fid)
{
printf("Fail to open file for reading.\n");
berror = 1;
return berror;
}
fseek (fid, 0, SEEK_END);
long fileSize = ftell(fid);
rewind(fid);
/* Read header */
char formatkey[] = "raw_image_stack_by_hpeng";
long lenkey = strlen(formatkey);
if (fileSize<lenkey+2+4*4+1) // datatype has 2 bytes, and sz has 4*4 bytes and endian flag has 1 byte.
{
printf("The size of your input file is too small and is not correct, -- it is too small to contain the legal header.\n");
printf("The fseek-ftell produces a file size = %ld.", fileSize);
berror = 1;
return berror;
}
char * keyread = (char*)Guarded_Malloc((lenkey+1)*sizeof(char), Program_Name());
if (!keyread)
{
printf("Fail to allocate memory.\n");
berror = 1;
return berror;
}
long nread = fread(keyread, 1, lenkey, fid);
if (nread!=lenkey)
{
printf("File unrecognized or corrupted file.\n");
berror = 1;
return berror;
}
keyread[lenkey] = '\0';
long i;
if (strcmp(formatkey, keyread)) /* is non-zero then the two strings are different */
{
printf("Unrecognized file format.\n");
if (keyread) {free(keyread); keyread=0;}
berror = 1;
return berror;
}
char endianCodeData;
fread(&endianCodeData, 1, 1, fid);
if (endianCodeData!='B' && endianCodeData!='L')
{
printf("This program only supports big- or little- endian but not other format. Check your data endian.\n");
berror = 1;
if (keyread) {free(keyread); keyread=0;}
return berror;
}
char endianCodeMachine;
endianCodeMachine = checkMachineEndian();
if (endianCodeMachine!='B' && endianCodeMachine!='L')
{
printf("This program only supports big- or little- endian but not other format. Check your data endian.\n");
berror = 1;
if (keyread) {free(keyread); keyread=0;}
return berror;
}
int b_swap = (endianCodeMachine==endianCodeData)?0:1;
printf("machine endian=[%c] data endian=[%c] b_swap=%d\n", endianCodeMachine, endianCodeData, b_swap);
short int dcode = 0;
fread(&dcode, 2, 1, fid); /* because I have already checked the file size to be bigger than the header, no need to check the number of actual bytes read. */
if (b_swap)
swap2bytes((void *)&dcode);
switch (dcode)
{
case 1:
datatype = 1; /* temporarily I use the same number, which indicates the number of bytes for each data point (pixel). This can be extended in the future. */
break;
case 2:
datatype = 2;
break;
case 4:
datatype = 4;
break;
default:
printf("Unrecognized data type code [%d]. The file type is incorrect or this code is not supported in this version.\n", dcode);
if (keyread) {free(keyread); keyread=0;}
berror = 1;
return berror;
}
long unitSize = datatype; // temporarily I use the same number, which indicates the number of bytes for each data point (pixel). This can be extended in the future.
printf("loadRaw2Stack unitSize=%d\n", unitSize);
unsigned int mysz[4];
mysz[0]=mysz[1]=mysz[2]=mysz[3]=0;
int tmpn=fread(mysz, 4, 4, fid); // because I have already checked the file size to be bigger than the header, no need to check the number of actual bytes read.
if (tmpn!=4)
{
printf("This program only reads [%d] units.\n", tmpn);
berror=1;
return berror;
}
if (b_swap)
{
for (i=0;i<4;i++)
{
//swap2bytes((void *)(mysz+i));
printf("mysz raw read unit[%ld]: [%d] ", i, mysz[i]);
swap4bytes((void *)(mysz+i));
printf("swap unit: [%d][%0x] \n", mysz[i], mysz[i]);
}
}
if (*sz) {free(*sz); *sz=0;}
*sz=(long*)Guarded_Malloc(4*sizeof(long), Program_Name());
if (!(*sz))
{
printf("Fail to allocate memory.\n");
if (keyread) {free(keyread); keyread=0;}
berror = 1;
return berror;
}
long totalUnit = 1;
for (i=0;i<4;i++)
{
(*sz)[i] = (long)mysz[i];
totalUnit *= (*sz)[i];
}
//mexPrintf("The input file has a size [%ld bytes], different from what specified in the header [%ld bytes]. Exit.\n", fileSize, totalUnit*unitSize+4*4+2+1+lenkey);
//mexPrintf("The read sizes are: %ld %ld %ld %ld\n", sz[0], sz[1], sz[2], sz[3]);
if ((totalUnit*unitSize+4*4+2+1+lenkey) != fileSize)
{
printf("The input file has a size [%ld bytes], different from what specified in the header [%ld bytes]. Exit.\n", fileSize, totalUnit*unitSize+4*4+2+1+lenkey);
printf("The read sizes are: %ld %ld %ld %ld\n", (*sz)[0], (*sz)[1], (*sz)[2], (*sz)[3]);
printf("The read sizes are: %d %d %d %d\n", mysz[0], mysz[1], mysz[2], mysz[3]);
if (keyread) {free(keyread); keyread=0;}
if (*sz) {free(*sz); *sz=0;}
berror = 1;
return berror;
}
if (*img) {free(*img); *img=0;}
long totalBytes = unitSize*totalUnit;
*img = (unsigned char *)Guarded_Malloc(totalBytes*sizeof(unsigned char), Program_Name());
if (*img==0 || *img==NULL)
{
fprintf(stderr, "Fail to allocate memory in loadRaw2Stack().\n");
if (keyread) {free(keyread); keyread=0;}
if (*sz) {free(*sz); *sz=0;}
berror = 1;
return berror;
}
long remainingBytes = totalBytes;
long nBytes2G = 1024L*1024L*1024L*2L;
long cntBuf = 0;
while (remainingBytes>0)
{
long curReadBytes = (remainingBytes<nBytes2G) ? remainingBytes : nBytes2G;
long curReadUnits = curReadBytes/unitSize;
nread = fread(*img+cntBuf*nBytes2G, unitSize, curReadUnits, fid);
if (nread!=curReadUnits)
{
printf("Something wrong in file reading. The program reads [%ld data points] but the file says there should be [%ld data points].\n", nread, totalUnit);
if (keyread) {free(keyread); keyread=0;}
if (*sz) {free(*sz); *sz=0;}
if (*img) {free(*img); *img=0;}
berror = 1;
return berror;
}
remainingBytes -= nBytes2G;
cntBuf++;
}
// swap the data bytes if necessary
if (b_swap==1)
{
if (unitSize==2)
{
for (i=0;i<totalUnit; i++)
{
swap2bytes((void *)(*img+i*unitSize));
}
}
else if (unitSize==4)
{
for (i=0;i<totalUnit; i++)
{
swap4bytes((void *)(*img+i*unitSize));
}
}
}
// clean and return
if (keyread) {free(keyread); keyread = 0;}
fclose(fid); //bug fix on 060412
double min=0.0, max=0.0;
if (datatype==1) {
findMinMax8bit(&min, &max, *img, totalUnit);
} else if (datatype==2) {
findMinMax16bit(&min, &max, *img, totalUnit);
} else if (datatype==4) {
findMinMaxFloat(&min, &max, *img, totalUnit);
}
printf("loadRaw2Stack() Min=%f Max=%f\n", min, max);
return berror;
}
Cardinal
Idb__BM_SwapRecordBytes (IDBRecordBufferPtr buffer)
{
/*
* Local variables
*/
Cardinal ndx; /* loop index */
IDBDummyRecordPtr idb_record; /* pointer to the generic IDB record */
IDBRecordHeaderPtr idb_header; /* pointer to hdr w/type and record # */
IDBHeaderRecordPtr header_rec; /* pointer to record type IDBrtHeader */
IDBHeaderHdrPtr header_hdr; /* pointer to the header in the header */
IDBIndexLeafRecordPtr leaf_rec; /* pointer to record type IDBrtIndexLeaf */
IDBIndexNodeRecordPtr node_rec; /* pointer to record type IDBrtIndexNode */
IDBridMapRecordPtr ridmap_rec; /* pointer to record type IDBrtRIDMap */
IDBDataRecordPtr data_rec; /* pointer to record type IDBrtData */
char err_msg[300] ;
if ( ! Idb__BM_Valid(buffer) )
return Urm__UT_Error("Idb__BM_MarkActivity", _MrmMMsg_0002,
NULL, NULL, MrmNOT_VALID) ;
/* load pointers to the record and record header */
idb_record = (IDBDummyRecordPtr) buffer->IDB_record ;
idb_header = (IDBRecordHeaderPtr)&idb_record->header ;
/* swap the remaining record entries in IDBRecordHeader */
swapbytes( idb_header->record_type ) ;
swapbytes( idb_header->record_num ) ;
/*
* Swap IDB record items based on record type
*/
switch ( idb_header->record_type )
{
case IDBrtHeader:
header_rec = (IDBHeaderRecordPtr)buffer->IDB_record ;
header_hdr = (IDBHeaderHdrPtr)&header_rec->header_hdr ;
/* swap the HeaderHdr first */
swapbytes( header_hdr->index_root );
swapbytes( header_hdr->num_indexed );
swapbytes( header_hdr->num_RID );
/* VAR check */
#ifdef WORD64
swap4bytes( header_hdr->next_RID.internal_id.map_rec );
swap4bytes( header_hdr->next_RID.internal_id.res_index );
#else
swap2bytes( header_hdr->next_RID.internal_id.map_rec );
swap2bytes( header_hdr->next_RID.internal_id.res_index );
#endif
swapbytes( header_hdr->last_record );
swapbytes( header_hdr->last_data_record );
for( ndx=0 ; ndx < URMgVecSize ; ndx++)
swapbytes(header_hdr->group_counts[ndx]);
for( ndx=0 ; ndx < IDBrtVecSize ; ndx++)
swapbytes(header_hdr->rt_counts[ndx]);
/* now swap the rest of the header */
/* VAR check */
for( ndx=0 ; ndx < IDBHeaderRIDMax ; ndx++)
{
swap2bytes(header_rec->RID_pointers[ndx].internal_id.rec_no);
swap2bytes(header_rec->RID_pointers[ndx].internal_id.item_offs);
}
swapbytes( header_rec->num_entry );
swapbytes( header_rec->last_entry );
swapbytes( header_rec->free_ptr );
swapbytes( header_rec->free_count );
break;
case IDBrtIndexLeaf:
leaf_rec = (IDBIndexLeafRecordPtr)buffer->IDB_record ;
swapbytes( leaf_rec->leaf_header.parent );
swapbytes( leaf_rec->leaf_header.index_count );
swapbytes( leaf_rec->leaf_header.heap_start );
swapbytes( leaf_rec->leaf_header.free_bytes );
for( ndx=0 ; ndx < leaf_rec->leaf_header.index_count ; ndx++ )
{
swapbytes( leaf_rec->index[ndx].index_stg );
swap2bytes( leaf_rec->index[ndx].data.internal_id.rec_no );
swap2bytes( leaf_rec->index[ndx].data.internal_id.item_offs );
}
break;
case IDBrtIndexNode:
node_rec = (IDBIndexNodeRecordPtr)buffer->IDB_record ;
swapbytes( node_rec->node_header.parent );
swapbytes( node_rec->node_header.index_count );
swapbytes( node_rec->node_header.heap_start );
swapbytes( node_rec->node_header.free_bytes );
for( ndx=0 ; ndx < node_rec->node_header.index_count ; ndx++ )
{
swapbytes( node_rec->index[ndx].index_stg );
swap2bytes( node_rec->index[ndx].data.internal_id.rec_no );
swap2bytes( node_rec->index[ndx].data.internal_id.item_offs );
swapbytes( node_rec->index[ndx].LT_record );
swapbytes( node_rec->index[ndx].GT_record );
}
break;
case IDBrtRIDMap:
ridmap_rec = (IDBridMapRecordPtr)buffer->IDB_record ;
ndx = 0;
while ( (ndx < IDBridPtrVecMax) &&
(ridmap_rec->pointers[ndx].internal_id.rec_no != 0) )
{
swap2bytes( ridmap_rec->pointers[ndx].internal_id.rec_no );
swap2bytes( ridmap_rec->pointers[ndx].internal_id.item_offs );
ndx++;
}
break;
case IDBrtData:
data_rec = (IDBDataRecordPtr)buffer->IDB_record ;
swapbytes( data_rec->data_header.num_entry );
swapbytes( data_rec->data_header.last_entry );
swapbytes( data_rec->data_header.free_ptr );
swapbytes( data_rec->data_header.free_count );
break;
default:
sprintf(err_msg, _MrmMMsg_0020, idb_header->record_num,
idb_header->record_type);
return Urm__UT_Error ("Idb__BM_SwapRecordBytes",
err_msg, NULL, NULL, MrmFAILURE) ;
}
return MrmSUCCESS ;
}
Cardinal
Urm__SwapRGMWidgetRecord(RGMWidgetRecordPtr widget_rec)
{
/*
* Local variables
*/
RGMArgListDescPtr arg_list; /* pointer to widget arglist */
RGMChildrenDescPtr child_list; /* pointer to the widgets children */
RGMResourceDescPtr res_desc; /* resource description literal */
RGMCallbackDescPtr callb_desc; /* pointer to a callback decriptor */
Cardinal ndx; /* loop index */
IDBridDesc *idb_rid_ptr;
void *offset; /* generic offset pointer */
char err_msg[300];
/* Swap the main part of the widget record */
swapbytes( widget_rec->size );
swapbytes( widget_rec->access );
swapbytes( widget_rec->lock );
swapbytes( widget_rec->type );
swapbytes( widget_rec->name_offs );
swapbytes( widget_rec->class_offs );
swapbytes( widget_rec->arglist_offs );
swapbytes( widget_rec->children_offs );
swapbytes( widget_rec->comment_offs );
swapbytes( widget_rec->creation_offs );
swapbytes( widget_rec->variety );
swapbytes( widget_rec->annex );
/* handle the argument list */
if (widget_rec->arglist_offs > 0)
{
arg_list = (RGMArgListDesc *)
((char *)widget_rec + widget_rec->arglist_offs);
swapbytes( arg_list->count );
swapbytes( arg_list->extra );
for ( ndx=0 ; ndx<arg_list->count ; ndx++ )
{
swapbytes( arg_list->args[ndx].tag_code );
swapbytes( arg_list->args[ndx].stg_or_relcode.tag_offs );
swapbytes( arg_list->args[ndx].arg_val.rep_type );
switch( arg_list->args[ndx].arg_val.rep_type )
{
case MrmRtypeInteger:
case MrmRtypeBoolean:
swapbytes( arg_list->args[ndx].arg_val.datum.ival );
break;
case MrmRtypeSingleFloat:
swapbytes( arg_list->args[ndx].arg_val.datum.ival );
_MrmOSIEEEFloatToHost((float *)
&(arg_list->args[ndx].arg_val.datum.ival));
default:
swapbytes( arg_list->args[ndx].arg_val.datum.offset );
break;
}
offset = ((char *)widget_rec+
arg_list->args[ndx].arg_val.datum.offset);
switch( arg_list->args[ndx].arg_val.rep_type )
{
/* these are immediate, do nothing special */
case MrmRtypeInteger:
case MrmRtypeBoolean:
case MrmRtypeSingleFloat:
break;
/* these are offsets into the file, handle them specially */
case MrmRtypeCallback:
callb_desc = (RGMCallbackDesc * )offset;
Urm__SwapRGMCallbackDesc( callb_desc, widget_rec );
break;
case MrmRtypeResource:
res_desc = (RGMResourceDesc *)offset;
Urm__SwapRGMResourceDesc( res_desc );
/* flag this resource as needing further byte swapping */
res_desc->cvt_type |= MrmResourceUnswapped;
break;
case MrmRtypeHorizontalInteger:
case MrmRtypeVerticalInteger:
case MrmRtypeHorizontalFloat:
case MrmRtypeVerticalFloat:
case MrmRtypeChar8:
case MrmRtypeChar8Vector:
case MrmRtypeCString:
case MrmRtypeCStringVector:
case MrmRtypeFloat:
case MrmRtypePixmapImage:
case MrmRtypePixmapDDIF:
case MrmRtypeNull:
case MrmRtypeAddrName:
case MrmRtypeIconImage:
case MrmRtypeFont:
case MrmRtypeFontList:
case MrmRtypeColor:
case MrmRtypeColorTable:
case MrmRtypeAny:
case MrmRtypeTransTable:
case MrmRtypeClassRecName:
case MrmRtypeIntegerVector:
case MrmRtypeXBitmapFile:
case MrmRtypeCountedVector:
case MrmRtypeKeysym:
case MrmRtypeWideCharacter:
case MrmRtypeFontSet:
sprintf(err_msg,_MrmMMsg_0022,
arg_list->args[ndx].arg_val.rep_type);
return Urm__UT_Error ("Urm__SwapRGMWidgetRecord",
err_msg, NULL, NULL, MrmFAILURE) ;
break;
}
}
}
/* handle the child list */
if (widget_rec->children_offs > 0)
{
child_list = (RGMChildrenDesc *)
((char *)widget_rec + widget_rec->children_offs);
swapbytes( child_list->count );
swapbytes( child_list->unused1 );
swapbytes( child_list->annex1 );
for ( ndx=0 ; ndx<child_list->count ; ndx++ )
{
swapbytes( child_list->child[ndx].annex1 );
if (child_list->child[ndx].type == URMrRID )
{
idb_rid_ptr = (IDBridDesc *)&(child_list->child[ndx].key.id);
#ifdef WORD64
swap4bytes( idb_rid_ptr->internal_id.map_rec );
swap4bytes( idb_rid_ptr->internal_id.res_index );
#else
swap2bytes( idb_rid_ptr->internal_id.map_rec );
swap2bytes( idb_rid_ptr->internal_id.res_index );
#endif
}
else
swapbytes( child_list->child[ndx].key.index_offs );
}
}
/* handle the creation callback, if any */
if (widget_rec->creation_offs > 0)
{
callb_desc = (RGMCallbackDesc * )
((char *)widget_rec + widget_rec->creation_offs);
Urm__SwapRGMCallbackDesc( callb_desc, widget_rec );
}
return MrmSUCCESS ;
}
