linse/sics
0
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
9388b5941d288e93ecd61cbf796b5130a6a1b45d
sics/nxio.c

748 lines
18 KiB
C
Raw Blame History

/**
* This file contains functions necessary to perform XML-I/O for
* NeXus with the mxml-library.
*
* Most notably it contains the callback function for reading and
* writing data
*
* Copyright (C) 2004 Mark Koennecke
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this library; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
* For further information, see <http://www.nexusformat.org>
*/
#ifdef NXXML
#include <mxml.h>
#include <assert.h>
#include "napi.h"
#include "nxio.h"
#include "nxdataset.h"
#include "napiconfig.h"
/* fix for mxml-2.3 */
#ifndef MXML_WRAP
#define MXML_WRAP 79
#endif
#ifdef _MSC_VER
#define snprintf _snprintf
#endif /* _MSC_VER */
/* #define TESTMAIN 1 */
/*=================== type code handling ================================= */
typedef struct {
char name[30];
char format[30];
int nx_type;
}type_code;
#define NTYPECODE 11
static type_code typecode[NTYPECODE];
/*-----------------------------------------------------------------------*/
void initializeNumberFormats(){
type_code myCode;
strcpy(myCode.name,"NX_FLOAT32");
strcpy(myCode.format,"%12.4f");
myCode.nx_type = NX_FLOAT32;
typecode[0] = myCode;
strcpy(myCode.name,"NX_FLOAT64");
strcpy(myCode.format,"%16.5f");
myCode.nx_type = NX_FLOAT64;
typecode[1] = myCode;
strcpy(myCode.name,"NX_INT8");
strcpy(myCode.format,"%5d");
myCode.nx_type = NX_INT8;
typecode[2] = myCode;
strcpy(myCode.name,"NX_UINT8");
strcpy(myCode.format,"%5d");
myCode.nx_type = NX_UINT8;
typecode[3] = myCode;
strcpy(myCode.name,"NX_INT16");
strcpy(myCode.format,"%8d");
myCode.nx_type = NX_INT16;
typecode[4] = myCode;
strcpy(myCode.name,"NX_UINT16");
strcpy(myCode.format,"%8d");
myCode.nx_type = NX_UINT16;
typecode[5] = myCode;
strcpy(myCode.name,"NX_INT32");
strcpy(myCode.format,"%12d");
myCode.nx_type = NX_INT32;
typecode[6] = myCode;
strcpy(myCode.name,"NX_UINT32");
strcpy(myCode.format,"%12d");
myCode.nx_type = NX_UINT32;
typecode[7] = myCode;
strcpy(myCode.name,"NX_INT64");
strcpy(myCode.format,"%24lld");
myCode.nx_type = NX_INT64;
typecode[8] = myCode;
strcpy(myCode.name,"NX_UINT64");
strcpy(myCode.format,"%24llu");
myCode.nx_type = NX_UINT64;
typecode[9] = myCode;
strcpy(myCode.name,"NX_CHAR");
strcpy(myCode.format,"%c");
myCode.nx_type = NX_CHAR;
typecode[10] = myCode;
}
/*----------------------------------------------------------------------*/
void setNumberFormat(int nx_type, char *format){
int i;
for(i = 0; i < NTYPECODE; i++){
if(typecode[i].nx_type == nx_type){
strncpy(typecode[i].format,format,29);
}
}
}
/*------------------------------------------------------------------*/
static void getNumberFormat(int nx_type, char format[30]){
int i;
for(i = 0; i < NTYPECODE; i++){
if(typecode[i].nx_type == nx_type){
strncpy(format,typecode[i].format,29);
}
}
}
/*----------------------------------------------------------------*/
void getNumberText(int nx_type, char *typestring, int typeLen){
int i;
for(i = 0; i < NTYPECODE; i++){
if(typecode[i].nx_type == nx_type){
strncpy(typestring,typecode[i].name,typeLen);
}
}
}
/*
* 'mxml_add_char()' - Add a character to a buffer, expanding as needed.
* copied here from mxml-file.c to achieve compatibility with mxml-2.1
* standard
*/
static int /* O - 0 on success, -1 on error */
myxml_add_char(int ch, /* I - Character to add */
char **bufptr, /* IO - Current position in buffer */
char **buffer, /* IO - Current buffer */
size_t *bufsize) /* IO - Current buffer size */
{
char *newbuffer; /* New buffer value */
if (*bufptr >= (*buffer + *bufsize - 4))
{
/*
* Increase the size of the buffer...
*/
if (*bufsize < 1024)
{
(*bufsize) *= 2;
}
else
{
(*bufsize) *= 3;
(*bufsize) /= 2;
}
newbuffer = (char *)malloc(*bufsize*sizeof(char));
if(!newbuffer){
free(*buffer);
mxml_error("Unable to expand string buffer to %d bytes!", *bufsize);
return (-1);
}
memset(newbuffer,0,*bufsize*sizeof(char));
memcpy(newbuffer,*buffer,*bufptr - *buffer);
free(*buffer);
*bufptr = newbuffer + (*bufptr - *buffer);
*buffer = newbuffer;
}
if (ch < 128)
{
/*
* Single byte ASCII...
*/
*(*bufptr)++ = ch;
}
else if (ch < 2048)
{
/*
* Two-byte UTF-8...
*/
*(*bufptr)++ = 0xc0 | (ch >> 6);
*(*bufptr)++ = 0x80 | (ch & 0x3f);
}
else if (ch < 65536)
{
/*
* Three-byte UTF-8...
*/
*(*bufptr)++ = 0xe0 | (ch >> 12);
*(*bufptr)++ = 0x80 | ((ch >> 6) & 0x3f);
*(*bufptr)++ = 0x80 | (ch & 0x3f);
}
else
{
/*
* Four-byte UTF-8...
*/
*(*bufptr)++ = 0xf0 | (ch >> 18);
*(*bufptr)++ = 0x80 | ((ch >> 12) & 0x3f);
*(*bufptr)++ = 0x80 | ((ch >> 6) & 0x3f);
*(*bufptr)++ = 0x80 | (ch & 0x3f);
}
return (0);
}
/*------------------------------------------------------------------*/
extern char *stptok(char *s, char *tok, size_t toklen, char *brk);
/*=====================================================================
actual stuff for implementing the callback functions
=====================================================================*/
/*
* if passed NX_CHAR, then returns dimension of -1 and the caller
* needs to do a strlen() or equivalent
*/
void analyzeDim(const char *typeString, int *rank,
int64_t *iDim, int *type){
char dimString[132];
char dim[20];
const char *dimStart, *dimEnd;
char* dimTemp;
int myRank;
if(strchr(typeString,(int)'[') == NULL){
*rank = 1;
switch(*type){
case NX_INT8:
case NX_UINT8:
case NX_INT16:
case NX_UINT16:
case NX_INT32:
case NX_UINT32:
case NX_INT64:
case NX_UINT64:
case NX_FLOAT32:
case NX_FLOAT64:
iDim[0] = 1;
break;
case NX_CHAR:
iDim[0] = -1; /* length unknown, caller needs to determine later */
break;
default:
mxml_error("ERROR: (analyzeDim) unknown type code %d for typeString %s", *type, typeString);
break;
}
} else {
/*
we have to determine rank and the dims.
Start by extracting the dimension string.
*/
dimStart = strchr(typeString,(int)'[') + 1;
dimEnd = strchr(typeString,(int)']');
if(!dimStart || !dimEnd) {
mxml_error("ERROR: malformed dimension string in %s",typeString);
return;
}
if((dimEnd - dimStart) > 131){
mxml_error("ERROR: run away dimension definition in %s",typeString);
return;
}
memset(dimString,0,132);
memcpy(dimString,dimStart,(dimEnd-dimStart)*sizeof(char));
dimTemp = stptok(dimString,dim,19,",");
myRank = 0;
while(dimTemp != NULL){
iDim[myRank] = atoi(dim);
dimTemp = stptok(dimTemp,dim,19,",");
myRank++;
}
*rank = myRank;
}
}
/*--------------------------------------------------------------------*/
int translateTypeCode(const char *code){
int i, result = -1;
for(i = 0; i < NTYPECODE; i++){
if(strstr(code,typecode[i].name) != NULL){
result = typecode[i].nx_type;
break;
}
}
return result;
}
/*
* This is used to locate an Idims node from the new style table data layout
*/
static mxml_node_t* findDimsNode(mxml_node_t *node)
{
mxml_node_t *tnode = NULL;
const char* name = node->value.element.name;
if ( (node->parent != NULL) && !strcmp(node->parent->value.element.name, DATA_NODE_NAME) )
{
tnode = mxmlFindElement(node->parent->parent, node->parent->parent, DIMS_NODE_NAME, NULL, NULL, MXML_DESCEND_FIRST);
if (tnode != NULL)
{
tnode = mxmlFindElement(tnode,tnode,name,NULL,NULL,MXML_DESCEND_FIRST);
}
}
return tnode;
}
/*---------------------------------------------------------------------*/
/*return 1 if in table mode , 0 if not */
static void analyzeDataType(mxml_node_t *parent, int *rank, int *type,
int64_t *iDim){
const char *typeString;
mxml_node_t* tnode;
int nx_type = -1;
int table_mode = 0;
*rank = 1;
*type = NX_CHAR;
iDim[0] = -1;
/*
get the type attribute. No attribute means: plain text
*/
tnode = findDimsNode(parent);
if (tnode != NULL)
{
table_mode = 1;
parent = tnode;
}
typeString = mxmlElementGetAttr(parent,TYPENAME);
if(typeString == NULL){
return;
}
nx_type = translateTypeCode((char *)typeString);
/*
assign type
*/
if(nx_type == -1){
mxml_error(
"ERROR: %s is an invalid NeXus type, I try to continue but may fail",
typeString);
*type =NX_CHAR;
return;
}
*type = nx_type;
analyzeDim(typeString, rank, iDim, type);
if (table_mode)
{
*rank = 1;
iDim[0] = 1;
}
return;
}
/*-------------------------------------------------------------------*/
void destroyDataset(void *data){
if(data != NULL){
dropNXDataset((pNXDS)data);
}
}
/*-------------------------------------------------------------------*/
static char *getNextNumber(char *pStart, char pNumber[80]){
int charCount = 0;
pNumber[0] = '\0';
/* advance to first digit */
while(isspace(*pStart) && *pStart != '\0'){
pStart++;
}
if(*pStart == '\0'){
return NULL;
}
/* copy */
while(!isspace(*pStart) && *pStart != '\0' && charCount < 78){
pNumber[charCount] = *pStart;
pStart++;
charCount++;
}
pNumber[charCount] = '\0';
return pStart;
}
/*--------------------------------------------------------------------*/
mxml_type_t nexusTypeCallback(mxml_node_t *parent){
const char *typeString;
if(strstr(parent->value.element.name,"?xml") != NULL ||
!strncmp(parent->value.element.name,"NX",2) ||
!strcmp(parent->value.element.name,DATA_NODE_NAME) ||
!strcmp(parent->value.element.name,DIMS_NODE_NAME)){
return MXML_ELEMENT;
} else {
/* data nodes do not habe TYPENAME in table style but are always CUSTOM */
if (parent->parent != NULL && !strcmp(parent->parent->value.element.name, DATA_NODE_NAME))
{
return MXML_CUSTOM;
}
if (parent->parent != NULL && !strcmp(parent->parent->value.element.name, DIMS_NODE_NAME))
{
return MXML_OPAQUE;
}
typeString = mxmlElementGetAttr(parent,TYPENAME);
if(typeString == NULL){
/*
MXML_TEXT seems more appropriate here. But mxml hacks text into
single words which is not what NeXus wants.
*/
return MXML_OPAQUE;
} else{
if(strstr(typeString,"NX_CHAR") != NULL){
return MXML_OPAQUE;
} else {
return MXML_CUSTOM;
}
}
}
}
/*----------------------------------------------------------------------*/
int nexusLoadCallback(mxml_node_t *node, const char *buffer){
mxml_node_t *parent = NULL;
int rank, type;
int64_t iDim[NX_MAXRANK];
char pNumber[80], *pStart;
long address, maxAddress;
pNXDS dataset = NULL;
parent = node->parent;
analyzeDataType(parent,&rank,&type,iDim);
if(iDim[0] == -1 || !strcmp(parent->parent->value.element.name, DIMS_NODE_NAME)){
iDim[0] = strlen(buffer);
node->value.custom.data = strdup(buffer);
node->value.custom.destroy = free;
return 0;
} else {
node->value.custom.data = createNXDataset(rank,type,iDim);
dataset = (pNXDS)node->value.custom.data;
if(dataset == NULL){
mxml_error("Failed to allocate custom dataset");
return 1;
}
node->value.custom.destroy = destroyDataset;
}
/*
load data
*/
pStart = (char *)buffer;
maxAddress = getNXDatasetLength(dataset);
address = 0;
while( (pStart = getNextNumber(pStart,pNumber)) != NULL &&
address < maxAddress){
putNXDatasetValueAt(dataset,address,atof(pNumber));
address++;
}
return 0;
}
/*---------------------------------------------------------------------*/
static void stringIntoBuffer(char **buffer, char **bufPtr, size_t *bufSize,
char *string){
size_t i;
for(i = 0; i < strlen(string); i++){
myxml_add_char(string[i],bufPtr,buffer,bufSize);
}
}
/*--------------------------------------------------------------------*/
static void formatNumber(double value, char *txt, int txtLen,
char *format, int type){
switch(type){
case NX_INT8:
case NX_UINT8:
case NX_INT16:
case NX_UINT16:
case NX_INT32:
case NX_UINT32:
snprintf(txt,txtLen,format,(int)value);
break;
case NX_INT64:
snprintf(txt,txtLen,format,(int64_t)value);
break;
case NX_UINT64:
snprintf(txt,txtLen,format,(uint64_t)value);
break;
case NX_FLOAT32:
case NX_FLOAT64:
snprintf(txt,txtLen,format,value);
break;
default:
/*assert(0); something is very wrong here */
printf("Problem\n");
break;
}
}
/*--------------------------------------------------------------------*/
static int countDepth(mxml_node_t *node){
int count = 0;
mxml_node_t *cur;
cur = node;
while(cur != NULL){
count++;
cur = cur->parent;
}
count--;
return count;
}
/*---------------------------------------------------------------------*/
char *nexusWriteCallback(mxml_node_t *node){
int type, col;
char pNumber[80], indent[80], format[30];
char *buffer, *bufPtr;
pNXDS dataset;
int currentLen, table_style = 0;
size_t i, bufsize, length;
int is_definition = 0;
/* this is set by nxconvert when making a definiton */
is_definition = (getenv("NX_IS_DEFINITION") != NULL);
if (!strcmp(node->parent->parent->value.element.name, DATA_NODE_NAME))
{
table_style = 1;
}
/*
allocate output buffer
*/
buffer = (char *)malloc(1024*sizeof(char));
if(buffer == NULL){
mxml_error("Unable to allocate buffer");
return NULL;
}
memset(buffer,0,1024);
bufPtr = buffer;
bufsize = 1024;
dataset = (pNXDS)node->value.custom.data;
/*
prepare indentation level
*/
col = countDepth(node)*2;
memset(indent,0,80);
for(i = 0; i < col; i++){
indent[i] = ' ';
}
/*
get dataset info
*/
type = getNXDatasetType(dataset);
if (is_definition) {
length = 1;
} else {
length = getNXDatasetLength(dataset);
}
if(dataset->format != NULL){
strcpy(format,dataset->format);
} else {
getNumberFormat(type,format);
}
/*
actually get the data out
*/
if (table_style)
{
for(i = 0; i < length; i++){
formatNumber(getNXDatasetValueAt(dataset,i),pNumber,79,format,type);
stringIntoBuffer(&buffer,&bufPtr,&bufsize,pNumber);
}
}
else
{
currentLen = col;
myxml_add_char('\n',&bufPtr,&buffer,&bufsize);
stringIntoBuffer(&buffer,&bufPtr,&bufsize,indent);
for(i = 0; i < length; i++){
formatNumber(getNXDatasetValueAt(dataset,i),pNumber,79,format,type);
if(currentLen + strlen(pNumber) > MXML_WRAP){
/*
wrap line
*/
myxml_add_char('\n',&bufPtr,&buffer,&bufsize);
stringIntoBuffer(&buffer,&bufPtr,&bufsize,indent);
currentLen = col;
}
stringIntoBuffer(&buffer,&bufPtr,&bufsize,pNumber);
myxml_add_char(' ',&bufPtr,&buffer,&bufsize);
currentLen += strlen(pNumber) + 1;
}
}
myxml_add_char('\0',&bufPtr,&buffer,&bufsize);
return (char *)buffer;
}
/*------------------------------------------------------------------*/
int isDataNode(mxml_node_t *node){
if(mxmlElementGetAttr(node,"name") != NULL){
return 0;
}
if(strcmp(node->value.element.name,"NXroot") == 0){
return 0;
}
if(strcmp(node->value.element.name,DIMS_NODE_NAME) == 0){
return 0;
}
if(strcmp(node->value.element.name,DATA_NODE_NAME) == 0){
return 0;
}
if(strcmp(node->value.element.name,"NAPIlink") == 0){
return 0;
}
return 1;
}
/*--------------------------------------------------------------------*/
static int isTextData(mxml_node_t *node){
const char *attr = NULL;
if(!isDataNode(node)){
return 0;
}
/*
test datasets
*/
attr = mxmlElementGetAttr(node,TYPENAME);
if(attr == NULL){
return 1;
}
if(strstr(attr,"NX_CHAR") != NULL){
return 1;
} else {
return 0;
}
}
/*---------------------------------------------------------------------*/
/*
* note: not reentrant or thead safe; returns pointer to static storage
*/
const char *NXwhitespaceCallback(mxml_node_t *node, int where){
static char *indent = NULL;
int len;
if(strstr(node->value.element.name,"?xml") != NULL){
return NULL;
}
if (node->parent != NULL && !strcmp(node->parent->value.element.name, DATA_NODE_NAME))
{
return NULL;
}
if (where == MXML_WS_BEFORE_CLOSE && !strcmp(node->value.element.name, DATA_NODE_NAME))
{
return NULL;
}
if(isTextData(node)){
if(where == MXML_WS_BEFORE_OPEN){
len = countDepth(node)*2 + 2;
if (indent != NULL)
{
free(indent);
indent = NULL;
}
indent = (char *)malloc(len*sizeof(char));
if(indent != NULL){
memset(indent,' ',len);
indent[0]= '\n';
indent[len-1] = '\0';
return (const char*)indent;
}
}
return NULL;
}
if(where == MXML_WS_BEFORE_OPEN || where == MXML_WS_BEFORE_CLOSE){
len = countDepth(node)*2 + 2;
if (indent != NULL)
{
free(indent);
indent = NULL;
}
indent = (char *)malloc(len*sizeof(char));
if(indent != NULL){
memset(indent,' ',len);
indent[0]= '\n';
indent[len-1] = '\0';
return (const char*)indent;
}
}
return NULL;
}
/*-----------------------------------------------------------------------*/
#ifdef TESTMAIN
#include <stdio.h>
int main(int argc, char *argv[]){
mxml_node_t *root = NULL;
FILE *f;
mxmlSetCustomHandlers(nexusLoadCallback, nexusWriteCallback);
initializeNumberFormats();
/*
read test
*/
f = fopen("dmc.xml","r");
root = mxmlLoadFile(NULL,f,nexusTypeCallback);
fclose(f);
/*
write test
*/
setNumberFormat(NX_INT32,"%8d");
setNumberFormat(NX_FLOAT32,"%8.2f");
f = fopen("dmc2.xml","w");
mxmlSaveFile(root,f,NXwhitespaceCallback);
fclose(f);
}
#endif
#endif /*NXXML*/
Reference in New Issue View Git Blame Copy Permalink