//--------------------------------------
// ParseStrainFile
//--------------------------------------
EStrainType ProcessStrainType( const vector< std::string > & Line,
int nLineNumber)
{
if( Line.size() < 2 )
{
std::cerr << "Line " << nLineNumber << std::endl
<< "StrainOpt: Strain Type expects an arguments \n [ Diag | Sym | Asym ]"
<< std::endl;
RUNTIME_ASSERT( 0, " Parsing Strain Optimization File Failed ");
}
EStrainType Method;
for( Size_Type j = 0; j < eNumStrainTypes; j++ )
{
if ( StrainTypeKeywords[j] == Line[1] )
Method = static_cast<EStrainType>( j );
}
if( Method >= eNumStrainTypes )
{
std::cerr << "Line " << nLineNumber << std::endl
<< "StrainOpt: Unknown strain type, choices are [ Diag | Sym | Asym ]"
<< std::endl;
RUNTIME_ASSERT( 0, " Parsing Strain Optimization File Failed ");
}
return Method;
}
//-------------------------------------------------------------------------------------
//
// FindBlocks
//
//-------------------------------------------------------------------------------------
Bool FindBlocks( vector<string> &vBlocks, const string & sBuf )
{
Size_Type nSearchPos = 0;
string::const_iterator pStringIt = sBuf.begin();
while ( nSearchPos < sBuf.size() )
{
Size_Type nStartPos = sBuf.find_first_of( '{', nSearchPos );
Size_Type nEndPos = sBuf.find_first_of( '}', nSearchPos );
RUNTIME_ASSERT( !( nStartPos == string::npos && nEndPos != string::npos ),
"[DetectorFile] ERROR: Invalid Detector Block: { expected\n");
RUNTIME_ASSERT( !( nStartPos != string::npos && nEndPos == string::npos ),
"[DetectorFile] ERROR: Invalid Detector Block: } expected\n");
// if neither are found, then job's finished here
if ( nStartPos == string::npos && nEndPos == string::npos )
{
break;
}
else
{
nSearchPos = nEndPos + 1; // advance search position
string sToInsert( pStringIt + nStartPos + 1, pStringIt + nEndPos );
vBlocks.push_back( sToInsert );
}
}
return ( vBlocks.size() > 0 );
}
//--------------------------------------
// ParseStrainFile
//--------------------------------------
EOptimizationMethod ProcessOptMethod( const vector< std::string > & Line,
int nLineNumber )
{
if( Line.size() < 2 )
{
std::cerr << "Line " << nLineNumber << std::endl
<< "StrainOpt: Optimization Method expects an argument" << std::endl
<< "[ MonteCarlo | ConjugateGradient ]" << std::endl;
RUNTIME_ASSERT( 0, " Parsing Strain Optimization File Failed ");
}
EOptimizationMethod Method;
for( Size_Type j = 0; j < eNumOptimizationMethods; j++ )
{
if ( OptMethodKeywords[j] == Line[1] )
Method = static_cast<EOptimizationMethod>( j );
}
if( Method >= eNumOptimizationMethods )
{
std::cerr << "Line " << nLineNumber << std::endl
<< "StrainOpt: Unknown strain optimization method, choices are [ MonteCarlo | ConjugateGradient ]"
<< std::endl;
RUNTIME_ASSERT( 0, " Parsing Strain Optimization File Failed ");
}
return Method;
}
//--------------------------------------
// ParseStrainFile
//--------------------------------------
std::pair<EConvergenceMethod, Float> ProcessConvergenceMethod( const vector< std::string > & Line,
int nLineNumber)
{
if( Line.size() < 3 )
{
std::cerr << "Line " << nLineNumber << std::endl
<< "StrainOpt: ConvergenceMethod expects two arguments " << std::endl
<< "[ Quality fQ | HitRatio fH | Differential fTol ]" << std::endl
<< std::endl;
RUNTIME_ASSERT( 0, " Parsing Strain Optimization File Failed ");
}
EConvergenceMethod Method;
for( Size_Type j = 0; j < eNumConvergenceMethods; j++ )
{
if ( ConvergenceMethodKeywords[j] == Line[1] )
Method = static_cast<EConvergenceMethod>( j );
}
if( Method >= eNumConvergenceMethods )
{
std::cerr << "Line " << nLineNumber << std::endl
<< "StrainOpt: Unknown ConvergenceMethod, choices are [ Quality fQ | HitRatio fH | Differential fTol ]" << std::endl
<< std::endl;
RUNTIME_ASSERT( 0, " Parsing Strain Optimization File Failed ");
}
return std::make_pair( Method, InitFileIO::ExtractReal( Line, nLineNumber ) );
}
static size_t
fill_buffer_from_fd(const int fd, void * const dst, const size_t buf_size)
{
char *buf = dst;
size_t pos = 0;
RUNTIME_ASSERT(buf);
RUNTIME_ASSERT(buf_size > 0);
RUNTIME_ASSERT((size_t) -1 != buf_size);
while (pos < buf_size) {
ssize_t ret;
size_t size;
size = buf_size - pos;
ret = read(fd, &buf[pos], size);
if ((ssize_t) -1 == ret) {
if (!is_temporary_error(errno) || wait_for_fd(fd) < 0) {
return -1;
}
} else if (0 == ret) {
if (pos != 0) {
errno = EIO;
return -1;
}
return 0; /* EOF */
} else {
RUNTIME_ASSERT((size_t) ret <= size);
pos += (size_t) ret;
}
}
return 1;
}
static void
hash_item_free(hashlist_t *hl, hash_item_t *item)
{
RUNTIME_ASSERT(hl != NULL);
RUNTIME_ASSERT(item != NULL);
mem_chunk_free(item, sizeof *item);
}
static int
http_send_str(http_t *ctx, const char *s)
{
RUNTIME_ASSERT(ctx);
RUNTIME_ASSERT(s);
return http_send(ctx, s, strlen(s));
}
void
ev_watcher_source_closed(ev_watcher_t *w, ev_source_t *evs)
{
ev_watcher_check(w);
ev_source_check(evs);
RUNTIME_ASSERT(ev_source_get_watcher(evs) == w);
RUNTIME_ASSERT(w->num_sources > 0);
}
static int
http_send(http_t *ctx, const void *data, size_t size)
{
RUNTIME_ASSERT(ctx);
RUNTIME_ASSERT(ctx->output);
RUNTIME_ASSERT(ctx->output->send);
return ctx->output->send(ctx->output, data, size);
}
/**
* Retrieves the payload pointer of the current item. This must not be
* used for empty lists.
*
* @param iter a valid hashlist_iter.
* @return the value of the item at the current position.
*/
void *
hashlist_iter_get_value(hashlist_iter_t *iter)
{
HASHLIST_ITER_CHECK(iter);
RUNTIME_ASSERT(iter->item != NULL);
RUNTIME_ASSERT(&iter->removed != iter->item);
return ((hash_item_t *) iter->item)->value;
}
static int
http_handle_referer_header(http_t *ctx, const char *name, char *value)
{
RUNTIME_ASSERT(ctx);
RUNTIME_ASSERT(name);
RUNTIME_ASSERT(value);
ACCLOG_SET(ctx->acclog, referer, value);
return 0;
}
static int
http_handle_proxy_header(http_t *ctx, const char *name, char *value)
{
RUNTIME_ASSERT(ctx);
RUNTIME_ASSERT(name);
RUNTIME_ASSERT(value);
ctx->proxied = true;
return 0;
}
int
http_send_line(http_t *ctx, const char *header)
{
RUNTIME_ASSERT(ctx != NULL);
RUNTIME_ASSERT(header != NULL);
if (0 != http_send_str(ctx, header) || 0 != http_send_str(ctx, "\r\n"))
return -1;
return 0;
}
//--------------------------------------------------------------------------------------------------------
//
// Private: ReadExperimentalData
//
//--------------------------------------------------------------------------------------------------------
Bool ReconstructionSetup::ReadExperimentalData( CSimulationData & oExpData, bool bServerMode )
{
const vector< SIntRange > & vFileRangeList = oExpSetup.GetFileRangeList();
const vector< SRange > & vOmegaRangeList = oExpSetup.GetOmegaRangeList();
const vector< CDetector > & vDetectorList = oExpSetup.GetDetectorList();
RUNTIME_ASSERT( vFileRangeList.size() == vDetectorList.size() && vDetectorList.size() > 0,
"ERROR: File range not specified for some detector(s) \n" );
//
// TODO: This needs to be more robust
//
oExpData.Initialize( vOmegaRangeList.size(), vDetectorList.size(),
vDetectorList[0].GetNumCols(), vDetectorList[0].GetNumRows() );
for ( Size_Type nDetector = 0; nDetector < vFileRangeList.size(); nDetector ++ )
{
Size_Type nNumFile = vFileRangeList[ nDetector ].nHigh - vFileRangeList[ nDetector ].nLow + 1;
RUNTIME_ASSERT( nNumFile == vOmegaRangeList.size(),
"ERROR: Number of files does not match specified number of omega inteval\n");
// Using -- openmp -- TODO - limit number of threads?
#pragma omp parallel for
for ( Int nFileNum = vFileRangeList[nDetector].nLow;
nFileNum <= vFileRangeList[nDetector].nHigh; nFileNum ++ )
{
Int nCurrentFileIndex = nFileNum - vFileRangeList[nDetector].nLow;
stringstream ssFilename;
ssFilename << InputParameters().InFileBasename
<< InitFileIO::NumToSuffix( nFileNum, InputParameters().InFileSerialLength )
<< "." << InputParameters().InFileExt << nDetector + oExpSetup.GetBCDetectorOffset();
Bool bSuccess = false;
switch( InputParameters().InFileType )
{
case eASCII:
bSuccess= oExpData.mImageMap[ nCurrentFileIndex ][ nDetector ].ReadCXDMSimulationDataFile( ssFilename.str() );
break;
case eBin:
bSuccess= oExpData.mImageMap[ nCurrentFileIndex ][ nDetector ].ReadCXDMSimulationUFFFile( ssFilename.str(), bServerMode );
break;
case eTif:
RUNTIME_ASSERT( 0, "Error: Tif input format not yet supported\n" );
break;
default:
RUNTIME_ASSERT( 0, "Error: Input File Type Not Recognized" );
}
DEBUG_ALERT( 0, ssFilename.str() + "\n" );
RUNTIME_ASSERT( bSuccess, "Error! Input data files cannot be read, please check file format and location\n" + ssFilename.str() );
}
}
return true;
}
static int
http_handle_if_modified_since_header(http_t *ctx, const char *name, char *value)
{
RUNTIME_ASSERT(ctx);
RUNTIME_ASSERT(name);
RUNTIME_ASSERT(value);
ctx->if_modified_since = 0 == http_parse_date(value, &ctx->ims_buf.tm)
? &ctx->ims_buf.tm
: NULL;
return 0;
}
static int
http_handle_range_header(http_t *ctx, const char *name, char *value)
{
RUNTIME_ASSERT(ctx);
RUNTIME_ASSERT(name);
RUNTIME_ASSERT(value);
if (0 == http_parse_range(value, &ctx->range_set)) {
DBUG("Ignoring unparsable Range header");
}
return 0;
}
int
dnslookup(dnslookup_ctx_t *ctx, const char *host, int *error)
{
RUNTIME_ASSERT(ctx);
RUNTIME_ASSERT(host);
RUNTIME_ASSERT(error);
ctx->i = 0;
ctx->he = gethostbyname(host);
if (!ctx->he) {
*error = h_errno;
}
return (ctx->he && ctx->he->h_addrtype == AF_INET) ? 0 : -1;
}
//------------------------------------------------------------------------
// InitializeWithDataFiles
//
// Purpose: This is the central point to read from all data/initialization
// file.
// Note: This function or InitializeWithRestore must be called beore
// any reconstruction!
//------------------------------------------------------------------------
void ReconstructionSetup::InitializeWithDataFiles( const CConfigFile & oConfigFile, bool bServerMode )
{
oExpSetup.SetConfigFile( oConfigFile );
std::cerr << "Before initialization " << std::endl;
oExpSetup.InitializeExperiment( ); // read in FZ files, omega files
std::cerr << "Before reading experimental data " << std::endl;
ReadExperimentalData( oExpData, bServerMode ); // read in experimental data
std::cerr << "After reading experimental data " << std::endl;
vector<SVector3> oFZEulerAngleList;
bool bSuccess = InitFileIO::ReadFundamentalZoneFile( oFZEulerAngleList, InputParameters().FundamentalZoneFilename );
RUNTIME_ASSERT( bSuccess, "InitializeWithDataFiles: Fundamental Zone File Not Found!\n");
for ( Size_Type i = 0; i < oFZEulerAngleList.size(); i ++)
{
SMatrix3x3 oOrient;
oOrient.BuildActiveEulerMatrix( oFZEulerAngleList[i].m_fX,
oFZEulerAngleList[i].m_fY,
oFZEulerAngleList[i].m_fZ );
oFZOrientationList.push_back( oOrient );
}
const vector< CDetector > & vDetectorList = oExpSetup.GetDetectorList();
oExpSetup.InitializeSample( oReconstructionLayer,
vDetectorList[ 0 ] ); // binding CurrentLayer to the first detector's limit
//
// TODO: Initialization should become uniform (or group together somewhere)
//
FPeakFilter.fMinEta = - InputParameters().fEtaLimit;
FPeakFilter.fMaxEta = InputParameters().fEtaLimit;
FPeakIntensityAccept.fMinEta = - InputParameters().fEtaLimit;
FPeakIntensityAccept.fMaxEta = InputParameters().fEtaLimit;
pPartialResult = MicIOFactory::Create( InputParameters().nMicGridType ); // initialize partial result
// Read partial result
if( InputParameters().bUsePartialResult )
{
const string & filename = InputParameters().PartialResultFilename;
std::cout << "before reading partial result " << std::endl;
// select out the correct result
RUNTIME_ASSERT( pPartialResult->Read( filename ),
"Failed to read partial result at: " + filename );
}
}
///////////////////////////////////////////////////////////
//
//
// ReadRotationIntervalFile (a.k.a "omegafiles")
//
// Given a filename, read in the range of data collection interval and
// the experimental file range
//
// TODO: Create a more flexible format to replace the omega files
//
bool ReadRotationIntervalFiles( vector<SRange> &oRotationRange,
vector<SIntRange> &oFileRange,
Size_Type nNumFileRange,
const string & filename )
{
char *pBuffer = NULL;
Size_Type nBufSize = 0;
vector< vector<string> > vsTokens;
pBuffer = ReadFileToBuf(nBufSize, filename);
if(pBuffer == NULL){
return false;
}
string sBuffStr( pBuffer, nBufSize );
GeneralLib::Tokenize( vsTokens, sBuffStr, ",# \t\n");
RUNTIME_ASSERT( vsTokens.size() >= 4,
"[ReadRotationIntervalFile] ERROR: Invalid file type (too short)\n");
// conform to existing omega file format, the first line is ignored
for ( Size_Type i = 1; i <= nNumFileRange; i ++)
{
SIntRange s;
s.nLow = atoi( vsTokens[i][0].c_str() );
s.nHigh = atoi( vsTokens[i][1].c_str() );
oFileRange.push_back( s );
}
//
// Get the omega ranges
//
for(Size_Type i = oFileRange.size() + 1; i < vsTokens.size(); i ++){
RUNTIME_ASSERT( (vsTokens[i].size() >= 2),
"[ReadRotationIntervalFiles] ERROR: Invalid file range\n");
SRange s;
s.fLow = DEGREE_TO_RADIAN( atof( vsTokens[i][0].c_str() ) );
s.fHigh = DEGREE_TO_RADIAN( atof( vsTokens[i][1].c_str() ) );
oRotationRange.push_back( s );
}
delete [] pBuffer;
return true;
}
/**
* Inserts a new node to the list before the current position. The nodes
* payload pointer will be set to ``ptr''.
*
* @param iter a valid list_iter.
* @param ptr the payload pointer for the new node.
* @return false if the item could not be prepended. Returns true on success.
*/
bool
list_iter_prepend(list_iter_t *iter, void *ptr)
{
node_t *n;
LIST_ITER_CHECK(iter);
/* Items must not be prepended to removed items! */
RUNTIME_ASSERT(&iter->removed != iter->node);
n = node_new(ptr);
if (!n)
return false;
n->prev = iter->node ? iter->node->prev : NULL;
n->next = iter->node;
if (!iter->l->last)
iter->l->last = n;
if (iter->l->first == iter->node)
iter->l->first = n;
if (iter->node)
iter->node->prev = n;
iter->stamp++;
iter->l->stamp++;
iter->l->length++;
LIST_CHECK(iter->l);
LIST_ITER_CHECK(iter);
return true;
}
static void
ev_watcher_collect_garbage(ev_watcher_t *w)
{
struct timeval tv;
size_t i;
ev_watcher_check(w);
compat_mono_time(&tv);
if (DIFFTIMEVAL(&tv, &w->last_gc) < 500) {
return;
}
w->last_gc = tv;
i = w->size_sources;
while (i-- > 0) {
ev_source_t *evs;
evs = w->sources[i];
if (evs) {
ev_source_check(evs);
if (ev_source_is_closed(evs)) {
ev_source_unref(evs);
w->sources[i] = NULL;
RUNTIME_ASSERT(w->num_sources > 0);
w->num_sources--;
} else {
/* Checks and delivers timeout */
ev_source_event(evs, EVT_NONE, &tv);
}
}
}
}
bool
dnslookup_next(dnslookup_ctx_t *ctx, uint32_t *addr)
{
const void *p;
RUNTIME_ASSERT(ctx);
RUNTIME_ASSERT(addr);
*addr = 0; /* Just in case */
p = ctx->he->h_addr_list[ctx->i];
if (p) {
memcpy(addr, p, sizeof *addr);
ctx->i++;
return true;
}
return false;
}
int
http_send_status_line(http_t *ctx, unsigned int code, const char *msg)
{
char buf[256], *p = buf;
size_t size = sizeof buf;
RUNTIME_ASSERT(code >= 100 && code <= 999);
ACCLOG_SET(ctx->acclog, code, code);
p = append_string(p, &size, "HTTP/1.1 ");
p = append_uint(p, &size, code);
p = append_char(p, &size, ' ');
p = append_string(p, &size, msg);
#if 0
DBUG("Sending HTTP response \"%s\"", buf);
#endif
p = APPEND_CRLF(p, &size);
p = APPEND_STATIC_CHARS(p, &size, "Date: ");
p = append_date(p, &size, compat_mono_time(NULL));
p = APPEND_CRLF(p, &size);
if (
0 != http_send(ctx, buf, sizeof buf - size) ||
0 != http_send_str(ctx, http_server_header)
)
return -1;
return 0;
}
/**
* Sets the default values for the given <major>.<minor> HTTP version.
*/
void
http_set_defaults(http_t *ctx)
{
RUNTIME_ASSERT(ctx);
ctx->keep_alive = http_at_least_ver(ctx, 1, 1) ? true : false;
}
void
dnslookup_ctx_free(dnslookup_ctx_t *ctx)
{
RUNTIME_ASSERT(ctx);
dnslookup_ctx_reset(ctx);
DO_FREE(ctx);
}
void RestrictedStratifiedGrid<SamplePointT, SamplePointGrid>
::InitializeRestart( const Mic & RecRegion_,
Mic & RestartPoint,
Float fMinAcceptThresh, // temporarily not using this - may need to add this back to improve efficiency
Float fMinSideLength_,
SVector3 oSampleCenter_,
Float fSampleRadius_ )
{
Initialize( RecRegion_, fMinSideLength_, oSampleCenter_, fSampleRadius_ );
typedef typename Mic::VoxelType_const_iterator const_iter;
int nPartialVoxelsAdded = 0;
if( RestartPoint.GetVoxels().size() > 0 )
{
Utilities::SetMinimumResolution( RestartPoint, fMinSideLength_ ); // make sure that side length is correct
for( const_iter pCur = RestartPoint.VoxelListBegin();
pCur != RestartPoint.VoxelListEnd(); ++ pCur )
{
SamplePointPtr pCenter = SolutionGrid( *pCur );
RUNTIME_ASSERT( SamplePointGrid::IsValid( pCenter ),
"[InitializeRestart:] Unexpected result from outside the solution region\n" );
*pCenter = *pCur;
// pCenter->nID = MultiStagedDetails::NOT_VISITED; // should allow option to set this
pCenter->nID = MultiStagedDetails::NOT_VISITED;
nPartialVoxelsAdded ++;
}
}
std::cout << "PartialVoxel Added: " << nPartialVoxelsAdded << std::endl;
}
static int
http_handle_transfer_encoding_header(http_t *ctx,
const char *name, char *value)
{
RUNTIME_ASSERT(ctx);
RUNTIME_ASSERT(name);
RUNTIME_ASSERT(value);
if (0 == strcasecmp(value, "chunked")) {
ctx->encoding = HTTP_TRANSFER_ENCODING_CHUNKED;
return 0;
}
http_set_status(ctx, 400, "Bad Request (Bad Transfer-Encoding)");
return -1;
}
/**
* @return
* -1 if a header was invalid (see http status for details).
* 0 if the end-of-headers was reached.
* 1 if a header was successfully parsed.
*/
int
http_parse_header(http_t *ctx, char *buf, size_t buf_size,
char **name_ptr, char **value_ptr)
{
char *value;
RUNTIME_ASSERT(ctx);
RUNTIME_ASSERT(HTTP_STATE_HEADERS == ctx->state);
if (name_ptr)
*name_ptr = NULL;
if (value_ptr)
*value_ptr = NULL;
switch (http_read_header(ctx, buf, buf_size)) {
case -1:
DBUG("http_read_header() failed: %u \"%s\"",
ctx->status_code, ctx->status_msg);
return -1;
case 0:
ctx->state = HTTP_STATE_BODY;
return 0;
case 1:
break;
default:
RUNTIME_ASSERT(0);
http_set_status(ctx, 500, "Internal Server Error");
return -1;
}
value = http_parse_header_name(buf);
if (!value) {
http_set_status(ctx, 400, "Bad Request (Bad Header)");
return -1;
}
if (name_ptr)
*name_ptr = buf;
if (value_ptr)
*value_ptr = skip_spaces(value);
return 1;
}
static int
http_handle_connection_header(http_t *ctx, const char *name, char *value)
{
const char *p;
RUNTIME_ASSERT(ctx);
RUNTIME_ASSERT(name);
RUNTIME_ASSERT(value);
for (p = skip_spaces(value); '\0' != *p; p = skip_spaces(p)) {
const char *token;
size_t len;
token = p;
while (http_is_tokenchar(*p))
p++;
len = p - token;
while ('\0' != *p && !http_is_tokenchar(*p))
p++;
#define TOKEN_MATCHES(x) \
(len == (sizeof (x) - 1) && NULL != skip_ci_prefix(token, (x)))
if (len > 0) {
if (TOKEN_MATCHES("close")) {
ctx->keep_alive = false;
#if 0
DBUG("keep-alive disabled");
#endif
} else if (TOKEN_MATCHES("keep-alive")) {
ctx->keep_alive = true;
#if 0
DBUG("keep-alive enabled");
#endif
} else {
DBUG("Unknown Connection value: \"%s\"", token);
}
}
#undef TOKEN_MATCHES
}
return 0;
}
/**
* Retrieves the payload pointer of the current node. This must not be
* used for empty lists unless list_iter points to the previously deleted
* only node.
*
* @param iter a valid list_iter.
* @return the payload pointer of the node at the current position.
*/
void *
list_iter_get_ptr(list_iter_t *iter)
{
LIST_ITER_CHECK(iter);
RUNTIME_ASSERT(iter->node != NULL);
return iter->node->ptr;
}