GIF_RETVAL readExtension(JNIEnv *env, GifDecoder *decoder, jobject currBlock) {
unsigned char extensionSize = *(decoder->inputPtr+2);
unsigned char extensionType;
if(decoder->bytesInBuffer < extensionSize + 3) { // Stop, we need more data
return STATUS_BUFFER_EMPTY;
}
decoder->inputPtr++; // Skip extension introducer
extensionType = *(decoder->inputPtr);
decoder->inputPtr += 2; // Skip size, already got it
decoder->bytesInBuffer -= 3; // Decrease buffer size as we advanced
switch(extensionType) {
case GRAPHIC_CONTROL_EXTENSION:
readGraphicControl(env, decoder, currBlock);
break;
case COMMENT_EXTENSION: {
decoder->inputPtr -= 1; // No extension size, usual sub-blocks, go back
decoder->bytesInBuffer += 1;
decoder->state = STATE_READING_COMMENT;
return readComment(env, decoder);
}
case APPLICATION_EXTENSION:
if(extensionSize == SIZE_NETSCAPE_EXT &&
!strncmp(decoder->inputPtr, "NETSCAPE2.0", SIZE_NETSCAPE_EXT)) {
if(*(decoder->inputPtr + extensionSize) == 3) { // Magic size of the sub-block in netscape ext
unsigned short loopCount;
decoder->inputPtr += extensionSize;
decoder->bytesInBuffer -= extensionSize;
loopCount = *((unsigned short *) (decoder->inputPtr+2));
(*env)->SetIntField(env, decoder->jDataStream, img_GIF_ds_loopCountID, loopCount);
return skipData(decoder);
} // If the extension is invalid proceed to default
}
case PLAIN_TEXT_EXTENSION:
default:
decoder->inputPtr += extensionSize;
decoder->bytesInBuffer -= extensionSize;
if(!(*(decoder->inputPtr))) { // No additional data
decoder->inputPtr++;
decoder->bytesInBuffer--;
decoder->state = STATE_BLOCK_BEGINNING;
} else {
decoder->state = STATE_SKIPPING_BLOCKS;
return skipData(decoder);
}
}
return STATUS_OK;
}
//------------------------------------------------------------------------------------------------
std::string readString( char * & data ) {
int strCount = readData<int>( data );
boost::shared_ptr<char> p( new char[strCount+1] );
memset( p.get(), 0, strCount+1 );
memcpy( p.get(), data, strCount );
std::string str = p.get();
skipData( data, strCount );
return str;
}
/** This method creates outputworkspace excluding monitors
*@param file :: -pointer to file
*@param period :: period number
*@param monitorList :: a list containing the spectrum numbers for monitors
*@param ws_sptr :: shared pointer to workspace
*/
void LoadRaw3::excludeMonitors(FILE *file, const int &period,
const std::vector<specnum_t> &monitorList,
DataObjects::Workspace2D_sptr ws_sptr) {
int64_t histCurrent = -1;
int64_t wsIndex = 0;
double histTotal = static_cast<double>(m_total_specs * m_numberOfPeriods);
// loop through the spectra
for (specnum_t i = 1; i <= m_numberOfSpectra; ++i) {
specnum_t histToRead = i + period * (m_numberOfSpectra + 1);
if ((i >= m_spec_min && i < m_spec_max) ||
(m_list &&
find(m_spec_list.begin(), m_spec_list.end(), i) !=
m_spec_list.end())) {
progress(m_prog, "Reading raw file data...");
// skip monitor spectrum
if (isMonitor(monitorList, i)) {
skipData(file, histToRead);
continue;
}
// read spectrum
if (!readData(file, histToRead)) {
throw std::runtime_error("Error reading raw file");
}
// set the workspace data
setWorkspaceData(ws_sptr, m_timeChannelsVec, wsIndex, i, m_noTimeRegimes,
m_lengthIn, 1);
// increment workspace index
++wsIndex;
if (m_numberOfPeriods == 1) {
if (++histCurrent % 100 == 0) {
setProg(static_cast<double>(histCurrent) / histTotal);
}
interruption_point();
}
} // end of if loop for spec min,max check
else {
skipData(file, histToRead);
}
} // end of for loop
}
void skipUselessChucks( WavFileHeader& header, QFile& file )
{
// We only care about the 'data' chuck
while ( memcmp( header.dataChuckID, "data", 4 ) != 0 )
{
int skipByteCount = header.dataSize;
std::vector<char> skipData( skipByteCount );
file.read( skipData.data(), skipByteCount );
file.read( (char*)&header.dataChuckID, 4 );
file.read( (char*)&header.dataSize, 4 );
}
}
void LoadRaw3::separateMonitors(FILE *file, const int64_t &period,
const std::vector<specnum_t> &monitorList,
DataObjects::Workspace2D_sptr ws_sptr,
DataObjects::Workspace2D_sptr mws_sptr) {
int64_t histCurrent = -1;
int64_t wsIndex = 0;
int64_t mwsIndex = 0;
double histTotal = static_cast<double>(m_total_specs * m_numberOfPeriods);
// loop through spectra
for (specnum_t i = 1; i <= m_numberOfSpectra; ++i) {
int64_t histToRead = i + period * (m_numberOfSpectra + 1);
if ((i >= m_spec_min && i < m_spec_max) ||
(m_list &&
find(m_spec_list.begin(), m_spec_list.end(), i) !=
m_spec_list.end())) {
progress(m_prog, "Reading raw file data...");
// read spectrum from raw file
if (!readData(file, histToRead)) {
throw std::runtime_error("Error reading raw file");
}
// if this a monitor store that spectrum to monitor workspace
if (isMonitor(monitorList, i)) {
setWorkspaceData(mws_sptr, m_timeChannelsVec, mwsIndex, i,
m_noTimeRegimes, m_lengthIn, 1);
++mwsIndex;
} else {
// not a monitor,store the spectrum to normal output workspace
setWorkspaceData(ws_sptr, m_timeChannelsVec, wsIndex, i,
m_noTimeRegimes, m_lengthIn, 1);
++wsIndex;
}
if (m_numberOfPeriods == 1) {
if (++histCurrent % 100 == 0) {
setProg(static_cast<double>(histCurrent) / histTotal);
}
interruption_point();
}
} else {
skipData(file, histToRead);
}
}
}
bool PlaylistImporter::parsePlaylist_wpl(QFile &data, QStringList &fileList, const QDir &baseDir, const QDir &rootDir)
{
bool foundAtLeastOneFile = false;
QRegExp skipData("<!--(.+)-->", Qt::CaseInsensitive);
QRegExp wplEntry("<(media|ref)[^<>]*(src|href)=\"([^\"]+)\"[^<>]*>", Qt::CaseInsensitive);
skipData.setMinimal(true);
QByteArray buffer = data.readAll();
QString line = QString::fromUtf8(buffer.constData(), buffer.size()).simplified();
buffer.clear();
int index = 0;
while((index = skipData.indexIn(line)) >= 0)
{
line.remove(index, skipData.matchedLength());
}
int offset = 0;
while((offset = wplEntry.indexIn(line, offset) + 1) > 0)
{
QFileInfo filename(QDir::fromNativeSeparators(unescapeXml(wplEntry.cap(3)).trimmed()));
filename.setCaching(false);
fixFilePath(filename, baseDir, rootDir);
if(filename.exists() && filename.isFile())
{
if(isPlaylist(filename.canonicalFilePath()) == notPlaylist)
{
fileList << filename.canonicalFilePath();
foundAtLeastOneFile = true;
}
}
}
return foundAtLeastOneFile;
}
/**This method creates outputworkspace including monitors
*@param file :: -pointer to file
*@param period :: period number
*@param ws_sptr :: shared pointer to workspace
*/
void LoadRaw3::includeMonitors(FILE *file, const int64_t &period,
DataObjects::Workspace2D_sptr ws_sptr) {
int64_t histCurrent = -1;
int64_t wsIndex = 0;
double histTotal = static_cast<double>(m_total_specs * m_numberOfPeriods);
// loop through spectra
for (specnum_t i = 1; i <= m_numberOfSpectra; ++i) {
int64_t histToRead = i + period * (m_numberOfSpectra + 1);
if ((i >= m_spec_min && i < m_spec_max) ||
(m_list &&
find(m_spec_list.begin(), m_spec_list.end(), i) !=
m_spec_list.end())) {
progress(m_prog, "Reading raw file data...");
// read spectrum from raw file
if (!readData(file, histToRead)) {
throw std::runtime_error("Error reading raw file");
}
// set workspace data
setWorkspaceData(ws_sptr, m_timeChannelsVec, wsIndex, i, m_noTimeRegimes,
m_lengthIn, 1);
++wsIndex;
if (m_numberOfPeriods == 1) {
if (++histCurrent % 100 == 0) {
setProg(double(histCurrent) / histTotal);
}
interruption_point();
}
} else {
skipData(file, histToRead);
}
}
// loadSpectra(file,period,m_total_specs,ws_sptr,m_timeChannelsVec);
}
/**
* Skip all spectra in a period.
* @param file :: -pointer to file
* @param period :: period number
*/
void LoadRaw3::skipPeriod(FILE *file, const int64_t &period) {
for (specnum_t i = 1; i <= m_numberOfSpectra; ++i) {
int64_t histToRead = i + period * (m_numberOfSpectra + 1);
skipData(file, histToRead);
}
}
/** Executes the algorithm. Reading in the file and creating and populating
* the output workspace
*
* @throw Exception::FileError If the RAW file cannot be found/opened
* @throw std::invalid_argument If the optional properties are set to invalid values
*/
void LoadRawBin0::exec()
{
// Retrieve the filename from the properties
m_filename = getPropertyValue("Filename");
bool bLoadlogFiles = getProperty("LoadLogFiles");
//open the raw file
FILE* file=openRawFile(m_filename);
// Need to check that the file is not a text file as the ISISRAW routines don't deal with these very well, i.e
// reading continues until a bad_alloc is encountered.
if( isAscii(file) )
{
g_log.error() << "File \"" << m_filename << "\" is not a valid RAW file.\n";
throw std::invalid_argument("Incorrect file type encountered.");
}
std::string title;
readTitle(file,title);
readworkspaceParameters(m_numberOfSpectra,m_numberOfPeriods,m_lengthIn,m_noTimeRegimes);
///
setOptionalProperties();
// to validate the optional parameters, if set
checkOptionalProperties();
// Calculate the size of a workspace, given its number of periods & spectra to read
m_total_specs = calculateWorkspaceSize();
//no real X values for bin 0,so initialize this to zero
boost::shared_ptr<MantidVec> channelsVec(new MantidVec(1,0));
m_timeChannelsVec.push_back(channelsVec);
double histTotal = static_cast<double>(m_total_specs * m_numberOfPeriods);
int64_t histCurrent = -1;
// Create the 2D workspace for the output xlength and ylength is one
DataObjects::Workspace2D_sptr localWorkspace = createWorkspace(m_total_specs, 1,1,title);
Run& run = localWorkspace->mutableRun();
if (bLoadlogFiles)
{
runLoadLog(m_filename,localWorkspace, 0.0, 0.0);
const int period_number = 1;
createPeriodLogs(period_number, localWorkspace);
}
// Set the total proton charge for this run
setProtonCharge(run);
WorkspaceGroup_sptr ws_grp = createGroupWorkspace();
setWorkspaceProperty("OutputWorkspace", title, ws_grp, localWorkspace,m_numberOfPeriods, false);
// Loop over the number of periods in the raw file, putting each period in a separate workspace
for (int period = 0; period < m_numberOfPeriods; ++period)
{
if (period > 0)
{
localWorkspace=createWorkspace(localWorkspace);
if (bLoadlogFiles)
{
//remove previous period data
std::stringstream prevPeriod;
prevPeriod << "PERIOD " << (period);
Run& runObj = localWorkspace->mutableRun();
runObj.removeLogData(prevPeriod.str());
runObj.removeLogData("current_period");
//add current period data
const int period_number = period + 1;
createPeriodLogs(period_number, localWorkspace);
}
}
skipData(file, period * (m_numberOfSpectra + 1));
int64_t wsIndex = 0;
for (specid_t i = 1; i <= m_numberOfSpectra; ++i)
{
int64_t histToRead = i + period * (m_numberOfSpectra + 1);
if ((i >= m_spec_min && i < m_spec_max) || (m_list && find(m_spec_list.begin(), m_spec_list.end(),
i) != m_spec_list.end()))
{
progress(m_prog, "Reading raw file data...");
//readData(file, histToRead);
//read spectrum
if (!readData(file, histToRead))
{
throw std::runtime_error("Error reading raw file");
}
int64_t binStart=0;
setWorkspaceData(localWorkspace, m_timeChannelsVec, wsIndex, i, m_noTimeRegimes,1,binStart);
++wsIndex;
if (m_numberOfPeriods == 1)
{
if (++histCurrent % 100 == 0)
{
m_prog = double(histCurrent) / histTotal;
}
interruption_point();
}
}
else
{
skipData(file, histToRead);
}
}
if(m_numberOfPeriods>1)
{
setWorkspaceProperty(localWorkspace, ws_grp, period, false);
// progress for workspace groups
m_prog = static_cast<double>(period) / static_cast<double>(m_numberOfPeriods - 1);
}
} // loop over periods
// Clean up
isisRaw.reset();
fclose(file);
}
/*
* Class: org_apache_harmony_awt_gl_image_GifDecoder
* Method: decode
* Signature: ([BIJLorg/apache/harmony/awt/gl/image/GifDecoder$GifDataStream;Lorg/apache/harmony/awt/gl/image/GifDecoder$GifGraphicBlock;)I
*/
JNIEXPORT jint JNICALL Java_org_apache_harmony_awt_gl_image_GifDecoder_decode
(JNIEnv *env,
jobject obj,
jbyteArray jInput,
jint bytesInBuffer,
jlong hDecoder,
jobject dataStream,
jobject currBlock) {
GIF_RETVAL retval = STATUS_OK;
GifDecoder *decoder = getDecoder(env, obj, dataStream, (GifDecoder*) ((IDATA)hDecoder));
int scanlinesDecoded;
decoder->input = decoder->inputPtr =
(*env)->GetPrimitiveArrayCritical(env, jInput, 0);
decoder->bytesInBuffer += bytesInBuffer;
bytesInBuffer = decoder->bytesInBuffer;
while(retval == STATUS_OK && decoder->bytesInBuffer > 0) {
switch(decoder->state) {
case STATE_INIT: {
retval = readHeader(env, decoder);
break;
}
case STATE_AT_GLOBAL_COLOR_TABLE: {
retval = loadColorTable(env, decoder->jGlobalColorTable, decoder);
break;
}
case STATE_AT_LOCAL_COLOR_TABLE: {
retval = loadColorTable(env, NULL, decoder);
break;
}
case STATE_BLOCK_BEGINNING: {
unsigned char blockLabel = *(decoder->inputPtr);
switch(blockLabel) {
case EXTENSION_INTRODUCER:
retval = readExtension(env, decoder, currBlock);
break;
case IMAGE_SEPARATOR:
retval = readImageDescriptor(env, currBlock, decoder);
break;
case GIF_TRAILER:
retval = STATUS_EOF;
break;
}
break;
}
case STATE_STARTING_DECOMPRESSION: {
retval = initDecompression(env, decoder, currBlock);
break;
}
case STATE_DECOMPRESSING: {
if(!decoder->interlace)
retval = decompress(env, currBlock, decoder);
else
retval = decompressInterlaced(env, currBlock, decoder);
break;
}
case STATE_READING_COMMENT: {
retval = readComment(env, decoder);
break;
}
case STATE_SKIPPING_BLOCKS: {
retval = skipData(decoder);
break;
}
default:
// Should never execute this!
break;
}
}
// Copy unconsumed data to the start of the input buffer
if(decoder->bytesInBuffer > 0) {
memmove(decoder->input, decoder->inputPtr, decoder->bytesInBuffer);
}
(*env)->ReleasePrimitiveArrayCritical(env, jInput, decoder->input, 0);
(*env)->SetIntField(
env,
obj,
img_GIF_bytesConsumedID,
bytesInBuffer - decoder->bytesInBuffer
);
if(decoder->stateVars.imageDataStarted) {
if(!decoder->interlace) {
scanlinesDecoded = decoder->pixelsDecoded / decoder->currentWidth -
decoder->oldPixelsDecoded / decoder->currentWidth;
decoder->oldPixelsDecoded = decoder->pixelsDecoded;
} else {
if(retval == STATUS_LINE_COMPLETED && decoder->pass < MAX_PASS) {
scanlinesDecoded = 1;
if(decoder->currScanline >= 0)
(*env)->SetIntField(env, currBlock, img_GIF_gb_currYID, decoder->currScanline);
decoder->scanlineOffset = 0;
} else {
scanlinesDecoded = 0;
}
}
} else {
scanlinesDecoded = 0;
}
if(retval == STATUS_FRAME_COMPLETED) {
decoder->oldPixelsDecoded = decoder->pixelsDecoded = 0;
}
// Free the decoder if decoding is finished
if(retval == STATUS_EOF) {
free(decoder);
decoder = NULL;
}
(*env)->SetLongField(env, obj, img_GIF_hNativeDecoderID, (jlong) ((IDATA)decoder));
return scanlinesDecoded;
}