void DoOverSampleSplitSubRegion(OptionsCls &options, char *dirName)
{
// look through a directory, and crop each file into its four base experiments
char destPath[4][2048];
DIR *d = opendir(options.expPath);
struct dirent *entry;
int osC[4] = {8,4,2,1};
int osS[4] = {1,2,4,8};
for(int i=0;i<4;i++)
sprintf(destPath[i],"%s_%d/%s",options.destPath,osC[i],dirName);
if(d)
{
while ((entry = readdir(d)) != NULL)
{
if ((entry->d_type != DT_DIR) && ((entry->d_name[0] == 'a') || entry->d_name[0] == 'b' || entry->d_name[0] == 'p'))
{
for(int i=0;i<4;i++)
{
// crop this file into its four sub-sampling files
options.oneFile = entry->d_name;
options.destPath = destPath[i];
options.OverSample_combine=osC[i];
options.OverSample_skip=osS[i];
options.skipCopy=1;
DoCrop(options);
}
}
}
closedir(d);
}
}
void subWorker(int os, int skip, char *tmpExpPath, char *tmpDestPath)
{
OptionsCls LocalOptions;
memcpy(&LocalOptions,&options,sizeof(LocalOptions));
LocalOptions.expPath=tmpExpPath;
LocalOptions.destPath=tmpDestPath;
LocalOptions.OverSample_combine = os;
LocalOptions.OverSample_skip = skip;
DoCrop(LocalOptions);
}
int main ( int argc, char *argv[] )
{
InitOptionsCls(options);
// int dont_retry = 0;
if ( argc == 1 ) {
usage ( options.cropx, options.cropy, options.cropw, options.croph );
}
int argcc = 1;
while ( argcc < argc ) {
switch ( argv[argcc][1] ) {
case 'a':
options.doAscii = 1;
break;
case 'x':
argcc++;
options.cropx = atoi ( argv[argcc] );
break;
case 'y':
argcc++;
options.cropy = atoi ( argv[argcc] );
break;
case 'w':
argcc++;
options.cropw = atoi ( argv[argcc] );
break;
case 'h':
argcc++;
// don't segfault if called with -h (user expects help)
if ( argcc >= argc ) {
usage ( options.cropx, options.cropy, options.cropw, options.croph );
}
options.croph = atoi ( argv[argcc] );
break;
case 's':
argcc++;
options.expPath = argv[argcc];
break;
case 'f':
argcc++;
options.oneFile = argv[argcc];
break;
case 'z':
options.dont_retry = 1;
break;
case 'p':
options.pfc=1;
options.cropx=0;
options.cropy=0;
options.cropw=0;
options.croph=0;
break;
case 'c':
options.vfc=1;
options.cropx=0;
options.cropy=0;
options.cropw=0;
options.croph=0;
break;
case 'b':
options.OverSamplingSplit=1;
options.cropx=0;
options.cropy=0;
options.cropw=0;
options.croph=0;
break;
case 'n':
options.vfc=0;
break;
case 'v':
fprintf ( stdout, "%s", IonVersion::GetFullVersion ( "Crop" ).c_str() );
exit ( 0 );
break;
case 'H':
usage ( options.cropx, options.cropy, options.cropw, options.croph );
break;
case 'd':
argcc++;
options.destPath = argv[argcc];
break;
case 'r':
options.regBasedAcq=1;
break;
case 'l':
options.TimeBasedAcq=1;
break;
case 't':
argcc++;
options.separatorIn = argv[argcc];
break;
case 'e':
argcc++;
options.t0In = argv[argcc];
options.useSeparatorT0File = false;
break;
case 'q':
argcc++;
strncpy(ImageTransformer::PCATest , argv[argcc], sizeof(ImageTransformer::PCATest)-1);
break;
case 'u':
argcc++;
options.PCAOpts=argv[argcc];
break;
case 'g':
argcc++;
options.excludeMaskFile = argv[argcc];
options.excludeMask = 1;
break;
case 'i':
argcc++;
options.OverSample_combine = atoi(argv[argcc]);
argcc++;
options.OverSample_skip = atoi(argv[argcc]);
break;
case 'j':
argcc++;
numThreads = atoi(argv[argcc]);
break;
case 'C':
options.doColumnCorrection=1;
if(argv[argcc+1][0] != '-'){
argcc++;
if(argc <= argcc || (argv[argcc][0] != '0' && argv[argcc][0] != '1')){
printf("Bad option on column noise correction\n");
exit(-1);
}
options.cncType = atoi(argv[argcc]);
}
break;
case 'D':
options.doColumnCorrectionTn=1;
break;
case 'E':
options.T0Test=1;
break;
case 'F':
argcc++;
options.cmpFile = argv[argcc];
break;
case 'G':
options.subtractAverage=1;
break;
case 'I':
if(argv[argcc+1][0] != '-'){
argcc++;
options.chipType = argv[argcc];
}
break;
case 'J':
options.applyRowCorrection = 1;
break;
case 'K':
options.applyColCorrection = 1;
break;
case 'L':
if(argv[argcc+1][0] != '-'){
argcc++;
sscanf(argv[argcc],"%f",&options.applyXtalkCorrection1);
}
else
options.applyXtalkCorrection1 = 0.2;
break;
case 'M':
if(argv[argcc+1][0] != '-'){
argcc++;
sscanf(argv[argcc],"%f",&options.applyXtalkCorrection2);
}
else
options.applyXtalkCorrection2 = 0.2;
break;
default:
fprintf ( stdout, "unknown option %s\n",argv[argcc] );
argcc++;
break;
}
argcc++;
}
if(options.OverSamplingSplit)
{
// crop an entire directory many times
DoOverSampleSplit(options);
}
else
{
DoCrop(options);
}
}
void CCropDialog::on_pushButtonCrop_clicked()
{
/* *************************
m_pCropThread = new CCropThread(this);
m_pCropThread->start();
**************************** */
QString strTemplateFilename(tr("%1/%2")
.arg(ui.lineEditSourceFolder->text())
.arg(sTEMPLATE_IMAGE_FILENAME));
if(QFile::exists(strTemplateFilename) != true)
{
QMessageBox::critical(this, tr("Missing the template image file"),
tr("%1 is necessary to crop the image stacks.")
.arg(sTEMPLATE_IMAGE_FILENAME));
return;
}
// make sub folders for cropped data
QString strZoomOutFolder, strColumnFolder;
QDir Dir;
m_bStartCropping = true;
ui.pushButtonCrop->setEnabled(false);
ui.pushButtonPauseResume->setEnabled(true);
ui.listWidgetOutput->clear();
m_bProcessFinished = true;
m_bPause = false;
////////////////////////////////
// ZO_1 is not a part of ZoomOutLevel, but needs to be made.
for(quint32 i = 0, nZoomOutLevel = 1;
i < m_TissueBlock.m_nNumZoomLevel+1; i++, nZoomOutLevel *= 2)
{
strZoomOutFolder = ui.lineEditDestFolder->text()
+ "/"
+ QString(sZOOM_OUT_DIR_PREFIX"%1")
.arg(nZoomOutLevel);
Dir.mkdir(strZoomOutFolder);
PrintToOutput(strZoomOutFolder + " folder created.");
for(quint32 j = 0; j < m_TissueBlock.m_nNumCol; j++)
{
strColumnFolder = strZoomOutFolder + "/" + QString("%1").arg(j);
Dir.mkdir(strColumnFolder);
PrintToOutput("\t" + strColumnFolder + " folder created.");
}
}
// open list for source image files
qint32 nOffset = (m_TissueBlock.m_nStartCol > m_TissueBlock.m_nEndCol) ?
-1 : 1;
//QString strSrcFile;
QString strLine;
quint32 nSrcStartCol = m_TissueBlock.m_nStartCol;
/////////////////////
// specify a task that processes only one column
quint32 nColsToCrop = m_TissueBlock.m_nNumCol;
quint32 iCol = 0;
//if(m_nSrcCropCol != -1) // an image stack number is specified
if(ui.comboBoxColumn->currentText() != "All")
{
int nSrcCropCol = ui.comboBoxColumn->currentText().toInt();
iCol = qAbs((int)nSrcStartCol - nSrcCropCol);//(int)m_nSrcCropCol);
nColsToCrop = iCol+1; // only one column
nSrcStartCol = nSrcCropCol;//m_nSrcCropCol;
}
//for( i = 0; i < m_TissueBlock.m_nNumCol; i++, nSrcStartCol+=nOffset)
for(; iCol < nColsToCrop; iCol++, nSrcStartCol+=nOffset)
{
#if 0
//////////////////////////////////////////////////////////////////////
// src image crop area
QString strCropFile(tr("%1/%2_crop_point.txt")
.arg(ui.lineEditSourceFolder->text())
.arg(nSrcStartCol));
QFile fileCrop(strCropFile);
if(!(fileCrop.open(QFile::ReadOnly | QFile::Text)))
{
PrintToOutput(tr("No %1 exists.").arg(strCropFile));
continue; // ignore no folder exists
//QMessageBox::critical(this, tr("File open error"),
// tr("No %1 exists.").arg(strCropFile));
//return;
}
QTextStream txtstrmCrop(&fileCrop);
while(!txtstrmCrop.atEnd())
{
strLine = txtstrmCrop.readLine();
if(strLine.isNull())
break;
m_TissueBlock.m_vCropStartX.append(strLine.toInt());
};
//////////////////////////////////////////////////////////////////////
// src image crop area index
QString strChunkPosFile(tr("%1/%2_chunk_pos.txt")
.arg(ui.lineEditSourceFolder->text())
.arg(nSrcStartCol));
QFile fileChunkPos(strChunkPosFile);
if(!fileChunkPos.open(QFile::ReadOnly | QFile::Text))
{
PrintToOutput(tr("No %1 exists.").arg(strChunkPosFile));
continue; // ignore no folder exists
//QMessageBox::critical(this, tr("File open error"),
// tr("No %1 exists.").arg(strChunkPosFile));
//return;
}
QTextStream txtstrmChunkPos(&fileChunkPos);
while(!txtstrmChunkPos.atEnd())
{
strLine = txtstrmChunkPos.readLine();
if(strLine.isNull())
break;
m_TissueBlock.m_vChunkPos.append(strLine.toDouble());
}
#endif
QString strSubFolder(tr("%1/%2")
.arg(ui.lineEditSourceFolder->text())
.arg(nSrcStartCol));
QDir dirDataFolder(strSubFolder);
QStringList slstFilters;
slstFilters << QString(tr("*%1").arg(m_Settings.m_strDestFileFormat));
dirDataFolder.setNameFilters(slstFilters);
QStringList slstEntry = dirDataFolder.entryList();
PrintToOutput(tr("Files: %1").arg(slstEntry.count()));
if(slstEntry.count() > 0)
ui.progressBarImage->setRange(0, slstEntry.count()-1);
QString strDestImage, strOptions, strSrcImage, strArgs;
//QStrinList strlstLine;
qreal rZ;
quint32 nImage;//, nStartImage;//, nIndexChunk = 0;
//bool bFirst = true;
//while(!txtstrmSrc.atEnd())
for(int iImage = 0; iImage < slstEntry.count(); iImage++)
{
//QStringList slstImageFile = slstEntry.at(nImage).split(".");
QString strImageFile = slstEntry.at(iImage);
// src image filename
//strLine = txtstrmSrc.readLine();
//if(strLine.isNull())
// break;
// get z coordinate value
int nPosZ = strImageFile.indexOf('z', 0);//strLine.indexOf('z', 0);
if(nPosZ == -1)
{
QMessageBox::critical(this, tr("Invalid src image filename"),
tr("%1 is an invalid src image filename.")
.arg(strImageFile)); //.arg(strLine));
m_bStartCropping = false;
ui.pushButtonCrop->setEnabled(true);
ui.pushButtonPauseResume->setEnabled(false);
return;
}
rZ = strImageFile.mid(nPosZ+1, 6).toDouble();//strLine.mid(nPosZ+1, 6).toDouble();
nImage = qRound((rZ - m_TissueBlock.m_rMinStartZ)\
/m_TissueBlock.m_rThickness);
//if(bFirst)
//{
// bFirst = false;
// nStartImage = nImage;
//}
#if 0
//if((nImage - nStartImage) == m_TissueBlock.m_vChunkPos[nIndexChunk])
if(rZ == m_TissueBlock.m_vChunkPos[nIndexChunk])
nIndexChunk++;
#endif
// make src filename
strSrcImage = QString(tr("%1/%2/%3")
.arg(ui.lineEditSourceFolder->text())
.arg(nSrcStartCol)
.arg(strImageFile));//.arg(strLine));
// make dest filename
QString strZoomOutDir = m_Settings.m_strZoomOutDirPrefix + "1";
//strDestImage = QString(tr("%1/%2/%3/%4%5")
// .arg(ui.lineEditDestFolder->text())
// .arg(strZoomOutDir)
// .arg(i)
// .arg(nImage)
// .arg(m_Settings.m_strDestFileFormat));
strDestImage.sprintf("%s/%s/%d/%05d%s",
ui.lineEditDestFolder->text().toStdString().c_str(),
strZoomOutDir.toStdString().c_str(),
iCol, // jrkwon: %05d
nImage,
m_Settings.m_strDestFileFormat.toStdString().c_str());
#if 0
strOptions = QString(tr("%1x%2+%3+%4")
.arg(m_TissueBlock.m_nWidth)
.arg(m_TissueBlock.m_nLength)
.arg(m_TissueBlock.m_vCropStartX[nIndexChunk])
.arg(0));
strArgs = QString(tr("%1 -crop %2 %3")
.arg(strSrcImage)
.arg(strOptions)
.arg(strDestImage));
PrintToOutput(strArgs);
QStringList strlstArgs;
strlstArgs << strSrcImage << tr("-crop") << strOptions << strDestImage;
QString strImageMagickConvert;
strImageMagickConvert = QString(tr("%1%2%3%4")
.arg(m_Settings.m_strProjectDir)
.arg(m_Settings.m_strToolkit)
.arg(m_Settings.m_strImageMagick)
.arg("/convert"));
#endif
ui.progressBarColumn->setValue(iCol);
ui.progressBarImage->setValue(iImage);
#if 0
while(m_bProcessFinished == false || m_bPause)
{
QCoreApplication::processEvents();
}
m_Process.start(strImageMagickConvert, strlstArgs);
m_bProcessFinished = false;
//PrintToOutput(strImageMagickConvert);
QCoreApplication::processEvents();
#endif
// see if there already is a dest file, and do this only no dest file exists
if(QFile::exists(strDestImage) == false)
{
quint32 nStartX;
if(GetCropX(strSrcImage, nStartX))
{
//DoCrop(m_TissueBlock.m_vCropStartX[nIndexChunk], 0,
DoCrop(nStartX, 0,
m_TissueBlock.m_nWidth, m_TissueBlock.m_nLength,
strSrcImage, strDestImage);
QString strMsg(tr("CropX: %1, Src: %2, Dest: %3")
.arg(nStartX).arg(strSrcImage).arg(strDestImage));
PrintToOutput(strMsg);
}
}
if(m_bStartCropping != true)
{
ui.pushButtonCrop->setEnabled(true);
ui.pushButtonPauseResume->setEnabled(false);
ui.progressBarColumn->setValue(0);
ui.progressBarImage->setValue(0);
return;
}
}
}
ui.pushButtonCrop->setEnabled(true);
ui.pushButtonPauseResume->setEnabled(false);
}
