Merge pull request #373 from slsdetectorgroup/ghdf5

Gotthard25um: virtual hdf5 image

RELEASE.txt

@@ -54,6 +54,7 @@ This document describes the differences between v7.0.0 and v6.x.x
 - added geometry to metadata
 - 10g eiger nextframenumber get fixed.
 - stop, able to set nextframenumber to a consistent (max + 1) for all modules if different (eiger/ctb/jungfrau/moench)
+- gotthard 25 um image reconstructed in gui and virtual hdf5 (firmware updated for slave to reverse channels)
 
 2. Resolved Issues
 ==================

slsReceiverSoftware/src/DataProcessor.cpp

@@ -200,7 +200,10 @@ void DataProcessor::CreateVirtualFile(
     if (virtualFile_) {
         delete virtualFile_;
     }
-    virtualFile_ = new HDF5VirtualFile(hdf5Lib);
+    bool gotthard25um =
+        ((detectorType_ == GOTTHARD || detectorType_ == GOTTHARD2) &&
+         (numModX * numModY) == 2);
+    virtualFile_ = new HDF5VirtualFile(hdf5Lib, gotthard25um);
 
     // maxframesperfile = 0 for infinite files
     uint32_t framesPerFile =
@@ -214,7 +217,7 @@ void DataProcessor::CreateVirtualFile(
         filePath, fileNamePrefix, fileIndex, overWriteEnable, silentMode,
         modulePos, numUnitsPerReadout, framesPerFile, numImages,
         generalData_->nPixelsX, generalData_->nPixelsY, dynamicRange,
-        numImagesProcessed, numModX, numModY, dataFile_->GetPDataType(),
+        numFramesCaught_, numModX, numModY, dataFile_->GetPDataType(),
         dataFile_->GetParameterNames(), dataFile_->GetParameterDataTypes());
 }
 

slsReceiverSoftware/src/HDF5VirtualFile.cpp

@@ -5,8 +5,8 @@
 
 #include <iomanip>
 
-HDF5VirtualFile::HDF5VirtualFile(std::mutex *hdf5Lib)
-    : File(HDF5), hdf5Lib_(hdf5Lib) {}
+HDF5VirtualFile::HDF5VirtualFile(std::mutex *hdf5Lib, bool g25)
+    : File(HDF5), hdf5Lib_(hdf5Lib), gotthard25um(g25) {}
 
 HDF5VirtualFile::~HDF5VirtualFile() { CloseFile(); }
 
@@ -73,12 +73,10 @@ void HDF5VirtualFile::CreateVirtualFile(
             "version", PredType::NATIVE_DOUBLE, dataspace_attr);
         attribute.write(PredType::NATIVE_DOUBLE, &dValue);
 
-        // virtual data dataspace
+        // virtual dataspace
         hsize_t vdsDims[3] = {numImagesCaught, numModY * nDimy,
                               numModZ * nDimz};
         DataSpace vdsDataSpace(3, vdsDims, nullptr);
-
-        // virtual parameter dataspace
         hsize_t vdsDimsPara[2] = {numImagesCaught,
                                   (unsigned int)numModY * numModZ};
         DataSpace vdsDataSpacePara(2, vdsDimsPara, nullptr);
@@ -91,37 +89,54 @@ void HDF5VirtualFile::CreateVirtualFile(
         // property list for parameters (datatype)
         std::vector<DSetCreatPropList> plistPara(paraSize);
 
-        // hyperslab
-        int numMajorHyperslab = numImagesCaught / maxFramesPerFile;
+        // hyperslab (files)
+        int numFiles = numImagesCaught / maxFramesPerFile;
         if (numImagesCaught % maxFramesPerFile)
-            ++numMajorHyperslab;
+            ++numFiles;
         uint64_t framesSaved = 0;
-        // loop through files
-        for (int hyperSlab = 0; hyperSlab < numMajorHyperslab; ++hyperSlab) {
+        for (int iFile = 0; iFile < numFiles; ++iFile) {
 
             uint64_t nDimx =
                 ((numImagesCaught - framesSaved) > maxFramesPerFile)
                     ? maxFramesPerFile
                     : (numImagesCaught - framesSaved);
-            hsize_t start[3] = {framesSaved, 0, 0};
-            hsize_t count[3] = {nDimx, nDimy, nDimz};
-            hsize_t startPara[2] = {framesSaved, 0};
-            hsize_t countPara[2] = {nDimx, 1};
-            // loop through readouts
-            for (unsigned int i = 0; i < numModY * numModZ; ++i) {
 
-                // setect data hyperslabs
-                vdsDataSpace.selectHyperslab(H5S_SELECT_SET, count, start);
+            hsize_t startLocation[3] = {framesSaved, 0, 0};
+            hsize_t strideBetweenBlocks[3] = {1, 1, 1};
+            hsize_t numBlocks[3] = {nDimx, nDimy, nDimz};
+            hsize_t blockSize[3] = {1, 1, 1};
 
-                // select parameter hyperslabs
-                vdsDataSpacePara.selectHyperslab(H5S_SELECT_SET, countPara,
-                                                 startPara);
+            hsize_t startLocationPara[2] = {framesSaved, 0};
+            hsize_t strideBetweenBlocksPara[3] = {1, 1};
+            hsize_t numBlocksPara[2] = {1, 1};
+            hsize_t blockSizePara[3] = {nDimx, 1};
+
+            // interleaving for g2
+            if (gotthard25um) {
+                strideBetweenBlocks[2] = 2;
+            }
+
+            for (unsigned int iReadout = 0; iReadout < numModY * numModZ;
+                 ++iReadout) {
+
+                // interleaving for g2 (startLocation is 0 and 1)
+                if (gotthard25um) {
+                    startLocation[2] = iReadout;
+                }
+
+                vdsDataSpace.selectHyperslab(H5S_SELECT_SET, numBlocks,
+                                             startLocation, strideBetweenBlocks,
+                                             blockSize);
+
+                vdsDataSpacePara.selectHyperslab(
+                    H5S_SELECT_SET, numBlocksPara, startLocationPara,
+                    strideBetweenBlocksPara, blockSizePara);
 
                 // source file name
                 std::ostringstream os;
                 os << filePath << "/" << fileNamePrefix << "_d"
-                   << (modulePos * numUnitsPerReadout + i) << "_f" << hyperSlab
-                   << '_' << fileIndex << ".h5";
+                   << (modulePos * numUnitsPerReadout + iReadout) << "_f"
+                   << iFile << '_' << fileIndex << ".h5";
                 std::string srcFileName = os.str();
                 LOG(logDEBUG1) << srcFileName;
 
@@ -138,25 +153,20 @@ void HDF5VirtualFile::CreateVirtualFile(
                 std::ostringstream osfn;
                 osfn << "/data";
                 if (numImages > 1)
-                    osfn << "_f" << std::setfill('0') << std::setw(12)
-                         << hyperSlab;
+                    osfn << "_f" << std::setfill('0') << std::setw(12) << iFile;
                 std::string srcDatasetName = osfn.str();
 
-                // source data dataspace
+                // source dataspace
                 hsize_t srcDims[3] = {nDimx, nDimy, nDimz};
                 hsize_t srcDimsMax[3] = {H5S_UNLIMITED, nDimy, nDimz};
                 DataSpace srcDataSpace(3, srcDims, srcDimsMax);
-
-                // source parameter dataspace
                 hsize_t srcDimsPara[1] = {nDimx};
                 hsize_t srcDimsMaxPara[1] = {H5S_UNLIMITED};
                 DataSpace srcDataSpacePara(1, srcDimsPara, srcDimsMaxPara);
 
-                // mapping of data property list
+                // mapping of property list
                 plist.setVirtual(vdsDataSpace, relative_srcFileName.c_str(),
                                  srcDatasetName.c_str(), srcDataSpace);
-
-                // mapping of parameter property list
                 for (unsigned int p = 0; p < paraSize; ++p) {
                     plistPara[p].setVirtual(
                         vdsDataSpacePara, relative_srcFileName.c_str(),
@@ -165,21 +175,23 @@ void HDF5VirtualFile::CreateVirtualFile(
 
                 // H5Sclose(srcDataspace);
                 // H5Sclose(srcDataspace_para);
-                start[2] += nDimz;
-                if (start[2] >= (numModZ * nDimz)) {
-                    start[2] = 0;
-                    start[1] += nDimy;
+
+                if (!gotthard25um) {
+                    startLocation[2] += nDimz;
+                    if (startLocation[2] >= (numModZ * nDimz)) {
+                        startLocation[2] = 0;
+                        startLocation[1] += nDimy;
+                    }
                 }
-                startPara[1]++;
+                startLocationPara[1]++;
             }
             framesSaved += nDimx;
         }
-        // data dataset
+        // datasets
         dataSetName_ = "data";
         DataSet vdsDataSet(fd_->createDataSet(dataSetName_.c_str(), dataType,
                                               vdsDataSpace, plist));
 
-        // parameter dataset
         for (unsigned int p = 0; p < paraSize; ++p) {
             DataSet vdsDataSetPara(fd_->createDataSet(
                 parameterNames[p].c_str(), parameterDataTypes[p],
@@ -196,4 +208,4 @@ void HDF5VirtualFile::CreateVirtualFile(
     if (!silentMode) {
         LOG(logINFO) << "Virtual File: " << fileName_;
     }
-}
+}

slsReceiverSoftware/src/HDF5VirtualFile.h

@@ -9,7 +9,7 @@
 class HDF5VirtualFile : private virtual slsDetectorDefs, public File {
 
   public:
-    HDF5VirtualFile(std::mutex *hdf5Lib);
+    HDF5VirtualFile(std::mutex *hdf5Lib, bool g25);
     ~HDF5VirtualFile();
 
     std::array<std::string, 2> GetFileAndDatasetName() const override;
@@ -30,4 +30,5 @@ class HDF5VirtualFile : private virtual slsDetectorDefs, public File {
     H5File *fd_{nullptr};
     std::string fileName_;
     std::string dataSetName_;
+    bool gotthard25um;
 };