Commit 2db201dc authored by Makayla Shepherd's avatar Makayla Shepherd
Browse files

Removed hdf5 serialization. Fixes #4795. 

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/ipce_FY17-Sprint1@7591 41f8697f-d340-4b68-9986-7bafba869bb8
parent a17060f5

isis/src/control/objs/BundleResults/BundleResults.cpp

+0 −608

File changed.

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isis/src/control/objs/BundleResults/BundleResults.h

+0 −11
Original line number Diff line number Diff line
@@ -30,11 +30,6 @@ 
#include <QString>

#include <QVector>



// hdf5 Library

#include <H5Cpp.h>

#include <hdf5_hl.h>

#include <hdf5.h>



// Isis Library

#include "BundleControlPoint.h"

#include "BundleObservationVector.h"
@@ -248,12 +243,6 @@ namespace Isis { 
      QDataStream &write(QDataStream &stream) const;

      QDataStream &read(QDataStream &stream);



      void createH5Group(hid_t locationId, QString locationName) const;// delete these

      void parseH5Group(hid_t locationId, QString locationName);       // delete these



      void createH5Group(H5::CommonFG &locationObject, QString locationName) const;

      void openH5Group(H5::CommonFG &locationObject, QString locationName);

      BundleResults(H5::CommonFG &locationObject, QString locationName);



    private:

      /**

isis/src/control/objs/BundleSolutionInfo/BundleSolutionInfo.cpp

+1 −271
Original line number Diff line number Diff line
@@ -7,10 +7,6 @@ 
#include <QUuid>

#include <QXmlStreamWriter>



#include <hdf5_hl.h> // in the hdf5 library

#include <hdf5.h>

#include <H5Cpp.h>



#include "BundleResults.h"

#include "ControlMeasure.h"

#include "ControlNet.h"
@@ -75,26 +71,6 @@ namespace Isis { 
    xmlReader->setErrorHandler(new XmlHandler(this, project));

  }



  /**

   * Constructor. Creates a BundleSolutionInfo.

   * 

   * @param bundleSolutionInfo Filename of another BundleSolutionInfo and reads the settings and 

   *        BundleResults from that.

   */

  BundleSolutionInfo::BundleSolutionInfo(FileName bundleSolutionInfoFile) {

    m_id = NULL;

    m_id = new QUuid(QUuid::createUuid());



    m_statisticsResults = NULL;

    m_statisticsResults = new BundleResults();



    m_settings = BundleSettingsQsp(new BundleSettings);



    m_images = NULL;

    m_images = new QList<ImageList *>;// change to QList<QStringList> ???



    openH5File(bundleSolutionInfoFile);

  }

  

  /**

   * Constructor. Creates a BundleSolutionInfo.
@@ -1747,250 +1723,4 @@ namespace Isis { 
    return bundleSolutionInfo.read(stream);

  }





  /**

   * Reads the settings and results from another BundleSolutionInfo

   * 

   * @throws IException::Io "No file with the given name was found."

   * @throws IException::Io "The given file is unsupported for constructing BundleSolutionInfo 

   *                        objects. Supported file types include [hdf]."

   * @throws IException::Unknown "H5 exception handler has detected an error when invoking the 

   *                             function"

   * @throws IException::Unknown "Unable to read bundle solution information from the given HDF5 

   *                             file"

   * 

   * @param bundleSolutionInfoFile The name of the BundleSolutionInfo we are reading from

   */

  void BundleSolutionInfo::openH5File(FileName bundleSolutionInfoFile) {



    try {

      if (!bundleSolutionInfoFile.fileExists()) {

        QString msg = "No file with the given name was found.";

        throw IException(IException::Io, msg, _FILEINFO_);

      }



      if (QString::compare(bundleSolutionInfoFile.extension(), "hdf", Qt::CaseInsensitive) != 0) {

        QString msg = "The given file is unsupported for constructing BundleSolutionInfo objects. "

                      "Supported file types include [hdf].";

        throw IException(IException::Io, msg, _FILEINFO_);

      }



      // catch H5 exceptions and rethrow

      try {

        /*

         * Turn off the auto-printing when failure occurs so that we can

         * handle the errors appropriately

         */

//        H5::Exception::dontPrint();//??? uncomment

    

        /* 

         * Create and open an H5File object with read-only access. This will throw an

         * H5 exception if the open fails.

         * 

         * The static H5Fopen() function will returns a negative file ID if it fails. So, in this

         * case, we would have to take the extra step of checking whether the return

         * is negative.

         */



        const H5std_string hdfFileName(bundleSolutionInfoFile.expanded().toStdString()); 

        H5::H5File hdfFile( hdfFileName, H5F_ACC_RDONLY ); // valgrind: Invalid read of size 4



        // get the BundleSolutionInfo group

        QString root = "/";

        QString bundleRunGroupName = root + "BundleSolutionInfo";

        H5::Group bundleRunGroup = hdfFile.openGroup(bundleRunGroupName.toLatin1());



        /* 

         * Add basic attributes

         */ 

        H5std_string attValue;



        Attribute att = bundleRunGroup.openAttribute("runTime");

        H5::StrType strDataType(H5::PredType::C_S1, att.getStorageSize());

        att.read(strDataType, attValue);

        m_runTime = QString::fromStdString(attValue);



        att = bundleRunGroup.openAttribute("controlNetworkFileName");

        strDataType = H5::StrType(H5::PredType::C_S1, att.getStorageSize());

        att.read(strDataType, attValue);

        m_controlNetworkFileName = new FileName(QString::fromStdString(attValue));



        m_settings->openH5Group(bundleRunGroup, bundleRunGroupName);

        m_statisticsResults->openH5Group(bundleRunGroup, bundleRunGroupName);



        // ???Let's just save off the image list file names for now...

        QString   imagesGroupName = bundleRunGroupName + "/imageLists";

        H5::Group imagesGroup     = bundleRunGroup.openGroup(imagesGroupName.toLatin1());

        int imagesGroupSize = (int)imagesGroup.getNumObjs();



        for (int i = 0; i < imagesGroupSize; i++) {

          H5std_string listGroupName = imagesGroup.getObjnameByIdx(i);

          H5::Group listGroup = imagesGroup.openGroup(listGroupName);

          

          H5std_string attValue;

          att = listGroup.openAttribute("path");

          strDataType = H5::StrType(H5::PredType::C_S1, att.getStorageSize());

          att.read(strDataType, attValue);

          QString listPath = QString::fromStdString(attValue);

          QString listName = QString::fromStdString(listGroupName).remove(imagesGroupName + "/");



          ImageList *imageList = new ImageList(listName, listPath);



          att = listGroup.openAttribute("fileNames");

          strDataType = H5::StrType(H5::PredType::C_S1, att.getStorageSize());

          att.read(strDataType, attValue);

          QStringList fileList = QString::fromStdString(attValue).split(",");

          for (int j = 0; j < fileList.size();j++) {

            imageList->append(new Image(fileList[j]));

          }



          m_images->append(imageList);// delete and null imageList???



        }

  #if 0

        

        QString   imagesGroupName = bundleRunGroupName + "/imageLists";

        H5::Group imagesGroup     = bundleRunGroup.openGroup(imagesGroupName.toLatin1());

        int imagesGroupSize = (int)imagesGroup.getNumObjs();



        for (int i = 0; i < imagesGroupSize; i++) {

          H5std_string listGroupName = imagesGroup.getObjnameByIdx(i);

          H5::Group listGroup = imagesGroup.openGroup(listGroupName);



          H5std_string attValue;

          att = listGroup.openAttribute("path");

          strDataType = H5::StrType(H5::PredType::C_S1, att.getStorageSize());

          att.read(strDataType, attValue);

          QString listPath = QString::fromStdString(attValue);

          QString listName = QString::fromStdString(listGroupName).remove(imagesGroupName + "/");



          ImageList *imageList = new ImageList(listName, listPath);

          imageList->openH5Group(bundleRunGroup, bundleRunGroupName);

          m_images.append(imageList);

        }

#endif



      }

      catch (H5::Exception error) {  //?? how to improve printed msg using major/minor error codes?

        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());

        IException hpfError(IException::Unknown, msg, _FILEINFO_);

        msg = "H5 exception handler has detected an error when invoking the function " 

              + QString::fromStdString(error.getFuncName()) + ".";

        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);

      }

    }

    catch (IException &e) {

      QString msg = "Unable to read bundle solution information from the given HDF5 file ["

                    + bundleSolutionInfoFile.expanded() + "].";

      throw IException(e, IException::Unknown, msg, _FILEINFO_);

    }

  }





  /**

   * Creates a new file using H5F_ACC_EXCL

   * 

   * @throws IException::Io "A file already exists with the given name ["

   * @throws IException::Unknown "H5 exception handler has detected an error when invoking the 

   *                             function"

   * @throws IException::Unknown "Unable to save bundle solution information to an HDF5 file."

   * 

   * @param outputFileName The name of the file we are creating.

   */

  void BundleSolutionInfo::createH5File(FileName outputFileName) const {



    try {

      if (outputFileName.fileExists()) {

        QString msg = "A file already exists with the given name ["

                      + outputFileName.expanded() + "].";

        throw IException(IException::Io, msg, _FILEINFO_);

      }



      // Try block to detect exceptions raised by any of the calls inside it

      try {

        /*

         * Turn off the auto-printing when failure occurs so that we can

         * handle the errors appropriately

         */

        //H5::Exception::dontPrint();



        /*

         * Create a new file using H5F_ACC_EXCL access,

         * default file creation properties, and default file

         * access properties.

         */

        const H5std_string hdfFileName(outputFileName.expanded().toStdString());

//        const H5std_string hdfFileName("./BundleSolutionInfo.hdf");

        H5::H5File hdfFile(hdfFileName, H5F_ACC_EXCL); // valgrind: Invalid read of size 4???



        // create BundleSolutionInfo group

        QString   root               = "/";

        QString   bundleRunGroupName = root + "BundleSolutionInfo";

        H5::Group bundleRunGroup     = hdfFile.createGroup(bundleRunGroupName.toLatin1());



        /* 

         * Add basic attributes

         */

        Attribute     att;

        H5::DataSpace spc(H5S_SCALAR); // single value space

        QString       attValue    = "";



        H5::StrType   strDataType(H5::PredType::C_S1, m_runTime.length());

        att = bundleRunGroup.createAttribute("runTime", strDataType, spc);

        att.write(strDataType, m_runTime.toStdString());



        attValue = m_controlNetworkFileName->expanded();

        strDataType = H5::StrType(H5::PredType::C_S1, attValue.length());

        att = bundleRunGroup.createAttribute("controlNetworkFileName", strDataType, spc);

        att.write(strDataType, attValue.toStdString());



        m_settings->createH5Group(bundleRunGroup, bundleRunGroupName);

        m_statisticsResults->createH5Group(bundleRunGroup, bundleRunGroupName);



        // Let's just save off the image list file names for now...

        QString   imagesGroupName = bundleRunGroupName + "/imageLists";

        H5::Group imagesGroup     = bundleRunGroup.createGroup(imagesGroupName.toLatin1());



        QString listGroupName = "";

        int     stringSize    = 0;



        for (int i = 0; i < m_images->size(); i++) {

          listGroupName = imagesGroupName + "/" + (*m_images)[i]->name();



          H5::Group listGroup = imagesGroup.createGroup(listGroupName.toLatin1());



          attValue = (*m_images)[i]->path();

          strDataType = H5::StrType(H5::PredType::C_S1, attValue.length());

          att = listGroup.createAttribute("path", strDataType, spc);

          att.write(strDataType, attValue.toStdString());



          QStringList fileList;

          for (int j = 0; j < (*m_images)[i]->size(); j++) {

            fileList += (*(*m_images)[i])[j]->fileName(); //???

          }



          QString fileNames = fileList.join(",");

          stringSize = qMax(fileNames.length(), 1);

          strDataType = H5::StrType(H5::PredType::C_S1, stringSize);

          att = listGroup.createAttribute("fileNames", strDataType, spc);

          att.write(strDataType, fileNames.toStdString());



        }

      }

      catch (H5::Exception error) {  //??? how to improve printed msg using major/minor error codes?

        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());

        IException hpfError(IException::Unknown, msg, _FILEINFO_);

        msg = "H5 exception handler has detected an error when invoking the function "

              + QString::fromStdString(error.getFuncName()) + ".";

        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);

      }

    }

    catch (IException &e) {

      throw IException(e,

                       IException::Unknown,

                       "Unable to save bundle solution information to an HDF5 file.",

                       _FILEINFO_);

    }

  }



}

isis/src/control/objs/BundleSolutionInfo/BundleSolutionInfo.h

+0 −6
Original line number Diff line number Diff line
@@ -105,7 +105,6 @@ namespace Isis { 
      BundleSolutionInfo(Project *project, 

                    XmlStackedHandlerReader *xmlReader, 

                    QObject *parent = 0);  //TODO does xml stuff need project???

      BundleSolutionInfo(FileName bundleSolutionInfoFile);

      BundleSolutionInfo(const BundleSolutionInfo &src);

      ~BundleSolutionInfo();

      BundleSolutionInfo &operator=(const BundleSolutionInfo &src);
@@ -140,11 +139,6 @@ namespace Isis { 
      QDataStream &write(QDataStream &stream) const;

      QDataStream &read(QDataStream &stream);



      void writeH5File(FileName outputFileName) const;

      void readH5File(FileName outputFileName) const;



      void createH5File(FileName outputFileName) const;

      void openH5File(FileName outputFileName);

//      BundleSolutionInfo(FileName bundleSolutionInfoFile);

      

      public slots:

isis/src/control/objs/BundleUtilities/BundleObservationSolveSettings.cpp

+0 −68
Original line number Diff line number Diff line
@@ -10,11 +10,6 @@ 
#include <QXmlInputSource>

#include <QXmlStreamWriter>



// in the hdf5 library

#include <hdf5.h>

#include <hdf5_hl.h> 

#include <H5Cpp.h>



#include "BundleImage.h"

#include "Camera.h"

#include "FileName.h"
@@ -1232,67 +1227,4 @@ namespace Isis { 
    return settings.read(stream);

  }





#if 0

  /** 

   *  H5 compound data type uses the offesets from the QDataStream returned by

   *  the write(QDataStream &stream) method.

   */

  H5::CompType BundleObservationSolveSettings::compoundH5DataType() {



    H5::CompType compoundDataType((size_t)   );



    size_t offset = 0;



    compoundDataType.insertMember("InstrumentId", offset, H5::PredType::C_S1);



    offset += sizeof(m_instrumentId);

    compoundDataType.insertMember("InstrumentPointingSolveOption", offset, H5::PredType::NATIVE_INT);



    offset += sizeof(m_instrumentId);

    compoundDataType.insertMember("NumCamAngleCoefSolved", offset, H5::PredType::NATIVE_INT);



    offset += sizeof(m_instrumentId);

    compoundDataType.insertMember("CkDegree", offset, H5::PredType::NATIVE_INT);



    offset += sizeof(m_instrumentId);

    compoundDataType.insertMember("CkSolveDegree", offset, H5::PredType::NATIVE_INT);



    offset += sizeof(m_instrumentId);

    compoundDataType.insertMember("SolveTwist", offset, H5::PredType::NATIVE_HBOOL);



    offset += sizeof(m_instrumentId);

    compoundDataType.insertMember("SolvePointingPolynomialOverExisting", offset, H5::PredType::NATIVE_HBOOL);



    offset += sizeof(m_instrumentId);

???    compoundDataType.insertMember("AnglesAprioriSigma", offset, H5::PredType::NATIVE_DOUBLE);



    offset += sizeof(m_instrumentId);

    compoundDataType.insertMember("PointingInterpolationType", offset, H5::PredType::NATIVE_INT);



    offset += sizeof(m_instrumentId);

    compoundDataType.insertMember("InstrumentPositionSolveOption", offset, H5::PredType::NATIVE_INT);



    offset += sizeof(m_instrumentId);

    compoundDataType.insertMember("NumCamPosCoefSolved", offset, H5::PredType::NATIVE_INT);



    offset += sizeof(m_numberCamPosCoefSolved);

    compoundDataType.insertMember("SpkDegree", offset, H5::PredType::NATIVE_INT);



    offset += sizeof(m_spkDegree);

    compoundDataType.insertMember("SpkSolveDegree", offset, H5::PredType::NATIVE_INT);



    offset += sizeof(m_spkSolveDegree);

    compoundDataType.insertMember("SolvePositionOverHermiteSpline", offset, H5::PredType::NATIVE_HBOOL);



    offset += sizeof(m_solvePositionOverHermiteSpline);

???    compoundDataType.insertMember("PositionAprioriSigma", offset, H5::PredType::NATIVE_DOUBLE);



    offset += sizeof(m_positionAprioriSigma);

    compoundDataType.insertMember("PositionInterpolationType", offset, H5::PredType::NATIVE_INT);



    return compoundDataType;



  }

#endif

}