Save and apply jigsaw adjustments

isis/src/base/objs/Table/Table.cpp

@@ -7,6 +7,7 @@ find files of those names at the top level of this repository. **/
 #include "Table.h"
 
 #include <fstream>
+#include <sstream>
 #include <string>
 
 #include "Blob.h"
@@ -137,6 +138,60 @@ namespace Isis {
     }
   }
 
+  /**
+   * This constructor takes in a string to create a Table object.
+   * 
+   * @param tableName The name o the Table to be read
+   * @param tableStr The table string
+   * @param fieldDelimiter The delimiter to separate fields with
+  */
+  Table::Table(const QString &tableName, const std::string &tableString, const char &fieldDelimiter) {
+    p_name = tableName;
+
+    std::stringstream tableStream;
+    tableStream << tableString;
+
+    // Create fieldNames  <-- refactor in progress
+    std::vector<std::string> tableLinesStringList;
+    std::string line;
+    while(std::getline(tableStream, line, '\n')) {
+      tableLinesStringList.push_back(line);
+    }
+
+    int numOfFieldValues = tableLinesStringList.size() - 1; // minus the header line 
+
+    std::string fieldNamesLineString = tableLinesStringList.front();
+    std::stringstream fieldNamesStringStream;
+    fieldNamesStringStream << fieldNamesLineString;
+
+    std::vector<QString> fieldNames;
+    std::string fieldNameString;
+    while(std::getline(fieldNamesStringStream, fieldNameString, fieldDelimiter)) {
+      fieldNames.push_back(QString::fromStdString(fieldNameString));
+    }
+
+    // Clear error flags and set pointer back to beginning
+    tableStream.clear();
+    tableStream.seekg(0, ios::beg);
+
+    // Add records to table
+    std::string recordString;
+    int index = 0;
+    while(std::getline(tableStream, recordString, '\n')) {
+      // skip first line bc that's the header line
+      if (index == 0) {
+        index++;
+        continue;
+      }
+
+      TableRecord tableRecord(recordString, fieldDelimiter, fieldNames, numOfFieldValues);
+      p_record = tableRecord;
+      std::cout << "Adding record" << std::endl;
+      this->operator+=(tableRecord);
+      index++;
+    }
+  }
+
 
   /**
    * Initialize a Table from a Blob that has been read from a file.

isis/src/base/objs/Table/Table.h

@@ -79,6 +79,7 @@ namespace Isis {
       Table(const QString &tableName, const QString &file,
             const Pvl &fileHeader);
       Table(const Table &other);
+      Table(const QString &tableName, const std::string &tableString, const char &fieldDelimiter);
       Table &operator=(const Isis::Table &other);
 
       ~Table();

isis/src/base/objs/TableRecord/TableRecord.cpp

@@ -8,6 +8,7 @@ find files of those names at the top level of this repository. **/
 #include "TableRecord.h"
 
 #include <iostream>
+#include <sstream>
 #include <string>
 #include <vector>
 
@@ -21,6 +22,21 @@ namespace Isis {
   TableRecord::TableRecord(){
   }
 
+  TableRecord::TableRecord(std::string tableRecordStr, char fieldDelimiter, 
+                            std::vector<QString> fieldNames, int numOfFieldValues) {
+    std::stringstream tableRecordStream;
+    tableRecordStream << tableRecordStr;
+
+    std::string fieldStr;
+    int i = 0;
+    while(std::getline(tableRecordStream, fieldStr, fieldDelimiter)) {
+      TableField tableField(fieldNames[i], TableField::Double);
+      tableField = std::stod(fieldStr); // convert string to double
+      p_fields.push_back(tableField);
+      i++;
+    }
+  }
+
   //! Destroys the TableRecord object
   TableRecord::~TableRecord() {
   }
@@ -155,7 +171,7 @@ namespace Isis {
       Isis::TableField &field = p_fields[f];
       field = (void *)&buf[sbyte];
       sbyte += field.bytes();
-    }
+    } 
   }
 
   /**

isis/src/base/objs/TableRecord/TableRecord.h

@@ -38,6 +38,8 @@ namespace Isis {
   class TableRecord {
     public:
       TableRecord();
+      TableRecord(std::string tableRecordStr, char fieldDelimiter, 
+                            std::vector<QString> fieldNames, int numOfFieldValues); 
       ~TableRecord();
 
 

isis/src/control/apps/jigsaw/jigsaw.cpp

@@ -7,13 +7,19 @@ find files of those names at the top level of this repository. **/
 /* SPDX-License-Identifier: CC0-1.0 */
 
 #include <iostream>
+#include <highfive/H5File.hpp>
+#include <highfive/H5DataType.hpp>
+#include <highfive/H5DataSet.hpp>
+#include <highfive/H5Group.hpp>
+#include <vector>
 
 #include <QDir>
 #include <QList>
 #include <QObject>
 #include <QSharedPointer>
 #include <QString>
 
+
 #include "Blob.h"
 #include "BundleAdjust.h"
 #include "BundleObservationSolveSettings.h"
@@ -35,6 +41,8 @@ find files of those names at the top level of this repository. **/
 #include "jigsaw.h"
 
 using namespace std;
+using namespace HighFive;
+
 
 namespace Isis {
 
@@ -130,24 +138,25 @@ namespace Isis {
         bundleSolution->outputResiduals();
       }
 
-    // write lidar csv output file
-    if (ui.GetBoolean("LIDAR_CSV")) {
-      bundleSolution->outputLidarCSV();
-    }
+      // write lidar csv output file
+      if (ui.GetBoolean("LIDAR_CSV")) {
+        bundleSolution->outputLidarCSV();
+      }
 
       // write updated control net
       bundleAdjustment->controlNet()->Write(ui.GetFileName("ONET"));
 
-    // write updated lidar data file
-    if (ui.WasEntered("LIDARDATA")) {
-      if (ui.GetString("OLIDARFORMAT") == "JSON") {
-        bundleAdjustment->lidarData()->write(ui.GetFileName("OLIDARDATA"),LidarData::Format::Json);
-      }
-      else {
-        bundleAdjustment->lidarData()->write(ui.GetFileName("OLIDARDATA"),LidarData::Format::Binary);
+      // write updated lidar data file
+      if (ui.WasEntered("LIDARDATA")) {
+        if (ui.GetString("OLIDARFORMAT") == "JSON") {
+          bundleAdjustment->lidarData()->write(ui.GetFileName("OLIDARDATA"),LidarData::Format::Json);
+        }
+        else {
+          bundleAdjustment->lidarData()->write(ui.GetFileName("OLIDARDATA"),LidarData::Format::Binary);
+        }
       }
-    }
       PvlGroup gp("JigsawResults");
+      QString adjustmentOutputFilename;
       // Update the cube pointing if requested but ONLY if bundle has converged
       if (ui.GetBoolean("UPDATE") ) {
         if ( !bundleAdjustment->isConverged() ) {
@@ -156,6 +165,19 @@ namespace Isis {
           throw IException(IException::Unknown, msg, _FILEINFO_);
         }
         else {
+          if (ui.GetFileName("ADJUSTMENT_OUTPUT") == NULL) {
+            gp += PvlKeyword("Status","If UPDATE=True then must specify bundle adjustment values to update cube files.");
+            QString msg = "ADJUSTMENT_OUTPUT value is missing";
+            throw IException(IException::Unknown, msg, _FILEINFO_);
+          }
+          adjustmentOutputFilename = ui.GetFileName("ADJUSTMENT_OUTPUT");
+          std::cout << "AdjustmentOutputFilename=" << adjustmentOutputFilename << std::endl;
+          // Initialize dataset for adjustment tables
+          File file(adjustmentOutputFilename.toStdString(), File::Truncate);
+
+
+          std::vector<std::string> adjustment_list;
+
           for (int i = 0; i < bundleAdjustment->numberOfImages(); i++) {
             Process p;
             CubeAttributeInput inAtt;
@@ -176,7 +198,9 @@ namespace Isis {
 
             //  Update the image parameters
             QString jigComment = "Jigged = " + Isis::iTime::CurrentLocalTime();
+
             if (c->hasBlob("CSMState", "String")) {
+              std::cout << "Cube has CSMState blob" << std::endl;
               Blob csmStateBlob("CSMState", "String");
               // Read the BLOB from the cube to propagate things like the model
               // and plugin name
@@ -193,9 +217,46 @@ namespace Isis {
               spvector.Label().addComment(jigComment);
               c->write(cmatrix);
               c->write(spvector);
+
+              QString serialNumber = bundleAdjustment->serialNumberList()->serialNumber(i);
+              QString cmatrixName = cmatrix.Name();
+              QString spvectorName = spvector.Name();
+              std::cout << "serialNumber=" << serialNumber.toStdString() << std::endl;
+
+              std::string cmatrixKey = serialNumber.toStdString() + "/" + cmatrixName.toStdString();
+              std::string spvectorKey = serialNumber.toStdString() + "/" + spvectorName.toStdString();
+
+              if (adjustmentOutputFilename != NULL) {
+
+                std::string cmatrixTableStr = Table::toString(cmatrix).toStdString();
+                DataSet dataset = file.createDataSet<std::string>(cmatrixKey, cmatrixTableStr);
+                std::string spvectorTableStr = Table::toString(spvector).toStdString();
+                dataset = file.createDataSet<std::string>(spvectorKey, spvectorTableStr);
+
+                // TODO: Add metadata to h5 file
+                PvlKeyword timeDependentFrames = c->label()->findObject(cmatrixName).findKeyword("TimeDependentFrames");
+              }
+              if (ui.WasEntered("ADJUSTMENT_INPUT")) {
+                QString adjustmentInputFilename = ui.GetFileName("ADJUSTMENT_INPUT");
+                std::cout << "AdjustmentInputFilename=" << adjustmentInputFilename << std::endl;
+                File fileRead(adjustmentInputFilename.toStdString(), File::ReadOnly);
+                DataSet datasetRead = fileRead.getDataSet(cmatrixKey);
+                std::vector<std::string> cmatrixData;
+                datasetRead.read(cmatrixData);
+                for (int i = 0; i < cmatrixData.size(); i++) {
+                  Table cmatrixTable(QString::fromStdString(cmatrixKey), cmatrixData[i], ',');
+                  // WIP <---
+                }
+              }
+
+              // flag = output to this file
             }
             p.WriteHistory(*c);
           }
+          // std::cout << "Writing out dataset" << std::endl;
+          // dataset.write(adjustment_list);
+          // std::cout <<"After writing to dataset" << std::endl;
+
           gp += PvlKeyword("Status", "Camera pointing updated");
         }
       }

isis/src/control/apps/jigsaw/jigsaw.xml

@@ -680,6 +680,34 @@
         </filter>
       </parameter>
 
+      <parameter name="ADJUSTMENT_OUTPUT">
+        <type>filename</type>
+        <fileMode>input</fileMode>
+        <brief>
+          Outputs adjustment values
+        </brief>
+        <description>
+          "Outputs adjustment values"
+        </description>
+        <filter>
+          *.h5
+        </filter>
+      </parameter>
+
+      <parameter name="ADJUSTMENT_INPUT">
+        <type>filename</type>
+        <fileMode>input</fileMode>
+        <brief>
+          Reads in adjustment values
+        </brief>
+        <description>
+          "Reads in adjustment values"
+        </description>
+        <filter>
+          *.h5
+        </filter>
+      </parameter>
+
       <parameter name="HELDLIST">
         <type>filename</type>
         <internalDefault>none</internalDefault>

isis/tests/TableTests.cpp

@@ -295,3 +295,33 @@ TEST(TableTests, Clear) {
 
   EXPECT_EQ(t.Records(), 0);
 }
+
+TEST(TableTests, FromString) {
+  std::string tableStr = "J2000Ang1,J2000Ang2,J2000Ang3\n"
+    "-1.0261086365746,1.3843980236775,0.97666760713915\n"
+    "-0.026127047776247,0.034245411189199,0.0052635095732964\n"
+    "-0.005717949450684,-0.0039014897927048,2.3750859084069e-05\n"
+    "260093852.48957,46.12915199995,2.0\n";
+
+  std::cout << "tableStr=" << tableStr << std::endl;
+
+  QString tableName = QString::fromStdString("TestTableName");
+
+  std::stringstream tableStrStream;
+  tableStrStream << tableStr;
+
+  Table table(tableName, tableStr, ',');
+  std::cout << "Created table with table string" << std::endl;
+  std::cout << "Table name=" << table.Name().toStdString() << std::endl;
+  std::cout << "Table recordFields=" << static_cast<int>(table.RecordFields()) << std::endl;
+  std::cout << "Table recordSize=" << static_cast<int>(table.RecordSize()) << std::endl;
+
+  for (int i = 0; i < table.Records(); i++) {
+    std::cout << "Table[" << i << "] record=" << TableRecord::toString(table[i]).toStdString() << std::endl;
+  }
+
+  QString tableToString = Table::toString(table);
+  std::cout << "tableToString=" << tableToString.toStdString() << std::endl;
+
+  EXPECT_EQ(tableStr, tableToString.toStdString());
+}