Save and apply jigsaw adjustments

CHANGELOG.md

@@ -57,6 +57,7 @@ release.
 - Fixed gllssi2isis to support V1.1 data [#5396](https://github.com/DOI-USGS/ISIS3/issues/5396)
 
 ### Added
+- Added option to save and apply bundle adjustment values in `jigsaw` [#4474](https://github.com/DOI-USGS/ISIS3/issues/4474)
 - Added versioned default values to lrowacphomap's PHOALGO and PHOPARCUBE parameters and updated lrowacphomap to handle them properly. [#5452](https://github.com/DOI-USGS/ISIS3/pull/5452)
 
 ## [8.2.0] - 2024-04-18

environment.yml

@@ -27,6 +27,7 @@ dependencies:
   - graphviz
   - conda-forge::gsl >=2.6, <2.7
   - hdf5
+  - highfive
   - icu
   - inja
   - jama

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 +138,63 @@ namespace Isis {
     }
   }
 
+  /**
+   * This constructor takes in a string to create a Table object.
+   * 
+   * @param tableName The name of 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;
+
+    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;
+      this->operator+=(tableRecord);
+      index++;
+    }
+
+    // Add fields
+    for (int f = 0; f < p_record.Fields(); f++) {
+      p_label.addGroup(p_record[f].pvlGroup());
+    }
+  }
+
 
   /**
    * 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 +22,29 @@ namespace Isis {
   TableRecord::TableRecord(){
   }
 
+  /**
+  * TableRecord constructor
+  * 
+  * @param tableRecordStr Table record string
+  * @param fieldDelimiter The delimiter to separate fields with
+  * @param fieldNames Table header names
+  * @param numOfFieldValues Number of fields (rows)
+  */
+  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
+      this->operator+=(tableField);
+      i++;
+    }
+  }
+
   //! Destroys the TableRecord object
   TableRecord::~TableRecord() {
   }
@@ -155,7 +179,7 @@ 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 {
 
@@ -130,23 +138,23 @@ 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");
       // Update the cube pointing if requested but ONLY if bundle has converged
       if (ui.GetBoolean("UPDATE") ) {
@@ -156,6 +164,29 @@ namespace Isis {
           throw IException(IException::Unknown, msg, _FILEINFO_);
         }
         else {
+
+          // Update the image parameters
+          QString jigComment = "Jigged = " + Isis::iTime::CurrentLocalTime();
+
+          // Need to prep the adjustment file first
+          QString adjustmentType;
+          unsigned adjustmentFileEnum = 0;
+          QString adjustmentFilename;
+          bool placeholderAdjustmentFileExists = false;
+          if (ui.WasEntered("ADJUSTMENT_OUTPUT")) {
+            adjustmentFilename = ui.GetFileName("ADJUSTMENT_OUTPUT");
+            adjustmentFileEnum = File::Truncate;
+          } else if (ui.WasEntered("ADJUSTMENT_INPUT")) {
+            adjustmentFilename = ui.GetFileName("ADJUSTMENT_INPUT");
+            adjustmentFileEnum = File::ReadOnly;
+          } else {
+            placeholderAdjustmentFileExists = true;
+            adjustmentFilename = "/tmp/placeholder_adj.tmp";
+            adjustmentFileEnum = File::Create;
+          }
+          File file(adjustmentFilename.toStdString(), adjustmentFileEnum);
+
+          // Loop through images
           for (int i = 0; i < bundleAdjustment->numberOfImages(); i++) {
             Process p;
             CubeAttributeInput inAtt;
@@ -174,8 +205,6 @@ namespace Isis {
               break;
             }
 
-            //  Update the image parameters
-            QString jigComment = "Jigged = " + Isis::iTime::CurrentLocalTime();
             if (c->hasBlob("CSMState", "String")) {
               Blob csmStateBlob("CSMState", "String");
               // Read the BLOB from the cube to propagate things like the model
@@ -185,17 +214,75 @@ namespace Isis {
               csmStateBlob.setData(modelState.c_str(), modelState.size());
               csmStateBlob.Label().addComment(jigComment);
               c->write(csmStateBlob);
-            }
-            else {
+            } else if (ui.WasEntered("ADJUSTMENT_OUTPUT")) {
+              // Write bundle adjustment values to cube
               Table cmatrix = bundleAdjustment->cMatrix(i);
               cmatrix.Label().addComment(jigComment);
               Table spvector = bundleAdjustment->spVector(i);
               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::string cmatrixKey = serialNumber.toStdString() + "/" + cmatrixName.toStdString();
+              std::string spvectorKey = serialNumber.toStdString() + "/" + spvectorName.toStdString();
+
+              // Save bundle adjustment values to HDF5 file
+              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);
+            } else if (ui.WasEntered("ADJUSTMENT_INPUT")) {
+              Table cmatrix = bundleAdjustment->cMatrix(i);
+              Table spvector = bundleAdjustment->spVector(i);
+
+              QString serialNumber = bundleAdjustment->serialNumberList()->serialNumber(i);
+              QString cmatrixName = cmatrix.Name();
+              QString spvectorName = spvector.Name();
+
+              std::string cmatrixKey = serialNumber.toStdString() + "/" + cmatrixName.toStdString();
+              std::string spvectorKey = serialNumber.toStdString() + "/" + spvectorName.toStdString();
+
+              // Read h5 into table
+              DataSet datasetRead = file.getDataSet(cmatrixKey);
+              auto cmatrixData = datasetRead.read<std::string>();
+              Table cmatrixTable(cmatrixName, cmatrixData, ',');
+
+              datasetRead = file.getDataSet(spvectorKey);
+              auto spvectorData = datasetRead.read<std::string>();
+              Table spvectorTable(spvectorName, spvectorData, ',');
+
+              // Write bundle adjustment values out
+              cmatrixTable.Label().addComment(jigComment);
+              c->write(cmatrixTable);
+              spvectorTable.Label().addComment(jigComment);
+              c->write(spvectorTable);
+            } else {
+              std::cout << "ADJUSTMENT ERROR????" << std::endl;
+              gp += PvlKeyword("Status","If UPDATE=True then must specify either ADJUSTMENT_OUTPUT or ADJUSTMENT_INPUT or must be csminit'd.");
+              QString msg = "If UPDATE=True, must run csminit on cubes or specify either ADJUSTMENT_OUTPUT or ADJUSTMENT_INPUT.";
+              throw IException(IException::Unknown, msg, _FILEINFO_);
             }
             p.WriteHistory(*c);
           }
+
+          // Check if temp adjustment file was created
+          // Delete if so
+          if (placeholderAdjustmentFileExists) {
+            int status = remove(adjustmentFilename.toStdString().c_str());
+            if (status != 0) {
+              PvlGroup tempAdjustmentFileWarning("TemporaryAdjustmentFileWarning");
+              tempAdjustmentFileWarning.addKeyword(PvlKeyword("Warning", "The placeholder adjustment file \
+                                                                              " + adjustmentFilename + "was \
+                                                                              not removed properly."));
+              if(log) {
+                log->addLogGroup(tempAdjustmentFileWarning);
+              }
+            }
+          }
           gp += PvlKeyword("Status", "Camera pointing updated");
         }
       }

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

@@ -885,7 +885,9 @@
           from the solution if the adjustment converges.  The results are written
           to the <def>SPICE</def> blobs attached to the cube, overwriting the previous
           values.  If this option is not selected, the <def>cube</def> files are not
-          changed.  All other output files are still created.
+          changed.  All other output files are still created. Unless the cubes have a
+          CSMState blob attached, must either define ADJUSTMENT_OUTPUT or ADJUSTMENT_INPUT
+          if UPDATE is true.
         </description>
         <type>boolean</type>
         <default>
@@ -1835,6 +1837,36 @@
             <item>no</item>
           </default>
         </parameter>
+
+        <parameter name="ADJUSTMENT_OUTPUT">
+          <type>filename</type>
+          <internalDefault>none</internalDefault>
+          <fileMode>input</fileMode>
+          <brief>
+            Outputs adjustment values
+          </brief>
+          <description>
+            "Outputs adjustment values"
+          </description>
+          <filter>
+            *.h5
+          </filter>
+        </parameter>
+
+        <parameter name="ADJUSTMENT_INPUT">
+          <type>filename</type>
+          <internalDefault>none</internalDefault>
+          <fileMode>input</fileMode>
+          <brief>
+            Reads in adjustment values
+          </brief>
+          <description>
+            "Reads in adjustment values"
+          </description>
+          <filter>
+            *.h5
+          </filter>
+        </parameter>
       </group>
 
     </groups>