Save and apply jigsaw adjustments (#5419)

* Current state

* Save and apply bundle values

* Add test

* Update changelog

* Update yaml and fix for loop issue

* Address test failures

* Make adjustment_output and _input optional

* Update workflow, added new param adjustmentout_h5, updated docs

* Add orientation check

* Update doc

* Address test failures

* Address comments

CHANGELOG.md

@@ -70,6 +70,7 @@ 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/SpiceRotation/SpiceRotation.cpp

@@ -1880,6 +1880,11 @@ namespace Isis {
                                     const std::vector<double> &coeffAng3,
                                     const Source type) {
 
+    if (type == PolyFunctionOverSpice && !m_orientation) {
+      QString msg = "The quaternion SPICE tables are no longer available. " 
+                    "Either re-run spiceinit or set OVEREXISTING to False.";
+      throw IException(IException::User, msg, _FILEINFO_);
+    }                             
     NaifStatus::CheckErrors();
     Isis::PolynomialUnivariate function1(p_degree);
     Isis::PolynomialUnivariate function2(p_degree);
@@ -3253,7 +3258,7 @@ namespace Isis {
    * @see SpiceRotation::SetEphemerisTime
    */
   void SpiceRotation::setEphemerisTimeMemcache() {
-   // If the cache has only one rotation, set it
+    // If the cache has only one rotation, set it
     NaifStatus::CheckErrors();
     if (p_cacheTime.size() == 1) {
       p_CJ = m_orientation->getRotations()[0].toRotationMatrix();
@@ -3487,23 +3492,23 @@ namespace Isis {
       p_av[index] += cacheVelocity[index];
     }
 
-   if (angles[0] <= -1 * pi_c()) {
-     angles[0] += twopi_c();
-   }
-   else if (angles[0] > pi_c()) {
-     angles[0] -= twopi_c();
-   }
+    if (angles[0] <= -1 * pi_c()) {
+      angles[0] += twopi_c();
+    }
+    else if (angles[0] > pi_c()) {
+      angles[0] -= twopi_c();
+    }
 
-   if (angles[2] <= -1 * pi_c()) {
-     angles[2] += twopi_c();
-   }
-   else if (angles[2] > pi_c()) {
-     angles[2] -= twopi_c();
-   }
+    if (angles[2] <= -1 * pi_c()) {
+      angles[2] += twopi_c();
+    }
+    else if (angles[2] > pi_c()) {
+      angles[2] -= twopi_c();
+    }
 
-   eul2m_c((SpiceDouble) angles[2], (SpiceDouble) angles[1], (SpiceDouble) angles[0],
-           p_axis3,                 p_axis2,                 p_axis1,
-           (SpiceDouble( *)[3]) &p_CJ[0]);
+    eul2m_c((SpiceDouble) angles[2], (SpiceDouble) angles[1], (SpiceDouble) angles[0],
+            p_axis3,                 p_axis2,                 p_axis1,
+            (SpiceDouble( *)[3]) &p_CJ[0]);
   }
 
 

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();