Blob Refactor (#4348)

* Updated to new blob structure * Clean up after being able to look at all of the changes at once * Changed the history read to return a history object rather than a pointer * Addressed PR feedback * Imagepolygon Update (#4308) * Converted Imagepolygon to no longer be a subclass of blob * Updated Imagepolygon with constructor chaining * Fixed error message * Refactor OriginalLabel class to remove inheritance from Blob (#4309) * Initial refactor of OriginalLabel class * Addressed PR feedback * Fixed error message Co-authored-by: Jesse Mapel <jmapel@usgs.gov> * Modified Table to not inherit from Blob anymore (#4312) * Ported Table test to gtest * Table refactor * Fixed merge issue * Fixed merge issues * Removes blob inheritance from OriginalXmlLabel (#4316) * Initial refactor of OriginalLabel class * Addressed PR feedback * Fixed error message * Remove blob inheritance from originalxmllabel * Removed commented / old code * Added byte order specification * History object tests (#4314) * Adds History object tests * Updated blob tests to use a non-pointer variable * Removed gisblob from isis (#4329) * Removed blob inheritance from stretchblob (#4331) * Removed blob inheritance from stretchblob * Addressed feedback + working read/write * Updated cubestretch with the stretch blob functionality * Removed stretchBlob and updated cubestretch/cube with read write functionality * Replaced readStretchBlob with readCubeStretch * Fixed segfault * Removed debug print statements * Added check for existence of OriginalLabel before attempting to propagate * Addressed PR feedback Co-authored-by: Adam Paquette <acpaquette@usgs.gov> * Removed StringBlob Class (#4321) * Converted StringBlob * Removed StretchBlob class * Changed Blob setData to copy * Added csminit change and docs * Removed old memcopy * History Blob Old Implementation (#4342) * Implemented old history functionality * Removed old history unit test * Fixed original label reading * Fixed Blob branch test failures (#4344) * Fixed test failures * More clean-up * Fixed marci2isis test * Blob final clean-up (#4346) * Redid Blob writing * Added docs * Review feedback * Fixed int comparison Co-authored-by: Adam Paquette <acpaquette@usgs.gov> Co-authored-by: AustinSanders <arsanders@usgs.gov>
DOI-USGS · Mar 9, 2021 · dbfb004 · dbfb004
1 parent a394b82
commit dbfb004
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Showing 122 changed files with 1,940 additions and 2,322 deletions.
diff --git a/isis/src/apollo/apps/apollofindrx/apollofindrx.cpp b/isis/src/apollo/apps/apollofindrx/apollofindrx.cpp
@@ -169,15 +169,14 @@ namespace Isis {
         }
 
         if (cube->label()->hasObject("History")) {
-            PvlObject histObj = cube->label()->findObject("History");
             // Record apollofindrx history to the cube
+            QString histName = (QString)cube->label()->findObject("History")["Name"];
             // create a History Blob with value found in the History PvlObject's Name keyword
-            Isis::History histBlob( (QString)histObj["Name"] );
             // read cube's History PvlObject data into the History Blob
-            cube->read(histBlob);
+            History hist = cube->readHistory(histName);
             // add apollofindrx History PvlObject into the History Blob and write to cube
-            histBlob.AddEntry();
-            cube->write(histBlob);
+            hist.AddEntry();
+            cube->write(hist);
             cube->close();
         }
     }

diff --git a/isis/src/apollo/apps/apollopaninit/main.cpp b/isis/src/apollo/apps/apollopaninit/main.cpp
@@ -261,8 +261,6 @@ void IsisMain() {
   //create a table from starttime to endtime (stretched by 3%) with NODES entries
   spPos->LoadCache(time0-0.015*(time1-time0), time1+0.015*(time1-time0), NODES);
   Table tableSunPos = spPos->Cache("SunPosition");
-  tableSunPos.Label() += PvlKeyword("SpkTableStartTime", toString(time0-0.015*(time1-time0)));
-  tableSunPos.Label() += PvlKeyword("SpkTablleEndTime", toString(time1+0.015*(time1-time0)));
   tableSunPos.Label() += PvlKeyword("Description", "Created by apollopaninit");
   panCube.write(tableSunPos);  //attach the table to the cube
 

diff --git a/isis/src/base/apps/caminfo/CamTools.cpp b/isis/src/base/apps/caminfo/CamTools.cpp
@@ -334,14 +334,8 @@ namespace Isis {
 
       if (getFootBlob && band == 0) {
         // Read the footprint from the image labels
-        ImagePolygon poly;
-        try {
-          cube.read(poly);
-        }
-        catch (IException &e) {
-          QString msg = "Error reading footprint blob from image labels";
-          throw IException(e, IException::User, msg, _FILEINFO_);
-        }
+        ImagePolygon poly = cube.readFootprint();
+        cube.close();
         geos::geom::MultiPolygon *multiP = poly.Polys();
         _polys.push_back(multiP->clone());
         _combined = multiP->clone();

diff --git a/isis/src/base/apps/caminfo/caminfo.cpp b/isis/src/base/apps/caminfo/caminfo.cpp
@@ -13,7 +13,6 @@
 #include "iTime.h"
 #include "LineManager.h"
 #include "OriginalLabel.h"
-#include "Process.h"
 #include "ProgramLauncher.h"
 #include "Progress.h"
 #include "Pvl.h"
@@ -82,8 +81,7 @@ namespace Isis{
 
       // Add the orginal label blob
       if(ui.GetBoolean("ORIGINALLABEL") && incube->label()->hasObject("OriginalLabel")) {
-        OriginalLabel orig;
-        incube->read(orig);
+        OriginalLabel orig = incube->readOriginalLabel();
         Pvl p = orig.ReturnLabels();
         p.setName("OriginalLabel");
         params.addObject(p);
@@ -372,7 +370,7 @@ namespace Isis{
           if (getFootBlob) {
             // Need to read history to obtain parameters that were used to
             // create the footprint
-            History hist("IsisCube", incube->fileName());
+            History hist = incube->readHistory();
             Pvl pvl = hist.ReturnHist();
             PvlObject::PvlObjectIterator objIter;
             bool found = false;

diff --git a/isis/src/base/apps/cathist/main.cpp b/isis/src/base/apps/cathist/main.cpp
@@ -5,7 +5,7 @@
 #include "FileName.h"
 #include "IString.h"
 #include "History.h"
-#include "Pvl.h"   
+#include "Pvl.h"
 #include "TextFile.h"
 
 using namespace Isis;
@@ -26,7 +26,8 @@ void IsisMain() {
   }
 
   // Extract history from file
-  History hist("IsisCube", fromfile.expanded());
+  Blob historyBlob("IsisCube", "History", fromfile.expanded());
+  History hist(historyBlob);
   Pvl pvl = hist.ReturnHist();
 
   // Print full history

diff --git a/isis/src/base/apps/copylabel/main.cpp b/isis/src/base/apps/copylabel/main.cpp
@@ -3,6 +3,7 @@
 #include "Application.h"
 #include "Cube.h"
 #include "History.h"
+#include "Process.h"
 #include "Pvl.h"
 #include "PvlGroup.h"
 #include "PvlObject.h"
@@ -227,22 +228,8 @@ void IsisMain() {
     subarea.UpdateLabel(&inOut, &inOut, results);
   }
 
-  // Add History
-  bool found = false;
-  for (int i = 0; i < mergeTo->objects() && !found; i++) {
-    if (mergeTo->object(i).isNamed("History")) {
-      History his((QString)mergeTo->object(i)["Name"]);
-      inOut.read(his);
-      his.AddEntry();
-      inOut.write(his);
-      found = true;
-    }
-  }
-  if (!found) {
-    History his("IsisCube");
-    his.AddEntry();
-    inOut.write(his);
-  }
+  Process process;
+  process.WriteHistory(inOut);
 
   inOut.close();
   sourceCube.close();
@@ -279,4 +266,3 @@ bool copyBlob(Cube * from, Cube * to, QString name, QString type, QString fname)
     return false;
   }
 }
-
diff --git a/isis/src/base/apps/csminit/csminit.cpp b/isis/src/base/apps/csminit/csminit.cpp
@@ -29,7 +29,6 @@ find files of those names at the top level of this repository. **/
 #include "Pvl.h"
 #include "PvlGroup.h"
 #include "PvlKeyword.h"
-#include "StringBlob.h"
 
 using namespace std;
 
@@ -364,54 +363,55 @@ namespace Isis {
     }
 
     // Save off all old Blobs to restore in the case of csminit failure
-    StringBlob originalCsmStateBlob("", "CSMState");
-    if (cube->hasBlob("String", "CSMState")) {
+    Blob originalCsmStateBlob("CSMState", "String");
+    if (cube->hasBlob("CSMState", "String")) {
       cube->read(originalCsmStateBlob);
     }
 
     Table originalInstrumentPointing("InstrumentPointing");
     if (cube->hasTable("InstrumentPointing")) {
-      cube->read(originalInstrumentPointing);
+      originalInstrumentPointing = cube->readTable("InstrumentPointing");
     }
 
     Table originalInstrumentPosition("InstrumentPosition");
     if (cube->hasTable("InstrumentPosition")) {
-      cube->read(originalInstrumentPosition);
+      originalInstrumentPosition = cube->readTable("InstrumentPosition");
     }
 
     Table originalBodyRotation("BodyRotation");
     if (cube->hasTable("BodyRotation")) {
-      cube->read(originalBodyRotation);
+      originalBodyRotation = cube->readTable("BodyRotation");
     }
 
     Table originalSunPosition("SunPosition");
     if (cube->hasTable("SunPosition")) {
-      cube->read(originalSunPosition);
+      originalSunPosition = cube->readTable("SunPosition");
     }
 
     Table originalCameraStatistics("CameraStatistics");
     if (cube->hasTable("CameraStatistics")) {
-      cube->read(originalCameraStatistics);
+      originalCameraStatistics = cube->readTable("CameraStatistics");
     }
 
     ImagePolygon originalFootprint;
-    if (cube->hasBlob("Polygon", "ImageFootprint")) {
-      cube->read(originalFootprint);
+    if (cube->hasBlob("ImageFootprint", "Polygon")) {
+      originalFootprint = cube->readFootprint();
     }
 
     // Remove blob from old csminit run
-    cube->deleteBlob("String", "CSMState");
+    cube->deleteBlob("CSMState", "String");
 
     // Remove tables from spiceinit before writing to the cube
-    cube->deleteBlob("Table", "InstrumentPointing");
-    cube->deleteBlob("Table", "InstrumentPosition");
-    cube->deleteBlob("Table", "BodyRotation");
-    cube->deleteBlob("Table", "SunPosition");
-    cube->deleteBlob("Table", "CameraStatistics");
-    cube->deleteBlob("Polygon", "Footprint");
+    cube->deleteBlob("InstrumentPointing", "Table");
+    cube->deleteBlob("InstrumentPosition", "Table");
+    cube->deleteBlob("BodyRotation", "Table");
+    cube->deleteBlob("SunPosition", "Table");
+    cube->deleteBlob("CameraStatistics", "Table");
+    cube->deleteBlob("Footprint", "Polygon");
 
     // Create our CSM State blob as a string and add the CSM string to the Blob.
-    StringBlob csmStateBlob(modelState, "CSMState");
+    Blob csmStateBlob("CSMState", "String");
+    csmStateBlob.setData(modelState.c_str(), modelState.size());
     PvlObject &blobLabel = csmStateBlob.Label();
     blobLabel += PvlKeyword("ModelName", modelName);
     blobLabel += PvlKeyword("PluginName", pluginName);
@@ -438,7 +438,7 @@ namespace Isis {
         cube->putGroup(originalCsmInfo);
       }
 
-      cube->deleteBlob("String", "CSMState");
+      cube->deleteBlob("CSMState", "String");
 
       // Restore the original blobs
       if (originalCsmStateBlob.Size() != 0) {
@@ -465,7 +465,9 @@ namespace Isis {
         cube->write(originalCameraStatistics);
       }
 
-      if (originalFootprint.Size() != 0) {
+
+      if (originalFootprint.Polys() != NULL &&
+          originalFootprint.Polys()->getNumGeometries() != 0) {
         cube->write(originalFootprint);
       }
 

diff --git a/isis/src/base/apps/cubeit/main.cpp b/isis/src/base/apps/cubeit/main.cpp
@@ -179,9 +179,7 @@ void IsisMain() {
   }
 
   // Delete any tracking tables from the input label if necessary
-  if (ocube->hasTable("InputImages")) {
-    ocube->deleteBlob("Table", "InputImages");
-  }
+  ocube->deleteBlob("InputImages", "Table");
 
   // Delete the Tracking group if it exists (3.6.0 and up)
   // The tracking group could be transfered from the first input cube, but it does not
@@ -220,9 +218,7 @@ void IsisMain() {
     Cube *icube = m.SetInputCube(newcubeList[i].toString(), attrib, 1, 1, 1, -1, -1, -1);
 
     // Delete any tracking tables from the input cube if necessary
-    if (icube->hasTable("InputImages")) {
-      icube->deleteBlob("Table", "InputImages");
-    }
+    icube->deleteBlob("InputImages", "Table");
 
     m.SetImageOverlay(ProcessMosaic::PlaceImagesOnTop);
     m.StartProcess(1, 1, sband);

diff --git a/isis/src/base/apps/demprep/demprep.cpp b/isis/src/base/apps/demprep/demprep.cpp
@@ -5,7 +5,6 @@
 #include "TProjection.h"
 #include "SpecialPixel.h"
 #include "LineManager.h"
-#include "OriginalLabel.h"
 #include "History.h"
 #include "Table.h"
 #include "Pvl.h"

diff --git a/isis/src/base/apps/desmile/main.cpp b/isis/src/base/apps/desmile/main.cpp
@@ -16,7 +16,7 @@
 #include "History.h"
 
 #include "Spectel.h"
-#include "SpectralDefinition.h" 
+#include "SpectralDefinition.h"
 #include "SpectralDefinitionFactory.h"
 #include "SpectralDefinition1D.h"
 #include "SpectralDefinition2D.h"
@@ -40,14 +40,14 @@ void IsisMain() {
   Cube *inCube = procSpectra.SetInputCube("FROM");
 
   // Get the spectral information for the input cube
-  FileName smileDef = ui.GetFileName("SMILEDEF"); 
+  FileName smileDef = ui.GetFileName("SMILEDEF");
   // TODO: May want to add the cube to the constructor args so some error checks can be done
-  SpectralDefinition* inputSpectralDef = SpectralDefinitionFactory::NewSpectralDefinition(smileDef); 
+  SpectralDefinition* inputSpectralDef = SpectralDefinitionFactory::NewSpectralDefinition(smileDef);
 
   // Get the spectral information for the output cube
   FileName smileObjective = ui.GetFileName("OBJECTIVE");
-  SpectralDefinition* outputSpectralDef = 
-      SpectralDefinitionFactory::NewSpectralDefinition(smileObjective); 
+  SpectralDefinition* outputSpectralDef =
+      SpectralDefinitionFactory::NewSpectralDefinition(smileObjective);
 
   // Set up the output cube. It may have a different number of bands than the input cube.
   Cube *outCube = procSpectra.SetOutputCube("TO", inCube->sampleCount(), inCube->lineCount(),
@@ -98,17 +98,15 @@ void IsisMain() {
     // Record apollofindrx history to the cube
 
   // create a History Blob with value found in the History PvlObject's Name keyword
-  PvlObject &histObj = inCube->label()->findObject("History");
-  Isis::History histBlob( (QString)histObj["Name"] );
-  // read cube's History PvlObject data into the History Blob
-  inCube->read(histBlob);
+  QString histName = (QString)inCube->label()->findObject("History")["Name"];
+  // read cube's History PvlObject data into the History Object
+  History histBlob = inCube->readHistory(histName);
   histBlob.AddEntry();
-  outCube->write(histBlob);
+  outCube->write(histBlob, histName);
 
   procSpectra.Finalize();
   delete outputSpectralDef;
   outputSpectralDef = NULL;
-  delete inputSpectralDef; 
+  delete inputSpectralDef;
   inputSpectralDef = NULL;
 }
-
diff --git a/isis/src/base/apps/editlab/main.cpp b/isis/src/base/apps/editlab/main.cpp
@@ -100,15 +100,7 @@ void IsisMain() {
 
   // Add history, write, and clean the data
   if(cube) {
-    History hist = History("IsisCube");
-    try {
-      // read history from cube, if it exists.
-      cube->read(hist);
-    }
-    catch(IException &e) {
-      // if the history does not exist in the cube, continue. In this case, 
-      // editlab will be the first History entry.
-    }
+    History hist = cube->readHistory();
     hist.AddEntry();
     cube->write(hist);
 
@@ -128,10 +120,10 @@ void IsisMain() {
 /**
  * Modifies the given keyword with the user entered value, units, and/or
  * comment.
- * 
+ *
  * @param ui UserInterface object for this application.
  * @param keyword PvlKeyword to be modified.
- * 
+ *
  * @return PvlKeyword Modified keyword.
  */
 PvlKeyword &modifyKeyword(UserInterface &ui, PvlKeyword &keyword) {