Merged in jaz_3.1 (pull request #21)

Jaz 3.1
3dem · Dec 3, 2018 · 11875c2 · 11875c2
2 parents 18fa37a + 6ac2951
commit 11875c2
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Showing 39 changed files with 319 additions and 1,275 deletions.
diff --git a/src/apps/ctf_mask_test.cpp b/src/apps/ctf_mask_test.cpp
@@ -51,9 +51,9 @@ int main(int argc, char *argv[])
     }
 
 	ObservationModel obsModel;	
-	MetaDataTable mdt0, opticsMdt;
+	MetaDataTable mdt0;
 
-	ObservationModel::loadSafely(starFn, obsModel, mdt0, opticsMdt);
+	ObservationModel::loadSafely(starFn, obsModel, mdt0);
 
 	std::vector<MetaDataTable> allMdts = StackHelper::splitByMicrographName(mdt0);
 	int opticsGroup = obsModel.getOpticsGroup(allMdts[mg], 0);

diff --git a/src/apps/demodulate.cpp b/src/apps/demodulate.cpp
@@ -8,7 +8,7 @@
 int main(int argc, char *argv[])
 {
 	std::string particlesFn, outPath;
-	MetaDataTable particlesMdt, opticsMdt;
+	MetaDataTable particlesMdt;
 	int nr_omp_threads;
 	bool r31;
 
@@ -45,7 +45,7 @@ int main(int argc, char *argv[])
 	ObservationModel obsModel;
 
 	ObservationModel::loadSafely(
-		particlesFn, obsModel, particlesMdt, opticsMdt);
+		particlesFn, obsModel, particlesMdt);
 
 
 	particlesMdt.read(particlesFn);
@@ -129,22 +129,22 @@ int main(int argc, char *argv[])
 				opticsGroup--;
 
 				double v;
-				opticsMdt.getValue(lab, v, opticsGroup);
+				obsModel.opticsMdt.getValue(lab, v, opticsGroup);
 				mdt1.setValue(lab, v, p);
 			}
 		}
 
-		opticsMdt.deactivateLabel(EMDL_IMAGE_OPTICS_GROUP);
+		obsModel.opticsMdt.deactivateLabel(EMDL_IMAGE_OPTICS_GROUP);
 
 		mdt1.setVersion(30000);
 	}
 	else
 	{
-		opticsMdt.deactivateLabel(EMDL_IMAGE_BEAMTILT_X);
-		opticsMdt.deactivateLabel(EMDL_IMAGE_BEAMTILT_Y);		
-		opticsMdt.deactivateLabel(EMDL_IMAGE_ODD_ZERNIKE_COEFFS);
+		obsModel.opticsMdt.deactivateLabel(EMDL_IMAGE_BEAMTILT_X);
+		obsModel.opticsMdt.deactivateLabel(EMDL_IMAGE_BEAMTILT_Y);		
+		obsModel.opticsMdt.deactivateLabel(EMDL_IMAGE_ODD_ZERNIKE_COEFFS);
 
-		opticsMdt.write(outPath+"demodulated_particles_optics.star");
+		obsModel.opticsMdt.write(outPath+"demodulated_particles_optics.star");
 	}
 
 	mdt1.write(outPath+"demodulated_particles.star");

diff --git a/src/apps/double_reconstruct_openmp.cpp b/src/apps/double_reconstruct_openmp.cpp
@@ -258,9 +258,9 @@ class reconstruct_parameters
 			Image<RFLOAT> vol, sub;
 
 			ObservationModel obsModel;
-			MetaDataTable mdt0, mdtOpt;
+			MetaDataTable mdt0;
 
-			ObservationModel::loadSafely(fn_sel, obsModel, mdt0, mdtOpt);
+			ObservationModel::loadSafely(fn_sel, obsModel, mdt0);
 			std::vector<double> angpix = obsModel.getPixelSizes();
 
 			const int optGroupCount = obsModel.numberOfOpticsGroups();

diff --git a/src/apps/free_aberration_plot.cpp b/src/apps/free_aberration_plot.cpp
diff --git a/src/apps/merge_particles.cpp b/src/apps/merge_particles.cpp
@@ -13,7 +13,7 @@ int main(int argc, char *argv[])
 	const int srcCount = argc - 2;
 	std::string destFn = argv[argc-1];
 
-	std::vector<MetaDataTable> particleMdts(srcCount), opticsMdts(srcCount);
+	std::vector<MetaDataTable> particleMdts(srcCount);
 	std::vector<ObservationModel> obsModels(srcCount);
 
 	std::cout << "merging: " << std::endl;
@@ -23,7 +23,7 @@ int main(int argc, char *argv[])
 		std::string srcFn = argv[i+1];
 
 		std::cout << "    " << srcFn << std::endl;
-		ObservationModel::loadSafely(srcFn, obsModels[i], particleMdts[i], opticsMdts[i]);
+		ObservationModel::loadSafely(srcFn, obsModels[i], particleMdts[i]);
 	}
 
 	std::cout << "into: " << destFn << std::endl;
@@ -35,12 +35,12 @@ int main(int argc, char *argv[])
 
 	for (int i = 0; i < srcCount; i++)
 	{
-		const int ogc = opticsMdts[i].numberOfObjects();
+		const int ogc = obsModels[i].opticsMdt.numberOfObjects();
 		optGrTransl[i].resize(ogc);
 
 		for (int g = 0; g < ogc; g++)
 		{
-			opticsOut.addObject(opticsMdts[i].getObject(g));
+			opticsOut.addObject(obsModels[i].opticsMdt.getObject(g));
 
 			const int ogNew = opticsOut.numberOfObjects() - 1;
 
@@ -66,7 +66,7 @@ int main(int argc, char *argv[])
 		}
 	}
 
-	ObservationModel::save(particleOut, opticsOut, destFn);
+	ObservationModel::saveNew(particleOut, opticsOut, destFn);
 
 	return 0;
 }