CTFFind,MotionCorr: check for missing columns

3dem · Oct 27, 2020 · c7546fe · c7546fe
1 parent 4e2f581
commit c7546fe
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Showing 3 changed files with 9 additions and 2 deletions.
diff --git a/src/ctffind_runner.cpp b/src/ctffind_runner.cpp
@@ -146,6 +146,9 @@ void CtffindRunner::initialise()
 		MetaDataTable MDin;
 		ObservationModel::loadSafely(fn_in, obsModel, MDin, "micrographs", verb);
 
+		if (MDin.numberOfObjects() > 0 && !MDin.containsLabel(EMDL_MICROGRAPH_NAME))
+			REPORT_ERROR("ERROR: There is no rlnMicrographName label in the input micrograph STAR file.");
+
 		if (do_use_without_doseweighting && MDin.numberOfObjects() > 0 && !MDin.containsLabel(EMDL_MICROGRAPH_NAME_WODOSE))
 			REPORT_ERROR("ERROR: You are using --use_noDW, but there is no rlnMicrographNameNoDW label in the input micrograph STAR file.");
 

diff --git a/src/filename.cpp b/src/filename.cpp
@@ -600,9 +600,11 @@ bool decomposePipelineSymlinkName(FileName fn_in, FileName &fn_pre, FileName &fn
 	if (!dont_expand && len != -1)
 	{
 			// This is a symbolic link!
-		if (linkname[len - 1] == '/')
-			linkname[len - 1] = '\0'; // remove trailing '/'
+
+			if (linkname[len - 1] == '/')
+				linkname[len - 1] = '\0'; // remove trailing '/'
 			linkname[len] = '\0';
+
 			FileName fn_link = std::string(linkname);
 			// TODO: FIXME: This condition is still not perfect. For example,
 			// Micrograph/mic001.mrc -> ../../../storage/mic001.mrc breaks the code.

diff --git a/src/motioncorr_runner.cpp b/src/motioncorr_runner.cpp
@@ -227,6 +227,8 @@ void MotioncorrRunner::initialise()
 	{
 		MetaDataTable MDin;
 		ObservationModel::loadSafely(fn_in, obsModel, MDin, "movies", verb);
+		if (MDin.numberOfObjects() > 0 && !MDin.containsLabel(EMDL_MICROGRAPH_MOVIE_NAME))
+			REPORT_ERROR("The input STAR file does not contain the rlnMicrographMovieName column. Are you sure you imported files as movies, not single frame images?");
 
 		fn_micrographs.clear();
 		optics_group_micrographs.clear();