Fixed bug in fbp preprocessing metadata handling.

arttumiettinen · Feb 1, 2024 · c56395c · c56395c
1 parent 235bfd7
commit c56395c
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Showing 3 changed files with 35 additions and 12 deletions.
diff --git a/itl2/imagemetadata.cpp b/itl2/imagemetadata.cpp
@@ -318,7 +318,7 @@ namespace itl2
 
 			// List as vector of Vec2f
 			vector<Vec2c> def;
-			vector<Vec2c> vlist = data.getList<Vec2c>("vec2_list", def);
+			vector<Vec2c> vlist = data.getList<Vec2c>("vec2_list", def, false);
 			if (testAssert(vlist.size() == 3, "vec2 list size"))
 			{
 				testAssert(vlist[0] == Vec2c(vectorElement(0, 0), vectorElement(0, 1)), "element");

diff --git a/itl2/imagemetadata.h b/itl2/imagemetadata.h
@@ -226,8 +226,9 @@ namespace itl2
 
 		/**
 		Gets item as a list of values.
+		@param squeeze If set to true, returns list of all elements of the value matrix irrespective of its shape; use, e.g., to always return a list of N numbers despite it being stored either as 1xN or Nx1 matrix. If set to false, the elements in the returned list correspond to the first dimension of the value matrix.
 		*/
-		template<typename T> std::vector<T> getList(const std::string& key, std::vector<T>& def) const
+		template<typename T> std::vector<T> getList(const std::string& key, std::vector<T>& def, bool squeeze) const
 		{
 			if (!contains(key))
 				return def;
@@ -240,12 +241,26 @@ namespace itl2
 			for(const std::vector<string>& row : mat)
 			{
 				if (row.size() == 1)
+				{
 					lst.push_back(fromString<T>(row[0]));
+				}
 				else
 				{
-					std::ostringstream str;
-					appendValueOrVector(str, row);
-					lst.push_back(fromString<T>(str.str()));
+					if (squeeze)
+					{
+						// Convert each element of the row to the output type.
+						for (const string& elem : row)
+						{
+							lst.push_back(fromString<T>(elem));
+						}
+					}
+					else
+					{
+						// Convert row of values to one value of output type.
+						std::ostringstream str;
+						appendValueOrVector(str, row);
+						lst.push_back(fromString<T>(str.str()));
+					}
 				}
 			}
 

diff --git a/itl2/tomo/fbp.cpp b/itl2/tomo/fbp.cpp
@@ -162,7 +162,7 @@ namespace itl2
 	void checkMetaItem(const string& item, const ImageMetadata& meta)
 	{
 		if (!meta.contains(item))
-			throw ITLException(item + " item is missing from image metadata.");
+			throw ITLException(string("'") + item + "' item is missing from image metadata.");
 	}
 
 	RecSettings RecSettings::fromMeta(ImageMetadata& meta)
@@ -172,7 +172,15 @@ namespace itl2
 
 		// Check that essential metadata exists.
 		checkMetaItem("source_to_ra", meta);
-		checkMetaItem("angles", meta);
+
+		//checkMetaItem("angles", meta);
+		string anglesName;
+		if (meta.contains("angles"))
+			anglesName = "angles";
+		else if (meta.contains("Angles [deg]"))
+			anglesName = "Angles [deg]";
+		else
+			throw ITLException("'angles' item or 'Angles [deg]' item is missing from image metadata.");
 
 
 		s.sourceToRA = meta.get("source_to_ra", s.sourceToRA);
@@ -211,13 +219,13 @@ namespace itl2
 		s.useShifts = meta.get("use_shifts", s.useShifts);
 
 		std::vector<float32_t> emptyV1;
-   		s.angles = meta.getList<float32_t>("angles", emptyV1);
+   		s.angles = meta.getList<float32_t>(anglesName, emptyV1, true);
 		std::vector<Vec2f> emptyV2;
    		std::vector<Vec3f> emptyV3;
-   		s.sampleShifts = meta.getList<Vec3f>("sample_shifts", emptyV3);
-   		s.sourceShifts = meta.getList<Vec3f>("source_shifts", emptyV3);
-   		s.cameraShifts = meta.getList<Vec3f>("camera_shifts", emptyV3);
-   		s.rotationAxisShifts = meta.getList<Vec3f>("rotation_axis_shifts", emptyV3);
+   		s.sampleShifts = meta.getList<Vec3f>("sample_shifts", emptyV3, false);
+   		s.sourceShifts = meta.getList<Vec3f>("source_shifts", emptyV3, false);
+   		s.cameraShifts = meta.getList<Vec3f>("camera_shifts", emptyV3, false);
+   		s.rotationAxisShifts = meta.getList<Vec3f>("rotation_axis_shifts", emptyV3, false);
 
    		// If there are no shifts supplied, set all shifts to zero.
    		if (s.sampleShifts.size() <= 0)