Check mrc header for sanity

Add functionality to check mrc density map headers for sanity.

Required for endianess correction, because the endianess stamp is not
guaranteed to be right for most .mrc maps.

Change-Id: I8956bcbc4b9fd7b3b6346c3b4cdd0022c9e3332a

diff --git a/src/gromacs/fileio/mrcdensitymapheader.cpp b/src/gromacs/fileio/mrcdensitymapheader.cpp
index 28842078ba275962092c779c3786478979e9a7e9..faaefc5773a77b12c7289d99fb48c91513739acc 100644 (file)
--- a/src/gromacs/fileio/mrcdensitymapheader.cpp
+++ b/src/gromacs/fileio/mrcdensitymapheader.cpp
@@ -50,10 +50,30 @@
 
 namespace gmx
 {
+
+namespace
+{
+
+//! Returns true if any of the argument values is smaller than zero.
+template<typename Container>
+bool anySmallerZero(Container values)
+{
+    return std::any_of(std::begin(values), std::end(values), [](auto v) { return v < 0; });
+}
+
+//! Returns true if any of the argument values is larger than a given boundary value.
+template<typename Container>
+bool anyLargerThanValue(Container values, typename Container::value_type boundaryValue)
+{
+    return std::any_of(std::begin(values), std::end(values),
+                       [boundaryValue](auto v) { return v > boundaryValue; });
+}
+
+} // namespace
+
 size_t numberOfExpectedDataItems(const MrcDensityMapHeader& header)
 {
-    if (std::any_of(std::begin(header.numColumnRowSection_), std::end(header.numColumnRowSection_),
-                    [](auto i) { return i < 0; }))
+    if (anySmallerZero(header.numColumnRowSection_))
     {
         GMX_THROW(
                 InternalError("Cannot determine data size, because the mrc "
@@ -95,4 +115,31 @@ dynamicExtents3D getDynamicExtents3D(const MrcDensityMapHeader& header)
              header.numColumnRowSection_[XX] };
 };
 
+bool mrcHeaderIsSane(const MrcDensityMapHeader& header)
+{
+    // Make sure all numbers of columns, row sections, extents and cell angles
+    // are positive
+    if (anySmallerZero(header.numColumnRowSection_) || anySmallerZero(header.cellAngles_)
+        || anySmallerZero(header.extent_))
+    {
+        return false;
+    }
+
+    // The maximum integer number in an mrc header to be considered sane
+    constexpr std::int32_t c_maxIntegerNumber = 100'000;
+    if (anyLargerThanValue(header.numColumnRowSection_, c_maxIntegerNumber)
+        || anyLargerThanValue(header.extent_, c_maxIntegerNumber))
+    {
+        return false;
+    }
+
+    constexpr std::int32_t c_maxCellAngle = 360;
+    if (anyLargerThanValue(header.cellAngles_, c_maxCellAngle))
+    {
+        return false; //NOLINT(readability-simplify-boolean-expr)
+    }
+
+    return true;
+}
+
 } // namespace gmx

diff --git a/src/gromacs/fileio/mrcdensitymapheader.h b/src/gromacs/fileio/mrcdensitymapheader.h
index f358efbaa2e1ca56384987f485942dd7cf45a369..82160127fa62ccda348df20c5480730169f5974c 100644 (file)
--- a/src/gromacs/fileio/mrcdensitymapheader.h
+++ b/src/gromacs/fileio/mrcdensitymapheader.h
@@ -190,5 +190,17 @@ TranslateAndScale getCoordinateTransformationToLattice(const MrcDensityMapHeader
  * \returns density data extents in three dimensions.
  */
 dynamicExtents3D getDynamicExtents3D(const MrcDensityMapHeader& header);
+
+/*! \brief Checks if the values in the header are sane.
+ *
+ * Checks extents and numbers of columns, rows and sections, as well as unit
+ * cell angles for positivity and to be within bounds.
+ *
+ * Bounds are set generously not to hamper future creative uses of mrc files.
+ *
+ * \returns true if all header values are within resonable albeit generous bounds
+ */
+bool mrcHeaderIsSane(const MrcDensityMapHeader& header);
+
 } // namespace gmx
 #endif /* end of include guard: GMX_FILEIO_MRCDENSITYMAPHEADER_H */

diff --git a/src/gromacs/fileio/tests/mrcdensitymapheader.cpp b/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
index ad303cad21672749cc815f76b2ab561e4bd7de9d..e9e17df359a87e4d0f267058456ed815e2964cd8 100644 (file)
--- a/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
+++ b/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
@@ -140,4 +140,22 @@ TEST(MrcDensityMapHeaderTest, GetsCorrectExtents)
     EXPECT_EQ(expectedExtents[ZZ], extents.extent(ZZ));
 }
 
+TEST(MrcDensityMapHeaderTest, IsSane)
+{
+    MrcDensityMapHeader header;
+    EXPECT_TRUE(mrcHeaderIsSane(header));
+
+    header.numColumnRowSection_[YY] = -1;
+    EXPECT_FALSE(mrcHeaderIsSane(header));
+
+    header.numColumnRowSection_[YY] = 10'000'000;
+    EXPECT_FALSE(mrcHeaderIsSane(header));
+
+    header = {};
+    EXPECT_TRUE(mrcHeaderIsSane(header));
+
+    header.cellAngles_[XX] = -20;
+    EXPECT_FALSE(mrcHeaderIsSane(header));
+}
+
 } // namespace gmx