Read mrc file using file name

Provide a higher level class for reading an mrc file given file name and
convert the information read from the density file into coordinate
transformation and three-dimensional density data.

Change-Id: I30ac5c044c5433043224be288340b794455f8fc9

diff --git a/src/gromacs/fileio/mrcdensitymap.cpp b/src/gromacs/fileio/mrcdensitymap.cpp
index 9c8385c7c2ef4112142d3abcb09b82a93266e295..0e251ee4e9dd6002ca62d2dd055fbd051b6d75be 100644 (file)
--- a/src/gromacs/fileio/mrcdensitymap.cpp
+++ b/src/gromacs/fileio/mrcdensitymap.cpp
@@ -48,8 +48,11 @@
 #include <algorithm>
 #include <vector>
 
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/gmxfio_xdr.h"
 #include "gromacs/fileio/mrcdensitymapheader.h"
 #include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/inmemoryserializer.h"
 #include "gromacs/utility/iserializer.h"
 
 #include "mrcserializer.h"
@@ -57,6 +60,43 @@
 namespace gmx
 {
 
+namespace
+{
+
+/*! \brief Read file into memory as vector of chars
+ *
+ * \param[in] filename of the file to be read
+ * \returns the file contents as a vector
+ * \throws FileIOError if file not found
+ * \throws FileIOError if reading was not successful
+ */
+std::vector<char> readCharBufferFromFile(const std::string &filename)
+{
+    if (!gmx_fexist(filename))
+    {
+        GMX_THROW(FileIOError("Error while reading '" + filename + "' - file not found."));
+    }
+    t_fileio *mrcFile = gmx_fio_open(filename.c_str(), "r");
+
+    // Determine file size
+    gmx_fseek(gmx_fio_getfp(mrcFile), 0, SEEK_END);
+    gmx_off_t fileSize = gmx_fio_ftell(mrcFile);
+    gmx_fseek(gmx_fio_getfp(mrcFile), 0, SEEK_SET);
+    // Read whole file into buffer the size of the file
+    std::vector<char> fileContentBuffer(fileSize);
+    size_t            readSize = fread(fileContentBuffer.data(), sizeof(char), fileContentBuffer.size(), gmx_fio_getfp(mrcFile));
+    gmx_fio_close(mrcFile);
+
+    if (fileContentBuffer.size() != readSize)
+    {
+        GMX_THROW(FileIOError("Error while reading '" + filename + "' - file size and read buffer size do not match."));
+    }
+
+    return fileContentBuffer;
+}
+
+}   // namespace
+
 /********************************************************************
  * MrcDensityMapOfFloatReader::Impl
  */
@@ -100,7 +140,7 @@ MrcDensityMapOfFloatReader::MrcDensityMapOfFloatReader(ISerializer *serializer)
 {
 }
 
-ArrayRef<const float> MrcDensityMapOfFloatReader::data() const
+ArrayRef<const float> MrcDensityMapOfFloatReader::constView() const
 {
     return impl_->data_;
 }
@@ -114,6 +154,65 @@ MrcDensityMapOfFloatReader::~MrcDensityMapOfFloatReader()
 {
 }
 
+/********************************************************************
+ * MrcDensityMapOfFloatFromFileReader::Impl
+ */
+
+
+class MrcDensityMapOfFloatFromFileReader::Impl
+{
+    public:
+        explicit Impl(const std::string &fileName);
+        ~Impl() = default;
+        const MrcDensityMapOfFloatReader &reader() const;
+    private:
+        std::vector<char>                 buffer_;
+        InMemoryDeserializer              serializer_;
+        const MrcDensityMapOfFloatReader  reader_;
+};
+
+MrcDensityMapOfFloatFromFileReader::Impl::Impl(const std::string &filename) :
+    buffer_(readCharBufferFromFile(filename)),
+    serializer_(buffer_, false),
+    reader_(&serializer_)
+{
+    layout_right::mapping<dynamicExtents3D> map(getDynamicExtents3D(reader_.header()));
+    if (map.required_span_size() != reader_.constView().ssize())
+    {
+        GMX_THROW(FileIOError("File header density extent information of "
+                              + filename + "' does not match density data size"));
+    }
+}
+
+const MrcDensityMapOfFloatReader &MrcDensityMapOfFloatFromFileReader::Impl::reader() const
+{
+    return reader_;
+}
+
+/********************************************************************
+ * MrcDensityMapOfFloatFromFileReader
+ */
+
+MrcDensityMapOfFloatFromFileReader::MrcDensityMapOfFloatFromFileReader(const std::string &filename)
+    : impl_(new Impl(filename))
+{}
+
+MrcDensityMapOfFloatFromFileReader::~MrcDensityMapOfFloatFromFileReader() = default;
+
+TranslateAndScale
+MrcDensityMapOfFloatFromFileReader::transformationToDensityLattice() const
+{
+    return getCoordinateTransformationToLattice(impl_->reader().header());
+}
+
+MultiDimArray<std::vector<float>, dynamicExtents3D>
+MrcDensityMapOfFloatFromFileReader::densityDataCopy() const
+{
+    MultiDimArray<std::vector<float>, dynamicExtents3D> result(getDynamicExtents3D(impl_->reader().header()));
+    std::copy(std::begin(impl_->reader().constView()), std::end(impl_->reader().constView()), begin(result.asView()));
+    return result;
+}
+
 /********************************************************************
  * MrcDensityMapOfFloatWriter::Impl
  */

diff --git a/src/gromacs/fileio/mrcdensitymap.h b/src/gromacs/fileio/mrcdensitymap.h
index 164859c309019f3952e4b46e9e3e38417de93085..6b9d0ec004a390c82e4af4e12a5883de8727b89f 100644 (file)
--- a/src/gromacs/fileio/mrcdensitymap.h
+++ b/src/gromacs/fileio/mrcdensitymap.h
@@ -41,6 +41,11 @@
  * \inlibraryapi
  * \ingroup module_fileio
  */
+#include <string>
+#include <vector>
+
+#include "gromacs/math/multidimarray.h"
+#include "gromacs/mdspan/extensions.h"
 #include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/classhelpers.h"
 
@@ -49,6 +54,7 @@ namespace gmx
 
 struct MrcDensityMapHeader;
 class ISerializer;
+class TranslateAndScale;
 
 /*! \libinternal \brief Read an mrc/ccp4 file that contains float values.
  */
@@ -65,8 +71,8 @@ class MrcDensityMapOfFloatReader
 
         ~MrcDensityMapOfFloatReader();
 
-        //! Return the data vector that holds the data on the density grid
-        ArrayRef<const float> data() const;
+        //! Return a view on the data of the density grid
+        ArrayRef<const float> constView() const;
         //! Return the header
         const MrcDensityMapHeader &header() const;
 
@@ -76,6 +82,43 @@ class MrcDensityMapOfFloatReader
 
 };
 
+/*! \libinternal \brief Read an mrc density map from a given file.
+ *
+ * Higher level class than MrcDensityMapOfFloatReader that takes a file name
+ * upon construction and returns coordinate transformation into the density
+ * lattice as well as the density data.
+ *
+ * \note File reading is completed during construction. When the constructor
+ *       completes succesfully, transformation to density lattice and density
+ *       data are valid, irrespective of the state of the read file.
+ */
+class MrcDensityMapOfFloatFromFileReader
+{
+    public:
+
+        MrcDensityMapOfFloatFromFileReader();
+
+        /*! \brief Read from filename.
+         * \throws FileIOError if file does not exist
+         * \throws FileIOError if read in buffer size does not match file size
+         * \throws FileIOError if header information does not match density
+         *                     data size
+         */
+        explicit MrcDensityMapOfFloatFromFileReader(const std::string &filename);
+
+        ~MrcDensityMapOfFloatFromFileReader();
+
+        //! Return the coordinate transformation into the density
+        TranslateAndScale transformationToDensityLattice() const;
+
+        //! Return a copy of the density data
+        MultiDimArray<std::vector<float>, dynamicExtents3D> densityDataCopy() const;
+
+    private:
+        class Impl;
+        PrivateImplPointer<Impl> impl_;
+};
+
 /*! \libinternal \brief Write an mrc/ccp4 file that contains float values.
  */
 class MrcDensityMapOfFloatWriter

diff --git a/src/gromacs/fileio/tests/mrcdensitymap.cpp b/src/gromacs/fileio/tests/mrcdensitymap.cpp
index e7272d22f0275adb451a19a658ee7bcd80a82424..a7cc86c905f1a8944053339e11c4db366b201003 100644 (file)
--- a/src/gromacs/fileio/tests/mrcdensitymap.cpp
+++ b/src/gromacs/fileio/tests/mrcdensitymap.cpp
@@ -43,17 +43,22 @@
 
 #include "gromacs/fileio/mrcdensitymap.h"
 
+#include <string>
+
 #include <gmock/gmock.h>
 #include <gtest/gtest.h>
 
 #include "gromacs/fileio/mrcdensitymapheader.h"
 #include "gromacs/utility/inmemoryserializer.h"
 
+#include "testutils/refdata.h"
 #include "testutils/testasserts.h"
+#include "testutils/testfilemanager.h"
 
 namespace gmx
 {
-
+namespace test
+{
 namespace
 {
 
@@ -76,7 +81,7 @@ TEST(MrcDensityMap, RoundTripIsIdempotent)
     InMemoryDeserializer       deserializer(serializedFile, false);
     MrcDensityMapOfFloatReader mrcDensityMapReader(&deserializer);
 
-    MrcDensityMapOfFloatWriter writerOfDeserializedOutput(mrcDensityMapReader.header(), mrcDensityMapReader.data());
+    MrcDensityMapOfFloatWriter writerOfDeserializedOutput(mrcDensityMapReader.header(), mrcDensityMapReader.constView());
     writerOfDeserializedOutput.write(&serializer);
 
     const auto roundTripResult = serializer.finishAndGetBuffer();
@@ -85,6 +90,53 @@ TEST(MrcDensityMap, RoundTripIsIdempotent)
     EXPECT_THAT(serializedFile, testing::Pointwise(testing::Eq(), roundTripResult));
 }
 
-} // namespace
+TEST(MrcDensityMap, ThrowsFileIOErrorWhenFileNotPresent)
+{
+    EXPECT_THROW(MrcDensityMapOfFloatFromFileReader(""), FileIOError);
+}
+
+TEST(MrcDensityMap, ReadsCoordinateTransformationFromFile)
+{
+    RVec coordinate1(0, 0, 0);
+    RVec coordinate2(0, 0, 1);
+    RVec coordinate3(1, 0, 0);
+    RVec coordinate4(0, 1, 0);
+
+    MrcDensityMapOfFloatFromFileReader mrcFileReader(TestFileManager::getInputFilePath("ellipsoid-density.mrc"));
+    TranslateAndScale                  coordinateTransformation(mrcFileReader.transformationToDensityLattice());
+
+    coordinateTransformation({&coordinate1, &coordinate1+1});
+    coordinateTransformation({&coordinate2, &coordinate2+1});
 
+    EXPECT_REAL_EQ(0, coordinate1[XX]);
+    EXPECT_REAL_EQ(-2, coordinate1[YY]);
+    EXPECT_REAL_EQ(0, coordinate1[ZZ]);
+
+    EXPECT_REAL_EQ(0, coordinate2[XX]);
+    EXPECT_REAL_EQ(-2, coordinate2[YY]);
+    EXPECT_REAL_EQ(1.25, coordinate2[ZZ]);
+
+    EXPECT_REAL_EQ(1, coordinate3[XX]);
+    EXPECT_REAL_EQ(0, coordinate3[YY]);
+    EXPECT_REAL_EQ(0, coordinate3[ZZ]);
+
+    EXPECT_REAL_EQ(0, coordinate4[XX]);
+    EXPECT_REAL_EQ(1, coordinate4[YY]);
+    EXPECT_REAL_EQ(0, coordinate4[ZZ]);
+}
+
+TEST(MrcDensityMap, ReadsDensityDataFromFile)
+{
+    MrcDensityMapOfFloatFromFileReader mrcFileReader(
+            TestFileManager::getInputFilePath("ellipsoid-density.mrc"));
+    const auto                         densityData = mrcFileReader.densityDataCopy();
+
+    TestReferenceData                  refData;
+    TestReferenceChecker               checker(refData.rootChecker());
+    checker.checkSequence(begin(densityData.asConstView()), end(densityData.asConstView()),
+                          "data ellipsoid density");
+}
+
+} // namespace
+} // namespace test
 } // namespace gmx

diff --git a/src/gromacs/fileio/tests/refdata/MrcDensityMap_ReadsDensityDataFromFile.xml b/src/gromacs/fileio/tests/refdata/MrcDensityMap_ReadsDensityDataFromFile.xml
new file mode 100644 (file)
index 0000000..a4399fa
--- /dev/null
+++ b/src/gromacs/fileio/tests/refdata/MrcDensityMap_ReadsDensityDataFromFile.xml
@@ -0,0 +1,493 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <Sequence Name="data ellipsoid density">
+    <Int Name="Length">486</Int>
+    <Real>1.1953919</Real>
+    <Real>1.6435194</Real>
+    <Real>2.1393259</Real>
+    <Real>2.632971</Real>
+    <Real>3.0569184</Real>
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+    <Real>3.2516041</Real>
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+    <Real>4.48736</Real>
+    <Real>4.1934929</Real>
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diff --git a/src/testutils/simulationdatabase/ellipsoid-density.mrc b/src/testutils/simulationdatabase/ellipsoid-density.mrc
new file mode 100644 (file)
index 0000000..44ed22c
Binary files /dev/null and b/src/testutils/simulationdatabase/ellipsoid-density.mrc differ