Add MRC file writing support (#147)

* Fix #108
* Add MRC file writing support
   - Implement MRC.write() method
   - Add Grid.export() integration for MRC format
   - Preserve header information and handle edge cases
*  Added Test
* update CHANGELOG

Author: Pradyumn-cloud

AUTHORS

@@ -28,3 +28,4 @@ Contributors:
 * Olivier Languin-Cattoën <ollyfutur>
 * Andrés Montoya <conradolandia> (logo)
 * Rich Waldo <plethorachutney>
+* Pradyumn Prasad <Pradyumn-cloud>

CHANGELOG

@@ -13,7 +13,7 @@ The rules for this file:
   * accompany each entry with github issue/PR number (Issue #xyz)
 
 ------------------------------------------------------------------------------
-??/??/???? IAlibay, ollyfutur, conradolandia, orbeckst, PlethoraChutney
+??/??/???? IAlibay, ollyfutur, conradolandia, orbeckst, PlethoraChutney, Pradyumn-cloud
   * 1.1.0
 
   Changes
@@ -30,6 +30,7 @@ The rules for this file:
     (PR #142)
   * `Grid` now allows forcing MRC/CCP4 maps to be read as volumes even when
     the header indicates they are stacks of 2D images. (#150, PR #149)
+  * Added MRC file writing support (Issue #108)
 
   Fixes
 

gridData/core.py

@@ -212,6 +212,7 @@ def __init__(self, grid=None, edges=None, origin=None, delta=None,
             'PKL': self._export_python,
             'PICKLE': self._export_python,  # compatibility
             'PYTHON': self._export_python,  # compatibility
+            'MRC': self._export_mrc,
         }
         self._loaders = {
             'CCP4': self._load_mrc,
@@ -600,6 +601,8 @@ def export(self, filename, file_format=None, type=None, typequote='"'):
 
         dx
             :mod:`OpenDX`
+        mrc
+            :mod:`mrc` MRC/CCP4 format
         pickle
             pickle (use :meth:`Grid.load` to restore); :meth:`Grid.save`
             is simpler than ``export(format='python')``.
@@ -609,7 +612,7 @@ def export(self, filename, file_format=None, type=None, typequote='"'):
         filename : str
             name of the output file
 
-        file_format : {'dx', 'pickle', None} (optional)
+        file_format : {'dx', 'pickle', 'mrc', None} (optional)
             output file format, the default is "dx"
 
         type : str (optional)
@@ -686,6 +689,41 @@ def _export_dx(self, filename, type=None, typequote='"', **kwargs):
         if ext == '.gz':
             filename = root + ext
         dx.write(filename)
+    
+    def _export_mrc(self, filename, **kwargs):
+        """Export the density grid to an MRC/CCP4 file.
+        
+        The MRC2014 file format is used via the mrcfile library.
+        
+        Parameters
+        ----------
+        filename : str
+            Output filename
+        **kwargs
+            Additional keyword arguments (currently ignored)
+        
+        Notes
+        -----
+        * Only orthorhombic unit cells are supported
+        * If the Grid was loaded from an MRC file, the original header
+          information (including axis ordering) is preserved
+        * For new grids, standard ordering (mapc=1, mapr=2, maps=3) is used
+        
+        .. versionadded:: 1.1.0
+        """
+        # Create MRC object and populate with Grid data
+        mrc_file = mrc.MRC()
+        mrc_file.array = self.grid
+        mrc_file.delta = numpy.diag(self.delta)
+        mrc_file.origin = self.origin
+        mrc_file.rank = 3
+        
+        # Transfer header if it exists (preserves axis ordering and other metadata)
+        if hasattr(self, '_mrc_header'):
+            mrc_file.header = self._mrc_header
+        
+        # Write to file
+        mrc_file.write(filename)
 
     def save(self, filename):
         """Save a grid object to `filename` and add ".pickle" extension.

gridData/mrc.py

@@ -85,7 +85,7 @@ class MRC(object):
     -----
     * Only volumetric (3D) densities are read.
     * Only orthorhombic unitcells supported (other raise :exc:`ValueError`)
-    * Only reading is currently supported.
+    * Reading and writing are supported.
 
 
     .. versionadded:: 0.7.0
@@ -160,5 +160,106 @@ def histogramdd(self):
         """Return array data as (edges,grid), i.e. a numpy nD histogram."""
         return (self.array, self.edges)
 
-
-
+    def write(self, filename):
+        """Write grid data to MRC/CCP4 file format.
+        
+        Parameters
+        ----------
+        filename : str
+            Output filename for the MRC file
+        
+        Notes
+        -----
+        The data array should be in xyz order (axis 0=X, axis 1=Y, axis 2=Z).
+        
+        If the MRC object was created by reading an existing file, the original
+        header information (including mapc, mapr, maps ordering) is preserved.
+        Otherwise, standard ordering (mapc=1, mapr=2, maps=3) is used.
+        
+        .. versionadded:: 1.1.0
+        """
+        if filename is not None:
+            self.filename = filename
+        
+        # Preserve header if it exists, otherwise use defaults
+        if hasattr(self, 'header'):
+            # File was read - preserve original ordering
+            h = self.header
+            axes_order = np.hstack([h.mapc, h.mapr, h.maps])
+            mapc, mapr, maps = int(h.mapc), int(h.mapr), int(h.maps)
+        else:
+            # New file - use standard ordering
+            axes_order = np.array([1, 2, 3])
+            mapc, mapr, maps = 1, 2, 3
+            h = None
+        
+        # Reverse the transformation done in read()
+        transpose_order = np.argsort(axes_order[::-1])
+        inverse_transpose_order = np.argsort(transpose_order)
+        
+        # Transform our xyz array back to the file's native ordering
+        data_for_file = np.transpose(self.array, axes=inverse_transpose_order)
+        
+        # Ensure proper data type (float32 is standard for mode 2)
+        data_for_file = data_for_file.astype(np.float32)
+        
+        # Create new MRC file
+        with mrcfile.new(filename, overwrite=True) as mrc:
+            mrc.set_data(data_for_file)
+            
+            # Set voxel size from delta (diagonal elements)
+            voxel_size = np.diag(self.delta).astype(np.float32)
+            mrc.voxel_size = tuple(voxel_size)
+            
+            # Set map ordering
+            mrc.header.mapc = mapc
+            mrc.header.mapr = mapr
+            mrc.header.maps = maps
+            
+            # Handle nstart and origin
+            if h is not None:
+                # Preserve original header values
+                nxstart = int(h.nxstart)
+                nystart = int(h.nystart)
+                nzstart = int(h.nzstart)
+                header_origin_xyz = np.array([h.origin.x, h.origin.y, h.origin.z], dtype=np.float32)
+                
+                mrc.header.mx = int(h.mx)
+                mrc.header.my = int(h.my)
+                mrc.header.mz = int(h.mz)
+                
+                # Preserve cell dimensions
+                if hasattr(h, 'cella'):
+                    mrc.header.cella.x = float(h.cella.x)
+                    mrc.header.cella.y = float(h.cella.y)
+                    mrc.header.cella.z = float(h.cella.z)
+                if hasattr(h, 'cellb'):
+                    mrc.header.cellb.alpha = float(h.cellb.alpha)
+                    mrc.header.cellb.beta = float(h.cellb.beta)
+                    mrc.header.cellb.gamma = float(h.cellb.gamma)
+                # Copy space group if available
+                if hasattr(h, 'ispg'):
+                    mrc.header.ispg = int(h.ispg)
+            else:
+                # For new files, calculate nstart from origin
+                if np.any(voxel_size <= 0):
+                    raise ValueError(f"Voxel size must be positive, got {voxel_size}")
+                
+                # Set header.origin = 0 and encode everything in nstart
+                header_origin_xyz = np.zeros(3, dtype=np.float32)
+                nxstart = int(np.round(self.origin[0] / voxel_size[0]))
+                nystart = int(np.round(self.origin[1] / voxel_size[1]))
+                nzstart = int(np.round(self.origin[2] / voxel_size[2]))
+            
+            # Set the start positions
+            mrc.header.nxstart = nxstart
+            mrc.header.nystart = nystart
+            mrc.header.nzstart = nzstart
+            
+            # Set explicit origin
+            mrc.header.origin.x = float(header_origin_xyz[0])
+            mrc.header.origin.y = float(header_origin_xyz[1])
+            mrc.header.origin.z = float(header_origin_xyz[2])
+            
+            # Update statistics only
+            mrc.update_header_stats()

gridData/tests/test_mrc.py

@@ -142,3 +142,170 @@ def test_origin(self, grid, ccp4data):
 
     def test_data(self, grid, ccp4data):
         assert_allclose(grid.grid, ccp4data.array)
+
+class TestMRCWrite:
+    """Tests for MRC write functionality"""
+    
+    def test_mrc_write_roundtrip(self, ccp4data, tmpdir):
+        """Test writing and reading back preserves data"""
+        outfile = str(tmpdir / "roundtrip.mrc")
+        
+        # Write the file
+        ccp4data.write(outfile)
+        
+        # Read it back
+        mrc_read = mrc.MRC(outfile)
+        
+        # Check data matches
+        assert_allclose(mrc_read.array, ccp4data.array)
+        assert_allclose(mrc_read.origin, ccp4data.origin, rtol=1e-5, atol=1e-3)
+        assert_allclose(mrc_read.delta, ccp4data.delta, rtol=1e-5)
+    
+    def test_mrc_write_header_preserved(self, ccp4data, tmpdir):
+        """Test that header fields are preserved"""
+        outfile = str(tmpdir / "header.mrc")
+        
+        ccp4data.write(outfile)
+        mrc_read = mrc.MRC(outfile)
+        
+        # Check axis ordering preserved
+        assert mrc_read.header.mapc == ccp4data.header.mapc
+        assert mrc_read.header.mapr == ccp4data.header.mapr
+        assert mrc_read.header.maps == ccp4data.header.maps
+        
+        # Check offsets preserved
+        assert mrc_read.header.nxstart == ccp4data.header.nxstart
+        assert mrc_read.header.nystart == ccp4data.header.nystart
+        assert mrc_read.header.nzstart == ccp4data.header.nzstart
+    
+    def test_mrc_write_new_file(self, tmpdir):
+        """Test creating new MRC file from scratch"""
+        outfile = str(tmpdir / "new.mrc")
+        
+        # Create new MRC object
+        mrc_new = mrc.MRC()
+        mrc_new.array = np.arange(24).reshape(2, 3, 4).astype(np.float32)
+        mrc_new.delta = np.diag([1.0, 2.0, 3.0])
+        mrc_new.origin = np.array([5.0, 10.0, 15.0])
+        mrc_new.rank = 3
+        
+        # Write and read back
+        mrc_new.write(outfile)
+        mrc_read = mrc.MRC(outfile)
+        
+        # Verify
+        assert_allclose(mrc_read.array, mrc_new.array, rtol=1e-5)
+        assert_allclose(mrc_read.origin, mrc_new.origin, rtol=1e-4)
+        assert_allclose(np.diag(mrc_read.delta), np.diag(mrc_new.delta), rtol=1e-5)
+    
+    def test_mrc_write_zero_voxel_raises(self, tmpdir):
+        """Test that zero voxel size raises ValueError"""
+        outfile = str(tmpdir / "invalid.mrc")
+        
+        mrc_obj = mrc.MRC()
+        mrc_obj.array = np.ones((2, 2, 2), dtype=np.float32)
+        mrc_obj.delta = np.diag([0.0, 1.0, 1.0])
+        mrc_obj.origin = np.array([0.0, 0.0, 0.0])
+        mrc_obj.rank = 3
+        
+        with pytest.raises(ValueError, match="Voxel size must be positive"):
+            mrc_obj.write(outfile)
+
+
+class TestGridMRCWrite:
+    """Tests for Grid.export() with MRC format"""
+    
+    def test_grid_export_mrc(self, tmpdir):
+        """Test Grid.export() with file_format='mrc'"""
+        outfile = str(tmpdir / "grid.mrc")
+        
+        # Create simple grid
+        data = np.arange(60).reshape(3, 4, 5).astype(np.float32)
+        g = Grid(data, origin=[0, 0, 0], delta=[1.0, 1.0, 1.0])
+        
+        # Export and read back
+        g.export(outfile, file_format='mrc')
+        g_read = Grid(outfile)
+        
+        # Verify
+        assert_allclose(g_read.grid, g.grid, rtol=1e-5)
+        assert_allclose(g_read.origin, g.origin, rtol=1e-4)
+        assert_allclose(g_read.delta, g.delta, rtol=1e-5)
+    
+    def test_grid_export_mrc_roundtrip(self, tmpdir):
+        """Test MRC → Grid → export → Grid preserves data"""
+        outfile = str(tmpdir / "roundtrip_grid.mrc")
+        
+        # Load original
+        g_orig = Grid(datafiles.CCP4_1JZV)
+        
+        # Export and reload
+        g_orig.export(outfile, file_format='mrc')
+        g_read = Grid(outfile)
+        
+        # Verify
+        assert_allclose(g_read.grid, g_orig.grid, rtol=1e-5)
+        assert_allclose(g_read.origin, g_orig.origin, rtol=1e-4)
+        assert_allclose(g_read.delta, g_orig.delta, rtol=1e-5)
+        assert_equal(g_read.grid.shape, g_orig.grid.shape)
+    
+    def test_grid_export_mrc_preserves_header(self, tmpdir):
+        """Test that Grid preserves MRC header through export"""
+        outfile = str(tmpdir / "header_grid.mrc")
+        
+        g_orig = Grid(datafiles.CCP4_1JZV)
+        orig_mapc = g_orig._mrc_header.mapc
+        orig_mapr = g_orig._mrc_header.mapr
+        orig_maps = g_orig._mrc_header.maps
+        
+        # Export and check
+        g_orig.export(outfile, file_format='mrc')
+        g_read = Grid(outfile)
+        
+        assert g_read._mrc_header.mapc == orig_mapc
+        assert g_read._mrc_header.mapr == orig_mapr
+        assert g_read._mrc_header.maps == orig_maps
+
+    def test_mrc_write_4x4x4_with_header(self, tmpdir):
+        """Test writing 4x4x4 MRC file with custom header values."""
+        
+        # Create 4x4x4 data
+        data = np.arange(64, dtype=np.float32).reshape((4, 4, 4))
+        outfile = str(tmpdir / "test_with_header.mrc")
+        
+        # Create and write MRC
+        m = mrc.MRC()
+        m.array = data
+        m.delta = np.diag([1.5, 2.0, 2.5])
+        m.origin = np.array([10.0, 20.0, 30.0])
+        m.rank = 3
+        m.write(outfile)
+        
+        # Read back and verify
+        m_read = mrc.MRC(outfile)
+        assert_allclose(m_read.array, data)
+        assert_allclose(np.diag(m_read.delta), [1.5, 2.0, 2.5])
+        assert_allclose(m_read.origin, [10.0, 20.0, 30.0], rtol=1e-4, atol=1.0)
+
+
+    def test_mrc_write_4x4x4_without_header(self, tmpdir):
+        """Test writing 4x4x4 MRC file with default header."""
+        
+        # Create 4x4x4 random data
+        np.random.seed(42)
+        data = np.random.rand(4, 4, 4).astype(np.float32)
+        outfile = str(tmpdir / "test_without_header.mrc")
+        
+        # Create and write MRC
+        m = mrc.MRC()
+        m.array = data
+        m.delta = np.diag([1.0, 1.0, 1.0])
+        m.origin = np.array([0.0, 0.0, 0.0])
+        m.rank = 3
+        m.write(outfile)
+        
+        # Read back and verify
+        m_read = mrc.MRC(outfile)
+        assert_allclose(m_read.array, data)
+        assert_allclose(np.diag(m_read.delta), [1.0, 1.0, 1.0])
+        assert_allclose(m_read.origin, [0.0, 0.0, 0.0], rtol=1e-4, atol=1.0)