API update from OpenDX and MRC

gridData/OpenDX.py

@@ -523,6 +523,33 @@ def __init__(self,classid='0',components=None,comments=None):
         self.components = components
         self.comments= comments
 
+    @staticmethod
+    def from_grid(grid, type=None, typequote='"', **kwargs):
+        comments = [
+            "OpenDX density file written by gridDataFormats.Grid.export()",
+            "File format: http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm#HDREDF",
+            "Data are embedded in the header and tied to the grid positions.",
+            "Data is written in C array order: In grid[x,y,z] the axis z is fastest",
+            "varying, then y, then finally x, i.e. z is the innermost loop.",
+        ]
+        if grid.metadata:
+            comments.append("Meta data stored with the python Grid object:")
+        for k in grid.metadata:
+            comments.append("   " + str(k) + " = " + str(grid.metadata[k]))
+        comments.append("(Note: the VMD dx-reader chokes on comments below this line)")
+
+        components = dict(
+            positions=gridpositions(1, grid.grid.shape, grid.origin, grid.delta),
+            connections=gridconnections(2, grid.grid.shape),
+            data=array(3, grid.grid, type=type, typequote=typequote),
+        )
+        dx_field = field('density', components=components, comments=comments)
+        return dx_field
+
+    @property
+    def native(self):
+        return self
+
     def _openfile_writing(self, filename):
         """Returns a regular or gz file stream for writing"""
         if filename.endswith('.gz'):

gridData/core.py

@@ -212,6 +212,12 @@ class Grid(object):
 
     #: Default format for exporting with :meth:`export`.
     default_format = 'DX'
+
+    converter = {
+        'MRC': mrc.MRC.from_grid, 
+        'VDB': None, 
+        'DX': OpenDX.field.from_grid,  
+    }
 
     def __init__(self, grid=None, edges=None, origin=None, delta=None,
                  metadata=None, interpolation_spline_order=3,
@@ -598,6 +604,32 @@ def _load_plt(self, filename, **kwargs):
         grid, edges = g.histogramdd()
         self._load(grid=grid, edges=edges, metadata=self.metadata)
 
+    def convert_to(self, format_specifier, tolerance=None, **kwargs):
+        """Generates an instance of the native object for a given format
+
+        Implemented formats:
+
+        DX
+            :mod:`OpenDX`
+        MRC
+            :mod:`mrc` MRC/CCP4 format
+
+        Parameters
+        ----------
+        format_specifier : str 
+
+        tolerance : float (default is None)
+
+        Returns
+        -------
+        native object
+
+        """
+        fmt_upper = format_specifier.upper()
+
+        wrapper = self.converter[fmt_upper](self, **kwargs)
+        return wrapper.native
+
     def export(self, filename, file_format=None, type=None, typequote='"'):
         """export density to file using the given format.
 
@@ -673,29 +705,8 @@ def _export_dx(self, filename, type=None, typequote='"', **kwargs):
         """
         root, ext = os.path.splitext(filename)
         filename = root + '.dx'
-
-        comments = [
-            'OpenDX density file written by gridDataFormats.Grid.export()',
-            'File format: http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm#HDREDF',
-            'Data are embedded in the header and tied to the grid positions.',
-            'Data is written in C array order: In grid[x,y,z] the axis z is fastest',
-            'varying, then y, then finally x, i.e. z is the innermost loop.']
-
-        # write metadata in comments section
-        if self.metadata:
-            comments.append('Meta data stored with the python Grid object:')
-        for k in self.metadata:
-            comments.append('   ' + str(k) + ' = ' + str(self.metadata[k]))
-        comments.append(
-            '(Note: the VMD dx-reader chokes on comments below this line)')
-
-        components = dict(
-            positions=OpenDX.gridpositions(1, self.grid.shape, self.origin,
-                                           self.delta),
-            connections=OpenDX.gridconnections(2, self.grid.shape),
-            data=OpenDX.array(3, self.grid, type=type, typequote=typequote),
-        )
-        dx = OpenDX.field('density', components=components, comments=comments)
+        dx = OpenDX.field.from_grid(self, type=type, typequote=typequote, **kwargs)
+
         if ext == '.gz':
             filename = root + ext
         dx.write(filename)
@@ -721,16 +732,7 @@ def _export_mrc(self, filename, **kwargs):
 
         .. 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
+        mrc_file = mrc.MRC.from_grid(self, **kwargs)
 
         # Write to file
         mrc_file.write(filename)

gridData/mrc.py

@@ -100,6 +100,25 @@ def __init__(self, filename=None, assume_volumetric=False):
         self.filename = filename
         if filename is not None:
             self.read(filename, assume_volumetric=assume_volumetric)
+
+    @staticmethod
+    def from_grid(grid, **kwargs):
+        mrc_obj = MRC()
+
+        mrc_obj.array = grid.grid
+        mrc_obj.delta = np.diag(grid.delta)
+        mrc_obj.origin = grid.origin
+        mrc_obj.rank = 3
+
+        if hasattr(grid, "_mrc_header"):
+            mrc_obj.header = grid._mrc_header
+
+        return mrc_obj
+
+    @property
+    def native(self):
+        """Native object is the MRC wrapper itself."""
+        return self
 
     def read(self, filename, assume_volumetric=False):
         """Populate the instance from the MRC/CCP4 file *filename*."""

gridData/tests/test_dx.py

@@ -90,3 +90,26 @@ def test_delta_precision(tmpdir):
         g.delta, g2.delta,
         decimal=7,
         err_msg="deltas of written grid do not match original")
+
+def test_dx_from_grid():
+    data = np.ones((5, 5, 5), dtype=np.float32)
+    g = Grid(data, origin=[1.0, 2.0, 3.0], delta=[0.5, 0.5, 0.5])
+    g.metadata['name'] = 'test_density'
+    g.metadata['author'] = 'test_user'
+
+    dx_field = gridData.OpenDX.field.from_grid(g)
+
+    assert isinstance(dx_field, gridData.OpenDX.field)
+
+    assert any('test_density' and 'test_user' in str(c) for c in dx_field.comments)
+    # assert any('test_user' in str(c) for c in dx_field.comments)
+
+    assert_equal(dx_field.components['data'].array, data)
+    assert_equal(dx_field.components['positions'].origin, g.origin)
+
+def test_dx_native():
+    data = np.ones((5, 5, 5))
+    g = Grid(data, origin=[0, 0, 0], delta=[1, 1, 1])
+
+    dx_field = gridData.OpenDX.field.from_grid(g)
+    assert dx_field.native is dx_field

gridData/tests/test_mrc.py

@@ -142,6 +142,27 @@ def test_origin(self, grid, ccp4data):
 
     def test_data(self, grid, ccp4data):
         assert_allclose(grid.grid, ccp4data.array)
+
+    def test_mrc_from_grid(self):
+        data = np.arange(27, dtype=np.float32).reshape((3, 3, 3))
+        g = Grid(data, origin=[1.0, 2.0, 3.0], delta=[0.5, 0.5, 0.5])
+
+        mrc_obj = mrc.MRC.from_grid(g)
+
+        assert isinstance(mrc_obj, mrc.MRC)
+
+        assert_equal(mrc_obj.array, data)
+        assert_allclose(mrc_obj.delta, np.diag(g.delta))
+        assert_allclose(mrc_obj.origin, g.origin)
+        assert mrc_obj.rank == 3
+
+    def test_mrc_native_property(self):
+        data = np.ones((3, 3, 3))
+        g = Grid(data, origin=[0, 0, 0], delta=[1, 1, 1])
+
+        mrc_obj = mrc.MRC.from_grid(g)
+
+        assert mrc_obj.native is mrc_obj
 
 class TestMRCWrite:
     """Tests for MRC write functionality"""