Merge pull request #100 from MDAnalysis/mrcfile

use mrcfile library for MRC/CCP4 file parsing

.github/workflows/gh-ci.yaml

@@ -49,7 +49,7 @@ jobs:
 
     - name: install package deps
       run: |
-        mamba install numpy scipy pytest pytest-cov codecov six
+        mamba install numpy scipy mrcfile six pytest pytest-cov codecov
 
     - name: check install
       run: |

CHANGELOG

@@ -13,6 +13,25 @@ The rules for this file:
   * accompany each entry with github issue/PR number (Issue #xyz)
 
 ------------------------------------------------------------------------------
+??/??/2022 orbeckst, tluchko, IAlibay
+
+  * 0.7.0
+
+  Enhancements
+
+  * use mrcfile library to parse MRC files (including CCP4) using the
+    new mrc.MRC class (issue #83)
+
+  Fixes
+
+  * The new mrc module correctly reorients the coordinate system based
+    on mapc, mapr, maps and correctly calculates the origin (issue #76)
+
+  Deprecations
+
+  * The CCP4 module (replaced by mrc) will be removed in 0.8.0.
+
+
 10/10/2021 eloyfelix, renehamburger1993, lilyminium, jvermaas, xiki-tempula,
            IAlibay, orbeckst
 

doc/source/gridData/formats.rst

@@ -27,7 +27,7 @@ small number of file formats is directly supported.
    ============================ ==========  =========  =====  =====  =========================================
    :mod:`~gridData.OpenDX`      OpenDX_     dx         x      x      subset of OpenDX implemented
    :mod:`~gridData.gOpenMol`    gOpenMol_   plt        x
-   :mod:`~gridData.CCP4`        CCP4_       ccp4       x             subset implemented
+   :mod:`~gridData.mrc`         CCP4_       ccp4,mrc   x             subset implemented
    :class:`~gridData.core.Grid` pickle      pickle     x      x      standard Python pickle of the Grid class
    ============================ ==========  =========  =====  =====  =========================================
 
@@ -38,7 +38,7 @@ small number of file formats is directly supported.
 .. _Chimera: https://www.cgl.ucsf.edu/chimera/
 .. _OpenDX: http://www.opendx.org/
 .. _gOpenMol: http://www.csc.fi/gopenmol/
-.. _CCP4: http://www.ccp4.ac.uk/html/maplib.html#description
+.. _CCP4: http://www.ccpem.ac.uk/mrc_format/mrc2014.php
 
 
 Format-specific modules
@@ -49,4 +49,5 @@ Format-specific modules
 
    formats/OpenDX
    formats/gOpenMol
+   formats/mrc
    formats/CCP4

doc/source/gridData/formats/mrc.rst

@@ -0,0 +1,2 @@
+.. automodule:: gridData.mrc
+   :members:

gridData/CCP4.py

@@ -6,11 +6,14 @@
 # Copyright Science and Technologies Facilities Council, 2015.
 
 """
-:mod:`CCP4` --- the CCP4 volumetric data format
-===============================================
+:mod:`CCP4` --- the CCP4 volumetric data format (DEPRECATED)
+============================================================
 
 .. versionadded:: 0.3.0
 
+.. deprecated:: 0.7.0 The CCP4 module is replaced by :mod:`gridData.mrc` and
+   will be removed in 0.8.0.
+
 .. _CCP4: http://www.ccp4.ac.uk/html/maplib.html#description
 
 The module provides a simple implementation of a reader for CCP4_
@@ -160,6 +163,10 @@ class CCP4(object):
        * symmetry records
        * index ordering besides standard column-major and row-major
        * non-standard fields, such any in filed in future use block
+
+
+    .. deprecated:: 0.7.0
+       Use :class:`gridData.mrc.MRC` instead. This class will be removed in 0.8.0.
     """
 
     _axis_map = {1: 'x', 2: 'y', 3: 'z'}
@@ -196,6 +203,10 @@ def __init__(self, filename=None):
         if filename is not None:
             self.read(filename)
 
+        warnings.warn("CCP4.CCP4 is being replaced by mrc.MRC and will be removed "
+                      "in release 0.8.0",
+                      category=DeprecationWarning)
+
     def read(self, filename):
         """Populate the instance from the ccp4 file *filename*."""
         if filename is not None:

gridData/__init__.py

@@ -93,16 +93,8 @@
 Formats
 -------
 
-The following formats are available (:ref:`supported-file-formats`):
-
-   :mod:`~gridData.OpenDX`
-        IBM's Data Explorer, http://www.opendx.org/
-   :mod:`~gridData.gOpenMol`
-        http://www.csc.fi/gopenmol/
-   :mod:`~gridData.CCP4`
-        CCP4 format http://www.ccp4.ac.uk/html/maplib.html#description
-   pickle
-        python pickle file (:mod:`pickle`)
+For the available file formats see :ref:`supported-file-formats`.
+
 
 
 """

gridData/core.py

@@ -40,7 +40,7 @@
 
 from . import OpenDX
 from . import gOpenMol
-from . import CCP4
+from . import mrc
 
 
 def _grid(x):
@@ -114,6 +114,10 @@ def __init__(self, grid=None, edges=None, origin=None, delta=None,
         .. versionchanged:: 0.5.0
            New *file_format* keyword argument.
 
+        .. versionchanged:: 0.7.0
+           CCP4 files are now read with :class:`gridData.mrc.MRC` and not anymore
+           with the deprecated/buggy `ccp4.CCP4`
+
         """
         # file formats are guess from extension == lower case key
         self._exporters = {
@@ -123,7 +127,8 @@ def __init__(self, grid=None, edges=None, origin=None, delta=None,
             'PYTHON': self._export_python,  # compatibility
         }
         self._loaders = {
-            'CCP4': self._load_cpp4,
+            'CCP4': self._load_mrc,
+            'MRC':  self._load_mrc,
             'DX': self._load_dx,
             'PLT': self._load_plt,
             'PKL': self._load_python,
@@ -471,12 +476,14 @@ def _load_python(self, filename):
                    edges=saved['edges'],
                    metadata=saved['metadata'])
 
-    def _load_cpp4(self, filename):
-        """Initializes Grid from a CCP4 file."""
-        ccp4 = CCP4.CCP4()
-        ccp4.read(filename)
-        grid, edges = ccp4.histogramdd()
+    def _load_mrc(self, filename):
+        """Initializes Grid from a MRC/CCP4 file."""
+        mrcfile = mrc.MRC(filename)
+        grid, edges = mrcfile.histogramdd()
         self._load(grid=grid, edges=edges, metadata=self.metadata)
+        # Store header for access from Grid object (undocumented)
+        # https://github.com/MDAnalysis/GridDataFormats/pull/100#discussion_r782604833
+        self._mrc_header = mrcfile.header.copy()
 
     def _load_dx(self, filename):
         """Initializes Grid from a OpenDX file."""

gridData/mrc.py

@@ -0,0 +1,149 @@
+# gridDataFormats --- python modules to read and write gridded data
+# Copyright (c) 2009-2021 Oliver Beckstein <[email protected]>
+# Released under the GNU Lesser General Public License, version 3 or later.
+#
+
+""":mod:`mrc` --- the mrc/CCP4 volumetric data format
+===================================================
+
+.. versionadded:: 0.7.0
+
+Reading of MRC/CCP4 volumetric files (`MRC2014 file format`_) using
+the mrcfile_ library [Burnley2017]_.
+
+This implementation replaces the :mod:`CCP4` module.
+
+.. _mrcfile: https://mrcfile.readthedocs.io/
+.. _`MRC2014 file format`: http://www.ccpem.ac.uk/mrc_format/mrc2014.php
+
+
+References
+----------
+
+.. [Burnley2017] Burnley T, Palmer C and Winn M (2017) Recent
+                 developments in the CCP-EM software suite. *Acta
+                 Cryst.* D73:469-477. doi: `10.1107/S2059798317007859`_
+
+
+.. _`10.1107/S2059798317007859`: https://doi.org/10.1107/S2059798317007859
+
+Classes
+-------
+
+"""
+from __future__ import absolute_import
+from six.moves import range
+
+import numpy as np
+import mrcfile
+
+
+class MRC(object):
+    """Represent a MRC/CCP4 file.
+
+    Load `MRC/CCP4 2014 <MRC2014 file format>`_ 3D volumetric data with
+    the mrcfile_ library.
+
+    Parameters
+    ----------
+    filename : str (optional)
+       input file (or stream), can be compressed
+
+
+    Attributes
+    ----------
+    header : numpy.recarray
+       Header data from the MRC file as a numpy record array.
+
+    array : numpy.ndarray
+       Data as a 3-dimensional array where axis 0 corresponds to X,
+       axis 1 to Y, and axis 2 to Z. This order is always enforced,
+       regardless of the order in the mrc file.
+
+    delta : numpy.ndarray
+       Diagonal matrix with the voxel size in X, Y, and Z direction
+       (taken from the :attr:`mrcfile.mrcfile.voxel_size` attribute)
+
+    origin : numpy.ndarray
+       numpy array with coordinates of the coordinate system origin
+       (taken from :attr:`header.origin`)
+
+    rank : int
+       The integer 3, denoting that only 3D maps are read.
+
+
+    Notes
+    -----
+    * Only volumetric (3D) densities are read.
+    * Only orthorhombic unitcells supported (other raise :exc:`ValueError`)
+    * Only reading is currently supported.
+
+
+    .. versionadded:: 0.7.0
+
+    """
+
+    def __init__(self, filename=None):
+        self.filename = filename
+        if filename is not None:
+            self.read(filename)
+
+    def read(self, filename):
+        """Populate the instance from the MRC/CCP4 file *filename*."""
+        if filename is not None:
+            self.filename = filename
+        with mrcfile.open(filename) as mrc:
+            if not mrc.is_volume():                           #pragma: no cover
+                raise ValueError(
+                    "MRC file {} is not a volumetric density.".format(filename))
+            self.header = h = mrc.header.copy()
+            # check for being orthorhombic
+            if not np.allclose([h.cellb.alpha, h.cellb.beta, h.cellb.gamma],
+                               [90, 90, 90]):
+                raise ValueError("Only orthorhombic unitcells are currently "
+                                 "supported, not "
+                                 "alpha={0}, beta={1}, gamma={2}".format(
+                                     h.cellb.alpha, h.cellb.beta, h.cellb.gamma))
+            # mrc.data[z, y, x] indexed: convert to x,y,z as used in GridDataFormats
+            # together with the axes orientation information in mapc/mapr/maps.
+            # mapc, mapr, maps = 1, 2, 3 for Fortran-ordering and 3, 2, 1 for C-ordering.
+            # Other combinations are possible. We reorder the data for the general case
+            # by sorting mapc, mapr, maps in ascending order, i.e., to obtain x,y,z.
+            # mrcfile provides the data in zyx shape (without regard to map*) so we first
+            # transpose it to xyz and then reorient with axes_c_order.
+            #
+            # All other "xyz" quantitities are also reordered.
+            axes_order = np.hstack([h.mapc, h.mapr, h.maps])
+            axes_c_order = np.argsort(axes_order)
+            transpose_order = np.argsort(axes_order[::-1])
+            self.array = np.transpose(mrc.data, axes=transpose_order)
+            self.delta = np.diag(np.array([mrc.voxel_size.x, mrc.voxel_size.y, mrc.voxel_size.z]))
+            # the grid is shifted to the MRC origin by offset
+            # (assume orthorhombic)
+            offsets = np.hstack([h.nxstart, h.nystart, h.nzstart])[axes_c_order] * np.diag(self.delta)
+            # GridData origin is centre of cell at x=col=0, y=row=0 z=seg=0
+            self.origin = np.hstack([h.origin.x, h.origin.y, h.origin.z]) + offsets
+            self.rank = 3
+
+    @property
+    def shape(self):
+        """Shape of the :attr:`array`"""
+        return self.array.shape
+
+    @property
+    def edges(self):
+        """Edges of the grid cells, origin at centre of 0,0,0 grid cell.
+
+        Only works for regular, orthonormal grids.
+        """
+        # TODO: Add triclinic cell support.
+        return [self.delta[d, d] * np.arange(self.shape[d] + 1) +
+                self.origin[d] - 0.5 * self.delta[d, d]
+                for d in range(self.rank)]
+
+    def histogramdd(self):
+        """Return array data as (edges,grid), i.e. a numpy nD histogram."""
+        return (self.array, self.edges)
+
+
+

gridData/tests/datafiles/__init__.py

@@ -10,6 +10,8 @@
 # from http://www.ebi.ac.uk/pdbe/coordinates/files/1jzv.ccp4
 # (see issue #57)
 CCP4_1JZV = resource_filename(__name__, '1jzv.ccp4')
+# from https://github.com/ccpem/mrcfile/blob/master/tests/test_data/EMD-3001.map.bz2
+MRC_EMD3001 = resource_filename(__name__, 'EMD-3001.map.bz2')
 # water density around M2 TM helices of nAChR from MD simulations
 # [O. Beckstein and M. S. P. Sansom. Physical Biology 3(2):147-159, 2006]
 gOpenMol = resource_filename(__name__, 'nAChR_M2_water.plt')

gridData/tests/test_ccp4.py

@@ -12,7 +12,12 @@
 
 @pytest.fixture(scope="module")
 def g():
-    return Grid(datafiles.CCP4)
+    with pytest.warns(DeprecationWarning,
+                      match="CCP4.CCP4 is being replaced by mrc.MRC and will be removed"):
+        ccp4 = CCP4.CCP4()
+    ccp4.read(datafiles.CCP4)
+    grid, edges = ccp4.histogramdd()
+    return Grid(grid=grid, edges=edges)
 
 def test_ccp4(g):
     POINTS = 192
@@ -24,7 +29,10 @@ def test_ccp4(g):
 
 @pytest.fixture(scope="module")
 def ccp4data():
-    return CCP4.CCP4(datafiles.CCP4_1JZV)
+    with pytest.warns(DeprecationWarning,
+                      match="CCP4.CCP4 is being replaced by mrc.MRC and will be removed"):
+        ccp4 = CCP4.CCP4(datafiles.CCP4_1JZV)
+    return ccp4
 
 @pytest.mark.parametrize('name,value', [
     ('nc', 96),