"""
This file contains the implementation of several functions that can be used to
read/write VolumeData objects to various file-types.
"""
import os
import numpy as np
import schrodinger.infra.mminit as mminit
import schrodinger.infra.mmsurf as mmsurf
from . import vdexception
from . import volumedata as volumedata
_X = 0
_Y = 1
_Z = 2
_VX = np.array([1.0, 0.0, 0.0])
_VY = np.array([0.0, 1.0, 0.0])
_VZ = np.array([0.0, 0.0, 1.0])
_MUST_SPECIFY_FILE = "Either stream or filename must be specified."
_NON_ORTHOGONAL = "Non-orthogonal axes are currently not permitted."
_DEFAULT_NAME = "VolumeData"
_PYTHON = "PYTHON"
_mmInitialiser = mminit.Initializer([mmsurf.mmvisio_initialize],
[mmsurf.mmvisio_terminate])
class _MMVol(object):
"""
The _MMVol class acts as a wrapper around low-level MMVol objects. The
class implements Python's context-manager interface to ensure that we
don't 'leak' MMVol objects in the event of an error.
"""
def __init__(self, mmvol=None):
"""
This function creates a new _MMVol object. It either explicitly
instantiates a MMVol object, or assumes control of the object passed
via mmvol.
:param mmvol: A valid MMVol handle, if specified
:type mmvol: `MMVol handle`
"""
if mmvol is None:
self._mmvol = mmsurf.mmvol_new()
else:
self._mmvol = mmvol
def __enter__(self):
"""
Called by the context-manager as part of a 'with' statement.
"""
return self._mmvol
def __exit__(self, type, value, traceback):
"""
Called by the context manager as part of a 'with' statement.
"""
mmsurf.mmvol_delete(self._mmvol)
return False
def _MMVolToVolumeData(mmvol, handleNonOrthogonalAxes=False):
"""
This function converts the specified mmvol object to a VolumeData instance.
:param mmvol: The MMVol object to be loaded into a VolumeData instance
:param mmvol: `MMVol handle`
:param handleNonOrthogonalAxes: True if the function should handle
non-orthogonal axes. False otherwise. [Currently this parameter is
ignored and the function will throw an exception if it encounters non-
orthogonal axes.
:type handleNonOrthogonalAxes: `bool`
:return: The newly constructed VolumeData instance
:rtype: ``VolumeData``
"""
# Query the object for its various dimensions and other data.
name = mmsurf.mmvol_get_name(mmvol)
data = mmsurf.mmvol_get_grid_data(mmvol)
N = np.array(mmsurf.mmvol_get_dimensions_array(mmvol))
resolution = np.array(mmsurf.mmvol_get_axis_scales_array(mmvol))
origin = np.array(mmsurf.mmvol_get_origin_array(mmvol))
# The orientations of the axes is important, currently we only handle
# orthogonal axes, but the hooks are in place for handling the non-
# orthogonal case.
axisOrientationX = mmsurf.mmvol_get_orientation_array(mmvol, _X)
axisOrientationY = mmsurf.mmvol_get_orientation_array(mmvol, _Y)
axisOrientationZ = mmsurf.mmvol_get_orientation_array(mmvol, _Z)
if not np.all(np.equal(axisOrientationX, _VX)) or \
not np.all(np.equal(axisOrientationY, _VY)) or \
not np.all(np.equal(axisOrientationZ, _VZ)):
if handleNonOrthogonalAxes:
# DDR: Should it ever be required; code to handle non-orthogonal
# axes can be included here. I'd suggest using scipy's
# interpolation algorithms to map the non-orthogonal data to
# an orthogonal system.
pass
else:
raise vdexception.VDException(_NON_ORTHOGONAL)
# Create the VolumeData object, set the data. We also set the name here,
# although that isn't technically part of the VolumeData specification.
ret = volumedata.VolumeData(N, resolution, origin)
ret.Name = name
ret.setData(data)
return ret
[docs]def LoadVisFile(filename):
"""
This function retrieves a VolumeData object from a Schrodinger .vis file.
:param filename: A Schrodinger .vis file containing a valid mmvol object
:type filename: `string`
:return: The VolumeData extracted from the contents of the .vis file
:rtype: ``VolumeData``
"""
# Load the mmvol object from the file.
with _MMVol(mmvol=mmsurf.mmvisio_read_volume_from_file(filename)) as mmvol:
return _MMVolToVolumeData(mmvol)
def _VolumeDataToMMVol(volumeData, mmvol):
"""
This function configures the specified mmvol object to be equivalent to
the specified VolumeData.
:param volumeData: The VolumeData object to be converted
:type volumeData: ``VolumeData``
:param mmvol: A pre-allocated mmvol handle which awaits configuration
:type mmvol: `MMVol handle`
"""
# BUGBUG: I'm not sure how many of these settings are required, or if they
# are complete. These settings were arrived at through trial and error.
# Name and trivial properties.
if hasattr(volumeData, "Name"):
mmsurf.mmvol_set_name(mmvol, volumeData.Name)
else:
mmsurf.mmvol_set_name(mmvol, _DEFAULT_NAME)
mmsurf.mmvol_set_comment(mmvol, _DEFAULT_NAME)
mmsurf.mmvol_set_property_name(mmvol, _DEFAULT_NAME)
mmsurf.mmvol_set_author_name(mmvol, _PYTHON)
# Data type and overall dimensionality.
mmsurf.mmvol_set_grid_type(mmvol, mmsurf.MMVOL_REGULAR)
mmsurf.mmvol_set_data_type(mmvol, mmsurf.MMVOL_FLOAT)
mmsurf.mmvol_set_num_dimensions(mmvol, 3)
mmsurf.mmvol_set_num_components(mmvol, 1)
# Axes directions.
mmsurf.mmvol_set_orientation(mmvol, _X, _VX)
mmsurf.mmvol_set_orientation(mmvol, _Y, _VY)
mmsurf.mmvol_set_orientation(mmvol, _Z, _VZ)
# Number of data points and axis scaling.
mmsurf.mmvol_set_dimensions(mmvol, volumeData.CoordinateFrame.N)
mmsurf.mmvol_set_axis_scales(mmvol, volumeData.CoordinateFrame.resolution)
mmsurf.mmvol_set_origin(mmvol, volumeData.CoordinateFrame.origin)
# Actual data.
mmsurf.mmvol_set_grid_data(mmvol,
np.ascontiguousarray(volumeData.getData()))
# Visibility.
mmsurf.mmvol_set_default_surf_visibility(mmvol, True)
mmsurf.mmvol_set_visible(mmvol, True)
# Data range. Currently contoured at the mean of the data.
# BUGBUG: Possibly better? Single contour for all +ve or all -ve data
# at the mean. Two contours at min / 2, max / 2 for +/- data.
min = np.min(volumeData.getData())
max = np.max(volumeData.getData())
sigma = np.std(volumeData.getData())
hints = np.array([(max + min) * 0.5])
colours = np.array([mmsurf.MMVOL_COLOR_CYAN])
# # Handle +/- data.
# if np.sign( min ) == np.sign( max ):
# hints = np.array( [ ( max + min ) * 0.5 ] )
# colours = np.array( [ mm.MMVOL_COLOR_CYAN ] )
# else:
# hints = np.array( [ min * 0.5, max * 0.5 ] )
# colours = np.array( [ mm.MMVOL_COLOR_RED, \
# mm.MMVOL_COLOR_CYAN ] )
mmsurf.mmvol_set_min_sample_value(mmvol, min)
mmsurf.mmvol_set_max_sample_value(mmvol, max)
mmsurf.mmvol_set_has_sample_range(mmvol, True)
mmsurf.mmvol_set_sigma(mmvol, sigma)
mmsurf.mmvol_set_contour_hints(mmvol, len(hints), hints, colours)
[docs]def SaveVisFile(volumeData, filename):
"""
This function saves a VolumeData object to a Schrodinger .vis file.
:param volumeData: The VolumeData to be serialised
:type volumeData: ``volumeData``
:param filename: Where to store the .vis file
:type filename: `string`
"""
with _MMVol() as mmvol:
_VolumeDataToMMVol(volumeData, mmvol)
# Attempt the save, before we can actually save we have to remove
# any file that has the specified name. This appears to be due to
# a complexity of the mmvisio library.
if os.path.isfile(filename):
os.remove(filename)
mmsurf.mmvisio_write_volume_to_file(filename, mmvol)
[docs]def SaveCCP4File(volumeData, filename):
"""
This function saves a VolumeData object to a CCP4 file.
:param volumeData: The VolumeData to be serialised
:type volumeData: ``VolumeData``
:param filename: Where to store the .CCP4 file
:type filename: `string`
"""
with _MMVol() as mmvol:
_VolumeDataToMMVol(volumeData, mmvol)
mmsurf.mmvisio_write_ccp4(mmvol, filename,
mmsurf.MMSURF_CNS_MAP_TYPE_CCP4,
mmsurf.MMSURF_CNS_MAP_TYPE_COMMENT_CCP4)
[docs]def LoadCNSFile(filename):
"""
This function loads a VolumeData object from a CNS file.
:param filename: The .cns formatted file
:type filename: `string`
:return: The VolumeData object extracted from the .cns file.
:rtype: ``VolumeData``
"""
# Attempt to load and parse the .cns file.
mmvol, centre, type, comments = mmsurf.mmvisio_read_cns(filename)
with _MMVol(mmvol=mmvol) as mmvol:
return _MMVolToVolumeData(mmvol)