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fix multiple __init__ calls #74

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Merged
orbeckst merged 2 commits into from
Jan 17, 2020
Merged

fix multiple __init__ calls #74

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df339ef
fix multiple __init__ calls
eloyfelix Nov 30, 2019
1bf3aec
update CHANGELOG
orbeckst Jan 17, 2020
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1 change: 1 addition & 0 deletions CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ The rules for this file:
Fixes

* fix initialization of mutable instance variable of Grid class (metadata dict) (#71)
* fix multiple __init__ calls (#73)


05/16/2019 giacomofiorin, orbeckst
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79 changes: 41 additions & 38 deletions gridData/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -157,38 +157,7 @@ def __init__(self, grid=None, edges=None, origin=None, delta=None,
if filename is not None:
self.load(filename, file_format=file_format)
else:
if edges is not None:
# set up from histogramdd-type data
self.grid = numpy.asanyarray(grid)
self.edges = edges
self._update()
elif origin is not None and delta is not None:
# setup from generic data
origin = numpy.asanyarray(origin)
delta = numpy.asanyarray(delta)
if len(origin) != grid.ndim:
raise TypeError(
"Dimension of origin is not the same as grid dimension.")
if delta.shape == () and numpy.isreal(delta):
delta = numpy.ones(grid.ndim) * delta
elif delta.ndim > 1:
raise NotImplementedError(
"Non-rectangular grids are not supported.")
elif len(delta) != grid.ndim:
raise TypeError("delta should be scalar or array-like of"
"len(grid.ndim)")
# note that origin is CENTER so edges must be shifted by -0.5*delta
self.edges = [origin[dim] +
(numpy.arange(m + 1) - 0.5) * delta[dim]
for dim, m in enumerate(grid.shape)]
self.grid = numpy.asanyarray(grid)
self._update()
else:
raise ValueError("Wrong/missing data to set up Grid. Use Grid() or "
"Grid(grid=<array>, edges=<list>) or "
"Grid(grid=<array>, origin=(x0, y0, z0), delta=(dx, dy, dz)):\n"
"grid={0} edges={1} origin={2} delta={3}".format(
grid, edges, origin, delta))
self._load(grid, edges, metadata, origin, delta)

@property
def interpolation_spline_order(self):
Expand Down Expand Up @@ -404,6 +373,40 @@ def _get_loader(self, filename, file_format=None):
file_format=file_format,
export=False)]

def _load(self, grid=None, edges=None, metadata=None, origin=None, delta=None):
if edges is not None:
# set up from histogramdd-type data
self.grid = numpy.asanyarray(grid)
self.edges = edges
self._update()
elif origin is not None and delta is not None:
# setup from generic data
origin = numpy.asanyarray(origin)
delta = numpy.asanyarray(delta)
if len(origin) != grid.ndim:
raise TypeError(
"Dimension of origin is not the same as grid dimension.")
if delta.shape == () and numpy.isreal(delta):
delta = numpy.ones(grid.ndim) * delta
elif delta.ndim > 1:
raise NotImplementedError(
"Non-rectangular grids are not supported.")
elif len(delta) != grid.ndim:
raise TypeError("delta should be scalar or array-like of"
"len(grid.ndim)")
# note that origin is CENTER so edges must be shifted by -0.5*delta
self.edges = [origin[dim] +
(numpy.arange(m + 1) - 0.5) * delta[dim]
for dim, m in enumerate(grid.shape)]
self.grid = numpy.asanyarray(grid)
self._update()
else:
raise ValueError("Wrong/missing data to set up Grid. Use Grid() or "
"Grid(grid=<array>, edges=<list>) or "
"Grid(grid=<array>, origin=(x0, y0, z0), delta=(dx, dy, dz)):\n"
"grid={0} edges={1} origin={2} delta={3}".format(
grid, edges, origin, delta))

def load(self, filename, file_format=None):
"""Load saved (pickled or dx) grid and edges from <filename>.pickle

Expand All @@ -425,30 +428,30 @@ def load(self, filename, file_format=None):
def _load_python(self, filename):
with open(filename, 'rb') as f:
saved = cPickle.load(f)
self.__init__(grid=saved['grid'],
edges=saved['edges'],
metadata=saved['metadata'])
self._load(grid=saved['grid'],
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()
self.__init__(grid=grid, edges=edges, metadata=self.metadata)
self._load(grid=grid, edges=edges, metadata=self.metadata)

def _load_dx(self, filename):
"""Initializes Grid from a OpenDX file."""
dx = OpenDX.field(0)
dx.read(filename)
grid, edges = dx.histogramdd()
self.__init__(grid=grid, edges=edges, metadata=self.metadata)
self._load(grid=grid, edges=edges, metadata=self.metadata)

def _load_plt(self, filename):
"""Initialize Grid from gOpenMol plt file."""
g = gOpenMol.Plt()
g.read(filename)
grid, edges = g.histogramdd()
self.__init__(grid=grid, edges=edges, metadata=self.metadata)
self._load(grid=grid, edges=edges, metadata=self.metadata)

def export(self, filename, file_format=None, type=None, typequote='"'):
"""export density to file using the given format.
Expand Down