Core functionality for storing n-D grids — gridData.core
¶
The core
module contains classes and functions that are
independent of the grid data format. In particular this module
contains the Grid
class that acts as a universal constructor
for specific formats:
g = Grid(**kwargs) # construct
g.export(filename, format) # export to the desired format
Some formats can also be read:
g = Grid() # make an empty Grid
g.load(filename) # populate with data from filename
Classes and functions¶
- class gridData.core.Grid(grid=None, edges=None, origin=None, delta=None, metadata=None, interpolation_spline_order=3, file_format=None)[source]¶
A multidimensional grid object with origin and grid spacings.
Grid
objects can be used in arithmetical calculations just like numpy arrays if they are compatible, i.e., they have the same shapes and lengths. In order to make arrays compatible, they an be resampled (resample()
) on a common grid.The attribute
grid
that holds the data is a standard numpy array and so the data can be directly manipulated.Data can be read from a number of molecular volume/density formats and written out in different formats with
export()
.- Parameters
grid (numpy.ndarray or str (optional)) – Build the grid either from a histogram or density (a numpy nD array) or read data from a filename.
edges (list (optional)) – List of arrays, the lower and upper bin edges along the axes (same as the output by
numpy.histogramdd()
)origin (
numpy.ndarray
(optional)) – Cartesian coordinates of the center of grid position at index[0, 0, ..., 0]
.delta (
numpy.ndarray
(optional)) – Eithern x n
array containing the cell lengths in each dimension, orn x 1
array for rectangular arrays.metadata (dict (optional)) – A user defined dictionary of arbitrary key/value pairs associated with the density; the class does not touch
metadata
but stores it withsave()
interpolation_spline_order (int (optional)) – Order of interpolation function for resampling with
resample()
; cubic splines = 3 and the default is 3file_format (str (optional)) – Name of the file format; only necessary when grid is a filename (see
load()
) and autodetection of the file format fails. The default isNone
and normally the file format is guessed from the file extension.
- Raises
TypeError – If the dimensions of the various input data do not agree with each other.
ValueError – If some of the required data are not provided in the keyword arguments, e.g., if only the grid is supplied as an array but not the edges or only grid and one of origin and delta.
NotImplementedError – If triclinic (non-orthorhombic) boxes are supplied in delta .. Note:: delta can only be a 1D array of length
grid.ndim
- grid¶
This array can be any number of dimensions supported by NumPy in order to represent high-dimensional data. When used with data that represents real space densities then the axis convention in GridDataFormats is that axis 0 corresponds to the Cartesian \(x\) component, axis 1 corresponds to the \(y\) component, and axis 2 to the \(z\) component.
- Type
- delta¶
Length of a grid cell (spacing or voxelsize) in \(x\), \(y\), \(z\) dimensions. This is a 1D array with length
Grid.grid.ndim
.- Type
- origin¶
Array with the Cartesian coordinates of the coordinate system origin, the center of cell
Grid.grid[0, 0, .., 0]
.- Type
- edges¶
List of arrays, one for each axis in
grid
. Each 1D edge array describes the edges of the grid cells along the corresponding axis. The length of an edge array for axisi
isgrid.shape[i] + 1
because it contains the lower boundary for the first cell, the boundaries between all grid cells, and the upper boundary for the last cell. The edges are assumed to be regular with spacing indicated indelta
, namelyGrid.delta[i]
for axisi
.- Type
- midpoints¶
List of arrays, one for each axis in
grid
. Each 1D midpoints array contains the midpoints of the grid cells along the corresponding axis.- Type
- metadata¶
A user-defined dictionary that can be used to annotate the data. The content is not touched by
Grid
. It is saved together with the other data withsave()
.- Type
Example
Create a Grid object from data.
From
numpy.histogramdd()
:grid, edges = numpy.histogramdd(...) g = Grid(grid, edges=edges)
From an arbitrary grid:
g = Grid(grid, origin=origin, delta=delta)
From a saved file:
g = Grid(filename)
or
g = Grid() g.load(filename)
Notes
In principle, the dimension (number of axes) is arbitrary but in practice many formats only support three and almost all functionality is only tested for this special case.
The
export()
method withformat='dx'
always exports a 3D object. Other methods might work for an array of any dimension (in particular the Python pickle output).Changed in version 0.5.0: New file_format keyword argument.
Changed in version 0.7.0: CCP4 files are now read with
gridData.mrc.MRC
and not anymore with the deprecated/buggy ccp4.CCP4- centers()[source]¶
Returns the coordinates of the centers of all grid cells as an iterator.
See also
numpy.ndindex()
- check_compatible(other)[source]¶
Check if other can be used in an arithmetic operation.
other is compatible if
other is a scalar
other is a grid defined on the same edges
In order to make other compatible, resample it on the same grid as this one using
resample()
.- Parameters
other (Grid or float or int) – Another object to be used for standard arithmetic operations with this
Grid
- Raises
TypeError – if not compatible
See also
- export(filename, file_format=None, type=None, typequote='"')[source]¶
export density to file using the given format.
The format can also be deduced from the suffix of the filename although the file_format keyword takes precedence.
The default format for
export()
is ‘dx’. Use ‘dx’ for visualization.Implemented formats:
- dx
OpenDX
- pickle
pickle (use
Grid.load()
to restore);Grid.save()
is simpler thanexport(format='python')
.
- Parameters
filename (str) – name of the output file
file_format ({'dx', 'pickle', None} (optional)) – output file format, the default is “dx”
type (str (optional)) –
for DX, set the output DX array type, e.g., “double” or “float”. By default (
None
), the DX type is determined from the numpy dtype of the array of the grid (and this will typically result in “double”).New in version 0.4.0.
typequote (str (optional)) –
For DX, set the character used to quote the type string; by default this is a double-quote character, ‘”’. Custom parsers like the one from NAMD-GridForces (backend for MDFF) expect no quotes, and typequote=’’ may be used to appease them.
New in version 0.5.0.
- property interpolated¶
B-spline function over the data grid(x,y,z).
The
interpolated()
function allows one to obtain data values for any values of the coordinates:interpolated([x1,x2,...],[y1,y2,...],[z1,z2,...]) -> F[x1,y1,z1],F[x2,y2,z2],...
The interpolation order is set in
Grid.interpolation_spline_order
.The interpolated function is computed once and is cached for better performance. Whenever
interpolation_spline_order
is modified,Grid.interpolated()
is recomputed.The value for unknown data is set in
Grid.interpolation_cval
(TODO: also recompute wheninterpolation_cval
value is changed.)Example
Example usage for resampling:
XX, YY, ZZ = numpy.mgrid[40:75:0.5, 96:150:0.5, 20:50:0.5] FF = interpolated(XX, YY, ZZ)
Note
Values are interpolated with a spline function. It is possible that the spline will generate values that would not normally appear in the data. For example, a density is non-negative but a cubic spline interpolation can generate negative values, especially at the boundary between 0 and high values.
Internally, the function uses
scipy.ndimage.map_coordinates()
withmode="constant"
whereby interpolated values outside the interpolated grid are determined by filling all values beyond the edge with the same constant value, defined by theinterpolation_cval
parameter, which when not set defaults to the minimum value in the interpolated grid.Changed in version 0.6.0: Interpolation outside the grid is now performed with
mode="constant"
rather thanmode="nearest"
, eliminating extruded volumes when interpolating beyond the grid.
- property interpolation_spline_order¶
Order of the B-spline interpolation of the data.
3 = cubic; 4 & 5 are also supported
Only choose values that are acceptable to
scipy.ndimage.spline_filter()
!See also
- load(filename, file_format=None)[source]¶
Load saved grid and edges from filename
The
load()
method calls the class’s constructor method and completely resets all values, based on the loaded data.
- resample(edges)[source]¶
Resample data to a new grid with edges edges.
This method creates a new grid with the data from the current grid resampled to a regular grid specified by edges. The order of the interpolation is set by
Grid.interpolation_spline_order
: change the value before callingresample()
.- Parameters
edges (tuple of arrays or Grid) – edges of the new grid or a
Grid
instance that providesGrid.edges
- Returns
a new
Grid
with the data interpolated over the new grid cells- Return type
Examples
Providing edges (a tuple of three arrays, indicating the boundaries of each grid cell):
g = grid.resample(edges)
As a convenience, one can also supply another
Grid
as the argument for this methodg = grid.resample(othergrid)
and the edges are taken from
Grid.edges
.
- resample_factor(factor)[source]¶
Resample to a new regular grid.
- Parameters
factor (float) – The number of grid cells are scaled with factor in each dimension, i.e.,
factor * N_i
cells along each dimension i. Must be positive, and cannot result in fewer than 2 cells along a dimension.- Returns
interpolated grid – The resampled data are represented on a
Grid
with the new grid cell sizes.- Return type
See also
Changed in version 0.6.0: Previous implementations would not alter the range of the grid edges being resampled on. As a result, values at the grid edges would creep steadily inward. The new implementation recalculates the extent of grid edges for every resampling.
- save(filename)[source]¶
Save a grid object to filename and add “.pickle” extension.
Internally, this calls
Grid.export(filename, format="python")
. A grid can be regenerated from the saved data withg = Grid(filename="grid.pickle")
Note
The pickle format depends on the Python version and therefore it is not guaranteed that a grid saved with, say, Python 2.7 can also be read with Python 3.5. The OpenDX format is a better alternative for portability.
- gridData.core.ndmeshgrid(*arrs)[source]¶
Return a mesh grid for N dimensions.
The input are N arrays, each of which contains the values along one axis of the coordinate system. The arrays do not have to have the same number of entries. The function returns arrays that can be fed into numpy functions so that they produce values for all points spanned by the axes arrs.
Original from http://stackoverflow.com/questions/1827489/numpy-meshgrid-in-3d and fixed.