crunchflow.output.spatial.SpatialProfile

class crunchflow.output.spatial.SpatialProfile(fileprefix, folder='.', output_times=None, suffix='.tec', warnings=True)

The SpatialProfile class for working with spatial_profile (.tec, .out and .dat) files.

Parameters:

fileprefixstr: file prefix of the tec file to read in, without the timestep number or “.tec” file ending. For example, if your files are “volume1.tec”, “volume2.tec”, etc., then fileprefix should be “volume”.
folderstr, optional: folder in which the .tec files are located. The default is the current directory
output_timeslist of float, optional: list of the actual output times at which the .tec files were output, in CrunchFlow time units
suffixstr, optional: file ending of the tec files to read in. This can vary depending on the version of CrunchTope used. The default is ‘.tec’, but ‘.out’ is also tried if ‘.tec’ files are not found.

Attributes:

timeslist of int: relative times at which .tec files were output, sorted
fileslist of str: ordered list of all files matching fileprefix
columnslist of str: list of all vars included within each .tec file
nxint: # of grid cells in the x direction. Typically only defined for 2D and 3D output
nyint: # of grid cells in the y direction. Typically only defined for 2D and 3D output
nzint: # of grid cells in the z direction. Typically only defined for 2D and 3D output
coordsndarray of float: (nx*ny*nz, 2) array of x, y coordinates of each node. Typically only defined for 2D and 3D output
griddedXndarray of float: (ny, nx) array of x coordinates; used for plotting. Typically only defined for 2D and 3D output
griddedYndarray of float: (ny, nx) array of y coordinates; used for plotting. Typically only defined for 2D and 3D output

Methods

__init__(fileprefix, folder, output_times, suffix)	Read in and get basic info about all .tec files matching fileprefix. For example, tec(‘volume’) will read in all files matching ‘volume[0-9]+.tec’
extract(variable, time)	Return the spatial profile of var at the given time.
plot(variable, time)	Plot .tec output from a single time step.
plot_series(variable)	Plot .tec output for a series of time steps.
outline(variable, value, time)	Get line segments that outline all the regions equal to the provided value.

Examples

>>> vol = SpatialProfile('volume')
>>> print(vol.columns)
>>> vol.plot('Calcite')
>>> calcite = vol.extract('Calcite', time=2)

extract(var, time=None, output_time=None)

Return the spatial profile of var at the given time.

Parameters:

varstr: variable to return (e.g., ‘Porosity’)
timeint: time slice at which to return the profile. By default, returns the first time slice.
output_timefloat: output time at which to return the profile. If provided, this will override the time parameter. If both time and output_time are provided, time will be ignored.

Returns:

datandarray of float: (ny, nx) numpy array of var

plot(var, time=None, output_time=None, plot_type='image', figsize=(12, 3), **kwargs)

Plot .tec output from a single time step.

Parameters:

varstr: variable to plot (e.g., ‘H+’)
timeint: which time slice to show. Refers to the file number, not the output time. By default, plots the first time slice.
output_timefloat: which output time to show. If provided, this will override the time parameter. If both time and output_time are provided, time will be ignored.
figsizetuple of int: figure size; default (12, 3)
plot_typestr: whether to display an image (‘image’) or a color-filled contour plot (‘contourf’)
**kwargsdict: args passed on to matplotlib plot function (either contourf or imshow)

Returns:

figpyplot object: matplotlib fig handle for the plot
axpyplot object: matplotlib ax handle for the plot

plot_series(var, times=None, output_times=None, plot_type='image', figsize=None, **kwargs)

Plot .tec output for a series of time steps.

Parameters:

varstr: variable to plot (e.g., ‘H+’)
timeslist: time steps to plot, must be either components of self.times or self.output_times; defaults to all time steps
plot_typestr: whether to display an image (‘image’) or a contour-filled contour plot (‘contourf’)
output_timeslist of float, optional: list of the actual output times at which the .tec files were output, in CrunchFlow time units. If provided, this will override the times parameter. If both times and output_times are provided, times will be ignored.
figsizetuple of int: figure size; default (12, 1.5 * # of timesteps)
**kwargsdict: args passed on to matplotlib’s imshow

Returns:

figpyplot object: matplotlib fig handle for the plot
axeslist of pyplot objects: list of matplotlib axes handles for each subplot

outline(var, value=None, time=None, output_time=None)

For a given .tec file, get line segments that outline all the regions equal to the provided value. Useful for generating outlines of areas of a model domain sharing a single attribute (e.g., permeability) and later adding the outlines to a plot of a different variable.

Parameters:

varstr: variable to outline (e.g., ‘Porosity’)
valuefloat: value to outline. The default is least-frequent value in array
timeint: time slice at which to create an outline. By default, outlines the first time slice.
output_timefloat: output time at which to create an outline. If provided, this will override the time parameter. If both time and output_time are provided, time will be ignored.

Returns:

segmentsndarray of float: array of (x,y) coordinate pairs for each line segment that comprises the outline

Examples

>>> # Get stratigraphy from permeability map
>>> perm = SpatialProfile('permeability')
>>> segments = perm.outline('X-Perm')
>>>
>>> # Plot stratigraphy outlines on O2 map
>>> conc = SpatialProfile('conc')
>>> fig, ax = conc.plot('O2(aq)')
>>> ax.plot(segments[:,0], segments[:,1])