output¶
Helper functions for reading and modifying flash output files. For more infromation on using this module to make figures with matplotlib and yt, please refer to the following presentation: http://flash.uchicago.edu/site/flashcode/user_support/yt_flash_informal.pdf
- flash.output.slice(axis, coord, field, pf, bounds=None, resolution=600, method='nearest', **kwargs)[source]¶
Grabs the slice of a certain field (parameter, data) from the flash output file pf. This slice is performed at the coord along the axis.
This function requires both scipy and yt and returns x, y, and z data that is suitable for plotting with matplotlib.imshow().
Parameters : axis : int
The axis along which to slice. Can be 0, 1, or 2 for x, y, z.
coord : float
The coordinate along the axis at which to slice. This is in “domain” coordinates.
field : str
A field to retrieve, e.g. ‘dens’.
pf : str or yt.data_objects.static_output
The checkpoint or plot file, may be either a path to the file or the yt object returned by pf.mods.load().
bounds : len-4 sequence of floats or None, optional
This defines the area within the domain that should be sliced. By default, the whole domain is taken. Applies the bounds in axes order, ie if axis=2 then bounds=[xmin, xmax, ymin, ymax].
resolution : int or len-2 sequence of ints, optional
If a list of intergers, this is the number of points (pixels) along each dimension. If a single integer, then this is the resolution the longest axis. The resolution on the other axis is then calculated to preserve the aspect ratio.
method : str, optional
Interpolation method flag, passed directly down to the function scipy.interpolate.griddata().
kwargs : optional
All other keyword arguments are passes to the slice() method on the pf.h object from yt.
Returns : xdat : 2d numpy array
Meshed data for x.
ydat : 2d numpy array
Meshed data for y.
zdat : 2d numpy array
Meshed data for z.
- flash.output.slice_gradient(axis, coord, field, pf, bounds=None, resolution=600, method='nearest', **kwargs)[source]¶
Grabs the gradient of a slice of a certain field (parameter, data) from the flash output file pf. This slice is performed at the coord along the axis.
This function requires both scipy and yt and returns x, y, and z data that is suitable for plotting with matplotlib.imshow().
Parameters : axis : int
The axis along which to slice. Can be 0, 1, or 2 for x, y, z.
coord : float
The coordinate along the axis at which to slice. This is in “domain” coordinates.
field : str
A field to retrieve, e.g. ‘dens’.
pf : str or yt.data_objects.static_output
The checkpoint or plot file, may be either a path to the file or the yt object returned by pf.mods.load().
bounds : len-4 sequence of floats or None, optional
This defines the area within the domain that should be sliced. By default, the whole domain is taken. Applies the bounds in axes order, ie if axis=2 then bounds=[xmin, xmax, ymin, ymax].
resolution : int or len-2 sequence of ints, optional
If a list of intergers, this is the number of points (pixels) along each dimension. If a single integer, then this is the resolution the longest axis. The resolution on the other axis is then calculated to preserve the aspect ratio.
method : str, optional
Interpolation method flag, passed directly down to the function scipy.interpolate.griddata().
kwargs : optional
All other keyword arguments are passes to the slice() method on the pf.h object from yt.
Returns : adat : 2d numpy array
Meshed data for the first non-axis axis, eg x when axis=z.
bdat : 2d numpy array
Meshed data for the second non-axis axis, eg y when axis=z.
dfdadat : 2d numpy array
Gradient of field along a.
dfdbdat : 2d numpy array
Gradient of field along b.
magdat : 2d numpy array
Magnitude of the gradient of field.
- flash.output.lineout(p1, p2, field, pf, **kwargs)[source]¶
Grabs a line out (ray) of a certain field (parameter, data) from the flash output file pf.
This function requires both scipy and yt and returns x, y, z and value data that is suitable for plotting with matplotlib.plot().
Parameters : p1 : three-tuple of floats
The first point in the line-out.
p2 : three-tuple of floats
The second point in the line-out.
field : str
A field to retrieve, e.g. ‘dens’.
pf : str or yt.data_objects.static_output
The checkpoint or plot file, may be either a path to the file or the yt object returned by pf.mods.load().
kwargs : optional
All other keyword arguments are passes to the ray() method on the pf.h object from yt.
Returns : x : 1D numpy array
Interpolated x data.
y : 1D numpy array
Interpolated y data.
z : 1D numpy array
Interpolated z data.
v : 1D numpy array
Interpolated field values along ray.
- flash.output.shock_on_lineout(p1, p2, field, pf, threshold=1e-06, min_threshold=1e-36, **kwargs)[source]¶
Finds the shock of a certain field (parameter, data) along a line out (ray) in a flash output file pf. Currently this assumes that p1 is closer to the center of the shock than p2. Moreover the geometry from the FLASH simulation must be cartesian or 2D cylindrical (rz).
Parameters : p1 : three-tuple of floats
The first point in the line-out.
p2 : three-tuple of floats
The second point in the line-out.
field : str
A field to retrieve, e.g. ‘dens’.
pf : str or yt.data_objects.static_output
The checkpoint or plot file, may be either a path to the file or the yt object returned by pf.mods.load().
threshold : float, optional
The value above which gradients must exceed to be considered a shock. Required for ignoring low-level noise.
min_threshold : float, optional
If a shock is not found at a given threshold level, the threshold value is reduced by an order of magnitude until a shock is found. This continues until a minimum threshold is reached.
kwargs : optional
All other keyword arguments are passes to the ray() method on the pf.h object from yt.
Returns : shock_p : three-tuple of floats
Shock position.
shock_v : field type (float)
Shock peak value.
See also
- flash.output.lineout
- Used to get the lineout from two points and a data file.
- flash.analysis.shock_detect
- Used to find the shock itself.
- flash.output.load_laser_dat(filename)[source]¶
Reads in a LaserEnergyProfile.dat file as a numpy structured array.
Parameters : filename : str or file-like
The string path to the file or an object which implements the file interface
Returns : dat : ndarray
This structured array has the following dtype and units:
Field
dtype
units
Step
int32
unitless
Time
float64
s
dt
float64
s
Energy In
float64
erg
Energy Out
float64
erg
dE In
float64
erg
dE Out
float64
erg
