BifrostDataCutter

class PlasmaCalcs.hookups.bifrost.bifrost_io_tools.BifrostDataCutter(snap, bcalc, *, new_snapname=UNSET)

Bases: BifrostVarPathsManager

interface for creating new data files cut from existing data files.

“cut” refers to indexing by simple slices, with trivial step (1 or None),

e.g. slice x by slice(500, 1000). But not by slice(500, 1000, 10).

(NEVER overwrites existing files; if any result files already exist, crash.)

self.kind2path = {kind: path}
self.kind2vars = {kind: [list of readable vars]}
self.var2kind = {var: kind}
self.var2path = {var: path}
self.path2kind = {path: kind}
self.path2vars = {path: [list of readable vars]}
self.var2index = {var: index of var in its path’s list of vars}

self.kind2newpath = {kind: newpath}
self.path2newpath = {original path: newpath}
self.newpath2path = {newpath: original path}

self.kinds: tuple of kinds with any vars in self.
self.vars: tuple of all vars in self.
self.paths: tuple of all paths with any vars in self.
self.newpaths: tuple of all newpaths with any vars in self.

kinds are: ‘snap’, ‘aux’, ‘hion’, ‘helium’, ‘ooe’.

if kind has no vars, do not include it in results.

snap: BifrostSnap

bcalc: BifrostCalculator

new_snapname: str or UNSET

new snapname to use for the cutted data files. UNSET –> ‘{self.snapname}_cut’

Methods

`cut`(*[, verbose])	cut all data & supporting files, writing results to new path based on self.new_snapname.
`cut_idl_file`()	cut idl_file, writing results to self.newpath(self.bcalc.idlfile).
`cut_kind`(kind)	cut data for this kind, writing results to self.kind2newpath[kind].
`cut_meshfile`()	cut meshfile, writing results to self.newpath(self.bcalc.meshfile).
`help`()	print docstring of self...
`init_aux_kind`()	vars stored in snapname_NNN.aux file.
`init_convenience`()	initialize convenience tuples.
`init_helium_kind`()	vars stored in snapname.helium_NNN.snap file.
`init_hion_kind`()	vars stored in snapname.hion_NNN.snap file.
`init_kinds`()	initialize all kinds in self, filling in all the details for self's storage dicts.
`init_new_paths`()	initialize self.kind2newpath, path2newpath and newpath2path
`init_ooe_kind`()	out of equilibrium vars.
`init_snap_kind`()	vars stored in snapname_NNN.snap file.
`init_storage`()	initialize storage dicts.
`kind2filebase`(kind)	returns file basename for this kind.
`new_file_paths`()	list of abspaths to all new files which self.cut() will create.
`newpath`(oldpath)	return newpath from oldpath.
`slices_tuple`()	returns tuple of slices to apply to array with (x, y, z) as first 3 dims.
`snappath`(filename)	returns os.path.join(self.snapdir, filename)
`_check_output_files_dont_exist`()	ensure that all output files do not exist yet.
`_data_array_shape_after_cut`()	returns shape each data array will be after cutting (using self.slices).
`_idl_file_path`()	path to idl file for self.snap.
`_init_kind_vars_path`(kind, vars, path)	updates self with corresponding kind, vars, and path.
`_new_idl_file_path`()	abspath to new idl file.
`_new_meshfile_path`()	abspath to new meshfile.
`_repr_contents`()	contents for repr(self), as list of strings

Attributes

`KIND2FILEBASE`
`KINDS`
`NNN`	(str) the NNN part of the snapname_NNN.idl filename.
`aux_todo`	list of all vars in 'aux' not yet handled by this VarPathsManager instance.
`calc`	gets self._calc(), or just self._calc if not self._calc_is_weakref.
`params`	alias to self.snap.params
`slices`	self.bcalc.slices, but ensuring all are slice objects and have trivial step (1 or None).
`snap`	gets self._snap(), or just self._snap if not self._snap_is_weakref.
`snapdir`	alias to self.calc.snapdir
`snapname`	alias to self.params['snapname']

property NNN: (str) the NNN part of the snapname_NNN.idl filename.

_check_output_files_dont_exist(): ensure that all output files do not exist yet.

_data_array_shape_after_cut(): returns shape each data array will be after cutting (using self.slices).

_idl_file_path(): path to idl file for self.snap. Equivalent: self.bcalc.snap_filepath(self.snap).

_init_kind_vars_path(kind, vars, path): updates self with corresponding kind, vars, and path.

_new_idl_file_path(): abspath to new idl file. Equivalent: self.newpath(self.bcalc.snap_filepath(self.snap)).

_new_meshfile_path(): abspath to new meshfile. Equivalent: self.newpath(self.bcalc.meshfile).

_repr_contents(): contents for repr(self), as list of strings

property aux_todo: list of all vars in ‘aux’ not yet handled by this VarPathsManager instance.

Presently, this means the list of all vars containing ‘xy’, ‘yz’, or ‘xz’.

property calc: gets self._calc(), or just self._calc if not self._calc_is_weakref.

cut(*, verbose=True): cut all data & supporting files, writing results to new path based on self.new_snapname.

(never edits any existing files, only makes new ones.)

returns list of all new file paths (i.e. self.new_file_paths())

verbose: bool

whether to print progress updates during cutting.

cut_idl_file(): cut idl_file, writing results to self.newpath(self.bcalc.idlfile).

the idlfile is the snapname_NNN.idl file; see self.bcalc.snap_filepath().

amount to cut is determined by self.bcalc.slices.

“cutting the idlfile” means replacing the relevant parameters in the idlfile:

‘mx’, ‘my’, ‘mz’ –> new sizes after cutting

‘snapname’ –> new snapname

‘meshfile’ –> new meshfile name

cut_kind(kind): cut data for this kind, writing results to self.kind2newpath[kind].

see self.kinds for options.

returns self.kind2newpath[kind], which is an abspath to the new path.

(NEVER overwrites existing data; if the newpath exists already, crash.)

amount to cut is determined by self.bcalc.slices.

size of arrays within memmap data files is determined by bcalc.data_array_shape.

cut_meshfile(): cut meshfile, writing results to self.newpath(self.bcalc.meshfile).

amount to cut is determined by self.bcalc.slices.

“cutting the meshfile” means apply slice_bifrost_meshfile()

help(): print docstring of self…

init_aux_kind(): vars stored in snapname_NNN.aux file.

init_convenience(): initialize convenience tuples.

init_helium_kind(): vars stored in snapname.helium_NNN.snap file.

init_hion_kind(): vars stored in snapname.hion_NNN.snap file.

init_kinds(): initialize all kinds in self, filling in all the details for self’s storage dicts.

init_new_paths(): initialize self.kind2newpath, path2newpath and newpath2path

init_ooe_kind(): out of equilibrium vars.

init_snap_kind(): vars stored in snapname_NNN.snap file.

init_storage(): initialize storage dicts.

kind2filebase(kind): returns file basename for this kind.

Equivalent: self.KIND2FILEBASE[kind].format(snapname=self.snapname, NNN=self.NNN)

new_file_paths(): list of abspaths to all new files which self.cut() will create.

These are self.newpaths, and the new path for the meshfile & idl file.

newpath(oldpath): return newpath from oldpath. (both are abspaths.)

newpath = oldpath, but replace self.bcalc.snapname (within oldpath basename) by new_snapname

crash if newpath == oldpath.

property params: alias to self.snap.params

property slices: self.bcalc.slices, but ensuring all are slice objects and have trivial step (1 or None).

Also ensures at least 1 nontrivial slice exists (i.e. not empty and not all slice(None).)

slices_tuple(): returns tuple of slices to apply to array with (x, y, z) as first 3 dims.

determined by self.slices.get(x, slice(None)) for x in ‘x’, ‘y’, ‘z’.

property snap: gets self._snap(), or just self._snap if not self._snap_is_weakref.

property snapdir: alias to self.calc.snapdir

property snapname: alias to self.params[‘snapname’]

snappath(filename): returns os.path.join(self.snapdir, filename)