stagyyparsers

Parsers of StagYY output files.

Note

These functions are low level utilities. You should not use these unless you know what you are doing. To access StagYY output data, use an instance of StagyyData.

time_series

time_series(
    timefile: Path, colnames: list[str]
) -> DataFrame | None

Read temporal series text file.

If colnames is too long, it will be truncated. If it is too short, additional numeric column names from 0 to N-1 will be attributed to the N extra columns present in timefile.

Parameters:

Name	Type	Description	Default
`timefile`	`Path`	path of the time.dat file.	required
`colnames`	`list[str]`	names of the variables expected in `timefile` (may be modified).	required

Returns:

Type	Description
`DataFrame \| None`	A `pandas.DataFrame` containing the time series, organized by variables in columns and time steps in rows.

time_series_h5

time_series_h5(
    timefile: Path, colnames: list[str]
) -> DataFrame | None

Read temporal series HDF5 file.

If colnames is too long, it will be truncated. If it is too short, additional column names will be deduced from the content of the file.

Parameters:

Name	Type	Description	Default
`timefile`	`Path`	path of the TimeSeries.h5 file.	required
`colnames`	`list[str]`	names of the variables expected in `timefile` (may be modified).	required

Returns:

Type	Description
`DataFrame \| None`	A `pandas.DataFrame` containing the time series, organized by variables in columns and the time steps in rows.

rprof

rprof(
    rproffile: Path, colnames: list[str]
) -> tuple[dict[int, DataFrame], DataFrame | None]

Extract radial profiles data.

If colnames is too long, it will be truncated. If it is too short, additional numeric column names from 0 to N-1 will be attributed to the N extra columns present in timefile.

Parameters:

Name	Type	Description	Default
`rproffile`	`Path`	path of the rprof.dat file.	required
`colnames`	`list[str]`	names of the variables expected in `rproffile`.	required

Returns:

Name	Type	Description
`profs`	`dict[int, DataFrame]`	a dict mapping istep to radial profiles.
`times`	`DataFrame \| None`	the time indexed by time steps.

rprof_h5

rprof_h5(
    rproffile: Path, colnames: list[str]
) -> tuple[dict[int, DataFrame], DataFrame | None]

Extract radial profiles data.

If colnames is too long, it will be truncated. If it is too short, additional column names will be deduced from the content of the file.

Parameters:

Name	Type	Description	Default
`rproffile`	`Path`	path of the rprof.h5 file.	required
`colnames`	`list[str]`	names of the variables expected in `rproffile`.	required

Returns:

Name	Type	Description
`profs`	`dict[int, DataFrame]`	a dict mapping istep to radial profiles.
`times`	`DataFrame \| None`	the time indexed by time steps.

refstate

refstate(
    reffile: Path, ncols: int = 8
) -> tuple[list[list[DataFrame]], list[DataFrame]] | None

Extract reference state profiles.

Parameters:

Name	Type	Description	Default
`reffile`	`Path`	path of the refstate file.	required
`ncols`	`int`	number of columns.	`8`

Returns:

Name	Type	Description
`syst`	`tuple[list[list[DataFrame]], list[DataFrame]] \| None`	list of list of `pandas.DataFrame` containing the reference state profiles for each system and each phase in these systems.
`adia`	`tuple[list[list[DataFrame]], list[DataFrame]] \| None`	list of `pandas.DataFrame` containing the adiabatic reference state profiles for each system, the last item being the combined adiabat.

field_istep

field_istep(fieldfile: Path) -> int | None

Read istep from binary field file.

Parameters:

Name	Type	Description	Default
`fieldfile`	`Path`	path of the binary field file.	required

Returns:

Type	Description
`int \| None`	the time step at which the binary file was written.

field_header

field_header(fieldfile: Path) -> dict[str, Any] | None

Read header info from binary field file.

Parameters:

Name	Type	Description	Default
`fieldfile`	`Path`	path of the binary field file.	required

Returns:

Type	Description
`dict[str, Any] \| None`	the header information of the binary file.

fields

fields(
    fieldfile: Path,
) -> tuple[dict[str, Any], NDArray[np.float64]] | None

Extract fields data.

Parameters:

Name	Type	Description	Default
`fieldfile`	`Path`	path of the binary field file.	required

Returns:

Type	Description
`tuple[dict[str, Any], NDArray[float64]] \| None`	the tuple `(header, fields)`. `fields` is an array of scalar fields indexed by variable, x-direction, y-direction, z-direction, block.

tracers

tracers(
    tracersfile: Path,
) -> dict[str, list[NDArray[np.float64]]] | None

Extract tracers data.

Parameters:

Name	Type	Description	Default
`tracersfile`	`Path`	path of the binary tracers file.	required

Returns:

Type	Description
`dict[str, list[NDArray[float64]]] \| None`	Tracers data organized by attribute names and blocks.

read_geom_h5

read_geom_h5(
    xdmf: FieldXmf, snapshot: int
) -> dict[str, Any]

Extract geometry information from hdf5 files.

Parameters:

Name	Type	Description	Default
`xdmf`	`FieldXmf`	xdmf file parser.	required
`snapshot`	`int`	snapshot number.	required

Returns:

Type	Description
`dict[str, Any]`	geometry information.

read_field_h5

read_field_h5(
    xdmf: FieldXmf,
    fieldname: str,
    snapshot: int,
    header: dict[str, Any] | None = None,
) -> tuple[dict[str, Any], NDArray[np.float64]] | None

Extract field data from hdf5 files.

Parameters:

Name	Type	Description	Default
`xdmf`	`FieldXmf`	xdmf file parser.	required
`fieldname`	`str`	name of field to extract.	required
`snapshot`	`int`	snapshot number.	required
`header`	`dict[str, Any] \| None`	geometry information.	`None`

Returns:

Type	Description
`tuple[dict[str, Any], NDArray[float64]] \| None`	geometry information and field data. None is returned if data is unavailable.

read_tracers_h5

read_tracers_h5(
    xdmf: TracersXmf, infoname: str, snapshot: int
) -> list[NDArray[np.float64]]

Extract tracers data from hdf5 files.

Parameters:

Name	Type	Description	Default
`xdmf`	`TracersXmf`	xdmf file parser.	required
`infoname`	`str`	name of information to extract.	required
`snapshot`	`int`	snapshot number.	required

Returns:

Type	Description
`list[NDArray[float64]]`	Tracers data organized by attribute and block.

read_time_h5

read_time_h5(h5folder: Path) -> Iterator[tuple[int, int]]

Iterate through (isnap, istep) recorded in h5folder/'time_botT.h5'.

Parameters:

Name	Type	Description	Default
`h5folder`	`Path`	directory of HDF5 output files.	required

Yields:

Type	Description
`tuple[int, int]`	tuple (isnap, istep).