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]
) -> Optional[DataFrame]

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
Optional[DataFrame]	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]
) -> Optional[DataFrame]

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
Optional[DataFrame]	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], Optional[DataFrame]]

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	Optional[DataFrame]	the time indexed by time steps.

rprof_h5

rprof_h5(
    rproffile: Path, colnames: list[str]
) -> tuple[dict[int, DataFrame], Optional[DataFrame]]

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	Optional[DataFrame]	the time indexed by time steps.

refstate

refstate(
    reffile: Path, ncols: int = 8
) -> Optional[
    tuple[list[list[DataFrame]], list[DataFrame]]
]

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	Optional[tuple[list[list[DataFrame]], list[DataFrame]]]	list of list of pandas.DataFrame containing the reference state profiles for each system and each phase in these systems.
adia	Optional[tuple[list[list[DataFrame]], list[DataFrame]]]	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) -> Optional[int]

Read istep from binary field file.

Parameters:

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

Returns:

Type	Description
Optional[int]	the time step at which the binary file was written.

field_header

field_header(fieldfile: Path) -> Optional[dict[str, Any]]

Read header info from binary field file.

Parameters:

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

Returns:

Type	Description
Optional[dict[str, Any]]	the header information of the binary file.

fields

fields(
    fieldfile: Path,
) -> Optional[tuple[dict[str, Any], NDArray]]

Extract fields data.

Parameters:

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

Returns:

Type	Description
Optional[tuple[dict[str, Any], NDArray]]	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,
) -> Optional[dict[str, list[NDArray]]]

Extract tracers data.

Parameters:

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

Returns:

Type	Description
Optional[dict[str, list[NDArray]]]	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: Optional[dict[str, Any]] = None,
) -> Optional[tuple[dict[str, Any], NDArray]]

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	Optional[dict[str, Any]]	geometry information.	None

Returns:

Type	Description
Optional[tuple[dict[str, Any], NDArray]]	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]

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]	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
int	tuple (isnap, istep).