data_extraction package¶

Submodules¶

data_extraction.extract_averages module¶

usage: extract_averages [-h] [--datapath DATAPATH] [--outpath OUTPATH]
                        [--pname PNAME [PNAME ...]] [--SI] [--verbose]
                        [--no_mpi] [--nprocs NPROCS] [--nskip NSKIP]
                        [--ifile IFILE] --fields FIELDS [FIELDS ...]
                        [--name NAME] [--normal {x,y,z}] [--location LOCATION]
                        [--rm_eb]

Named Arguments¶

--datapath

Path to the data files.

--outpath

Path to the output directory.

--pname

Name of plt files to plot (if empty, do all)

--SI

Flag to set the units to SI (default is cgs).

Default: False

--verbose

Flag to turn on various statements.

Default: False

--no_mpi

Flag to manually disable mpi features.

Default: False

--nprocs

Number of processors to devote to each file when operating inparallel mode

Default: 1

--nskip

Skip every “nskip” entries in “pname” list.

--ifile

Path to the input file for configuring plots.

--fields

Names of the data fields to extract.

--name

Name of the output data file (.pkl).

Default: “average_data”

--normal

Possible choices: x, y, z

Option to perform 2D slice (defaults to domain average).

--location

Physical location to perform the 2D slice (if normal is defined).

--rm_eb

Flag to explicitly remove all data in EB regions.

Default: False

Extracts domain averaged quantities and saves for plotting.

data_extraction.extract_averages.get_args(parser)[source]¶: Get the arguments from the parser.

data_extraction.extract_averages.get_base_parser()[source]¶: Get the base level parser primarily for documentation.

data_extraction.extract_averages.get_parser()[source]¶: Get the parser.

data_extraction.extract_averages.main()[source]¶

data_extraction.extract_grid_info module¶

usage: extract_grid_info [-h] [--datapath DATAPATH] [--outpath OUTPATH]
                         [--pname PNAME [PNAME ...]] [--SI] [--verbose]
                         [--no_mpi] [--nprocs NPROCS] [--nskip NSKIP]
                         [--ifile IFILE] [--name NAME]

Named Arguments¶

--datapath

Path to the data files.

--outpath

Path to the output directory.

--pname

Name of plt files to plot (if empty, do all)

--SI

Flag to set the units to SI (default is cgs).

Default: False

--verbose

Flag to turn on various statements.

Default: False

--no_mpi

Flag to manually disable mpi features.

Default: False

--nprocs

Number of processors to devote to each file when operating inparallel mode

Default: 1

--nskip

Skip every “nskip” entries in “pname” list.

--ifile

Path to the input file for configuring plots.

--name

Name of the output data file (.pkl).

Default: “average_data”

Extracts grid information at each level and saves to file.

data_extraction.extract_grid_info.get_args(parser)[source]¶: Get the arguments from the parser.

data_extraction.extract_grid_info.get_base_parser()[source]¶: Get the base level parser primarily for documentation.

data_extraction.extract_grid_info.get_parser()[source]¶: Get the parser.

data_extraction.extract_grid_info.main()[source]¶: Main function for grid info extraction.

data_extraction.extract_isosurfaces module¶

usage: extract_isosurfaces [-h] [--datapath DATAPATH] [--outpath OUTPATH]
                           [--pname PNAME [PNAME ...]] [--field FIELD] [--SI]
                           [--verbose] [--no_mpi] [--nprocs NPROCS]
                           [--nskip NSKIP] [--ifile IFILE] [--format FORMAT]
                           [--yt] [--do_ghost] [--single_level]
                           [--smooth SMOOTH]
                           [--iso_edge ISO_EDGE [ISO_EDGE ...]]
                           [--gradient {x,y,z,magnitude}]
                           (--value VALUE | --vfunction VFUNCTION [VFUNCTION ...])

Named Arguments¶

--datapath

Path to the data files.

--outpath

Path to the output directory.

--pname

Name of plt files to plot (if empty, do all)

--field

Name of the field for visualization.

--SI

Flag to set the units to SI (default is cgs).

Default: False

--verbose

Flag to turn on various statements.

Default: False

--no_mpi

Flag to manually disable mpi features.

Default: False

--nprocs

Number of processors to devote to each file when operating inparallel mode

Default: 1

--nskip

Skip every “nskip” entries in “pname” list.

--ifile

Path to the input file for configuring plots.

--format

Output format of the iso-surface.

Default: “ply”

--yt

Flag to enable yt iso-surface extraction when outputting in hdf5/xdmf format only (default to faster, custom routine).

Default: False

--do_ghost

Flag to get ghost cells before the iso-surface extraction.

Default: False

--single_level

Flag to only get single grid level for isosurface.

Default: False

--smooth

Smoothing value to apply to field before isosurface extract

--iso_edge

Physical box inside which we extract isosurfaces.

--gradient

Possible choices: x, y, z, magnitude

Choice to extract the gradient of the input field.

--value

Value of the iso surface to extract.

--vfunction

Value of the iso surface to extract as a function (start_time; start_value; end_time; end_value).

Extracts iso-surfaces from plot files and saves.

data_extraction.extract_isosurfaces.do_isosurface_extraction(dregion, ds_attributes, outformat, field, value, outpath, fname, comm, rank, size, do_ghost=False, do_yt=False, single_level=False, smooth=None, ds=None, iso_edge=None, do_gradient=False)[source]¶: Do the isosurface extraction according to the input parameters.

data_extraction.extract_isosurfaces.get_args(parser)[source]¶: Get the arguments from the parser.

data_extraction.extract_isosurfaces.get_base_parser()[source]¶: Get the base level parser primarily for documentation.

data_extraction.extract_isosurfaces.get_parser()[source]¶: Get the parser.

data_extraction.extract_isosurfaces.main()[source]¶: Main function for extracting isosurfaces.

data_extraction.extract_isosurfaces.retrieve_ghost_zones(cube, n_zones, fields, ds_left_edge, ds_right_edge, single_level, do_gradient)[source]¶

data_extraction.extract_isosurfaces.write_hdf5(verts, samples, faces, field, fname)[source]¶: Write the HDF5 file based on the extracted isosurface.

data_extraction.extract_isosurfaces.write_xdmf(fbase, fhdf5, field, ftype, ctype, value, time, conn_shape, coord_shape, field_shape)[source]¶: Write the XDMF wrapper based on the hdf5 data.

data_extraction.extract_slices module¶

usage: extract_slices [-h] [--datapath DATAPATH] [--outpath OUTPATH]
                      [--pname PNAME [PNAME ...]] [--field FIELD] [--SI]
                      [--verbose] [--no_mpi] [--nprocs NPROCS] [--nskip NSKIP]
                      [--ifile IFILE] [--normal NORMAL]
                      [--grid_offset GRID_OFFSET] --min MIN --max MAX
                      --num_slices NUM_SLICES [--gradient {x,y,z,magnitude}]

Named Arguments¶

--datapath

Path to the data files.

--outpath

Path to the output directory.

--pname

Name of plt files to plot (if empty, do all)

--field

Name of the field for visualization.

--SI

Flag to set the units to SI (default is cgs).

Default: False

--verbose

Flag to turn on various statements.

Default: False

--no_mpi

Flag to manually disable mpi features.

Default: False

--nprocs

Number of processors to devote to each file when operating inparallel mode

Default: 1

--nskip

Skip every “nskip” entries in “pname” list.

--ifile

Path to the input file for configuring plots.

--normal

Normal direction for the slice plot.

Default: “z”

--grid_offset

Amount to offset center to avoid grid alignment vis issues.

Default: 0.0

--min

Index of the first slice to extract in the normal direction.

--max

Index of the last slice to extract in the normal direction.

--num_slices

Number of slices to extract in normal direction.

--gradient

Possible choices: x, y, z, magnitude

Choice to extract the gradient of the input field.

Extracts slices from plot files and saves.

data_extraction.extract_slices.get_args(parser)[source]¶: Get the arguments from the parser.

data_extraction.extract_slices.get_base_parser()[source]¶: Get the base level parser primarily for documentation.

data_extraction.extract_slices.get_parser()[source]¶: Get the parser.

data_extraction.extract_slices.main()[source]¶

Module contents¶

class data_extraction.ListScriptsAction(option_strings, dest, nargs=None, const=None, default=None, type=None, choices=None, required=False, help=None, metavar=None)[source]¶: Bases: Action

data_extraction.list_scripts(directory)[source]¶

data_extraction.main()[source]¶