Results

Generic results and snapshots

class astrophysix.simdm.results.generic.GenericResult(**kwargs)

Experiment generic result class

Parameters:

name (string) – result name (mandatory)
description (string) – result description
directory_path (string) – result data directory path

__eq__(other)

GenericResult comparison method

other: GenericResult: generic result to compare to

__ne__(other)

Not an implied relationship between “rich comparison” equality methods in Python 2.X but only in Python 3.X see https://docs.python.org/2.7/reference/datamodel.html#object.__ne__

other: other instance to compare to

__unicode__(): String representation of the instance

property catalogs

Result Catalog list (ObjectList)

New in version 0.5.0

property datafiles: Result Datafile list (ObjectList)

property description: Result description. Can be set to any string value.

property directory_path: Result directory.path. Can be set to any string value.

galactica_valid_alias(alias_value)

galactica_validity_check(**kwargs)

Perform validity checks on this instance and eventually log warning messages.

Parameters:: kwargs (dict) – keyword arguments (optional)

property name: Result name. Can be set to a non-empty string value.

property uid

class astrophysix.simdm.results.snapshot.Snapshot(**kwargs)

Experiment snapshot class (Simulation data model)

Parameters:

name (string) – snapshot name (mandatory)
description (string) – snapshot description
directory_path (string) – snapshot directory path
time ((float, Unit) tuple) – snapshot time info (value, unit) tuple
physical_size ((float, Unit) tuple) – snapshot physical size info (value, unit) tuple
data_reference (string) – snapshot data reference (e.g. data directory name, snapshot number) string

__eq__(other)

Snapshot comparison method

other: Snapshot: snapshot to compare to

__ne__(other)

Not an implied relationship between “rich comparison” equality methods in Python 2.X but only in Python 3.X see https://docs.python.org/2.7/reference/datamodel.html#object.__ne__

other: other instance to compare to

__unicode__(): String representation of the instance

property catalogs

Result Catalog list (ObjectList)

New in version 0.5.0

property data_reference: Snapshot data reference (e.g. data directory name, snapshot number). Can be set to any string value.

property datafiles: Result Datafile list (ObjectList)

property description: Result description. Can be set to any string value.

property directory_path: Result directory.path. Can be set to any string value.

galactica_valid_alias(alias_value)

galactica_validity_check(**kwargs)

Perform validity checks on this instance and eventually log warning messages.

Parameters:: kwargs (dict) – keyword arguments (optional)

property name: Result name. Can be set to a non-empty string value.

property physical_size

Snapshot physical size info (value, unit) tuple . Can be set to a float value (unitless) or a (float, Unit) tuple.

Example

>>> sn = Snapshot(name="My super snapshot")
>>> sn.physical_size = "0.256"
>>> sn.physical_size = ("0.24", U.pc)
>>> sn.physical_size = ("0.45", "kpc")
>>> sn.physical_size[1] == U.kpc
True
>>> sn.physical_size = 4.46
>>> sn.physical_size = (7.89e2, "Mpc")
>>> sn.physical_size[1] == U.Mpc
True
>>> sn.physical_size = (78.54, U.ly)

property processing_services: DataProcessingService list (ObjectList)

property time

Snapshot time info (value, unit) tuple . Can be set to a float value (unitless) or a (float, Unit) tuple.

Example

>>> sn = Snapshot(name="My super snapshot")
>>> sn.time = "0.256"
>>> sn.time[1] == U.none
True
>>> sn.time = ("0.24", U.year)
>>> sn.time = ("0.45", "Myr")
>>> sn.time[1] == U.Myr
True
>>> sn.time = (7.89e2, "Gyr")
>>> sn.time = (78.54, U.min)

property uid

Datafiles

Datafile and AssociatedFile

class astrophysix.simdm.datafiles.Datafile(**kwargs)

Datafile class

Parameters:

name (string) – datafile name (mandatory)
description (string) – datafile description

Example

>>> from astrophysix.utils import FileType
>>> from astrophysix.simdm.datafiles import JpegImageFile
>>> df = Datafile(name="Pre-stellar cores mass spectrum")
>>> df[FileType.PNG_FILE] = "/data/SIMUS/result_spectrum/mass_spectrum.png"
>>> df[FileType.FITS_FILE] = "/data/SIMUS/result_spectrum/pre-stellar-core-mass-hist.fits"
>>> df[FileType.PNG_FILE] = JpegImageFile.load_file("/data/SIMUS/result_spectrum/hist.jpg")
ValueError: Datafile associated file type mismatch : expected PngImageFile object but JpegImageFile was provided.
>>> df[FileType.PNG_FILE] = "/data/SIMUS/result_spectrum/hist.jpg"
AttributeError: Invalid filename for a PNG file (/data/SIMUS/result_spectrum/hist.jpg).
>>> # Removing a file
>>> del df[FileType.FITS_FILE]

__delitem__(ftype)

Remove associated file given its file type.

Parameters:: item (FileType)
Raises:: KeyError – if the search index type is not a FileType instance or if there is no associated file with the required file type.

__eq__(other)

Datafile comparison method

Parameters:: other (Datafile) – datafile to compare to:

__getitem__(ftype)

Get an associated file from the data file, given its file type.

Parameters:: ftype (FileType) – Associated file type
Returns:: f – datafile associated file for the required file type.
Return type:: AssociatedFile
Raises:: KeyError – if the search index type is not a FileType instance or if there is no associated file with the required file type.

__ne__(other)

Not an implied relationship between “rich comparison” equality methods in Python 2.X but only in Python 3.X see https://docs.python.org/2.7/reference/datamodel.html#object.__ne__

other: other instance to compare to

__setitem__(filetype, ass_file)

Set an associated file with a given file type into the data file.

Parameters:

filetype (FileType) – Associated file type
ass_file (string or AssociatedFile) – Associated file path or instance

__unicode__(): String representation of the data file instance

property description: Datafile description. Can be set to any string value.

display_files()

Show tabulated view of associated files

Example

>>> df.display_files()
[My best datafile] datafile. Attached files :
+-----------+-----------------------------+
| File type |          Filename           |
+-----------+-----------------------------+
| PNG       | CEA.png                     |
+-----------+-----------------------------+
| JPEG      | irfu_simple.jpg             |
+-----------+-----------------------------+
| FITS      | cassiopea_A_0.5-1.5keV.fits |
+-----------+-----------------------------+
| TARGZ     | archive.tar.gz              |
+-----------+-----------------------------+
| JSON      | test_header_249.json        |
+-----------+-----------------------------+
| YAML      | config.yml                  |
+-----------+-----------------------------+
| ASCII     | abstract.txt                |
+-----------+-----------------------------+
| HDF5      | study.h5                    |
+-----------+-----------------------------+
| PICKLE    | dict_saved.pkl              |
+-----------+-----------------------------+

galactica_valid_alias(alias_value)

galactica_validity_check(**kwargs)

Perform validity checks on this instance and eventually log warning messages.

Parameters:: kwargs (dict) – keyword arguments (optional)

property name: Datafile name. Can be set to a non-empty string value.

property plot_info: Datafile plot information. Can be set to a PlotInfo instance.

property uid

class astrophysix.simdm.datafiles.file.AssociatedFile(**kwargs)

class astrophysix.simdm.datafiles.file.FitsFile(**kwargs)

Bases: AssociatedFile

Datafile associated FITS_FILE file class.

property filename: Gets associated file name. Cannot be edited.

property last_modified: Returns file last modification time. Cannot be edited.

classmethod load_file(filepath)

Loads an AssociatedFile object from a filepath

Parameters:: filepath (string) – path of the file to load.
Returns:: f – Loaded associatedfile
Return type:: AssociatedFile instance

property raw_file_data

File binary raw data. Cannot be edited.

Returns:: raw_data
Return type:: bytes

save_to_disk(filepath=None)

Save associated file to an external file on the local filesystem

Parameters:: filepath (string) – external file path

class astrophysix.simdm.datafiles.file.PickleFile(**kwargs)

Bases: AssociatedFile

Datafile associated PICKLE_FILE file class.

property filename: Gets associated file name. Cannot be edited.

property last_modified: Returns file last modification time. Cannot be edited.

classmethod load_file(filepath)

Loads an AssociatedFile object from a filepath

Parameters:: filepath (string) – path of the file to load.
Returns:: f – Loaded associatedfile
Return type:: AssociatedFile instance

property raw_file_data

File binary raw data. Cannot be edited.

Returns:: raw_data
Return type:: bytes

save_to_disk(filepath=None)

Save associated file to an external file on the local filesystem

Parameters:: filepath (string) – external file path

class astrophysix.simdm.datafiles.file.AsciiFile(**kwargs)

Bases: AssociatedFile

Datafile associated ASCII_FILE file class.

property filename: Gets associated file name. Cannot be edited.

property last_modified: Returns file last modification time. Cannot be edited.

classmethod load_file(filepath)

Loads an AssociatedFile object from a filepath

Parameters:: filepath (string) – path of the file to load.
Returns:: f – Loaded associatedfile
Return type:: AssociatedFile instance

property raw_file_data

File binary raw data. Cannot be edited.

Returns:: raw_data
Return type:: bytes

save_to_disk(filepath=None)

Save associated file to an external file on the local filesystem

Parameters:: filepath (string) – external file path

class astrophysix.simdm.datafiles.file.HDF5File(**kwargs)

Bases: AssociatedFile

Datafile associated HDF5_FILE file class.

property filename: Gets associated file name. Cannot be edited.

property last_modified: Returns file last modification time. Cannot be edited.

classmethod load_file(filepath)

Loads an AssociatedFile object from a filepath

Parameters:: filepath (string) – path of the file to load.
Returns:: f – Loaded associatedfile
Return type:: AssociatedFile instance

property raw_file_data

File binary raw data. Cannot be edited.

Returns:: raw_data
Return type:: bytes

save_to_disk(filepath=None)

Save associated file to an external file on the local filesystem

Parameters:: filepath (string) – external file path

class astrophysix.simdm.datafiles.file.JsonFile(**kwargs)

Bases: AssociatedFile

Datafile associated JSON_FILE file class.

property filename: Gets associated file name. Cannot be edited.

property last_modified: Returns file last modification time. Cannot be edited.

classmethod load_file(filepath)

Loads an AssociatedFile object from a filepath

Parameters:: filepath (string) – path of the file to load.
Returns:: f – Loaded associatedfile
Return type:: AssociatedFile instance

property raw_file_data

File binary raw data. Cannot be edited.

Returns:: raw_data
Return type:: bytes

save_to_disk(filepath=None)

Save associated file to an external file on the local filesystem

Parameters:: filepath (string) – external file path

class astrophysix.simdm.datafiles.file.CSVFile(**kwargs)

Bases: AssociatedFile

Datafile associated CSV_FILE file class.

property filename: Gets associated file name. Cannot be edited.

property last_modified: Returns file last modification time. Cannot be edited.

classmethod load_file(filepath)

Loads an AssociatedFile object from a filepath

Parameters:: filepath (string) – path of the file to load.
Returns:: f – Loaded associatedfile
Return type:: AssociatedFile instance

property raw_file_data

File binary raw data. Cannot be edited.

Returns:: raw_data
Return type:: bytes

save_to_disk(filepath=None)

Save associated file to an external file on the local filesystem

Parameters:: filepath (string) – external file path

class astrophysix.simdm.datafiles.file.YamlFile(**kwargs)

Bases: AssociatedFile

Datafile associated YAML_FILE file class.

property filename: Gets associated file name. Cannot be edited.

property last_modified: Returns file last modification time. Cannot be edited.

classmethod load_file(filepath)

Loads an AssociatedFile object from a filepath

Parameters:: filepath (string) – path of the file to load.
Returns:: f – Loaded associatedfile
Return type:: AssociatedFile instance

property raw_file_data

File binary raw data. Cannot be edited.

Returns:: raw_data
Return type:: bytes

save_to_disk(filepath=None)

Save associated file to an external file on the local filesystem

Parameters:: filepath (string) – external file path

class astrophysix.simdm.datafiles.file.TarGzFile(**kwargs)

Bases: AssociatedFile

Datafile associated TARGZ_FILE file class.

property filename: Gets associated file name. Cannot be edited.

property last_modified: Returns file last modification time. Cannot be edited.

classmethod load_file(filepath)

Loads an AssociatedFile object from a filepath

Parameters:: filepath (string) – path of the file to load.
Returns:: f – Loaded associatedfile
Return type:: AssociatedFile instance

property raw_file_data

File binary raw data. Cannot be edited.

Returns:: raw_data
Return type:: bytes

save_to_disk(filepath=None)

Save associated file to an external file on the local filesystem

Parameters:: filepath (string) – external file path

class astrophysix.simdm.datafiles.image.PngImageFile(**kwargs)

Bases: ImageFile

Datafile associated PNG_FILE image file class.

property filename: Gets associated file name. Cannot be edited.

property last_modified: Returns file last modification time. Cannot be edited.

classmethod load_file(filepath)

Loads an AssociatedFile object from a filepath

Parameters:: filepath (string) – path of the file to load.
Returns:: f – Loaded associatedfile
Return type:: AssociatedFile instance

property pil_image: Pillow image (JPEG/PNG) image property getter. Implements lazy I/O.

property raw_file_data

File binary raw data. Cannot be edited.

Returns:: raw_data
Return type:: bytes

save_to_disk(filepath=None)

Save associated file to an external file on the local filesystem

Parameters:: filepath (string) – external file path

class astrophysix.simdm.datafiles.image.JpegImageFile(**kwargs)

Bases: ImageFile

Datafile associated JPEG_FILE image file class.

property filename: Gets associated file name. Cannot be edited.

property last_modified: Returns file last modification time. Cannot be edited.

classmethod load_file(filepath)

Loads an AssociatedFile object from a filepath

Parameters:: filepath (string) – path of the file to load.
Returns:: f – Loaded associatedfile
Return type:: AssociatedFile instance

property pil_image: Pillow image (JPEG/PNG) image property getter. Implements lazy I/O.

property raw_file_data

File binary raw data. Cannot be edited.

Returns:: raw_data
Return type:: bytes

save_to_disk(filepath=None)

Save associated file to an external file on the local filesystem

Parameters:: filepath (string) – external file path

Plot information

class astrophysix.simdm.datafiles.plot.PlotType(value)

Plot type enum

Example

>>> pt = PlotType.HISTOGRAM_2D
>>> pt.alias
"2d_hist"
>>> pt.display_name
"2D histogram"
>>> pt.ndimensions
2

HISTOGRAM = ('hist', 'Histogram', 1, 1)

HISTOGRAM_2D = ('2d_hist', '2D histogram', 2, 1)

IMAGE = ('img', 'Image', 2, 1)

LINE_PLOT = ('line', 'Line plot', 1, 0)

MAP_2D = ('2d_map', '2D map', 2, 1)

SCATTER_PLOT = ('scatter', 'Scatter plot', 1, 0)

property alias: Plot type alias

property axis_size_offset

property display_name: Plot type verbose name

classmethod from_alias(alias)

Find a PlotType according to its alias

Parameters:: alias (string) – required plot type alias
Returns:: ft – Plot type matching the requested alias.
Return type:: PlotType
Raises:: ValueError – if requested alias does not match any plot type.

Example

>>> pt = PlotType.from_alias("hist")
>>> pt.display_name
"Histogram"
>>> pt2 = PlotType.from_alias("MY_UNKNOWN_PLOT_YPE")
ValuerError: No PlotType defined with the alias 'MY_UNKNOWN_PLOT_YPE'.

property ndimensions: Plot type number of dimensions

class astrophysix.simdm.datafiles.plot.PlotInfo(**kwargs)

Datafile class (Simulation data model)

Parameters:

plot_type (PlotType or string) – Plot type or plot type alias (mandatory)
xaxis_values (numpy.ndarray) – x-axis coordinate values numpy 1D array (mandatory).
yaxis_values (numpy.ndarray) – y-axis coordinate numpy 1D array (mandatory).
values (numpy.ndarray) – plot data values numpy array (mandatory for 2D plots).
xlabel (string) – x-axis label
ylabel (string) – y-axis label
values_label (string) – plot values label
xaxis_unit – TODO
yaxis_unit – TODO
values_unit – TODO
xaxis_log_scale (bool) – TODO
yaxis_log_scale (bool) – TODO
values_log_scale (bool) – TODO
plot_title (string) – Plot title.

__eq__(other_plot_info)

PlotInfo comparison method

Parameters:: other_plot_info (PlotInfo) – plot info object to compare to:

__unicode__(): String representation of the instance

galactica_validity_check(**kwargs)

Perform validity checks on this instance and eventually log warning messages.

Parameters:: kwargs (dict) – keyword arguments (optional)

gald3_render(open_browser=True, local_http_port=8076)

Exports the PlotInfo object into a temporary JSON file and opens a web browser window to render it using the Galactica GalD3.js javascript library.

Parameters:

open_browser (: obj:bool) – open a web browser window. Default True. Set to False if already opened
local_http_port (int) – localhost http port to use in the URL

property plot_type: Returns the plot type (PlotType). Cannot be edited.

save_json_plot_data(json_filepath)

Save plot information into an external JSON file on the local filesystem

Parameters:: json_filepath (string) – valid external JSON file path

set_data(xaxis_values, yaxis_values, values=None)

Set plot data arrays.

Parameters:

xaxis_values (numpy.ndarray) – x-axis coordinate array
yaxis_values (numpy.ndarray) – TODO
values (numpy.ndarray) – TODO

property title: Plot title. Can be set to any string value.

property values: Plot values array. Cannot be edited. Implements lazy I/O.

Note

To edit plot values, see PlotInfo.set_data() method.

property values_label: plot values label. Can be set to any string value.

property values_log_scale: value log scale boolean flag. Can be edited to any bool value.

property values_unit: TODO

property xaxis_log_scale: x-axis log scale boolean flag. Can be edited to any bool value.

property xaxis_unit: TODO

property xaxis_values: Plot x-axis coordinate array (numpy.ndarray). Cannot be edited. Implements lazy I/O.

Note

To edit plot values, see PlotInfo.set_data() method.

property xlabel: x-axis label. Can be set to any string value.

property yaxis_log_scale: y-axis log scale boolean flag. Can be edited to any bool value.

property yaxis_unit: TODO

property yaxis_values: Plot y-axis coordinate array (numpy.ndarray). Cannot be edited. Implements lazy I/O.

Note

To edit plot values, see PlotInfo.set_data() method.

property ylabel: y-axis label. Can be set to any string value.