morphfits.config#

Configure and setup a program execution of the MorphFITS program.

Attributes#

logger

Logger object for this module.

LowerStr

Lowercase string type for pydantic model.

Classes#

FICL

Configuration model for a single FICL.

MorphFITSConfig

Configuration model for a program execution of MorphFITS.

Functions#

create_config(→ MorphFITSConfig)

Create a MorphFITS configuration object from hierarchically preferred

Module Contents#

morphfits.config.logger#

Logger object for this module.

morphfits.config.LowerStr#

Lowercase string type for pydantic model.

class morphfits.config.FICL(/, **data: Any)#

Bases: pydantic.BaseModel

Configuration model for a single FICL.

FICL is an abbreviation for the field, image version, catalog version, and filter of a JWST science observation. Each FICL corresponds to a single observation.

Parameters:

BaseModel (class) – Base pydantic model class for type validation.

field#

Field of observation, e.g. “abell2744clu”.

Type:

str

image_version#

Version string of JWST image processing, e.g. “grizli-v7.2”.

Type:

str

catalog_version#

Version string of JWST cataloging, e.g. “dja-v7.2”.

Type:

str

filter#

Observational filter band, e.g. “f140w”.

Type:

str

objects#

Integer IDs of galaxies or cluster targets in catalog, e.g. [1003, 6371].

Type:

list[int]

pixscale#

Pixel scale along x and y axes, in arcseconds per pixel.

Type:

tuple[float, float]

Notes

All strings are converted to lowercase upon validation.

field: Annotated[str, StringConstraints(to_lower=True)]#
image_version: Annotated[str, StringConstraints(to_lower=True)]#
catalog_version: Annotated[str, StringConstraints(to_lower=True)]#
filter: Annotated[str, StringConstraints(to_lower=True)]#
objects: list[int]#
pixscale: tuple[float, float]#
__str__() → str#

Return str(self).

class morphfits.config.MorphFITSConfig(/, **data: Any)#

Bases: pydantic.BaseModel

Configuration model for a program execution of MorphFITS.

Parameters:

BaseModel (class) – Base pydantic model class to enforce type validation upon creation.

input_root#

Path to root input directory.

Type:

Path

output_root#

Path to root output directory.

Type:

Path

product_root#

Path to root products directory.

Type:

Path

run_root#

Path to root runs directory.

Type:

Path

datetime#

Datetime at start of program run.

Type:

datetime

run_number#

Number of run ordering runs with the same datetime.

Type:

int

fields#

List of fields over which to fit.

Type:

list[str]

image_versions#

List of image versions over which to fit.

Type:

list[str]

filters#

List of filters over which to fit.

Type:

list[str]

catalog_versions#

List of catalog versions over which to fit, by default only the v7.2 DJA catalog.

Type:

list[str], optional

objects#

List of object IDs within the catalog over which to fit, by default empty (all items in catalog).

Type:

list[int], optional

morphfits_root#

Path to root directory containing all of input, product, and output directories, by default the repository root.

Type:

Path, optional

wrappers#

List of morphology fitting algorithms to run, by default only GALFIT.

Type:

list[str], optional

galfit_path#

Path to GALFIT binary, by default None.

Type:

Path

input_root: pathlib.Path#
output_root: pathlib.Path#
product_root: pathlib.Path#
run_root: pathlib.Path#
datetime: datetime.datetime#
run_number: int#
fields: list[str]#
image_versions: list[str]#
filters: list[str]#
catalog_versions: list[str] = ['dja-v7.2']#
objects: list[int] = []#
morphfits_root: pathlib.Path#
wrappers: list[str] = ['galfit']#
galfit_path: pathlib.Path = None#
get_FICLs(pre_input: bool = False) → Generator[FICL, None, None]#

Generate all FICL permutations for this configuration object, and return those with the necessary input files.

Parameters:

pre_input (bool, optional) – Skip file checks if this function is called prior to download.

Yields:

FICL – FICL permutation with existing input files.

setup_paths(display_progress: bool = False, pre_input: bool = False)#

Create product and output directories for each FICLO of this configuration object.

Parameters:

  • display_progress (bool, optional) – Display setup progress via tqdm, by default False.

  • pre_input (bool, optional) – Skip file checks if this function is called prior to download.

clean_paths(display_progress: bool = False)#

Remove product and output directories for skipped FICLOs of this configuration object.

Parameters:

display_progress (bool, optional) – Display cleaning progress via tqdm, by default False.

write()#

Write configurations settings for a program run to a YAML file in the corresponding run directory.

morphfits.config.create_config(config_path: str | pathlib.Path | None = None, morphfits_root: str | pathlib.Path | None = None, input_root: str | pathlib.Path | None = None, output_root: str | pathlib.Path | None = None, product_root: str | pathlib.Path | None = None, run_root: str | pathlib.Path | None = None, fields: list[str] | None = None, image_versions: list[str] | None = None, catalog_versions: list[str] | None = None, filters: list[str] | None = None, objects: list[int] | None = None, wrappers: list[str] | None = None, galfit_path: str | pathlib.Path | None = None, display_progress: bool = False, download: bool = False) → MorphFITSConfig#

Create a MorphFITS configuration object from hierarchically preferred variables, in order of values from

  1. CLI call from terminal

  2. Specified config file,

  3. Filesystem discovery

Parameters:

  • config_path (str | Path | None, optional) – Path to user config yaml file, by default None (no user config file provided).

  • morphfits_root (str | Path | None, optional) – Path to root directory of MorphFITS filesystem, by default None (not passed through CLI).

  • input_root (str | Path | None, optional) – Path to root directory of input products, e.g. catalogs, science images, and PSFs, by default None (not passed through CLI).

  • output_root (str | Path | None, optional) – Path to root directory of GALFIT output products, e.g. morphology model and plots, by default None (not passed through CLI).

  • product_root (str | Path | None, optional) – Path to root directory of products generated by this program to execute GALFIT, e.g. cutouts/stamps, masks, and feedfiles, by default None (not passed through CLI).

  • run_root (str | Path | None, optional) – Path to root directory of records generated by this program for each run, by default None (not passed through CLI).

  • fields (list[str] | None, optional) – List of fields over which to execute GALFIT, by default None (not passed through CLI).

  • image_versions (list[str] | None, optional) – List of image versions over which to execute GALFIT, by default None (not passed through CLI).

  • catalog_versions (list[str] | None, optional) – List of catalog versions over which to execute GALFIT, by default None (not passed through CLI).

  • filters (list[str] | None, optional) – List of filter bands over which to execute GALFIT, by default None (not passed through CLI).

  • objects (list[int] | None, optional) – List of target IDs over which to execute GALFIT, for each catalog, by default None (not passed through CLI).

  • wrappers (list[str], optional) – List of morphology fitting algorithms to run, by default only GALFIT.

  • galfit_path (str | Path | None, optional) – Path to GALFIT binary file, by default None (not passed through CLI).

  • display_progress (bool, optional) – Display progress via tqdm, by default False.

  • download (bool, optional) – Create configuration in download mode, i.e. create directory structure if missing, by default False.

Returns:

A configuration object for this program execution.

Return type:

MorphFITSConfig

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