## \package pts.do.modeling.list_parameters
# -----------------------------------------------------------------
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.tools import formatting as fmt
from pts.modeling.config.parameters import possible_parameter_types, possible_parameter_types_descriptions, default_units
from pts.core.units.stringify import represent_unit as ru
from pts.core.basics.configuration import ConfigurationDefinition
# -----------------------------------------------------------------
definition = ConfigurationDefinition()
definition.add_positional_optional("modeling_type", "string", "modeling type")
print("")
for parameter_types in possible_parameter_types:
print(fmt.green + fmt.bold + parameter_types + fmt.reset)
print("")
print(
" - Description: " +
possible_parameter_types_descriptions[parameter_types].split(" (")[0])
print(" - Default unit: " + ru(default_units[parameter_types]))
print("")
# -----------------------------------------------------------------
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.tools import filesystem as fs
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.core.basics.log import log
from pts.magic.core.image import Image
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition()
definition.add_required("add_to", "file_path", "add to this FITS file")
definition.add_required("add_from", "file_path", "add from this FITS file")
definition.add_flag("frames", "add frames", True)
definition.add_flag("masks", "add masks", True)
definition.add_flag("segments", "add segmentation maps", True)
definition.add_flag("replace", "replace planes", False)
definition.add_flag("replace_frames", "replace frames", False)
definition.add_flag("replace_masks", "replace masks", False)
definition.add_flag("replace_segments", "replace segmentation maps", False)
definition.add_flag("backup", "make backup", False)
config = parse_arguments("interpolate", definition)
# -----------------------------------------------------------------
if config.replace: config.replace_frames = config.replace_masks = config.replace_segments = True
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.modeling.plotting.preparation import PreparationPlotter
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition(log_path="log", config_path="config")
# Add settings
definition.add_positional_optional("features", "string_list", "features to be plotted", choices=PreparationPlotter.features())
# -----------------------------------------------------------------
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.core.remote.host import find_host_ids
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
# Add required
definition.add_required("remote", "string", "name of the remote host", choices=find_host_ids())
definition.add_positional_optional("id", "positive_integer", "simulation ID")
definition.add_optional("name", "string", "simulation name")
# Additional relative error
definition.add_optional("additional_error", "percentage", "additional percentual error for the observed flux points")
# Flags
definition.add_flag("write", "write the results", True)
# -----------------------------------------------------------------
## \package pts.do.core.normalizations Show the normalizations of stellar components in a ski file.
# -----------------------------------------------------------------
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.core.simulation.skifile import SkiFile
from pts.core.simulation.skifile import show_normalizations
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
# Ski path
definition.add_required("ski", "file_path", "path of the ski file")
# Optional
definition.add_optional("flux", "photometric_unit", "also show flux in a particular unit")
# -----------------------------------------------------------------
# Parse the arguments into a configuration
config = parse_arguments("normalizations", definition, "Show the normalizations of stellar components in a ski file")
# -----------------------------------------------------------------
# Load the ski file
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.core.remote.host import find_host_ids
# -----------------------------------------------------------------
# Create definition
definition = ConfigurationDefinition(write_config=False)
# Number of frames
definition.add_optional("nframes", "positive_integer", "number of frames", 2)
# Size of frames
definition.add_optional("npixels", "positive_integer",
"number of pixels of the frames", 500)
# Number of sources
definition.add_optional("nrandom_sources", "positive_integer",
"number of point sources", 100)
# Flags
definition.add_flag("vary_fwhm", "vary the FWHM", False)
# PSF model
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import standard modules
import subprocess
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.core.tools import introspection
from pts.core.prep.update import PTSUpdater
# -----------------------------------------------------------------
# Configuration definition
definition = ConfigurationDefinition()
# Required parameters
definition.add_required("message", "string", "the commit message")
# Optional parameters
definition.add_positional_optional("git_remotes",
"string_list",
"the remote(s) to commit to",
default="origin")
definition.add_optional("remote", "string",
"the remote on which to pull the changes")
# -----------------------------------------------------------------
# Get the configuration
# Import the relevant PTS classes and modules
from pts.core.tools import filesystem as fs
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.core.basics.animation import Animation
from pts.core.basics.apng import APNG
from pts.core.basics.numpngw import write_apng
# -----------------------------------------------------------------
formats = ["avi", "gif", "apng"]
default_format = "gif"
# -----------------------------------------------------------------
# Create the definition
definition = ConfigurationDefinition()
# File format
definition.add_optional("format", "string", "output format", default_format, choices=formats)
definition.add_optional("fps", "positive_integer", "frames per second", 10)
# Parse the command line arguments
config = parse_arguments("animate", definition)
# -----------------------------------------------------------------
# Add the frames
paths = fs.files_in_cwd(extension="png", sort=int)
# Determine path
path = "animation." + config.format
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.modeling.fitting.component import get_populations
from pts.modeling.fitting.run import get_generations_table, get_generation_path
from pts.modeling.fitting.generation import Generation
from pts.modeling.core.environment import verify_modeling_cwd
from pts.modeling.fitting.run import FittingRuns
# -----------------------------------------------------------------
modeling_path = verify_modeling_cwd()
runs = FittingRuns(modeling_path)
# -----------------------------------------------------------------
# Create configuration definition
definition = ConfigurationDefinition()
# -----------------------------------------------------------------
# FITTING RUN
if runs.empty: raise RuntimeError("No fitting runs are present (yet)")
elif runs.has_single: definition.add_fixed("fitting_run", "name of the fitting run", runs.single_name)
else: definition.add_required("fitting_run", "string", "name of the fitting run", choices=runs.names)
# Create the configuration
config = parse_arguments("check_populations", definition)
# -----------------------------------------------------------------
# Load populations table
populations = get_populations(modeling_path)
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
# -----------------------------------------------------------------
# Create configuration definition
definition = ConfigurationDefinition()
# Add optional arguments
definition.add_positional_optional("host_id", "string", "install SKIRT/PTS remotely")
definition.add_optional("repository", "string", "repository name from which to clone (only possible when installing remotely and SKIRT/PTS is already installed locally)")
# Add flags
definition.add_flag("private", "use the private SKIRT/PTS repository")
# Advanced
definition.add_flag("force", "force re-installation when already present", letter="f")
definition.add_flag("force_conda", "force installation of conda and creation of a conda environment even when it is already present")
definition.add_flag("finish", "finish previously initiated installation")
# Add flag
#definition.add_flag("all_remotes", "update on all remote hosts")
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.core.remote.host import find_host_ids
from pts.core.tools import introspection
from pts.core.tools import filesystem as fs
from pts.core.simulation.simulation import RemoteSimulation
from pts.core.remote.remote import Remote
from pts.core.basics.log import log
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
# Add settings
definition.add_positional_optional("remotes", "string_list", "the IDs of the remote hosts for which to clear the simulations", choices=find_host_ids(), default=find_host_ids())
definition.add_positional_optional("ids", "integer_list", "the IDs of the simulations to clear")
definition.add_flag("full", "fully clear the simulations, also remove remote simulation directories")
# -----------------------------------------------------------------
# Parse the arguments into a configuration
config = parse_arguments("clear_tasks", definition, description="Clear PTS tasks for a certain remote host")
# -----------------------------------------------------------------
# Loop over the remote hosts
for host_id in config.remotes:
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.modeling.fitting.component import get_generation_names, get_last_finished_generation
from pts.core.tools import filesystem as fs
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition(log_path="log", config_path="config")
# Add settings
definition.add_positional_optional("features", "string_list", "features to be plotted")
definition.add_positional_optional("generation", "string", "generation for which to plot the features", choices=get_generation_names(fs.cwd()), default=get_last_finished_generation(fs.cwd()))
# -----------------------------------------------------------------
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.core.remote.host import find_host_ids
from pts.core.config.analyse_simulation import definition as analysis_definition
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition(write_config=False)
# Add positional optional
definition.add_positional_optional("host_ids", "string_list", "name of the remote host(s) for which to show/retrieve simulations and tasks", choices=find_host_ids())
definition.add_positional_optional("ids", "string_integer_list_dictionary", "simulation IDs for the different remote hosts")
# Add flag
definition.add_flag("show_progress", "show the progress of the simulation that is still running (only if there is just one)", False)
definition.add_flag("debug_output", "show all simulation output in debug mode")
# -----------------------------------------------------------------
definition.add_flag("retrieve", "retrieve finished simulations", True)
definition.add_flag("analyse", "analyse retrieved simulations", True)
# -----------------------------------------------------------------
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.tools import introspection
from pts.core.tools import filesystem as fs
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.core.remote.host import find_host_ids
from pts.core.remote.remote import Remote
from pts.core.tools import time
# -----------------------------------------------------------------
# Create definition
definition = ConfigurationDefinition()
definition.add_positional_optional("remote", "string", "remote host on which to clear the temporary directory", choices=find_host_ids())
definition.add_optional("names", "string_list", "remove temporary directories matching these names (e.g. 'installation' matches 'installation_2017-05-03--08-45-44-410', 'installation_2017-05-03--13-52-28-371', etc. and also exact matches")
# Create setter
config = parse_arguments("clear_temp", definition)
# -----------------------------------------------------------------
# Remote
if config.remote is not None:
# Create the remote
remote = Remote(host_id=config.remote)
# Check whether names are given
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import standard modules
import StringIO
# Import the relevant PTS classes and modules
from pts.core.prep.smile import SKIRTSmileSchema
from pts.core.tools import formatting as fmt
from pts.core.tools import stringify
from pts.core.basics.configuration import ConfigurationDefinition, write_definition, parse_arguments
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition()
definition.add_positional_optional("match", "string", "only show types with names that contain this string")
definition.add_flag("definitions", "format the properties for each item as a configuration definition")
# Parse
config = parse_arguments("skirt_items", definition)
# -----------------------------------------------------------------
# Create the SKIRT smile schema
smile = SKIRTSmileSchema()
print("")
# Loop over the concrete types
for name in smile.concrete_types:
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition()
# Add optional arguments
definition.add_section("wavelengths")
definition.sections["wavelengths"].add_optional("unit", str, "the unit of the wavelengths", "micron")
definition.sections["wavelengths"].add_optional("min", float, "the minimum wavelength", 0.09)
definition.sections["wavelengths"].add_optional("max", float, "the maximum wavelength", 2000)
definition.sections["wavelengths"].add_optional("npoints", int, "the number of wavelength points", 100)
definition.sections["wavelengths"].add_optional("min_zoom", float, "the minimum wavelength of the zoomed-in grid", 1)
definition.sections["wavelengths"].add_optional("max_zoom", float, "the maximum wavelength of the zoomed-in grid", 30)
definition.sections["wavelengths"].add_optional("npoints_zoom", int, "the number of wavelength points in the zoomed-in grid", 100)
definition.add_optional("packages", float, "the number of photon packages per wavelength", 2e5)
definition.add_flag("selfabsorption", "enable dust self-absorption")
definition.add_optional("dust_grid", str, "the type of dust grid to use (bintree, octtree or cartesian)", "bintree")
# -----------------------------------------------------------------
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.core.plot.sed import plot_sed
from pts.core.plot.distribution import plot_distribution
from pts.core.tools import formatting as fmt
from pts.core.tools import sequences
from pts.core.tools.stringify import tostr
from pts.core.basics.structure import load_structure, filetypes, composite, table, dictionary, sed, distribution, regions
# -----------------------------------------------------------------
# Create configuration definition
definition = ConfigurationDefinition(write_config=False)
definition.add_required("filetype", "string", "type of file", choices=filetypes)
definition.add_required("filename", "file_path", "path of the dictionary file")
# As table?
definition.add_flag("table", "show as table")
# Displaying and formatting
definition.add_flag("interactive", "display tables interactively", False)
definition.add_flag("latex", "print as latex")
# Modyfying the table
definition.add_optional("columns", "string_list", "only show these columns")
definition.add_optional("sort", "string", "sort the entries on this column")
# Extra options
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.core.config.plot import definition as plot_definition
from pts.core.basics.plot import plotting_libraries, mpl
# -----------------------------------------------------------------
formats = ["pdf", "png"]
default_format = "pdf"
normalizations = ["max", "sum"]
# -----------------------------------------------------------------
# Create configuration definition
definition = ConfigurationDefinition()
# Distributions
definition.add_positional_optional("distributions", "filepath_list", "distribution files to be plotted")
definition.add_flag("panels", "plot the distributions in separate panels")
definition.add_flag("recursive", "search distribution files recursively in the working directory")
definition.add_optional("normalize", "string", "normalize all distributions by a certain method", choices=normalizations)
definition.add_optional("normalization_value", "real", "value for normalization", 1.)
# Add plotting options
definition.import_section("plot", "plotting options", plot_definition)
definition.sections["plot"].optional["xsize"].default = 8
definition.sections["plot"].optional["ysize"].default = 4
definition.add_flag("logscale", "use value log scale")
definition.add_flag("logfrequency", "use log scale for frequency")
definition.add_optional("bar_width", "positive_real", "relative width of the bars (1 means edges touch)", 1.)
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.core.remote.host import find_host_ids
# -----------------------------------------------------------------
# Create configuration definition
definition = ConfigurationDefinition()
# Add optional
definition.add_positional_optional("ski", "file_path", "ski file to be used (if not specified, all ski files in the current directory will be used)")
# Add flag
definition.add_flag("recursive", "look for ski files recursively")
# Add optional
definition.add_optional("remote", "string", "the remote host (no schedulers) on which to launch the simulations", choices=find_host_ids(schedulers=False))
# Add optional
definition.add_optional("nprocesses", "integer", "number of processes to use", 1)
definition.add_flag("data_parallel", "use data parallelization mode")
# -----------------------------------------------------------------
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.core.basics.plot import normal_colormaps
from pts.magic.plot.imagegrid import default_cmap, light_theme, themes
# ------------------------------------------------------------------------------
# Create definition
definition = ConfigurationDefinition(write_config=False)
# From directory
definition.add_optional("from_directory", "directory_path", "load images from directory")
# Colormap
definition.add_optional("cmap", "string", "colormap", default_cmap, choices=normal_colormaps)
# Options
definition.add_optional("axes_label_size", "positive_integer", "axes label size", 14)
definition.add_optional("ticks_label_size", "positive_integer", "ticks label size", 8)
definition.add_optional("legend_fontsize", "positive_integer", "legend fontsize", 14)
definition.add_optional("legend_markers_cale", "positive_integer", "legend marker scale", 0)
definition.add_optional("lines_marker_size", "positive_real", "lines marker size", 2.5)
definition.add_optional("linewidth", "positive_integer", "linewidth", 1)
# Dark or light theme?
## \package pts.do.developer.sessions Check screen/tmux sessions on the remote host.
# -----------------------------------------------------------------
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.basics.log import log
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.core.remote.remote import Remote
# -----------------------------------------------------------------
definition = ConfigurationDefinition()
definition.add_required("remote", "string", "remote host ID")
setter = parse_arguments("sessions", definition)
# -----------------------------------------------------------------
remote = Remote()
if not remote.setup(config.remote):
raise RuntimeError("The remote host '" + config.remote +
"' is not available at the moment")
screen_names = remote.screen_names()
tmux_names = remote.tmux_names()
print("SCREEN")
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.magic.maps.colour.colour import colour_strings
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition()
# Add optional
definition.add_positional_optional("colours", "string_list", "colour maps to make", default=colour_strings, suggestions=colour_strings)
# -----------------------------------------------------------------
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
# Flags
definition.add_flag("recursive",
"look for simulation in directories recursively", True)
# Output
definition.add_optional("output",
"directory_path",
"output directory",
letter="o")
# Flags
definition.add_flag("other", "also plot the 'other' phases")
definition.add_flag(
"group",
"group timelines for the same number of processes in the same plot")
# -----------------------------------------------------------------
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.remote.remote import Remote
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.core.tools import introspection
from pts.core.basics.log import log
# -----------------------------------------------------------------
# Create configuration definition
definition = ConfigurationDefinition()
# Add required
definition.add_required("remote", "string", "the remote host ID")
# Add flags
definition.add_flag("versions", "compare versions", "v")
# Get configuration
config = parse_arguments("compare_python_packages", definition)
# -----------------------------------------------------------------
# Create the remote execution environment
remote = Remote()
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.remote.host import find_host_ids
from pts.core.basics.configuration import ConfigurationDefinition
from pts.core.tools import introspection
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
# Add optional
host_ids = find_host_ids()
if len(host_ids) > 0:
definition.add_positional_optional("host_ids",
"string_list",
"remote host ids",
choices=host_ids,
default=host_ids)
else:
definition.add_fixed("host_ids", "remote host_ids", [])
# Add optional
definition.add_optional("pts_repo_name",
"string",
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.evolve.solve.extremizer import genetic_definition
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition()
# Genetic settings
definition.import_section("genetic", "genetic algorithm settings",
genetic_definition)
# Add
definition.sections["genetic"].add_optional("ngenerations", "positive_integer",
"number of generations", 10)
definition.sections["genetic"].add_optional(
"nindividuals", "even_integer", "number of individuals per generation",
100)
# -----------------------------------------------------------------
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.core.remote.host import find_host_ids
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
# Add required
definition.add_positional_optional("remote", "string", "name of the remote host", choices=find_host_ids())
definition.add_positional_optional("matching", "string", "only adapt settings with a name matching this string")
definition.add_positional_optional("ids", "integer_list", "simulation IDs (if none specified, all simulation IDs will be used)")
definition.add_optional("names", "string_list", "simulation names")
definition.add_flag("from_directories", "use directory names as simulation names")
# -----------------------------------------------------------------
# Select certain properties
definition.add_optional("contains", "string", "only adapt properties containing this string in their name")
definition.add_optional("not_contains", "string", "don't adapt properties containing this string in their name")
definition.add_optional("exact_name", "string", "only adapt properties with this exact string as their name")
definition.add_optional("exact_not_name", "string", "don't adapt properties with this exact string as their name")
definition.add_optional("startswith", "string", "only adapt properties whose name starts with this string")
from pts.modeling.core.environment import verify_modeling_cwd
# -----------------------------------------------------------------
# Set modeling path
modeling_path = verify_modeling_cwd()
# -----------------------------------------------------------------
default_fitting_method = get_default_fitting_method(modeling_path)
cache_host_id = get_cache_host_id(modeling_path)
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition()
# Add flags
definition.add_flag("check_hosts",
"check the availability of the remote hosts", True)
definition.add_flag("deploy", "deploy SKIRT and PTS where necessary", False)
definition.add_flag("check_versions",
"check versions of SKIRT and PTS where necessary", True)
definition.add_flag("update_dependencies", "update PTS dependencies", False)
# Advanced settings
definition.add_flag("local", "keep computationaly heavy computations local")
definition.add_optional(
"remotes",
"string_list",
"remote hosts for computationally heavy computations (overrule the modeling configuration)",
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
# Optional
definition.add_optional("default_fwhm",
"quantity",
"default FWHM",
"2.0 arcsec",
convert_default=True)
definition.add_optional("sigma_level", "real", "sigma level", 4.0)
# -----------------------------------------------------------------
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
# -----------------------------------------------------------------
# Create configuration definition
definition = ConfigurationDefinition()
# Add required
definition.add_required("ski", "file_path", "path to the ski file")
# Add optional
definition.add_optional("input", "directory_path", "path to the input directory")
# Add optional
definition.add_optional("nwavelengths", "integer", "the number of wavelengths (useful for when a file wavelength grid is used and the file is not present)")
definition.add_optional("ncells", "integer", "number of dust cells (useful only when the ski file includes a tree dust grid)")
# Add flag
definition.add_flag("probe", "probe the number of cells (or memory usage) by launching a dry-run of the simulation, if necessary (tree dust grid and ncells not specified)", True)
# Add optional
definition.add_optional("nprocesses", "integer_list", "number of processes", [1, 2, 4, 8, 12, 20])
# -----------------------------------------------------------------
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.core.remote.host import all_host_ids
from pts.core.simulation.remote import get_simulation_for_host
from pts.core.launch.analyser import reanalyse_simulation, all_steps
from pts.core.basics.log import log
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
definition.add_required("remote", "string", "remote host to mount", choices=all_host_ids())
definition.add_required("ids", "integer_list", "simulation IDs")
definition.add_positional_optional("steps", "string_list", "re-analyse only certain steps", choices=all_steps, default=all_steps)
definition.add_positional_optional("features", "string_list", "re-analyse only certain features (if a single step is defined)")
definition.add_optional("not_steps", "string_list", "don't analyse these steps", choices=all_steps)
definition.add_optional("not_features", "string_list", "don't analyse these features (if a single not_step is defined)")
# Read the command line arguments
config = parse_arguments("reanalyse", definition, description="Re-analyse a certain simulation")
# -----------------------------------------------------------------
# Loop over the simulations
for simulation_id in config.ids:
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.core.remote.host import find_host_ids
# -----------------------------------------------------------------
# Create definition
definition = ConfigurationDefinition(write_config=False)
definition.add_flag("plot", "do plotting", False)
definition.add_flag("rotate", "rotation", True)
definition.add_optional("nrandom_sources", "positive_integer",
"number of random sources", 100)
definition.add_flag("vary_fwhm", "vary the FWHM slightly for each star", True)
definition.add_flag("add_catalogued_sources", "add catalogued sources", False)
definition.add_optional("point_source_catalogs", "string_list",
"point source catalogs", ["II/246"])
definition.add_optional("nfilters_stars", "positive_integer",
# *****************************************************************
## \package pts.do.magic.rebin Rebin a set of images to the same pixel grid.
# -----------------------------------------------------------------
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.magic.core.list import NamedFrameList
from pts.core.tools import filesystem as fs
from pts.magic.basics.coordinatesystem import CoordinateSystem
# -----------------------------------------------------------------
# Create the definition
definition = ConfigurationDefinition()
# Select files
definition.add_optional("contains", "string_list",
"only files whose name contain one of these strings")
# Options
definition.add_optional("name", "string", "rebin to this name")
definition.add_optional("wcs", "file_path",
"path to the file from which to take the WCS")
# Flags
definition.add_flag("backup", "make backups", True)
# Parse the command line arguments
config = parse_arguments("rebin", definition)
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import standard modules
import numpy as np
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.magic.core.image import Image
from pts.core.tools import filesystem as fs
from pts.core.basics.log import log
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition()
definition.add_required("file_path", "file_path", "path of the image")
definition.add_required("factor", "real", "multiplication factor")
definition.add_flag("backup", "make a backup of each image that is multiplied", False)
config = parse_arguments("multiply", definition)
# -----------------------------------------------------------------
# BACKUP FIRST
if config.backup:
# Inform the user
log.info("Making a backup of the original image ...")
# Determine new filepath and copy
new_filepath = fs.appended_filepath(config.filepath, "_backup")
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.modeling.reporting.reporting import steps
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition(log_path="log", config_path="config")
# The modeling step for which to create the report
definition.add_required("step", "string", "the modeling step", choices=steps)
# -----------------------------------------------------------------
# Import the relevant PTS classes and modules
from pts.core.tools import time
from pts.core.tools import filesystem as fs
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.dustpedia.core.sample import DustPediaSample
from pts.dustpedia.core.database import DustPediaDatabase, get_account
from pts.core.tools import formatting as fmt
from pts.core.tools import introspection
from pts.dustpedia.core.photometry import DustPediaPhotometry
from pts.core.tools import stringify
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
# The galaxy name
definition.add_required("galaxy", "string", "galaxy name")
# Get configuration
config = parse_arguments("strategy", definition)
# -----------------------------------------------------------------
sample = DustPediaSample()
# Database
username, password = get_account()
database = DustPediaDatabase()
database.login(username, password)
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.core.remote.host import find_host_ids
from pts.modeling.tests.base import default_free_parameters, possible_free_parameters
from pts.evolve.solve.extremizer import genetic_definition
# -----------------------------------------------------------------
# Create definition
definition = ConfigurationDefinition(write_config=False)
# Optional settings
definition.add_optional("nwavelengths", "positive_integer", "number of wavelengths for the reference simulation", 50)
definition.add_optional("npackages", "positive_integer", "number of photon packages per wavelength for the reference simulation", int(1e5))
definition.add_optional("dust_grid_relative_scale", "real", "smallest scale of the dust grid relative to the pixelscale of the input maps", 2.)
definition.add_optional("dust_grid_min_level", "positive_integer", "level for the dust grid", 2)
definition.add_optional("dust_grid_max_mass_fraction", "positive_real", "max mass fraction for the dust grid", 1e-6)
# Flags
definition.add_flag("transient_heating", "enable transient heating", False)
definition.add_flag("selfabsorption", "enable dust selfabsorption", False)
# For remote execution
definition.add_optional("host_ids", "string_list", "remote hosts to use for heavy computations and simulations", choices=find_host_ids())
definition.add_flag("attached", "launch remote executions in attached mode", False)
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.tools import filesystem as fs
from pts.dustpedia.core.database import DustPediaDatabase, get_account
from pts.dustpedia.core.sample import DustPediaSample
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.magic.services.s4g import get_galaxy_names, has_galaxy
from pts.core.basics.map import Map
from pts.core.basics.log import log
from pts.core.basics.table import SmartTable
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition()
#
definition.add_optional("ngalaxies", "positive_integer", "max number of galaxies")
# Get configuration
config = parse_arguments("plot_galaxies", definition)
# -----------------------------------------------------------------
# Create the database instance
database = DustPediaDatabase()
#username, password = get_account()
#database.login(username, password)
# -----------------------------------------------------------------
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.magic.config.extract import definition as extraction_definition
from pts.magic.config.subtract_sky import definition as subtraction_definition
from pts.core.tools.parallelization import ncores
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition()
# The dataset or image
definition.add_positional_optional("dataset", "file_path",
"name of the dataset file or image file")
# The maximum FWHM (minimum resolution that has to be retained in the convolved frames)
definition.add_optional("max_fwhm", "quantity", "maximum FWHM for convolution")
# The minimum pixel size (minimum resolution that has to be retained in the rebinned frames)
definition.add_optional("max_pixelscale", "quantity",
"maximum pixelscale for rebinning")
# Add input section
#definition.add_section("input", "the names of the input files")
#definition.sections["input"].add_required("image", "image_path", "name of the input image")
# *****************************************************************
## \package pts.do.core.mount Mount a remote configured in PTS into a local directory.
# -----------------------------------------------------------------
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.core.remote.mounter import mount_and_open
from pts.core.remote.host import all_host_ids
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
definition.add_required("remote", "string", "remote host to mount", choices=all_host_ids())
definition.add_positional_optional("path", "directory_path", "path of directory in which to create the mount point")
# Read the command line arguments
config = parse_arguments("mount", definition, description="Mount a remote configured in PTS into the local filesystem")
# -----------------------------------------------------------------
# Mount and open
mount_and_open(config.remote, path=config.path)
# -----------------------------------------------------------------
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.core.remote.host import smb_host_ids
# -----------------------------------------------------------------
default_host_name = "www"
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition(log_path="log", config_path="config")
# Upload
definition.add_optional("host_name",
"string",
"remote host name",
default_host_name,
choices=smb_host_ids())
# Flags
definition.add_flag("regenerate", "regenerate the pages", False)
definition.add_flag("replot", "make plots again", False)
# -----------------------------------------------------------------
## \package pts.do.modeling.clear Clear the output of one of the radiative transfer modeling steps.
# -----------------------------------------------------------------
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.tools import logging, time
from pts.core.tools import filesystem as fs
from pts.core.basics.configuration import ConfigurationDefinition, ConfigurationReader
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
# Add setting
definition.add_required("step", str, "the modeling step for which to clear the output")
# Get the configuration
reader = ConfigurationReader("clear")
config = reader.read(definition)
# -----------------------------------------------------------------
# Determine the log file path
logfile_path = fs.join(fs.cwd(), "log", time.unique_name("log") + ".txt") if config.arguments.report else None
# Determine the log level
level = "DEBUG" if config.arguments.debug else "INFO"
#!/usr/bin/env python # -*- coding: utf8 -*- # ***************************************************************** # ** PTS -- Python Toolkit for working with SKIRT ** # ** © Astronomical Observatory, Ghent University ** # ***************************************************************** # Import the relevant PTS classes and modules from pts.core.basics.configuration import ConfigurationDefinition # ----------------------------------------------------------------- # Create the configuration definition definition = ConfigurationDefinition() # -----------------------------------------------------------------
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.core.remote.host import find_host_ids
from pts.core.tools import filesystem as fs
from pts.core.remote.remote import Remote
from pts.core.basics.task import Task
from pts.core.tools import introspection
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
# Add required
definition.add_required("remote",
"string",
"name of the remote host",
choices=find_host_ids())
definition.add_required("id", "positive_integer", "task ID")
# -----------------------------------------------------------------
# Parse the arguments into a configuration
#setter = InteractiveConfigurationSetter("show_log", "Show the log output of a remote PTS task")
config = parse_arguments(
"show_task_log",
definition,
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
# -----------------------------------------------------------------
methods = ["skirt", "pts"]
default_method = "pts"
default_downsample_factor = 2.
default_parallelization = "2:1:2" # 2 cores, 1 process, 2 threads per core
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition(log_path="log", config_path="config")
# Method
definition.add_optional("method",
"string",
"method for deprojection",
default_method,
choices=methods)
# Downsample
definition.add_optional(
"downsample_factor", "positive_real",
"downsample factor of the deprojected map w.r.t the original map",
default_downsample_factor)
# Writing
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
# Required arguments
definition.add_required(
"ski_path", "file_path",
"the name of the ski file to be used for the scaling test")
definition.add_required("remote", "string", "the name of the remote host")
definition.add_required("mode",
"string",
"the parallelization mode for the scaling test",
choices=["mpi", "hybrid", "threads"])
# Optional arguments
definition.add_positional_optional("maxnodes", "real",
"the maximum number of nodes", 1)
definition.add_positional_optional(
"minnodes", "real",
"the minimum number of nodes. In hybrid mode, this also defines the number of threads per process",
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition()
# Number of processes to use
definition.add_optional("nprocesses", "positive_integer", "number of parallel processes", 8)
# Flags
definition.add_flag("write", "write results", True)
# -----------------------------------------------------------------
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.magic.core.cutout import interpolation_methods
# -----------------------------------------------------------------
default_method = "pts"
default_interpolation_method = "pts"
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition()
definition.add_required("image", "string", "name of the input image")
definition.add_required("regions", "string", "name of the regions file over which to interpolate")
definition.add_flag("write_mask", "write out the mask")
definition.add_optional("color", "string", "only interpolate over the shapes with this color")
definition.add_optional("ignore_color", "string", "ignore shapes with this particular color")
definition.add_optional("shapes", "string_list", "only interpolate over these kinds of shapes")
definition.add_optional("input", "string", "name of the input directory", letter="i")
definition.add_optional("output", "string", "name of the output directory", letter="o")
definition.add_optional("method", "string", "interpolation method to use", default=default_method)
definition.add_optional("interpolation_method", "string", "interpolation method", default_interpolation_method, choices=interpolation_methods)
definition.add_flag("sigma_clip", "apply sigma clipping before interpolation", True)
definition.add_optional("source_outer_factor", "real", "outer factor", 1.4)
definition.add_flag("plot", "plot after interpolation", False)
definition.add_flag("replace", "allow the original image to be replaced", False)
definition.add_flag("backup", "backup if replaced", True)
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
# -----------------------------------------------------------------
# Create
definition = ConfigurationDefinition()
# Commands to be run
definition.add_optional("commands", "string_list", "commands to be run in interactive mode")
# Interactive mode
definition.add_flag("interactive", "use interactive mode", default=None)
# -----------------------------------------------------------------
# Showing
definition.add_flag("show", "show stuff", True)
definition.add_flag("show_components", "show the model components", False)
# Plotting
definition.add_flag("plot", "do plotting", True)
# Writing
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.core.remote.host import find_host_ids
from pts.core.tools import introspection
from pts.core.tools import filesystem as fs
from pts.core.simulation.simulation import RemoteSimulation
from pts.core.remote.remote import Remote
from pts.core.basics.log import log
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
# Add settings
definition.add_positional_optional(
"remotes",
"string_list",
"the IDs of the remote hosts for which to clear the simulations",
choices=find_host_ids(),
default=find_host_ids())
definition.add_positional_optional("ids", "integer_list",
"the IDs of the simulations to clear")
definition.add_flag(
"full",
"fully clear the simulations, also remove remote simulation directories")
# -----------------------------------------------------------------
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
# Optional
definition.add_optional("default_fwhm", "quantity", "default FWHM", "2.0 arcsec", convert_default=True)
definition.add_optional("sigma_level", "real", "sigma level", 4.0)
# -----------------------------------------------------------------
# -----------------------------------------------------------------
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.modeling.core.environment import find_modeling_environment_up_cwd
from pts.magic.plot.imagegrid import ResidualImageGridPlotter
from pts.core.tools import filesystem as fs
from pts.magic.core.frame import Frame
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
definition.add_optional("not_filters", "lazy_broad_band_filter_list", "don't show these filters")
definition.add_flag("downsample", "perform downsampling")
definition.add_optional("max_npixels", "positive_integer", "maximum number of pixels to enabled downsampling", 400)
definition.add_flag("truncate", "truncate the images", True)
definition.add_flag("distributions", "show residual distributions", False)
# Extra
definition.add_flag("normalize", "normalize the images")
definition.add_optional("share_scale_with", "string", "share the scale of all other images with this image")
definition.add_optional("colormap", "string", "colormap", "viridis")
# Extra
definition.add_flag("write_data", "write data")
# -----------------------------------------------------------------
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.tools import logging
from pts.magic.tools import catalogs
from pts.core.tools import filesystem as fs
from pts.core.basics.configuration import ConfigurationDefinition, ConfigurationReader
# -----------------------------------------------------------------
# Create the configuration
definition = ConfigurationDefinition()
# Add required settings
definition.add_required("name", str, "the name of the galaxy")
# Get configuration
reader = ConfigurationReader("setup")
config = reader.read(definition)
# -----------------------------------------------------------------
# Determine the log level
level = "DEBUG" if config.debug else "INFO"
# Initialize the logger
log = logging.setup_log(level=level)
from pts.modeling.component.component import get_log_file_paths
from pts.core.tools import filesystem as fs
from pts.core.basics.log import log
from pts.core.tools import time
from pts.core.tools import formatting as fmt
# -----------------------------------------------------------------
# Get the modeling commands
modeling_path = verify_modeling_cwd()
filepaths = get_log_file_paths(modeling_path)
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
# Add settings
definition.add_required("match", "string", "(partial) command name")
# Get configuration
config = parse_arguments("previous_config", definition)
# -----------------------------------------------------------------
matches = defaultdict(list)
# -----------------------------------------------------------------
# Loop over the filepaths
for filepath in filepaths:
## \package pts.do.modeling.clear Clear the output of one of the radiative transfer modeling steps.
# -----------------------------------------------------------------
# Ensure Python 3 compatibility
from __future__ import absolute_import, division, print_function
# Import the relevant PTS classes and modules
from pts.core.tools import logging, time
from pts.core.tools import filesystem as fs
from pts.core.basics.configuration import ConfigurationDefinition, ConfigurationReader
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
# Add setting
definition.add_required("step", str, "the modeling step for which to clear the output")
# Get the configuration
reader = ConfigurationReader("clear")
config = reader.read(definition)
# -----------------------------------------------------------------
# Determine the log file path
logfile_path = fs.join(fs.cwd(), "log", time.unique_name("log") + ".txt") if config.arguments.report else None
# Determine the log level
level = "DEBUG" if config.arguments.debug else "INFO"
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition
from pts.magic.tools.catalogs import stellar_catalog_descriptions
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
definition.add_flag(
"use_frame_fwhm",
"If possible, avoid the fitting procedure and use the FWHM defined by the frame",
True)
definition.add_optional("input_path", "directory_path",
"path to the input directory")
definition.add_optional("output_path", "directory_path",
"path to the output directory")
definition.add_flag("track_record", "track record", False)
definition.add_flag("plot_track_record_if_exception", True)
definition.add_optional("manual_region", "file_path", "manual star region")
definition.add_flag("remove", "remove stars from the frame", True)
definition.add_flag("find_saturation", "find saturated stars", True)
# -----------------------------------------------------------------
