def screenlog_path(self):
"""
This function ...
:return:
"""
if self.output_path is None: return None
the_index = 0
the_path = None
# Find screenlog file
for path in self.remote.files_in_path(self.output_path):
name = fs.name(path)
if name.startswith("screenlog"):
index = int(name.split(".")[1])
if the_path is None:
the_path = path
the_index = index
elif index > the_index:
the_path = path
the_index = index
# Return the path
return the_path
def set_reference_images(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Setting the reference images ...")
# Remove reference images
self.fski.remove_all_reference_images()
# Set reference images
for name in self.image_paths:
# Get filename
path = self.image_paths[name]
filename = fs.name(path)
# Set FWHM
if "u" in filename: kernel_fwhm = 1.7
elif "g" in filename: kernel_fwhm = 1.6
else: raise NotImplementedError("Not implemented")
# Ranges (for both stellar components)
luminosity_range = RealRange(min_luminosity, max_luminosity)
luminosity_ranges = [luminosity_range, luminosity_range]
# Add reference image
self.fski.add_reference_image(filename, luminosity_ranges,
kernel_fwhm, self.config.kernel_type,
self.config.kernel_dimension)
def screenlog_path(self):
"""
This function ...
:return:
"""
if self.output_path is None: return None
the_index = 0
the_path = None
# Find screenlog file
for path in self.remote.files_in_path(self.output_path):
name = fs.name(path)
if name.startswith("screenlog"):
index = int(name.split(".")[1])
if the_path is None:
the_path = path
the_index = index
elif index > the_index:
the_path = path
the_index = index
# Return the path
return the_path
def image_name(self):
"""
This function ...
:return:
"""
return fs.name(self.config.image)
def filename(self):
"""
This function ...
:return:
"""
return fs.strip_extension(fs.name(self.config.image))
def adjust_fski(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Creating the fski file ...")
# Set ski name
self.fski.set_ski_name(fs.name(self.reference_ski_path))
# Set the parameter ranges
self.set_parameter_ranges()
# Set the reference images
self.set_reference_images()
# Set the genetic options
self.set_genetic_options()
# Load the wavelength grid
grid = fitting_run.get_wavelength_grid_data_grid(name)
# Determine the new path
path = fitting_run.get_wavelength_grid_path(name)
# Save
grid.to_skirt_input(path)
# -----------------------------------------------------------------
# Grid path is given
if config.grid_path is not None:
# Set wavelength grid
grid_name = fs.strip_extension(fs.name(config.grid_path))
# Load the grid
if config.skirt: wavelength_grid = WavelengthGrid.from_skirt_input(config.grid_path)
else: wavelength_grid = WavelengthGrid.from_file(config.grid_path)
# Grid name is given
else:
# Set wavelength grid name
grid_name = config.name
# Load the wavelength grid
if config.name not in fitting_run.wavelength_grid_names: raise ValueError("Wavelength grid '" + config.name + "' does not exist")
wavelength_grid = fitting_run.get_wavelength_grid(config.name)
# -----------------------------------------------------------------
# Create the configuration definition
definition = ConfigurationDefinition()
definition.add_required("files", "filepath_list",
"list of the data file paths")
definition.add_flag("loglog", "use log-log scale", False)
# Parse
config = parse_arguments("plot_curves", definition)
# -----------------------------------------------------------------
curves = dict()
for filepath in config.files:
name = fs.strip_extension(fs.name(filepath))
curves[name] = Curve.from_data_file(filepath)
# -----------------------------------------------------------------
plot = MPLPlot()
for name in curves:
plot.add_curve(curves[name], name)
# -----------------------------------------------------------------
if config.loglog:
plot.set_x_log_scale()
plot.set_y_log_scale()
# -----------------------------------------------------------------
# Required
definition.add_required("local_path", "string", "path or name of the file or directory to send")
definition.add_required("remote", "string", "the remote host to send to", choices=find_host_ids())
# Remote path
definition.add_positional_optional("remote_path", "string", "path of the remote directory to send to")
# Create configuration
config = parse_arguments("send", definition, "Send a file or directory to a remote host")
# -----------------------------------------------------------------
# Create remote
remote = Remote(host_id=config.remote)
# -----------------------------------------------------------------
# Set full path of origin
origin = fs.absolute_or_in_cwd(config.local_path)
name = fs.name(origin)
# Set full path to the destination
if config.remote_path is None: destination = fs.join(remote.home_directory, name)
else: destination = remote.absolute_path(config.remote_path)
# Upload
remote.upload(origin, destination)
# -----------------------------------------------------------------
remote.setup(config.remote)
# Remove specification of the remote
arguments_no_remote = arguments[:-2]
# Make a new temporary directory remotely
remote_path = fs.join(remote.home_directory, temp_name)
remote.create_directory(remote_path)
remote.change_cwd(remote_path)
# Send the appropriate command
remote.launch_pts_command("get_poisson_errors", arguments_no_remote)
# Retrieve the remote directory
remote.download(remote_path, fs.cwd(), show_output=True)
local_path = fs.join(fs.cwd(), fs.name(remote_path))
# Remove the temporary remote directory
remote.remove_directory(remote_path)
# Locally
else:
# Make a local directory
local_path = fs.join(fs.cwd(), temp_name)
fs.create_directory(local_path)
# Create the DustPedia data processing instance
dpdp = DustPediaDataProcessing()
# GALEX
# Create config
config = parse_arguments("view", definition)
# -----------------------------------------------------------------
stylesheet_url = "https://users.ugent.be/~sjversto/stylesheet.css"
background_color = "white"
page_style = "ugentstyle"
# -----------------------------------------------------------------
# Create CSS for the page width
css = html.make_page_width(config.page_width)
# Get name
name = fs.strip_extension(fs.name(config.image))
title = name
# Create list of css scripts
css_paths = css_scripts[:]
css_paths.append(stylesheet_url)
# Create the page
page = html.HTMLPage(title,
css=css,
body_settings=body_settings,
style=page_style,
css_path=css_paths,
javascript_path=javascripts,
footing=html.updated_footing())
definition = ConfigurationDefinition()
definition.add_required("local_path", "string",
"path or name of the file or directory to send")
definition.add_required("remote",
"string",
"the remote host to send to",
choices=find_host_ids())
definition.add_optional("remote_path", "string",
"path of the remote directory to send to")
config = parse_arguments("send", definition)
# -----------------------------------------------------------------
# Create remote
remote = Remote(host_id=config.remote)
# -----------------------------------------------------------------
# Set full path of origin
origin = fs.absolute_or_in_cwd(config.local_path)
name = fs.name(origin)
# Set full path to the destination
if config.path is not None: destination = fs.join(remote.home_directory, name)
else: destination = remote.absolute_path(config.remote_path)
# Upload
remote.upload(origin, destination)
# -----------------------------------------------------------------
# -----------------------------------------------------------------
# Create the command-line parser
parser = argparse.ArgumentParser()
# Basic options
parser.add_argument("filename",
type=str,
help="the name of the input image file")
# Parse the command line arguments
arguments = parser.parse_args()
# -----------------------------------------------------------------
# Open the original image
image = imageio.imread(arguments.filename)
# Invert the colours
invert_colors(image)
# Determine output name
name = fs.strip_extension(fs.name(arguments.filename))
newname = name + "_inverted.png"
# Write the inverted image
imageio.imwrite(newname, image)
# -----------------------------------------------------------------
prep_path = fs.join(modeling_path, "prep")
# -----------------------------------------------------------------
progress = defaultdict(dict)
# -----------------------------------------------------------------
# Loop over all images of the initial dataset
#for path in fs.files_in_path(prep_path, recursive=True, exact_name="initialized"):
for directory_path in fs.directories_in_path(prep_path):
# Directory path
#directory_path = fs.directory_of(path)
image_name = fs.name(directory_path)
# Determine filter
fltr = parse_filter(image_name)
# Sort
label, filepath = sort_image(image_name, directory_path, read_only=True)
category = fltr.instrument if fltr.instrument is not None else "other"
# Add to progress data
progress[category][fltr.band] = label
# -----------------------------------------------------------------
print("")
# -----------------------------------------------------------------
# Loop over the generations
for generation_name in config.generations:
# Loop over the simulations
for simulation in get_simulations(modeling_path, generation_name):
# Inform the user
log.info("Plotting SED for simulation '" + simulation.name + "' of generation '" + generation_name + "' ...")
# Determine plot path
plot_dir_path = fs.join(simulation.base_path, "plot")
plot_path = fs.join(plot_dir_path, "sed.pdf")
# Create SED plotter
plotter = SEDPlotter()
# Add observed sed
plotter.add_sed(observed_sed, "observation")
# Add simulated sed(s)
for path in simulation.seddatpaths():
sed = SED.from_skirt(path)
plotter.add_sed(sed, fs.name(path))
# Run the plotter
plotter.run(output=plot_path)
# -----------------------------------------------------------------
definition.add_optional("not_columns", "string_list", "don't use these columns")
# Parse
config = parse_arguments("merge_tables", definition)
# -----------------------------------------------------------------
# Load the tables
tables = []
for filepath in config.files:
table = SmartTable.from_file(filepath)
tables.append(table)
# -----------------------------------------------------------------
filenames = [fs.strip_extension(fs.name(filepath)) for filepath in config.files]
# -----------------------------------------------------------------
table = merge_tables(*tables, column_name=config.column, labels=filenames, differences=config.differences,
rel_differences=config.rel_differences, percentual=config.percentual, columns=config.columns, not_columns=config.not_columns)
# -----------------------------------------------------------------
# Show the table
if config.show: print(table)
# Write the table
if config.write:
# Determine path
# -----------------------------------------------------------------
remote_host_id = "nancy"
session = AttachedPythonSession.from_host_id(remote_host_id)
# -----------------------------------------------------------------
# Paths
paths = fs.files_in_path(galex_images_path, extension="fits", contains="poisson") + fs.files_in_path(sdss_images_path, extension="fits", contains="poisson")
# Loop over the GALEX poisson frames
for path in paths:
# Image name
name = fs.strip_extension(fs.name(path))
# Get instrument and band
galaxy_name, instrument, band, _ = name.split("_")
# Create the filter
fltr = BroadBandFilter.from_instrument_and_band(instrument, band)
# Load the frame
poisson = Frame.from_file(path)
# Get the attenuation
att = attenuation.extinction_for_filter(fltr)
# CORRECT FOR GALACTIC EXTINCTION
poisson *= 10**(0.4 * att)
# -----------------------------------------------------------------
# Inform the user
log.info("Loading the FITS file ...")
# Load the FITS file
frame = Frame.from_file(config.filename)
# -----------------------------------------------------------------
if config.output is not None: filepath = fs.absolute_or_in(config.output, fs.cwd())
else:
# Determine the path
name = fs.strip_extension(fs.name(config.filename))
filepath = fs.absolute_path(name + ".png")
# -----------------------------------------------------------------
# Max npixels
if config.max_npixels is not None:
# Determine downsample factor
if frame.xsize > config.max_npixels or frame.ysize > config.max_npixels:
factor = max(frame.xsize, frame.ysize) / float(config.max_npixels)
# Make integer
#numbers.round_up_to_int(factor)
#if factor < 2.: factor = 2
config.downsample = factor
if not remote.is_directory(
remote_prep_path) or not remote.is_directory(
remote_image_directory_path) or not remote.is_file(
remote_initialized_path):
log.warning("The initialized '" + name +
"' image is not found, skipping ...")
continue
# Cache
# Create directory for the image
# Get the path
path = paths[name]
# Get filename
filename = fs.strip_extension(fs.name(path))
#print(filename)
# Determine origin from filename
#origin = instrument_to_origin(filename.split("_")[1])
# Other way
origin = fs.name(fs.directory_of(path))
# CHeck
#if origin != origin_alt: raise ValueError(origin + " != " + origin_alt)
# Create remote directory
remote_image_directory = fs.join(remote_data_path, origin)
if not remote.is_directory(remote_image_directory):
# Loop over the generations
for generation_name in config.generations:
# Loop over the simulations
for simulation in get_simulations(modeling_path, generation_name):
# Inform the user
log.info("Plotting SED for simulation '" + simulation.name +
"' of generation '" + generation_name + "' ...")
# Determine plot path
plot_dir_path = fs.join(simulation.base_path, "plot")
plot_path = fs.join(plot_dir_path, "sed.pdf")
# Create SED plotter
plotter = SEDPlotter()
# Add observed sed
plotter.add_sed(observed_sed, "observation")
# Add simulated sed(s)
for path in simulation.seddatpaths():
sed = SED.from_skirt(path)
plotter.add_sed(sed, fs.name(path))
# Run the plotter
plotter.run(output=plot_path)
# -----------------------------------------------------------------
# User-specified color
elif "," in config.color: red, blue, green = map(int, config.color.split(","))
# Invalid
else: raise ValueError("Invalid input")
# Check dimensions
if image.shape[2] == 3:
shape = list(image.shape)
old_image = image
shape[2] = 4
shape = tuple(shape)
image = np.ones(shape) * 255
image[:, :, :3] = old_image
# Set transparent
if config.gradient: set_transparency_gradient(image, (red, blue, green,), config.scale)
else: set_transparent_color(image, (red, blue, green,), tolerance=config.tolerance)
# Determine output name
name = fs.strip_extension(fs.name(filename))
#extension = fs.get_extension(filename)
extension = "png" # because transparancy has to be supported
newname = name + "_transparent." + extension
# Write the inverted image
imageio.imwrite(newname, image)
# -----------------------------------------------------------------
remote.setup(config.remote)
# Remove specification of the remote
arguments_no_remote = arguments[:-2]
# Make a new temporary directory remotely
remote_path = fs.join(remote.home_directory, temp_name)
remote.create_directory(remote_path)
remote.change_cwd(remote_path)
# Send the appropriate command
remote.launch_pts_command("get_poisson_errors", arguments_no_remote)
# Retrieve the remote directory
remote.download(remote_path, fs.cwd(), show_output=True)
local_path = fs.join(fs.cwd(), fs.name(remote_path))
# Remove the temporary remote directory
remote.remove_directory(remote_path)
# Locally
else:
# Make a local directory
local_path = fs.join(fs.cwd(), temp_name)
fs.create_directory(local_path)
# Create the DustPedia data processing instance
dpdp = DustPediaDataProcessing()
# GALEX
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
## \package pts.do.magic.show_image_info Show basic info of a FITS image.
# -----------------------------------------------------------------
# Import the relevant PTS classes and modules
from pts.core.basics.configuration import ConfigurationDefinition, parse_arguments
from pts.magic.tools.info import get_image_info_strings_from_header_file
from pts.core.tools import filesystem as fs
# -----------------------------------------------------------------
# Create the definition
definition = ConfigurationDefinition()
definition.add_required("file_path", "file_path", "name of the input image file")
# Parse the command line arguments
config = parse_arguments("show_image_info", definition)
# -----------------------------------------------------------------
filename = fs.strip_extension(fs.name(config.file_path))
for line in get_image_info_strings_from_header_file(filename, config.file_path, name=False): print(line)
# -----------------------------------------------------------------
# Create configuration
definition = ConfigurationDefinition(write_config=False)
#definition.add_required("filename", "file_path", "table file")
definition.add_required("columns", "string_list", "names of columns")
definition.add_optional("method", "string", "table reading method", "lines")
config = parse_arguments("remove_columns", definition)
# -----------------------------------------------------------------
# Find table files
filepaths = fs.files_in_cwd(extension="dat", recursive=True)
for filepath in filepaths:
#print(filepath)
directory_name = fs.name(fs.directory_of(filepath))
filename = fs.name(filepath)
# Get column names
column_names = fs.get_column_names(filepath)
if not sequences.contains_any(column_names, config.columns): continue
print(directory_name, filename, column_names)
# -----------------------------------------------------------------
# Load the table
table = SmartTable.from_file(filepath, method=config.method)
# -----------------------------------------------------------------
from pts.core.plot.sed import SEDPlotter
# -----------------------------------------------------------------
# Set the log level
level = "DEBUG"
# Initialize the logger
log = logging.setup_log(level=level)
log.start("Starting compare_sed ...")
# -----------------------------------------------------------------
fit_path = fs.absolute_path("../../../../../")
modeling_path = fs.directory_of(fit_path)
galaxy_name = fs.name(modeling_path)
# -----------------------------------------------------------------
# Create the plotter
plotter = SEDPlotter()
# Add the SEDs
filename = galaxy_name + "_earth_sed.dat"
sed = SED.from_skirt(filename)
# Load the reference SED
reference_sed_path = fs.join(modeling_path, "sed.dat")
reference_sed = ObservedSED.from_file(reference_sed_path)
plotter.add_sed(sed, "simulation")
#parser.add_argument("fwhm", type=float, help="the FWHM of the stars (in pixels)")
#parser.add_argument("sigma_level", type=float, nargs='?', help="the sigma level", default=3.0)
#parser.add_argument("--color", type=str, help="the color", default="blue")
config = parse_arguments("catalog_to_regions", definition)
# -----------------------------------------------------------------
# Load the catalog
#catalog_name = os.path.splitext(os.path.basename(arguments.catalog))[0]
#catalog = tables.from_file(arguments.catalog)
# Open the frame
#frame = Frame.from_file(arguments.image)
# -----------------------------------------------------------------
catalog_name = fs.strip_extension(fs.name(config.path))
# -----------------------------------------------------------------
# Load the catalog
if config.type == "extended": catalog = ExtendedSourceCatalog.from_file(config.path)
elif config.type == "point": catalog = PointSourceCatalog.from_file(config.path)
else: raise ValueError("Invalid catalog type")
# -----------------------------------------------------------------
# -----------------------------------------------------------------
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:
# Get the modeling command
filename = fs.name(filepath)
command = filename.split("__")[0]
# Skip other commands
if not command.startswith(config.match): continue
# Add filepath
matches[command].append(filepath)
# -----------------------------------------------------------------
if len(matches) > 1: raise ValueError("Ambigious command: matches are " + ", ".join(matches.keys()))
# -----------------------------------------------------------------
single_command = matches.keys()[0]
from pts.core.plot.sed import SEDPlotter
# -----------------------------------------------------------------
# Set the log level
level = "DEBUG"
# Initialize the logger
log = logging.setup_log(level=level)
log.start("Starting compare_sed ...")
# -----------------------------------------------------------------
fit_path = fs.absolute_path("../../../../../")
modeling_path = fs.directory_of(fit_path)
galaxy_name = fs.name(modeling_path)
# -----------------------------------------------------------------
# Create the plotter
plotter = SEDPlotter()
# Add the SEDs
filename = galaxy_name + "_earth_sed.dat"
sed = SED.from_skirt(filename)
# Load the reference SED
reference_sed_path = fs.join(modeling_path, "sed.dat")
reference_sed = ObservedSED.from_file(reference_sed_path)
plotter.add_sed(sed, "simulation")
from pts.core.basics.rgbimage import invert_colors
from pts.core.tools import filesystem as fs
# -----------------------------------------------------------------
# Create the command-line parser
parser = argparse.ArgumentParser()
# Basic options
parser.add_argument("filename", type=str, help="the name of the input image file")
# Parse the command line arguments
arguments = parser.parse_args()
# -----------------------------------------------------------------
# Open the original image
image = imageio.imread(arguments.filename)
# Invert the colours
invert_colors(image)
# Determine output name
name = fs.strip_extension(fs.name(arguments.filename))
newname = name + "_inverted.png"
# Write the inverted image
imageio.imwrite(newname, image)
# -----------------------------------------------------------------
#parser.add_argument("sigma_level", type=float, nargs='?', help="the sigma level", default=3.0)
#parser.add_argument("--color", type=str, help="the color", default="blue")
config = parse_arguments("catalog_to_regions", definition)
# -----------------------------------------------------------------
# Load the catalog
#catalog_name = os.path.splitext(os.path.basename(arguments.catalog))[0]
#catalog = tables.from_file(arguments.catalog)
# Open the frame
#frame = Frame.from_file(arguments.image)
# -----------------------------------------------------------------
catalog_name = fs.strip_extension(fs.name(config.path))
# -----------------------------------------------------------------
# Load the catalog
if config.type == "extended":
catalog = ExtendedSourceCatalog.from_file(config.path)
elif config.type == "point":
catalog = PointSourceCatalog.from_file(config.path)
else:
raise ValueError("Invalid catalog type")
# -----------------------------------------------------------------
# -----------------------------------------------------------------