def make_animation(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Making animation ...")
# Get the best
best = self.optimizer.best
# Determine path
temp_path = self.optimizer.config.path
filepath = fs.join(temp_path, "best.png")
# Make plot of best
# Create animated gif
animation = Animation()
# Open the images present in the directory
for path in fs.files_in_path(temp_path, extension="png", exact_not_name="best"):
# Add frame to the animation
animation.add_frame_from_file(path)
# Save the animation
animation_path = fs.join(temp_path, "animation.gif")
animation.saveto(animation_path)
def make_animation(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Making animation ...")
# Get the best
best = self.optimizer.best
# Determine path
temp_path = self.optimizer.config.path
filepath = fs.join(temp_path, "best.png")
# Make plot of best
# Create animated gif
animation = Animation()
# Open the images present in the directory
for path in fs.files_in_path(temp_path, extension="png", exact_not_name="best"):
# Add frame to the animation
animation.add_frame_from_file(path)
# Save the animation
animation_path = fs.join(temp_path, "animation.gif")
animation.saveto(animation_path)
def setup(self, **kwargs):
"""
This function ...
:param kwargs:
:return:
"""
# Call the setup function of the base class
super(M81TestBase, self).setup(**kwargs)
# Reference base path
self.reference_path = fs.create_directory_in(self.path, "ref")
# Reference wcs path
self.reference_wcs_path = fs.join(self.reference_path, "wcs.txt")
# Reference ski path
self.reference_ski_path = fs.join(self.reference_path, "M81.ski")
# Determine the simulation input and output path
self.simulation_input_path = fs.create_directory_in(self.reference_path, "in")
self.simulation_output_path = fs.create_directory_in(self.reference_path, "out")
self.simulation_extract_path = fs.create_directory_in(self.reference_path, "extr")
self.simulation_plot_path = fs.create_directory_in(self.reference_path, "plot")
self.simulation_misc_path = fs.create_directory_in(self.reference_path, "misc")
# Determine the path to the wavelength grid file
self.wavelength_grid_path = fs.join(self.simulation_input_path, reference_wavelength_grid_filename)
# Create the plot path
self.plot_path = fs.create_directory_in(self.path, "plot")
# Set the execution platforms
self.set_platforms()
def create_dataset(self, masks=None):
"""
This function ...
:param masks:
:return:
"""
# Inform the user
log.info("Creating the dataset ...")
# Initialize
self.dataset = DataSet()
# Add the frames
for fltr in self.frames:
# Determine name for the image
name = str(fltr)
# Determine path for this frame
path = fs.join(self.data_frames_path, name + ".fits")
# Debugging
log.debug("Saving the frame ...")
# Save the frame
self.frames[fltr].saveto(path)
# Debugging
log.debug("Adding the '" + name + "' image to the dataset ...")
# Add the frame to the dataset
self.dataset.add_path(name, path)
# Determine the path for the mask
mask_path = fs.join(self.data_masks_path, name + ".fits")
# Mask
if masks is not None and fltr in masks:
# Debugging
log.debug("Saving the mask ...")
# Save
masks[fltr].saveto(mask_path)
# Debugging
log.debug("Adding mask ...")
# Add the mask
self.dataset.add_mask_path(name, mask_path)
# Determine database path
path = fs.join(self.path, "database.dat")
# Write the dataset
self.dataset.saveto(path)
def import_package_update(self, name, as_name=None, from_name=None, show_output=False):
"""
Thins function ...
:param name:
:param as_name:
:param from_name:
:param show_output:
:return:
"""
# Try to import
success, module_name, import_statement = self.import_package(name, as_name=as_name, from_name=from_name, show_output=show_output, return_false_if_fail=True, return_failed_module=True)
# Not succesful, try updating the module on which it failed
if not success:
# No problem module, show import statement
if module_name is None: raise RuntimeError("Unsolvable import error occured at: '" + import_statement + "'")
# Debugging
log.debug("Import of '" + name + "' was unsuccesful: trying updating the '" + module_name + "' package ...")
from ..prep.update import update_pts_dependencies_remote
# Find conda
conda_installation_path, conda_main_executable_path = self.remote.find_conda()
# Determine the conda environment for PTS
env_name = self.remote.conda_environment_for_pts
if env_name is None: raise Exception("Cannot determine the conda environment used for pts")
conda_environment = env_name
environment_bin_path = fs.join(conda_installation_path, "envs", conda_environment, "bin")
if not self.remote.is_directory(environment_bin_path): raise RuntimeError("The environment directory is not present")
conda_executable_path = fs.join(environment_bin_path, "conda")
# Set ...
conda_pip_path = fs.join(environment_bin_path, "pip")
conda_python_path = fs.join(environment_bin_path, "python")
conda_easy_install_path = fs.join(environment_bin_path, "easy_install")
# Update the module
packages = [module_name]
update_pts_dependencies_remote(self.remote, packages, conda_executable_path,
conda_environment, conda_python_path, conda_pip_path,
conda_easy_install_path)
# Try again
success, module_name, import_statement = self.import_package(name, as_name=as_name, from_name=from_name,
show_output=show_output, return_false_if_fail=True,
return_failed_module=True)
# Not succesful again
if not success: raise ImportError("The import statement '" + import_statement + "' failed on remote host '" + self.host_id + "'")
def old(self):
"""
This function ...
:return:
"""
exit()
# FWHM of all the images
fwhm = 11.18 * u("arcsec")
fwhm_pix = (fwhm / frame.average_pixelscale).to("pix").value
sigma = fwhm_pix * statistics.fwhm_to_sigma
# Get the center pixel of the galaxy
parameters_path = fs.join(components_path, "parameters.dat")
parameters = load_parameters(parameters_path)
center = parameters.center.to_pixel(frame.wcs)
# Create a source around the galaxy center
ellipse = PixelEllipseRegion(center, 20.0*sigma)
source = Source.from_ellipse(model_residual, ellipse, 1.5)
source.estimate_background("polynomial")
source.plot()
position = source.center
model = source.subtracted.fit_model(position, "Gaussian")
rel_center = center - Extent(source.x_min, source.y_min)
rel_model = fitting.shifted_model(model, -source.cutout.x_min, -source.cutout.y_min)
plotting.plot_peak_model(source.cutout, rel_center.x, rel_center.y, rel_model)
model_fwhm_pix = fitting.fwhm(model)
model_fwhm = (model_fwhm_pix * frame.average_pixelscale).to("arcsec")
print("Model FWHM: ", model_fwhm)
evaluated_model = source.cutout.evaluate_model(model)
all_residual = Frame(np.copy(model_residual))
all_residual[source.y_slice, source.x_slice] -= evaluated_model
all_residual.saveto(fs.join(residuals_path, "all_residual.fits"))
model = Gaussian2D(amplitude=0.0087509425805, x_mean=center.x, y_mean=center.y, x_stddev=sigma, y_stddev=sigma)
rel_model = fitting.shifted_model(model, -source.cutout.x_min, -source.cutout.y_min)
plotting.plot_peak_model(source.cutout, rel_center.x, rel_center.y, rel_model)
evaluated_model = source.cutout.evaluate_model(model)
all_residual2 = Frame(np.copy(model_residual))
all_residual2[source.y_slice, source.x_slice] -= evaluated_model
all_residual2.saveto(fs.join(residuals_path, "all_residual2.fits"))
def setup(self, **kwargs):
"""
This function ...
:param kwargs:
:return:
"""
# Call the
super(GalaxyTest, self).setup(**kwargs)
# Reference ski path
self.reference_ski_path = fs.join(self.path, "galaxy_clumpy.ski")
# Determine the simulation output path
self.simulation_output_path = fs.join(self.path, "ref")
def model(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Performing the modelling ...")
# Settings
settings_model = dict()
settings_model["ngenerations"] = 4
settings_model["nsimulations"] = 20
settings_model["fitting_settings"] = {"spectral_convolution": False}
# Input
input_model = dict()
# Set galaxy properties
input_model["properties"] = self.properties
# Set SEDs
input_model["seds"] = dict()
# Set images dictionary
images = dict()
for filter_name in fitting_filter_names:
images[filter_name] = fs.join("../ref/images",
filter_name + ".fits")
input_model["images"] = images
def uninstall_conda_remote(self):
"""
This function ...
:return:
"""
# Inform the user
log.info(
"Uninstalling the Conda python distribution on the remote host ..."
)
# Determine path of miniconda installation
installation_path = fs.join(self.remote.home_directory, "miniconda")
if not self.remote.is_directory(installation_path):
log.warning("Conda was not found on the remote host")
return
# Debugging
log.debug("Removing the Conda directory ...")
# Remove the directory
self.remote.remove_directory(installation_path)
# Debugging
log.debug("Removing lines from shell configuration ...")
# Remove lines from shell configuration file
comment = "For Conda, added by PTS (Python Toolkit for SKIRT)"
self.remote.remove_aliases_and_variables_with_comment(comment)
self.remote.remove_from_path_variable_containing("miniconda/bin")
def create_ski(self):
"""
This function ...
"""
# Inform the user
log.info("Creating ski file ...")
fraction = 0.5
count = 1000
radius = parse_quantity("10 pc")
cutoff = False
kernel_type = "uniform"
# Determine the ski path
ski_path = fs.join(this_dir_path, "galaxy.ski")
# Create clumpy ski file
self.ski = LabeledSkiFile(ski_path)
# Set instrument
self.set_instrument()
# Set stellar components
self.set_stellar_components()
# Set dust components
self.set_dust_components()
# Save as new ski file
self.ski.saveto(self.reference_ski_path)
def run_script(matches, args):
"""
This function ...
:param matches:
:param args:
:return:
"""
if args.remote is not None: raise ValueError("This do command cannot be executed remotely")
match = matches[0]
# Execute the matching script, after adjusting the command line arguments so that it appears that the script was executed directly
target = fs.join(introspection.pts_do_dir, match[0], match[1])
sys.argv[0] = target
del sys.argv[1]
print("Executing: " + match[0] + "/" + match[1] + " " + " ".join(sys.argv[1:]))
#command_name = match[1]
# Set target
#def start(): exec open(target)
# Start # DOESN'T WORK WHEN THE SCRIPT FILE DEFINES A FUNCTION
#start_target(command_name, start)
exec open(target)
def run_script(matches, args):
"""
This function ...
:param matches:
:param args:
:return:
"""
if args.remote is not None:
raise ValueError("This do command cannot be executed remotely")
match = matches[0]
# Execute the matching script, after adjusting the command line arguments so that it appears that the script was executed directly
target = fs.join(introspection.pts_do_dir, match[0], match[1])
sys.argv[0] = target
del sys.argv[1]
print("Executing: " + match[0] + "/" + match[1] + " " +
" ".join(sys.argv[1:]))
#command_name = match[1]
# Set target
#def start(): exec open(target)
# Start # DOESN'T WORK WHEN THE SCRIPT FILE DEFINES A FUNCTION
#start_target(command_name, start)
exec open(target)
def uninstall_conda_remote(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Uninstalling the Conda python distribution on the remote host ...")
# Determine path of miniconda installation
installation_path = fs.join(self.remote.home_directory, "miniconda")
if not self.remote.is_directory(installation_path):
log.warning("Conda was not found on the remote host")
return
# Debugging
log.debug("Removing the Conda directory ...")
# Remove the directory
self.remote.remove_directory(installation_path)
# Debugging
log.debug("Removing lines from shell configuration ...")
# Remove lines from shell configuration file
comment = "For Conda, added by PTS (Python Toolkit for SKIRT)"
self.remote.remove_aliases_and_variables_with_comment(comment)
self.remote.remove_from_path_variable_containing("miniconda/bin")
def load_i1(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Loading the IRAC 3.6 micron image ...")
# Determine the path to the truncated 3.6 micron image
#path = fs.join(truncation_path, "IRAC I1.fits")
path = fs.join(self.prep_path, "IRAC I1", "result.fits")
frame = Frame.from_file(path)
# Convert the frame to Jy/pix
conversion_factor = 1.0
conversion_factor *= 1e6
# Convert the 3.6 micron image from Jy / sr to Jy / pixel
pixelscale = frame.average_pixelscale
pixel_factor = (1.0/pixelscale**2).to("pix2/sr").value
conversion_factor /= pixel_factor
frame *= conversion_factor
frame.unit = "Jy"
# Set the frame
self.i1_jy = frame
def check_reference_data(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Checking the reference data ...")
# Determine simulation directory
if self.config.reference_path is not None:
data_path = self.config.reference_path
elif self.config.reference_test is not None:
data_path = fs.join(introspection.pts_tests_dir,
self.config.reference_test, "data")
else:
raise ValueError(
"Reference path and reference test settings are None")
# Check whether directory exist and not empty
if not fs.is_directory(data_path):
raise ValueError("Directory does not exist: " + data_path)
if fs.is_empty(data_path):
raise ValueError("Empty directory: " + data_path)
# Remove data directory for this test
fs.remove_directory(self.data_path)
# Set data path
self.data_path = data_path
def uninstall_conda_local(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Uninstalling the Conda python distribution locally ...")
# Check installation
installation_path = fs.join(fs.home, "miniconda")
if not fs.is_directory(installation_path):
log.warning("Conda was not found locally")
return
# Debugging
log.debug("Removing the Conda directory ...")
# Remove the directory
fs.remove_directory(installation_path)
# Debugging
log.debug("Removing lines from shell configuration ...")
# Remove lines from shell configuration file
comment = "For Conda, added by PTS (Python Toolkit for SKIRT)"
terminal.remove_aliases_and_variables_with_comment(comment)
terminal.remove_from_path_variable_containing("miniconda/bin")
def restore_chi_squared(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Restoring the chi squared tables ...")
# Loop over the generations
for generation_name in self.generation_names:
# Has generation?
if not self.has_generation(generation_name): continue
# Debugging
log.debug("Creating backup of chi squared table for generation '" + generation_name + "' ...")
# Get the generation
generation = self.generations[generation_name]
# Get the generation path
generation_path = self.get_generation_restore_path(generation_name)
# Determine the filepath
filepath = fs.join(generation_path, "chi_squared.dat")
# Copy the file
fs.copy_file(filepath, generation.chi_squared_table_path)
def make_young_stars_maps(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Making maps of young stars ...")
# Get input
fuv = self.get_frame("FUV")
fuv_attenuation = self.get_map(fuv_attenuation_filename)
old_disk = self.get_map(old_disk_filename)
factor = 0.25 # to be determined for each galaxy
# Make the map of young stars
young_stars = make_young_stellar_map(
self.get_frame("FUV"), self.get_map(fuv_attenuation_filename),
old_disk, factor)
# Determine the path
path = fs.join(self.maps_path, young_stars_filename)
# Save the map
young_stars.saveto(path)
def create_wcs(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Creating the WCS ...")
min_pixelscale = None
# Determine the path to the headers directory
headers_path = fs.join(m81_data_path, "headers")
# Loop over the header files
for path, name in fs.files_in_path(headers_path, extension="txt", returns=["path", "name"]):
# Get the filter
fltr = parse_filter(name)
filter_name = str(fltr)
# Set the path of the file for the filter name
self.wcs_paths[filter_name] = path
# Get WCS
wcs = CoordinateSystem.from_header_file(path)
# Adjust the pixelscale
if min_pixelscale is None:
min_pixelscale = wcs.pixelscale
self.wcs = wcs
elif min_pixelscale > wcs.pixelscale:
min_pixelscale = wcs.pixelscale
self.wcs = wcs
def create_wcs(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Creating the WCS ...")
min_pixelscale = None
# Determine the path to the headers directory
headers_path = fs.join(m81_data_path, "headers")
# Loop over the header files
for path, name in fs.files_in_path(headers_path, extension="txt", returns=["path", "name"]):
# Get the filter
fltr = parse_filter(name)
filter_name = str(fltr)
# Set the path of the file for the filter name
self.wcs_paths[filter_name] = path
# Get WCS
wcs = CoordinateSystem.from_header_file(path)
# Adjust the pixelscale
if min_pixelscale is None:
min_pixelscale = wcs.pixelscale
self.wcs = wcs
elif min_pixelscale > wcs.pixelscale:
min_pixelscale = wcs.pixelscale
self.wcs = wcs
def uninstall_conda_local(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Uninstalling the Conda python distribution locally ...")
# Check installation
installation_path = fs.join(fs.home(), "miniconda")
if not fs.is_directory(installation_path):
log.warning("Conda was not found locally")
return
# Debugging
log.debug("Removing the Conda directory ...")
# Remove the directory
fs.remove_directory(installation_path)
# Debugging
log.debug("Removing lines from shell configuration ...")
# Remove lines from shell configuration file
comment = "For Conda, added by PTS (Python Toolkit for SKIRT)"
terminal.remove_aliases_and_variables_with_comment(comment)
terminal.remove_from_path_variable_containing("miniconda/bin")
def load_i1(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Loading the IRAC 3.6 micron image ...")
# Determine the path to the truncated 3.6 micron image
#path = fs.join(truncation_path, "IRAC I1.fits")
path = fs.join(self.prep_path, "IRAC I1", "result.fits")
frame = Frame.from_file(path)
# Convert the frame to Jy/pix
conversion_factor = 1.0
conversion_factor *= 1e6
# Convert the 3.6 micron image from Jy / sr to Jy / pixel
pixelscale = frame.average_pixelscale
pixel_factor = (1.0 / pixelscale**2).to("pix2/sr").value
conversion_factor /= pixel_factor
frame *= conversion_factor
frame.unit = "Jy"
# Set the frame
self.i1_jy = frame
def setup_modelling(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Setting up the modeling ...")
# Settings
settings_setup = dict()
settings_setup["type"] = "images"
settings_setup["name"] = "NGC4013"
settings_setup["fitting_host_ids"] = None
# Create object config
object_config = dict()
ski_path = fs.join(this_dir_path, "NGC4013.ski")
object_config["ski"] = ski_path
object_config["images"] = self.image_paths.values()
# Create input dict for setup
input_setup = dict()
input_setup["object_config"] = object_config
# Construct the command
setup_command = Command("setup", "setup the modelling", settings_setup,
input_setup, ".")
# Run the command
tool = self.run_command(setup_command)
def load_reference(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Loading the reference simulation ...")
# Determine simulation directory
if self.config.reference_path is not None:
simulation_path = self.config.reference_path
elif self.config.reference_test is not None:
simulation_path = fs.join(introspection.pts_tests_dir,
self.config.reference_test, "ref")
else:
raise ValueError(
"Reference path and reference test settings are None")
# Check whether present
if not fs.is_directory(simulation_path):
raise ValueError(
"The reference simulation path could not be found")
# Look for simulation
prefix, ski_path, in_path, out_path = find_one_simulation_in_path(
simulation_path)
# Load the ski file
self.ski = LabeledSkiFile(ski_path)
# Other paths
extr_path = fs.join(simulation_path, "extr")
plot_path = fs.join(simulation_path, "plot")
misc_path = fs.join(simulation_path, "misc")
# Check existence
if not fs.is_directory(extr_path):
raise IOError("Extraction directory not found")
if not fs.is_directory(plot_path):
raise IOError("Plotting directory not found")
if not fs.is_directory(misc_path):
raise IOError("Misc directory not found")
# Copy
self.copy_reference(ski_path, in_path, out_path, extr_path, plot_path,
misc_path)
def restore_configuration_path(self):
"""
This function ...
:return:
"""
return fs.join(self.restore_path, "configuration.cfg")
def modeling_path(self):
"""
This function ...
:return:
"""
return fs.join(self.path, self.modeling_name)
def restore_prob_path(self):
"""
This function ...
:return:
"""
return fs.join(self.restore_path, "prob")
def write_mask(self):
"""
Thisfunction ...
:return:
"""
path = fs.join(output_path, "mask.fits")
mask.saveto(path, header=header)
def restore_weights_path(self):
"""
This function ...
:return:
"""
return fs.join(self.restore_path, "weights.dat")
def restore_generations_path(self):
"""
This function ...
:return:
"""
return fs.join(self.restore_path, "generations")
def restore_best_parameters_path(self):
"""
This function ...
:return:
"""
return fs.join(self.restore_path, "best_parameters.dat")
def write_tour_to_img(self, tour):
"""
The function to plot the graph
:param tour:
"""
padding = 20
coords = [(x+padding,y+padding) for (x,y) in self.coordinates]
maxx, maxy = 0, 0
for x, y in coords:
maxx = max(x, maxx)
maxy = max(y, maxy)
maxx += padding
maxy += padding
img = Image.new("RGB",(int(maxx),int(maxy)),color=(255,255,255))
font = ImageFont.load_default()
d = ImageDraw.Draw(img)
num_cities = len(tour)
# Loop over the cities
for i in range(num_cities):
j = (i+1) % num_cities
city_i = tour[i]
city_j = tour[j]
x1,y1 = coords[city_i]
x2,y2 = coords[city_j]
d.line((int(x1),int(y1),int(x2),int(y2)),fill=(0,0,0))
d.text((int(x1)+7,int(y1)-5),str(i),font=font,fill=(32,32,32))
for x, y in coords:
x, y = int(x),int(y)
d.ellipse((x-5,y-5,x+5,y+5),outline=(0,0,0),fill=(196,196,196))
del d
# Save
if self.output_path is not None:
# Determine the plot path
path = fs.join(self.output_path, str(self.counter) + ".png")
# Debugging
log.debug("Saving the plot to '" + path + "' ...")
# Save
img.save(path, "PNG")
else: raise RuntimeError("Cannot show the plot, specify an output path")
def elitism_table_path_for_generation(self, generation_name):
"""
This function ...
:param generation_name:
:return:
"""
return fs.join(self.fitting_run.generations_path, generation_name, "elitism.dat")
def get_generation_restore_path(self, generation_name):
"""
This function ...
:param generation_name:
:return:
"""
return fs.join(self.restore_generations_path, generation_name)
def write_input(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the simulation input ...")
# Write wavelength grid
self.wavelength_grid.to_skirt_input(self.wavelength_grid_path)
# Write maps
self.maps["old"].saveto(fs.join(self.simulation_input_path, old_filename))
self.maps["young"].saveto(fs.join(self.simulation_input_path, young_filename))
self.maps["ionizing"].saveto(fs.join(self.simulation_input_path, ionizing_filename))
self.maps["dust"].saveto(fs.join(self.simulation_input_path, dust_filename))
def load_seds(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Loading the SEDs ...")
observed_sed_path = fs.join(this_dir_path, "DustPedia.dat")
sim_sed_path_1 = fs.join(this_dir_path, "M81_earth_sed1.dat")
sim_sed_path_2 = fs.join(this_dir_path, "M81_earth_sed2.dat")
mock_sed_path = fs.join(this_dir_path, "M81_earth_fluxes.dat")
self.observed_sed = ObservedSED.from_file(observed_sed_path)
self.model_sed_1 = SED.from_skirt(sim_sed_path_1)
self.model_sed_2 = SED.from_skirt(sim_sed_path_2)
self.mock_sed = ObservedSED.from_file(mock_sed_path)
def load_seds(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Loading the SEDs ...")
observed_sed_path = fs.join(this_dir_path, "DustPedia.dat")
sim_sed_path_1 = fs.join(this_dir_path, "M81_earth_sed1.dat")
sim_sed_path_2 = fs.join(this_dir_path, "M81_earth_sed2.dat")
mock_sed_path = fs.join(this_dir_path, "M81_earth_fluxes.dat")
self.observed_sed = ObservedSED.from_file(observed_sed_path)
self.model_sed_1 = SED.from_skirt(sim_sed_path_1)
self.model_sed_2 = SED.from_skirt(sim_sed_path_2)
self.mock_sed = ObservedSED.from_file(mock_sed_path)
def get_map(self, name):
"""
This function ...
:param name:
:return:
"""
# Determine path
path = fs.join(self.maps_path, name)
return Frame.from_file(path)
def restore_path(self):
"""
This function ...
:return:
"""
path = fs.join(self.fitting_run.refitting_path, self.config.name)
if not fs.is_directory(path): raise ValueError("'" + self.config.name + "' is not a backup of a fit")
return path
def restore_fluxes_plots(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Making a backup of the mock fluxes plots ...")
# Loop over the generations
for generation_name in self.generation_names:
# Has generation?
if not self.has_generation(generation_name): continue
# Debugging
log.debug("Creating backups for generation '" + generation_name + "' ...")
# Get the generation
generation = self.generations[generation_name]
# Get restore path
generation_path = self.get_generation_restore_path(generation_name)
# Loop over the simulations
for simulation_name in generation.simulation_names:
# Set simulation path
simulation_path = fs.join(generation_path, simulation_name)
# Check whether fluxes are present
filepath = fs.join(simulation_path, "earth_fluxes.pdf")
if not fs.is_file(filepath):
log.warning("No mock SED plot for simulation '" + simulation_name + "' of generation '" + generation_name + "'")
continue
# Debugging
log.debug("Restoring fluxes plot for simulation '" + simulation_name + "' ...")
# Copy the plot file
fs.copy_file(filepath, generation.get_mock_sed_plot_path(simulation_name))
def restore_differences(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Making a backup of the flux differences ...")
# Loop over the generations
for generation_name in self.generation_names:
# Has generation?
if not self.has_generation(generation_name): continue
# Debugging
log.debug("Creating backups for generation '" + generation_name + "' ...")
# Get the generation
generation = self.generations[generation_name]
# Get restore path
generation_path = self.get_generation_restore_path(generation_name)
# Loop over the simulations
for simulation_name in generation.simulation_names:
# Set simulation path
simulation_path = fs.join(generation_path, simulation_name)
# Check whether the simulation has differences
filepath = fs.join(simulation_path, "differences.dat")
if not fs.is_file(filepath):
log.warning("No differences table for simulation '" + simulation_name + "' of generation '" + generation_name + "'")
continue
# Debugging
log.debug("Restoring differences table for simulation '" + simulation_name + "' ...")
# Copy the file
fs.copy_file(filepath, generation.get_simulation_sed_differences_path(simulation_name))
def get_map(self, name):
"""
This function ...
:param name:
:return:
"""
# Determine path
path = fs.join(self.maps_path, name)
return Frame.from_file(path)
def load_components(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Loading the components ...")
# Determine paths
path = fs.join(m81_data_path, "components")
bulge_path = fs.join(path, "bulge.mod")
disk_path = fs.join(path, "disk.mod")
# Load bulge model
self.bulge = load_3d_model(bulge_path)
# Load disk model
self.disk = load_3d_model(disk_path)
def write_residuals(self):
"""
This function ...
:return:
"""
# Bulge residual
path = fs.join(self.components_residuals_path, "bulge.fits")
self.bulge_residual.saveto(path)
# Bulge2D residual
path = fs.join(self.components_residuals_path, "bulge2D.fits")
self.bulge2d_residual.saveto(path)
# Disk residual
path = fs.join(self.components_residuals_path, "disk.fits")
self.disk_residual.saveto(path)
# Calculate the model residual frame
path = fs.join(self.components_residuals_path, "model.fits")
self.model_residual.saveto(path)
def load_model(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Loading the model image ...")
# Determine the path to the truncated model image
path = fs.join(self.components_images_path, "model.fits")
self.model_jy = Frame.from_file(path)
def load_disk(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Loading the disk image ...")
# Determine the path to the disk image
path = fs.join(self.components_images_path, "disk.fits")
self.disk_jy = Frame.from_file(path)
def load_bulge2d(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Loading the bulge 2D image ...")
# Determine the path to the bulge 2D image
path = fs.join(self.components_images_path, "bulge2D.fits")
self.bulge2d_jy = Frame.from_file(path)
def load_model(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Loading the model image ...")
# Determine the path to the truncated model image
path = fs.join(self.components_images_path, "model.fits")
self.model_jy = Frame.from_file(path)
def write_residuals(self):
"""
This function ...
:return:
"""
# Bulge residual
path = fs.join(self.components_residuals_path, "bulge.fits")
self.bulge_residual.saveto(path)
# Bulge2D residual
path = fs.join(self.components_residuals_path, "bulge2D.fits")
self.bulge2d_residual.saveto(path)
# Disk residual
path = fs.join(self.components_residuals_path, "disk.fits")
self.disk_residual.saveto(path)
# Calculate the model residual frame
path = fs.join(self.components_residuals_path, "model.fits")
self.model_residual.saveto(path)
def load_disk(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Loading the disk image ...")
# Determine the path to the disk image
path = fs.join(self.components_images_path, "disk.fits")
self.disk_jy = Frame.from_file(path)
def write_sources(self):
"""
THis function ...
:return:
"""
# Inform the user
log.info("Writing the sources frame with noise ...")
# Determine the path
path = fs.join(self.path, "sources_noise.fits")
# Save the frame
self.sources_with_noise.saveto(path)
def write_residual(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the residual map ...")
# Determine the path
path = fs.join(self.path, "residual.fits")
# Save
self.sky_residual.saveto(path)
def write_statistics(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the statistics ...")
# Determine the path
path = fs.join(self.path, "statistics.dat")
# Write
save_mapping(path, self.statistics)
def write_frame(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the frame ...")
# Determine the path
path = fs.join(self.path, "frame.fits")
# SAve the frame
self.frame.saveto(path)
def write_subtracted(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the sky-subtracted frame ...")
# Determine the path
path = fs.join(self.path, "subtracted.fits")
# Save
self.subtracted.saveto(path)
def write_estimated_sky(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the estimated sky map ...")
# Determine the path
path = fs.join(self.path, "estimated_sky.fits")
# Save
self.estimated_sky.saveto(path)
def write_reference_sky(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the reference sky map ...")
# Determine the path
path = fs.join(self.path, "reference_sky.fits")
# Save
self.reference_sky.saveto(path)
def write_galaxy_mask(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the galaxy mask ...")
# Determine the path
path = fs.join(self.path, "galaxy_mask.fits")
# Save
self.galaxy_mask.saveto(path)
