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 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 get_map(self, name):
"""
This function ...
:param name:
:return:
"""
# Determine path
path = fs.join(self.maps_path, name)
return Frame.from_file(path)
def young_stars_map(self):
"""
This function ...
:return:
"""
# young stars
young_map = Frame.from_file(young_map_path)
young_map.wcs = self.wcs
return young_map
def dust_map(self):
"""
This function ...
:return:
"""
# Dust
dust_map = Frame.from_file(dust_map_path)
dust_map.wcs = self.wcs
return dust_map
def ionizing_stars_map(self):
"""
This function ....
:return:
"""
# Ionizing stars
ionizing_map = Frame.from_file(ionizing_map_path)
ionizing_map.wcs = self.wcs
return ionizing_map
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 old_stars_map(self):
"""
This function ...
:return:
"""
# Old stars
old_map = Frame.from_file(old_map_path)
old_map.wcs = self.wcs
return old_map
def load_maps(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Loading the input maps ...")
# Determine path to maps directory
maps_path = fs.join(m81_data_path, "maps")
# Determine the path to the header file
header_path = fs.join(maps_path, "header.txt")
header = Header.fromtextfile(header_path)
wcs = CoordinateSystem(header=header)
# Old stars
old_map_path = fs.join(maps_path, old_filename)
old_map = Frame.from_file(old_map_path)
old_map.wcs = wcs
self.maps["old"] = old_map
# young stars
young_map_path = fs.join(maps_path, young_filename)
young_map = Frame.from_file(young_map_path)
young_map.wcs = wcs
self.maps["young"] = young_map
# Ionizing stars
ionizing_map_path = fs.join(maps_path, ionizing_filename)
ionizing_map = Frame.from_file(ionizing_map_path)
ionizing_map.wcs = wcs
self.maps["ionizing"] = ionizing_map
# Dust
dust_map_path = fs.join(maps_path, dust_filename)
dust_map = Frame.from_file(dust_map_path)
dust_map.wcs = wcs
self.maps["dust"] = dust_map
def dust_map(self):
"""
This function ...
:return:
"""
# Dust
dust_map = Frame.from_file(dust_map_path)
dust_map.wcs = self.wcs
return dust_map
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_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 ionizing_stars_map(self):
"""
This function ....
:return:
"""
# Ionizing stars
ionizing_map = Frame.from_file(ionizing_map_path)
ionizing_map.wcs = self.wcs
return ionizing_map
def young_stars_map(self):
"""
This function ...
:return:
"""
# young stars
young_map = Frame.from_file(young_map_path)
young_map.wcs = self.wcs
return young_map
def old_stars_map(self):
"""
This function ...
:return:
"""
# Old stars
old_map = Frame.from_file(old_map_path)
old_map.wcs = self.wcs
return old_map
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_images(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Loading the images ...")
# The common wcs of the images
wcs = None
# Loop over the images in the data directory
for path, filename in fs.files_in_path(self.data_path,
extension="fits",
returns=["path", "name"]):
# Load the frame
frame = Frame.from_file(path)
# Set filter
previous_filter = frame.filter
frame.filter = parse_filter(filename.split("_norm")[0])
if previous_filter != frame.filter: frame.save()
# Check filter
if str(frame.filter) not in [
str(fltr) for fltr in self.config.fitting_filters
]:
continue
# Determine name
name = str(frame.filter)
# Check wcs
if wcs is None: wcs = frame.wcs
elif wcs == frame.wcs: pass
else:
raise IOError("The coordinate system of image '" + filename +
"' does not match that of other images")
# Debugging
log.debug("Adding frame '" + filename + "' ...")
# Add to dictionary
self.images[name] = frame
# Set original path
self.image_paths[name] = path
# Set the wcs
self.wcs = wcs
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 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)
#continue
# Loop over the images
for step in paths:
# Get the path
path = paths[step]
# Check whether the correction has already been performed
backup_filepath = fs.appended_filepath(path, "_backup")
if fs.is_file(path): # local
if fs.is_file(backup_filepath): # already corrected
# Check
corrected = Frame.from_file(path)
backup = Frame.from_file(backup_filepath)
ratio = corrected / backup
ratios = ratio[np.isfinite(ratio)]
if not np.all(np.isclose(ratios, factor)):
raise RuntimeError("Correction was not OK for " +
prep_name + " after the " + step +
" step: mean ratio of " +
str(np.mean(ratios)))
log.success("The " + prep_name + " image after the " + step +
" step has already been corrected (locally)")
continue
else:
if np.isclose(factor, config.factor, rtol=0.01):
the_image_path = image_path
break
# Check
if the_image_path is None:
raise ValueError("Could not find the truncated " + filter_name +
" image with a truncation factor of " +
str(config.factor))
# -----------------------------------------------------------------
# Download the image to a temporary path
filename = time.unique_name("truncated_" + filter_name + "_" +
str(config.factor))
filepath = remote.download_file_to(the_image_path,
pts_temp_dir,
new_name=filename)
# -----------------------------------------------------------------
# Open the image
frame = Frame.from_file(filepath)
# -----------------------------------------------------------------
# Plot the truncated image
plotting.plot_box(frame)
# -----------------------------------------------------------------
# Create the command-line parser
parser = argparse.ArgumentParser()
parser.add_argument("region", type=str, help="the name of the region file")
parser.add_argument("image", type=str, help="the name of the image file")
parser.add_argument("value", type=float, nargs='?', help="the fill value", default='nan')
parser.add_argument("--data", action="store_true", help="use the original data for pixels that are not masked")
parser.add_argument('--invert', action="store_true", help="invert the mask so that mask covers outside regions")
# Parse the command line arguments
arguments = parser.parse_args()
# -----------------------------------------------------------------
# Load the image
frame = Frame.from_file(arguments.image)
# Load the region
region_name = os.path.splitext(os.path.basename(arguments.region))[0]
region = load_as_pixel_region_list(arguments.region, frame.wcs)
# Create the mask
mask = region.to_mask(x_size=frame.xsize, y_size=frame.ysize)
# Calculate the inverse, if requested
if arguments.invert: mask = mask.inverse()
# -----------------------------------------------------------------
if arguments.data:
the_image_path = None
# Find the image corresponding to the specified factor
for image_path, image_name in fs.files_in_path(lowres_path,
extension="fits",
returns=["path", "name"]):
# Determine the factor
factor = real(image_name)
# If the factor corresponds to the specified factor, take this image
if np.isclose(factor, config.factor, rtol=0.01):
the_image_path = image_path
break
# Check
if the_image_path is None:
raise ValueError("No truncated " + filter_name +
" image found for a factor of " + str(config.factor))
# Add the image
frame = Frame.from_file(the_image_path)
plotter.add_image(frame, filter_name)
# -----------------------------------------------------------------
# Run the plotter
plotter.run()
# -----------------------------------------------------------------
definition.add_optional("alpha", "string", "alpha method", default_alpha_method, suggestions=alpha_methods)
definition.add_flag("no_alpha", "no alpha", False)
definition.add_optional("output", "string", "output filepath", letter="o")
definition.add_optional("peak_alpha", "real", "alpha of peak value", 1.)
definition.add_optional("max_npixels", "positive_integer", "maximum number of pixels")
definition.add_optional("downsample", "positive_real", "downsample with this factor")
definition.add_flag("show", "show after creating", False)
config = parse_arguments("fits_to_png", definition)
# -----------------------------------------------------------------
# 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:
name = fs.strip_extension(fs.name(filepath))
# Get header
header = get_header(filepath)
# Get the filter
fltr = get_filter(name, header=header)
# Check whether the filter is in the list of filters to be plotted
if fltr not in config.filters: continue
# Get the index for this filter
index = config.filters.index(fltr)
# Load the image
frame = Frame.from_file(filepath)
# Replace zeroes and negatives
frame.replace_zeroes_by_nans()
frame.replace_negatives_by_nans()
# Set the image
mock_images[index] = frame
# ------------------------------------------------------------------------------
# Get the observed images
observed_images = []
for fltr in config.filters:
# Check
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)
# CONVERT UNIT to MJy/sr
poisson *= 1e-6
poisson /= poisson.pixelarea.to("sr").value
poisson.unit = "MJy/sr"
# Make frame remote
remote_frame = RemoteFrame.from_local(poisson, remote_host_id)
modeling_path = config.path
galaxy_name = fs.name(modeling_path)
fit_best_images_path = fs.join(modeling_path, "fit", "best", "images", "test")
simulated = dict()
for path, name in fs.files_in_path(fit_best_images_path,
extension="fits",
returns=["path", "name"]):
if name == galaxy_name + "_earth_total": continue
frame = Frame.from_file(path)
if "2MASS" in str(frame.filter): continue
if "I4" in str(frame.filter): continue
if "W3" in str(frame.filter): continue
if frame.filter is None: raise ValueError("No filter for " + name)
simulated[str(frame.filter)] = frame
trunc_path = fs.join(modeling_path, "truncated")
observed = dict()
for path, name in fs.files_in_path(trunc_path,
extension="fits",
# return the MSE, the lower the error, the more "similar"
# the two images are
return err
# -----------------------------------------------------------------
# Loop over the different kinds of maps
for which_map in config.maps:
# Get the map path
path = map_paths[which_map]
# Load the map
the_map = Frame.from_file(path)
# Set psf filter
the_map.psf_filter = "Pacs red"
# Loop over the maps
if which_map == "dust": maps = collection.get_dust_maps(flatten=True)
elif which_map == "old": maps = collection.get_old_maps(flatten=True)
elif which_map == "young": maps = collection.get_young_maps(flatten=True)
elif which_map == "ionizing":
maps = collection.get_ionizing_maps(flatten=True)
else:
raise ValueError("Invalid map type: '" + which_map + "'")
similarities = dict()
plotter.config.max_nrows = 3
plotter.config.ngrids = 4
# Write data
plotter.config.write = config.write_data
# Crop to
plotter.crop_to = environment.truncation_box
# -----------------------------------------------------------------
# Loop over the frames in the current working directory
for path, name in fs.files_in_cwd(extension="fits", returns=["path", "name"]):
# Load the frame
frame = Frame.from_file(path)
# Get the filter
fltr = frame.filter
filter_name = str(fltr)
# Do we have a photometry image for this filter
if not environment.has_photometry_for_filter(fltr): continue
# Get the photometry image
reference_path = environment.photometry_image_paths_for_filters[fltr]
reference = Frame.from_file(reference_path)
# Add row
plotter.add_row(reference, frame, filter_name)
#finder.config.point_sources_catalog = ...
# Set the output directory
finder.config.output = output_find_name
# Set options for extended sources, point sources and other sources
# For extended source options: see 'definition' in pts.magic.config.find_extended.py
# For point source options: see 'definition' in pts.magic.config.find_point.py
# For other source options: see 'definition' in pts.magic.config.find_other.py
#finder.config.extended. .. = ...
#finder.config.point. ... = ...
#finder.config.other. ... = ...
## Add your image frame(s)
# Output path can be specified seperately for each frame
frame = Frame.from_file("testIm-i.fits")
#finder.add_frame(frame="J000002.00+051717.0_1237678777941229794-g.fits", name=name, output_path='output/')
#finder.add_frame(...)
#...
## Start the source finder:
# various kinds of input can be passed here:
# - frames: a FrameList instance
# - dataset: a DataSet instance
# - output_paths: a dictionary of output paths for each frame
# - star_finder_settings: different settings for each frame
# - ignore: ignore images (list of names)
# - ignore_stars: ignore stars for these images (list of names)
# - ignore_other_sources: ignore other sources for these images (list of names)
# - extended_source_catalog: object of ExtendedSourceCatalog class
nargs='?',
help="the sigma level",
default=3.0)
parser.add_argument("--color", type=str, help="the color", default="blue")
# Parse the command line arguments
arguments = parser.parse_args()
# -----------------------------------------------------------------
# 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)
# -----------------------------------------------------------------
# Determine the path to the region file
path = os.path.join(os.getcwd(), catalog_name + ".reg")
# Create a file
f = open(path, 'w')
# Initialize the region string
print("# Region file format: DS9 version 4.1", file=f)
# Create the list of stars
for i in range(len(catalog)):
definition.add_optional("colours", "string", "colour or colour scale", "red")
definition.add_optional("alpha", "string", "alpha method", default_alpha_method, suggestions=alpha_methods)
definition.add_optional("output", "string", "output filepath", letter="o")
definition.add_optional("peak_alpha", "real", "alpha of peak value", 1.)
definition.add_optional("max_npixels", "positive_integer", "maximum number of pixels")
definition.add_optional("downsample", "positive_real", "downsample with this factor")
definition.add_flag("show", "show after creating", False)
config = parse_arguments("fits_to_png", definition)
# -----------------------------------------------------------------
# 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:
prep_names_column = []
names = ["Image name", "Image path", "Preparation name"]
# Loop over all subdirectories of the data directory
for path, name in fs.directories_in_path(fs.join(config.path, "data"),
not_contains="bad",
returns=["path", "name"]):
# Loop over all FITS files found in the current subdirectory
for image_path, image_name in fs.files_in_path(path,
extension="fits",
not_contains="_Error",
returns=["path", "name"]):
# Open the image frame
frame = Frame.from_file(image_path)
# Determine the preparation name
if frame.filter is not None: prep_name = str(frame.filter)
else: prep_name = image_name
# Set the row entries
names_column.append(image_name)
paths_column.append(image_path)
prep_names_column.append(prep_name)
# Create the table
data = [names_column, paths_column, prep_names_column]
table = tables.new(data, names)
# Check whether the preparation directory exists
trunc_path = fs.join(modeling_path, "truncated")
prep_path = fs.join(modeling_path, "prep")
observed = dict()
# Loop over the directories in the preparation directory
for path, name in fs.directories_in_path(prep_path, returns=["path", "name"]):
# Skip Halpha
if "Halpha" in name: continue
# Determine the path to the prepared image
result_path = fs.join(path, "result.fits")
# Load the frame
frame = Frame.from_file(result_path)
if frame.filter is None: raise ValueError("No filter for " + name)
observed[str(frame.filter)] = frame
# Sort the filter names on wavelength
sorted_filter_names = sorted(observed.keys(), key=lambda key: observed[key].filter.pivotwavelength())
sorted_filter_names = sorted_filter_names[0:6]
##### CAN BE REMOVED ########
"""
plt.figure()
x = []
y = []
data_images_path = get_data_images_path(modeling_path)
# -----------------------------------------------------------------
shapes = dict()
# Loop over the images
for image_path, image_name in fs.files_in_path(data_images_path,
extension="fits",
not_contains="poisson",
returns=["path", "name"],
recursive=True,
recursion_level=1):
# Load the image
frame = Frame.from_file(image_path, silent=True)
# Determine filter name
filter_name = frame.filter_name
# Set pixel shape
shapes[filter_name] = frame.shape
# -----------------------------------------------------------------
# Sort on shape
sorted_filter_names = sorted(shapes.keys(), key=lambda name: shapes[name])
# -----------------------------------------------------------------
print("")
fltr = parse_filter(name)
filter_name = str(fltr)
# Initializ variable
the_image_path = None
# Find the image corresponding to the specified factor
for image_path, image_name in fs.files_in_path(lowres_path, extension="fits", returns=["path", "name"]):
# Determine the factor
factor = real(image_name)
# If the factor corresponds to the specified factor, take this image
if np.isclose(factor, config.factor, rtol=0.01):
the_image_path = image_path
break
# Check
if the_image_path is None: raise ValueError("No truncated " + filter_name + " image found for a factor of " + str(config.factor))
# Add the image
frame = Frame.from_file(the_image_path)
plotter.add_image(frame, filter_name)
# -----------------------------------------------------------------
# Run the plotter
plotter.run()
# -----------------------------------------------------------------
log.start("Starting decomposition_residuals ...")
# -----------------------------------------------------------------
components_path = fs.join(config.path, "components")
truncation_path = fs.join(config.path, "truncated")
residuals_path = fs.join(config.path, "residuals")
# -----------------------------------------------------------------
# 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")
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"
frame.save(fs.join(residuals_path, "i1_jy.fits"))
# Inform the user
# -----------------------------------------------------------------
names_column = []
paths_column = []
prep_names_column = []
names = ["Image name", "Image path", "Preparation name"]
# Loop over all subdirectories of the data directory
for path, name in fs.directories_in_path(fs.join(config.path, "data"), not_contains="bad", returns=["path", "name"]):
# Loop over all FITS files found in the current subdirectory
for image_path, image_name in fs.files_in_path(path, extension="fits", not_contains="_Error", returns=["path", "name"]):
# Open the image frame
frame = Frame.from_file(image_path)
# Determine the preparation name
if frame.filter is not None: prep_name = str(frame.filter)
else: prep_name = image_name
# Set the row entries
names_column.append(image_name)
paths_column.append(image_path)
prep_names_column.append(prep_name)
# Create the table
data = [names_column, paths_column, prep_names_column]
table = tables.new(data, names)
# Check whether the preparation directory exists