def spectrum_view(library, spec_id):
lambda_min = 3600
lambda_max = 9600
try:
lambda_min = float(request.form.get("lambda_min"))
except (TypeError, ValueError):
pass
try:
lambda_max = float(request.form.get("lambda_max"))
except (TypeError, ValueError):
pass
parent_url = url_for("library_search", library=library)
self_url = url_for("spectrum_view", library=library, spec_id=spec_id)
txt_url = url_for("spectrum_txt", library=library, spec_id=spec_id)
data_url = url_for("spectrum_json", library=library, spec_id=spec_id)
png_url = url_for("spectrum_png", library=library, spec_id=spec_id, lambda_min=lambda_min, lambda_max=lambda_max)
path = os_path.join(args.path, library)
x = SpectrumLibrarySqlite(path=path)
metadata_keys = x.list_metadata_fields()
metadata_keys.sort()
metadata = x.get_metadata(ids=int(spec_id))[0]
metadata["spectrum_id"] = spec_id
return render_template('spectrum.html', path=args.path, library=library, metadata_keys=metadata_keys,
parent_url=parent_url, metadata=metadata,
txt_url=txt_url, data_url=data_url, png_url=png_url,
self_url=self_url, lambda_min=lambda_min, lambda_max=lambda_max)
time_start = time.time()
stellar_labels = rv_code.fit_rv(test_spectrum_with_rv)
time_end = time.time()
# If this is the first object, write column headers
if not column_headings_written:
line1 = "# {:5s} {:7s} {:11s} ".format("Steps", "Time", "RV_in")
line2 = "# {:5d} {:7d} {:11d} ".format(1, 2, 3)
column_counter = 3
stellar_label_names = list(stellar_labels.keys())
stellar_label_names.sort()
for key in stellar_label_names:
column_counter += 1
line2 = "%-*s %s" % (len(line1), line2, column_counter)
line1 += "{}_out ".format(key)
for key in test_library.list_metadata_fields():
column_counter += 1
line2 = "%-*s %s" % (len(line1), line2, column_counter)
line1 += "{} ".format(key)
output.write("{}\n{}\n".format(line1, line2))
column_headings_written = True
# Write a line to the output data file
line = "{:5d} {:9.1f} {:11.3f} ".format(rv_code.n_steps,
time_end - time_start,
radial_velocity)
for key in stellar_label_names:
line += "{} ".format(stellar_labels.get(key, "-"))
for key in test_library.list_metadata_fields():
line += "{} ".format(test_spectrum.metadata.get(key, "-"))
def tabulate_labels(library_list, label_list, output_file, workspace=None):
"""
Take a SpectrumLibrary and tabulate a list of the stellar parameters of the stars within it.
:param workspace:
Path to the workspace where we expect to find SpectrumLibraries stored
:param library_list:
A list of the SpectrumLibraries we are to tabulate the contents of
:param label_list:
A list of the labels whose values we are to tabulate
:param output_file:
The filename of the ASCII output file we are to produce
:return:
None
"""
# Set path to workspace where we expect to find libraries of spectra
if workspace is None:
our_path = os_path.split(os_path.abspath(__file__))[0]
workspace = os_path.join(our_path, "../../../../workspace")
# Open output data file
with open(output_file, "w") as output:
# Loop over each spectrum library in turn
for library in library_list:
# Extract name of spectrum library we are to open. Filter off any constraints which follow the name in []
test = re.match("([^\[]*)\[(.*)\]$", library)
if test is None:
library_name = library
else:
library_name = test.group(1)
# Open spectrum library and extract list of metadata fields which are defined on this library
library_path = os_path.join(workspace, library_name)
library_object = SpectrumLibrarySqlite(path=library_path,
create=False)
metadata_fields = library_object.list_metadata_fields()
# Now search library for spectra matching any input constraints, with additional constraint on only
# returning continuum normalised spectra, if that field is defined for this library
constraints = {}
if "continuum_normalised" in metadata_fields:
constraints["continuum_normalised"] = 1
library_spectra = SpectrumLibrarySqlite.open_and_search(
library_spec=library,
workspace=workspace,
extra_constraints=constraints)
# Write column headers at the top of the output
columns = label_list if label_list is not None else library_object.list_metadata_fields(
)
output.write("# ")
for label in columns:
output.write("{} ".format(label))
output.write("\n")
# Loop over objects in each spectrum library
for item in library_spectra["items"]:
metadata = library_object.get_metadata(ids=item['specId'])[0]
for label in columns:
output.write("{} ".format(metadata.get(label, "-")))
output.write("\n")