def toJSON(args):
spectrum_file = args.input
spectrum_data = read_spectra_file_simple(spectrum_file)
spectrum = SimpleSpectrum('fits2JSON', spectrum_data)
asjson = utils.toMarzJSON(spectrum)
print(json.dumps(asjson, indent=2), flush=True)
def reduce(self, argument):
"""Implementation of the Marz CLI
Parameters
----------
argument : str
Path to the FITS file containing the spectrum to be fit
Returns
-------
Float
The fitted redshift of the input spectrum
String
The name of the fitted template of the input spectrum
"""
import os
from subprocess import run, Popen, PIPE, STDOUT
spectrum = SimpleSpectrum('fits2JSON', argument)
spectrum_json = json.dumps(utils.toMarzJSON(spectrum), indent=2)
plugin_dir = os.path.dirname(os.path.abspath(__file__))
marzcli_path = plugin_dir + '/marzcli.js'
cmd = plugin_dir + '/marzcli.sh ' + marzcli_path
if sys.version_info[:3] >= (3, 7):
proc = run(cmd,
shell=True,
input=spectrum_json,
text=True,
stdout=PIPE,
stderr=STDOUT,
close_fds=True)
else:
proc = run(cmd,
shell=True,
input=spectrum_json,
universal_newlines=True,
stdout=PIPE,
stderr=STDOUT,
close_fds=True)
lines = proc.stdout.split('\n')
print("=" * 20 + " Marz CLI Plugin " + "=" * 20)
for line in lines[:-6:-1]:
print(line)
tokens = lines[-5].split(',')
bestfit_redshift = float(tokens[8])
bestfit_template = tokens[7].strip()
print(f"BEST REDSHIFT = {bestfit_redshift}")
print(f"BEST TEMPLATE = {bestfit_template}")
return bestfit_redshift, bestfit_template
def test_fits2json_2(self, shared_datadir):
from ssv.viewer import read_spectra_file, read_spectra_file_simple, SimpleSpectrum
from ssv import utils
spectrum_file = shared_datadir / "marz/spec-4444-55538-1000.fits"
formats = loaders.whatformat(spectrum_file)
if len(formats) > 1:
loaders.unregister(formats[0])
spectrum_data = read_spectra_file_simple(spectrum_file)
loaders.restore_registered_loaders()
spectrum = SimpleSpectrum('fits2JSON', spectrum_data)
asjson = utils.toMarzJSON(spectrum)
def test_fits2json_1(self, shared_datadir):
from ssv.viewer import SimpleSpectrum
from ssv import utils
spectrum_file = shared_datadir / "marz/emlLinearVacuumNoHelio.fits"
formats = ssv.ssvloaders.whatformat(spectrum_file)
if len(formats) > 1:
ssv.ssvloaders.unregister(formats[0])
spectrum_data = utils.read_spectra_file(spectrum_file)
ssv.ssvloaders.restore_registered_loaders()
spectrum = SimpleSpectrum('fits2JSON', spectrum_data)
asjson = utils.toMarzJSON(spectrum)
def jsonFitsFile(request, fits_id):
fitsfile = FitsFiles.objects.get(pk=fits_id)
#
datadir = Path('../../../')
anyFILE = datadir / fitsfile.filepath
formats = ssv.loaders.whatformat(anyFILE)
if len(formats) > 1:
ssv.loaders.unregister(formats[0])
spectrum_data = read_spectra_file_simple(anyFILE)
ssv.loaders.restore_registered_loaders()
spectrum = SimpleSpectrum('Test SSV', spectrum_data)
js_data = utils.toMarzJSON(spectrum)
return JsonResponse(js_data, safe=False)
def main():
args = parse_args(sys.argv[1:])
print("fits file to use {}".format(args.input))
spectrum_filename = os.path.basename(args.input)
spectrum_file = args.input
formats = ssv.loaders.whatformat(spectrum_file)
if len(formats) > 1:
ssv.loaders.unregister(formats[0])
spectrum_data = read_spectra_file_simple(spectrum_file)
ssv.loaders.restore_registered_loaders()
template_data = read_template_file(templatedir / TEMPLATE_FILENAME)
# best_fit_redshift, best_fit_template = fit_template_and_redshift(str(spectrum_file))
template_list = [template.meta['purpose'] for template in template_data]
best_fit_redshift = 0
best_fit_template = template_list[0]
best_fit_template_index = template_list.index(best_fit_template)
smoothing_function_list = [box_smooth, gaussian_smooth, trapezoid_smooth, median_smooth]
##### Streamlit Layout #####
st.sidebar.write(spectrum_filename)
show_sky = st.sidebar.checkbox("Show Sky", True, key=1)
show_templates = st.sidebar.checkbox("Show Templates", True, key=2)
show_variance = st.sidebar.checkbox("Show Variance", False, key=3)
show_processed_data = st.sidebar.checkbox("Process Data", True, key=5)
show_continuum_subtracted = st.sidebar.checkbox("Subtract Continuum", False, key=6)
top_controls = st.beta_container()
chart_container = st.beta_container()
# lower_controls = st.beta_container()
lower_controls = st.beta_columns(2)
template_choice = lower_controls[0].selectbox("Template", template_list, index=best_fit_template_index)
smoothing_choice = lower_controls[0].selectbox("Smoothing Function", smoothing_function_list, format_func=lambda x: x.__name__, index=0)
smoothing_width = lower_controls[0].slider("Smoothing Width", min_value=1, max_value=51, step=2, value=7)
show_scaled_spectra = lower_controls[1].checkbox("Scale Spectra", True, key=4)
scaling_maximum = lower_controls[1].text_input("Scaling Maximum Value", value=1.0) # This should be replaced with a number_input
scaling_max = float(scaling_maximum) # but currently it doesn't seem to save value between runs
# Streamlit widgets automatically run the script from top to bottom. Since
# this button is not connected to any other logic, it just causes a plain
# rerun.
st.button("Re-run")
##### Main Code #####
spectrum = SimpleSpectrum('Test SSV', spectrum_data)
spectrum.set_visible_traces('reduced')
flux_range = spectrum.flux_range('reduced')
spectrum.set_variance_visible('reduced', show_variance)
spectrum.set_trace_visible('sky', show_sky)
spectrum.set_transform_functions('reduced', transform_function_array(scaled=show_scaled_spectra, scaling_max=scaling_max, processed=show_processed_data, subtract_continuum=show_continuum_subtracted, smoothing_function=smoothing_choice, smoothing_width=smoothing_width))
spectrum.set_transform_functions('sky', transform_function_array(scaled=show_scaled_spectra, scaling_max=scaling_max, smoothing_function=smoothing_choice, smoothing_width=smoothing_width))
# spectrum2 = SimpleSpectrum('Test SSV 2', spectrum_data)
# spectrum2.set_visible_traces('sky')
# spectrum2.offset_flux(-100, 'sky')
lines = SimpleSpectralLines()
lines.redshift_wavelength(best_fit_redshift)
templates = SimpleSpectrum('Templates', template_data)
templates.set_visible_traces(template_choice)
templates.set_trace_visible(template_choice, show_templates)
templates.redshift_wavelength(best_fit_redshift, best_fit_template)
templates.set_transform_functions(template_choice, transform_function_array(scaled=show_scaled_spectra, scaling_max=scaling_max, processed=show_processed_data, subtract_continuum=show_continuum_subtracted, smoothing_function=smoothing_choice, smoothing_width=smoothing_width))
viewer = SimpleSpectrumViewer('Simple')
viewer.add_spectrum(spectrum)
viewer.add_spectrum(templates)
viewer.add_lines(lines)
viewer.show_grid(True)
viewer.show_legend(True)
viewer.set_chart_width_height(height=500)
chart_container.altair_chart(viewer.build_chart(), use_container_width=True)
def vegaFitsFile(request, fits_id):
fitsfile = FitsFiles.objects.get(pk=fits_id)
#
datadir = Path('../../../')
templatedir = Path('../../../tests/data/marz/')
TEMPLATE_FILENAME = 'MarzTemplates.json'
anyFILE = datadir / fitsfile.filepath
formats = ssv.loaders.whatformat(anyFILE)
if len(formats) > 1:
ssv.loaders.unregister(formats[0])
spectrum_data = read_spectra_file_simple(anyFILE)
ssv.loaders.restore_registered_loaders()
template_data = read_template_file(templatedir / TEMPLATE_FILENAME)
spectrum = SimpleSpectrum('Test SSV', spectrum_data)
spectrum.set_visible_traces('reduced')
spectrum2 = SimpleSpectrum('Test SSV 2', spectrum_data)
spectrum2.set_visible_traces('sky')
spectrum2.set_transform_functions('sky', [utils.remove_spurious_points])
spectrum2.offset_flux(-100, 'sky')
lines = SimpleSpectralLines()
templates = SimpleSpectrum('Templates', template_data)
templates.set_visible_traces('Quasar')
#templates.subtract_continuum()
viewer = SimpleSpectrumViewer('Simple')
viewer.add_spectrum(spectrum)
viewer.add_spectrum(spectrum2)
#if showTemplates:
# viewer.add_spectrum(templates)
viewer.add_lines(lines)
viewer.show_grid(True)
viewer.show_legend(True)
js_data = viewer.build_chart().to_json()
return JsonResponse(json.loads(js_data), safe=False)
def test_ozdes_smooth(self, shared_datadir):
spectrum_file = shared_datadir / OZDES_TEST_FILENAME
formats = ssv.ssvloaders.whatformat(spectrum_file)
if len(formats) > 1:
ssv.ssvloaders.unregister(formats[0])
spectrum_data = utils.read_spectra_file(spectrum_file)
ssv.ssvloaders.restore_registered_loaders()
show_sky = True
show_templates = True
show_variance = True
show_processed_data = True
show_continuum_subtracted = False
show_scaled_spectra = True
scaling_max = 1.0
smoothing_choice = box_smooth
smoothing_width = 3
spectrum = SimpleSpectrum('Test SSV', spectrum_data)
spectrum.set_visible_traces('reduced')
flux_range = spectrum.flux_range('reduced')
spectrum.set_variance_visible('reduced', show_variance)
spectrum.set_trace_visible('sky', show_sky)
spectrum.set_transform_functions(
'reduced',
transform_function_array(
scaled=show_scaled_spectra,
scaling_max=scaling_max,
processed=show_processed_data,
subtract_continuum=show_continuum_subtracted,
smoothing_function=smoothing_choice,
smoothing_width=smoothing_width))
spectrum.set_transform_functions(
'sky',
transform_function_array(scaled=show_scaled_spectra,
scaling_max=scaling_max,
smoothing_function=smoothing_choice,
smoothing_width=smoothing_width))
best_fit_redshift = 0
best_fit_template = 'Quasar'
best_fit_template_index = 12
lines = SimpleSpectralLines()
lines.redshift_wavelength(best_fit_redshift)
templatedir = Path('./tests/data/marz/')
TEMPLATE_FILENAME = 'MarzTemplates.json'
template_data = utils.read_template_file(templatedir /
TEMPLATE_FILENAME)
templates = SimpleSpectrum('Templates', template_data)
template_choice = 'Quasar'
templates.set_visible_traces(template_choice)
templates.set_trace_visible(template_choice, show_templates)
templates.redshift_wavelength(best_fit_redshift, best_fit_template)
templates.set_transform_functions(
template_choice,
transform_function_array(
scaled=show_scaled_spectra,
scaling_max=scaling_max,
processed=show_processed_data,
subtract_continuum=show_continuum_subtracted,
smoothing_function=smoothing_choice,
smoothing_width=smoothing_width))
viewer = SimpleSpectrumViewer('Simple')
viewer.add_spectrum(spectrum)
viewer.add_spectrum(templates)
viewer.add_lines(lines)
viewer.show_grid(True)
viewer.show_legend(True)
viewer.set_chart_width_height(height=500)
viewer.build_chart()