Merge branch 'main' into version-3-0-alpha

Author: jchate6

docs/api/tom_dataproducts/data_processing.md

@@ -11,9 +11,9 @@ The ``DataProductUploadView`` calls ``run_data_processor`` upon saving the ``Dat
 instantiates the ``DATA_PROCESSOR_CLASS``, which can be specified in ``settings.py``. ``run_data_processor`` then
 processes the uploaded ``DataProduct`` based on the tag value, which can either be Photometry or Spectroscopy.
 
-In the case of spectra, the default behavior is that ``DataProduct`` is converted into a ``specutils.Spectrum1D`` from
+In the case of spectra, the default behavior is that ``DataProduct`` is converted into a ``specutils.Spectrum`` from
 either a CSV or a FITS file. The spectrum is multiplied by the flux constant of the facility it was taken at, or not
-multiplied. The ``Spectrum1D`` is then serialized into JSON for database via the ``SpectrumSerializer``.
+multiplied. The ``Spectrum`` is then serialized into JSON for database via the ``SpectrumSerializer``.
 
 For photometry, the default behavior is simply to read the CSV and convert it to JSON for database storage.
 

docs/managing_data/customizing_data_processing.rst

@@ -149,7 +149,7 @@ Just like the ``PhotometryProcessor``, this class inherits from
 ``DataProcessor`` and implements ``process_data()``. This is a
 requirement for a custom DataProcessor! This ``process_data()`` method
 handles two file types, unlike the previous example, each of which calls
-an internal method that returns a ``Spectrum1D`` object. Again, like the
+an internal method that returns a ``Spectrum`` object. Again, like the
 ``PhotometryProcessor``, a list of 2-tuples is created, with the first
 value being the timestamp, and the second being the JSON spectrum.
 

poetry.lock

@@ -57,7 +57,7 @@ dependencies = [
     "crispy-bootstrap4 >=2023.1,<2024.11",
     "django-extensions >=3.0.0,<4.0.0",
     "django-filter >=23,<25",
-    "django-tables2 <3",
+    "django-tables2 >=3.0,<4",
     "django-gravatar2 >=1.0.0,<2.0.0",
     "django-guardian >=2.0.0,<3.0.0",
     "django-htmx >=1.0.0,<2.0.0",
@@ -67,7 +67,7 @@ dependencies = [
     "plotly <6",
     "python-dateutil <3",
     "requests <3",
-    "specutils <2",
+    "specutils >=1.20.0,<3",
     "importlib-resources >=6.4.5,<6.5.0",
     "django-tasks (>=0.6.1,<0.7.0)",
     "alerce >=2.0,<3.0",

pyproject.toml

@@ -13,7 +13,7 @@
       <tr>
           {% for column in table.columns %}
               <th {{ column.attrs.th.as_html }}
-                  hx-get="{% querystring table.prefixed_order_by_field=column.order_by_alias.next %}"
+                  hx-get="{% querystring_replace table.prefixed_order_by_field=column.order_by_alias.next %}"
                   hx-trigger="click"
                   hx-target="div.table-container"
                   hx-swap="outerHTML"
@@ -30,7 +30,7 @@
 {# Pagination block overrides #}
 {% block pagination.previous %}
     <li class="previous page-item">
-        <div hx-get="{% querystring table.prefixed_page_field=table.page.previous_page_number %}"
+        <div hx-get="{% querystring_replace table.prefixed_page_field=table.page.previous_page_number %}"
              hx-trigger="click"
              hx-target="div.table-container"
              hx-swap="outerHTML"
@@ -45,7 +45,7 @@
     {% for p in table.page|table_page_range:table.paginator %}
         <li class="page-item{% if table.page.number == p %} active{% endif %}">
             <div class="page-link"
-                 {% if p != '...' %}hx-get="{% querystring table.prefixed_page_field=p %}"{% endif %}
+                 {% if p != '...' %}hx-get="{% querystring_replace table.prefixed_page_field=p %}"{% endif %}
                  hx-trigger="click"
                  hx-target="div.table-container"
                  hx-swap="outerHTML"
@@ -57,7 +57,7 @@
 {% endblock pagination.range %}
 {% block pagination.next %}
     <li class="next page-item">
-        <div hx-get="{% querystring table.prefixed_page_field=table.page.next_page_number %}"
+        <div hx-get="{% querystring_replace table.prefixed_page_field=table.page.next_page_number %}"
              hx-trigger="click"
              hx-target="div.table-container"
              hx-swap="outerHTML"

tom_common/templates/tom_common/bootstrap_htmx.html

@@ -1,6 +1,6 @@
 from astropy.units import photon, Quantity, spectral_density
 from django.db import migrations
-from specutils import Spectrum1D
+from specutils import Spectrum
 
 from tom_dataproducts.processors.data_serializers import SpectrumSerializer
 
@@ -11,9 +11,9 @@ def photon_spectrum_to_energy_spectrum(apps, schema_editor):
     of this code.
 
     def photon_spectrum_to_energy_spectrum(wavelength, photon_counts):
-        photon_spectrum = specutils.Spectrum1D(flux=photon_counts, spectral_axis=wavelength)
+        photon_spectrum = specutils.Spectrum(flux=photon_counts, spectral_axis=wavelength)
         energy_spectrum = photon_spectrum.flux * (photon_spectrum.energy / u.photon)
-        return specutils.Spectrum1D(spectral_axis=wavelength,
+        return specutils.Spectrum(spectral_axis=wavelength,
                                     flux=energy_spectrum.to('erg / (s cm2 AA)', u.spectral_density(wavelength)))
     """
     reduced_datum = apps.get_model('tom_dataproducts', 'ReducedDatum')
@@ -24,9 +24,9 @@ def photon_spectrum_to_energy_spectrum(wavelength, photon_counts):
         if all(k in row.value.keys() for k in ['photon_flux', 'photon_flux_units', 'wavelength', 'wavelength_units']):
             photon_counts = Quantity(value=row.value['photon_flux'], unit=row.value['photon_flux_units'])
             wavelength = Quantity(value=row.value['wavelength'], unit=row.value['wavelength_units'])
-            photon_spectrum = Spectrum1D(flux=photon_counts, spectral_axis=wavelength)
+            photon_spectrum = Spectrum(flux=photon_counts, spectral_axis=wavelength)
             energy_spectrum = photon_spectrum.flux * (photon_spectrum.energy / photon)
-            energy_spectrum_object = Spectrum1D(
+            energy_spectrum_object = Spectrum(
                                         spectral_axis=wavelength,
                                         flux=energy_spectrum.to('erg / (s cm2 AA)', spectral_density(wavelength)))
             row.value = spectrum_serializer.serialize(energy_spectrum_object)

tom_dataproducts/migrations/0010_manual_20210305_fix_spectroscopy.py

@@ -1,16 +1,16 @@
-from specutils import Spectrum1D
+from specutils import Spectrum
 from astropy.units import Quantity
 
 
 class SpectrumSerializer():
 
-    def serialize(self, spectrum: Spectrum1D) -> dict:
+    def serialize(self, spectrum: Spectrum) -> dict:
         """
-        Serializes a Spectrum1D in order to store in a ReducedDatum object. The serialization stores only what's
-        necessary to rebuild the Spectrum1D--namely, flux and wavelength, and their respective units.
+        Serializes a Spectrum in order to store in a ReducedDatum object. The serialization stores only what's
+        necessary to rebuild the Spectrum--namely, flux and wavelength, and their respective units.
 
-        :param spectrum: Spectrum1D to be serialized
-        :type spectrum: specutils.Spectrum1D
+        :param spectrum: Spectrum to be serialized
+        :type spectrum: specutils.Spectrum
 
         :returns: JSON representation of spectrum
         :rtype: dict
@@ -22,17 +22,17 @@ def serialize(self, spectrum: Spectrum1D) -> dict:
         serialized['wavelength_units'] = spectrum.wavelength.unit.to_string()
         return serialized
 
-    def deserialize(self, spectrum: dict) -> Spectrum1D:
+    def deserialize(self, spectrum: dict) -> Spectrum:
         """
-        Constructs a Spectrum1D from the spectrum value stored in a ReducedDatum
+        Constructs a Spectrum from the spectrum value stored in a ReducedDatum
 
-        :param spectrum: JSON representation used to construct the Spectrum1D
+        :param spectrum: JSON representation used to construct the Spectrum
         :type spectrum: dict
 
-        :returns: Spectrum1D representing the spectrum information
-        :rtype: specutil.Spectrum1D
+        :returns: Spectrum representing the spectrum information
+        :rtype: specutil.Spectrum
         """
         flux = Quantity(value=spectrum['flux'], unit=spectrum['flux_units'])
         wavelength = Quantity(value=spectrum['wavelength'], unit=spectrum['wavelength_units'])
-        spectrum = Spectrum1D(flux=flux, spectral_axis=wavelength)
+        spectrum = Spectrum(flux=flux, spectral_axis=wavelength)
         return spectrum

tom_dataproducts/processors/data_serializers.py

@@ -7,7 +7,7 @@
 from astropy.io import fits, ascii as astropy_ascii
 from astropy.time import Time
 from astropy.wcs import WCS
-from specutils import Spectrum1D
+from specutils import Spectrum
 
 from tom_dataproducts.data_processor import DataProcessor
 from tom_dataproducts.exceptions import InvalidFileFormatException
@@ -46,16 +46,16 @@ def process_data(self, data_product):
 
     def _process_spectrum_from_fits(self, data_product):
         """
-        Processes the data from a spectrum from a fits file into a Spectrum1D object, which can then be serialized and
+        Processes the data from a spectrum from a fits file into a Spectrum object, which can then be serialized and
         stored as a ReducedDatum for further processing or display. File is read using specutils as specified in the
         below documentation.
         # https://specutils.readthedocs.io/en/doc-testing/specutils/read_fits.html
 
-        :param data_product: Spectroscopic DataProduct which will be processed into a Spectrum1D
+        :param data_product: Spectroscopic DataProduct which will be processed into a Spectrum
         :type data_product: tom_dataproducts.models.DataProduct
 
-        :returns: Spectrum1D object containing the data from the DataProduct
-        :rtype: specutils.Spectrum1D
+        :returns: Spectrum object containing the data from the DataProduct
+        :rtype: specutils.Spectrum
 
         :returns: Datetime of observation, if it is in the header and the file is from a supported facility, current
             datetime otherwise
@@ -86,13 +86,13 @@ def _process_spectrum_from_fits(self, data_product):
         header['CUNIT1'] = 'Angstrom'
         wcs = WCS(header=header, naxis=1)
 
-        spectrum = Spectrum1D(flux=flux, wcs=wcs)
+        spectrum = Spectrum(flux=flux, wcs=wcs)
 
         return spectrum, Time(date_obs).to_datetime(), facility_name
 
     def _process_spectrum_from_plaintext(self, data_product):
         """
-        Processes the data from a spectrum from a plaintext file into a Spectrum1D object, which can then be serialized
+        Processes the data from a spectrum from a plaintext file into a Spectrum object, which can then be serialized
         and stored as a ReducedDatum for further processing or display. File is read using astropy as specified in
         the below documentation. The file is expected to be a multi-column delimited file, with headers for wavelength
         and flux. The file also requires comments containing, at minimum, 'DATE-OBS: [value]', where value is an
@@ -102,11 +102,11 @@ def _process_spectrum_from_plaintext(self, data_product):
 
         Parameters
         ----------
-        :param data_product: Spectroscopic DataProduct which will be processed into a Spectrum1D
+        :param data_product: Spectroscopic DataProduct which will be processed into a Spectrum
         :type data_product: tom_dataproducts.models.DataProduct
 
-        :returns: Spectrum1D object containing the data from the DataProduct
-        :rtype: specutils.Spectrum1D
+        :returns: Spectrum object containing the data from the DataProduct
+        :rtype: specutils.Spectrum
 
         :returns: Datetime of observation, if it is in the comments and the file is from a supported facility, current
             datetime otherwise
@@ -132,6 +132,6 @@ def _process_spectrum_from_plaintext(self, data_product):
 
         spectral_axis = np.array(data['wavelength']) * wavelength_units
         flux = np.array(data['flux']) * flux_constant
-        spectrum = Spectrum1D(flux=flux, spectral_axis=spectral_axis)
+        spectrum = Spectrum(flux=flux, spectral_axis=spectral_axis)
 
         return spectrum, Time(date_obs).to_datetime(), facility_name

tom_dataproducts/processors/spectroscopy_processor.py

@@ -17,7 +17,7 @@
 from django.utils import timezone, text
 from guardian.shortcuts import assign_perm
 import numpy as np
-from specutils import Spectrum1D
+from specutils import Spectrum
 from unittest.mock import patch
 
 from tom_dataproducts.exceptions import InvalidFileFormatException
@@ -417,7 +417,7 @@ def setUp(self):
     def test_serialize_spectrum(self):
         flux = np.arange(1, 200) * units.Jy
         wavelength = np.arange(1, 200) * units.Angstrom
-        spectrum = Spectrum1D(spectral_axis=wavelength, flux=flux)
+        spectrum = Spectrum(spectral_axis=wavelength, flux=flux)
         serialized = self.serializer.serialize(spectrum)
 
         self.assertTrue(isinstance(serialized, dict))
@@ -439,7 +439,7 @@ def test_deserialize_spectrum(self):
         }
         deserialized = self.serializer.deserialize(serialized_spectrum)
 
-        self.assertTrue(isinstance(deserialized, Spectrum1D))
+        self.assertTrue(isinstance(deserialized, Spectrum))
         self.assertEqual(deserialized.flux.mean().value, 1.5)
         self.assertEqual(deserialized.wavelength.mean().value, 1.5)
 
@@ -484,15 +484,15 @@ def test_process_spectrum_from_fits(self):
         with open('tom_dataproducts/tests/test_data/test_spectrum.fits', 'rb') as spectrum_file:
             self.data_product.data.save('spectrum.fits', spectrum_file)
             spectrum, _, _ = self.spectrum_data_processor._process_spectrum_from_fits(self.data_product)
-            self.assertTrue(isinstance(spectrum, Spectrum1D))
+            self.assertTrue(isinstance(spectrum, Spectrum))
             self.assertAlmostEqual(spectrum.flux.mean().value, 2.295068e-14, places=19)
             self.assertAlmostEqual(spectrum.wavelength.mean().value, 6600.478789, places=5)
 
     def test_process_spectrum_from_plaintext(self):
         with open('tom_dataproducts/tests/test_data/test_spectrum.csv', 'rb') as spectrum_file:
             self.data_product.data.save('spectrum.csv', spectrum_file)
             spectrum, _, _ = self.spectrum_data_processor._process_spectrum_from_plaintext(self.data_product)
-            self.assertTrue(isinstance(spectrum, Spectrum1D))
+            self.assertTrue(isinstance(spectrum, Spectrum))
             self.assertAlmostEqual(spectrum.flux.mean().value, 1.166619e-14, places=19)
             self.assertAlmostEqual(spectrum.wavelength.mean().value, 3250.744489, places=5)
 

tom_dataproducts/tests/tests.py

@@ -43,7 +43,7 @@
 VALID_OBSERVING_STATES = ['TRIGGERED', 'ON_HOLD']
 TERMINAL_OBSERVING_STATES = ['TRIGGERED', 'ON_HOLD']
 
-# Units of flux and wavelength for converting to Specutils Spectrum1D objects
+# Units of flux and wavelength for converting to Specutils Spectrum objects
 FLUX_CONSTANT = (1 * u.erg) / (u.cm ** 2 * u.second * u.angstrom)
 WAVELENGTH_UNITS = u.angstrom