Test metadata loading in all the viz

jdaviz/configs/cubeviz/plugins/tests/test_parsers.py

@@ -5,6 +5,8 @@
 from astropy.wcs import WCS
 from specutils import Spectrum1D
 
+from jdaviz.utils import PRIHDR_KEY
+
 
 @pytest.fixture
 def image_hdu_obj():
@@ -58,6 +60,12 @@ def test_fits_image_hdu_parse_from_file(tmpdir, image_hdu_obj, cubeviz_helper):
 
     # This tests the same data as test_fits_image_hdu_parse above.
 
+    cubeviz_helper.app.data_collection[0].meta['EXTNAME'] == 'FLUX'
+    cubeviz_helper.app.data_collection[1].meta['EXTNAME'] == 'MASK'
+    cubeviz_helper.app.data_collection[2].meta['EXTNAME'] == 'ERR'
+    for i in range(3):
+        assert cubeviz_helper.app.data_collection[i].meta[PRIHDR_KEY]['BITPIX'] == 8
+
     flux_viewer = cubeviz_helper.app.get_viewer('flux-viewer')
     flux_viewer.on_mouse_or_key_event({'event': 'mousemove', 'domain': {'x': 0, 'y': 0}})
     assert flux_viewer.label_mouseover.pixel == 'x=00.0 y=00.0'
@@ -114,6 +122,7 @@ def test_spectrum1d_parse(spectrum1d, cubeviz_helper):
 
     assert len(cubeviz_helper.app.data_collection) == 1
     assert cubeviz_helper.app.data_collection[0].label.endswith('[FLUX]')
+    assert cubeviz_helper.app.data_collection[0].meta['uncertainty_type'] == 'std'
 
     # Coordinate display is only for spatial image, which is missing here.
     flux_viewer = cubeviz_helper.app.get_viewer('flux-viewer')

jdaviz/configs/mosviz/plugins/parsers.py

@@ -221,8 +221,13 @@ def mos_spec1d_parser(app, data_obj, data_labels=None):
 
     with app.data_collection.delay_link_manager_update():
 
-        for i in range(len(data_obj)):
-            app.add_data(data_obj[i], data_labels[i], notify_done=False)
+        for cur_data, cur_label in zip(data_obj, data_labels):
+            # Make metadata layout conform with other viz.
+            if 'header' in cur_data.meta:
+                cur_data.meta.update(cur_data.meta['header'])
+                del cur_data.meta['header']
+
+            app.add_data(cur_data, cur_label, notify_done=False)
 
         _add_to_table(app, data_labels, '1D Spectra')
 

jdaviz/configs/mosviz/tests/test_data_loading.py

@@ -9,13 +9,17 @@
 import pytest
 from specutils import Spectrum1D
 
+from jdaviz.utils import PRIHDR_KEY
+
 
 def test_load_spectrum1d(mosviz_helper, spectrum1d):
     label = "Test 1D Spectrum"
     mosviz_helper.load_1d_spectra(spectrum1d, data_labels=label)
 
     assert len(mosviz_helper.app.data_collection) == 2
-    assert mosviz_helper.app.data_collection[0].label == label
+    dc_0 = mosviz_helper.app.data_collection[0]
+    assert dc_0.label == label
+    assert dc_0.meta['uncertainty_type'] == 'std'
 
     table = mosviz_helper.app.get_viewer('table-viewer')
     table.widget_table.vue_on_row_clicked(0)
@@ -24,7 +28,7 @@ def test_load_spectrum1d(mosviz_helper, spectrum1d):
 
     assert isinstance(data[label], Spectrum1D)
 
-    with pytest.raises(TypeError):
+    with pytest.raises(AttributeError):
         mosviz_helper.load_1d_spectra([1, 2, 3])
 
 
@@ -34,7 +38,10 @@ def test_load_image(mosviz_helper, mos_image):
     mosviz_helper.load_images(mos_image, data_labels=label)
 
     assert len(mosviz_helper.app.data_collection) == 2
-    assert mosviz_helper.app.data_collection[0].label == f"{label} 0"
+    dc_0 = mosviz_helper.app.data_collection[0]
+    assert dc_0.label == f"{label} 0"
+    assert PRIHDR_KEY not in dc_0.meta
+    assert dc_0.meta['RADESYS'] == 'ICRS'
 
     table = mosviz_helper.app.get_viewer('table-viewer')
     table.widget_table.vue_on_row_clicked(0)
@@ -51,7 +58,9 @@ def test_load_spectrum_collection(mosviz_helper, spectrum_collection):
     mosviz_helper.load_1d_spectra(spectrum_collection, data_labels=labels)
 
     assert len(mosviz_helper.app.data_collection) == 6
-    assert mosviz_helper.app.data_collection[0].label == labels[0]
+    dc_0 = mosviz_helper.app.data_collection[0]
+    assert dc_0.label == labels[0]
+    assert dc_0.meta['uncertainty_type'] == 'std'
 
     table = mosviz_helper.app.get_viewer('table-viewer')
     table.widget_table.vue_on_row_clicked(0)
@@ -68,7 +77,9 @@ def test_load_list_of_spectrum1d(mosviz_helper, spectrum1d):
     mosviz_helper.load_1d_spectra(spectra, data_labels=labels)
 
     assert len(mosviz_helper.app.data_collection) == 4
-    assert mosviz_helper.app.data_collection[0].label == labels[0]
+    dc_0 = mosviz_helper.app.data_collection[0]
+    assert dc_0.label == labels[0]
+    assert dc_0.meta['uncertainty_type'] == 'std'
 
     table = mosviz_helper.app.get_viewer('table-viewer')
     table.widget_table.vue_on_row_clicked(0)
@@ -85,7 +96,9 @@ def test_load_mos_spectrum2d(mosviz_helper, mos_spectrum2d):
     mosviz_helper.load_2d_spectra(mos_spectrum2d, data_labels=label)
 
     assert len(mosviz_helper.app.data_collection) == 2
-    assert mosviz_helper.app.data_collection[0].label == label
+    dc_0 = mosviz_helper.app.data_collection[0]
+    assert dc_0.label == label
+    assert dc_0.meta['INSTRUME'] == 'nirspec'
 
     table = mosviz_helper.app.get_viewer('table-viewer')
     table.widget_table.vue_on_row_clicked(0)
@@ -140,7 +153,7 @@ def test_load_single_image_multi_spec(mosviz_helper, mos_image, spectrum1d, mos_
 
 @pytest.mark.filterwarnings('ignore')
 @pytest.mark.remote_data
-def test_nirpsec_loader(mosviz_helper, tmpdir):
+def test_nirspec_loader(mosviz_helper, tmpdir):
     '''
     Tests loading our default MosvizExample notebook data
     '''
@@ -157,12 +170,30 @@ def test_nirpsec_loader(mosviz_helper, tmpdir):
     mosviz_helper.load_data(directory=data_dir, instrument='nirspec')
 
     assert len(mosviz_helper.app.data_collection) == 16
-    assert "MOS Table" in mosviz_helper.app.data_collection
-    assert "Image 4" in mosviz_helper.app.data_collection
-    assert "1D Spectrum 4" in mosviz_helper.app.data_collection
-    assert "2D Spectrum 4" in mosviz_helper.app.data_collection
+
+    dc_0 = mosviz_helper.app.data_collection[0]
+    assert dc_0.label == "MOS Table"
+    assert len(dc_0.meta) == 0
+
+    dc_5 = mosviz_helper.app.data_collection[5]
+    assert dc_5.label == "Image 4"
+    assert PRIHDR_KEY not in dc_5.meta
+    assert dc_5.meta['WCSAXES'] == 2
+
+    dc_10 = mosviz_helper.app.data_collection[10]
+    assert dc_10.label == "1D Spectrum 4"
+    assert PRIHDR_KEY not in dc_10.meta
+    assert 'header' not in dc_10.meta
+    assert dc_10.meta['TARGNAME'] == 'FOO'
+
+    dc_15 = mosviz_helper.app.data_collection[15]
+    assert dc_15.label == "2D Spectrum 4"
+    assert PRIHDR_KEY not in dc_15.meta
+    assert 'header' not in dc_15.meta
+    assert dc_15.meta['SOURCEID'] == 2315
 
 
+# This is another version of test_niriss_parser in test_parsers.py
 @pytest.mark.remote_data
 def test_niriss_loader(mosviz_helper, tmpdir):
 
@@ -183,7 +214,7 @@ def test_niriss_loader(mosviz_helper, tmpdir):
 
 
 @pytest.mark.remote_data
-def test_nirpsec_fallback(mosviz_helper, tmpdir):
+def test_nirspec_fallback(mosviz_helper, tmpdir):
     '''
     When no instrument is provided, mosviz.load_data is expected to fallback to the nirspec loader.
     Naturally, the nirspec dataset should then work without any instrument keyword

jdaviz/configs/mosviz/tests/test_parsers.py

@@ -1,10 +1,13 @@
-import pytest
 from zipfile import ZipFile
 import pathlib
 
+import pytest
 from astropy.utils.data import download_file
 
+from jdaviz.utils import PRIHDR_KEY
 
+
+# This is another version of test_niriss_loader in test_data_loading.py
 @pytest.mark.remote_data
 def test_niriss_parser(mosviz_helper, tmpdir):
 
@@ -20,5 +23,23 @@ def test_niriss_parser(mosviz_helper, tmpdir):
     mosviz_helper.load_niriss_data(data_dir)
 
     assert len(mosviz_helper.app.data_collection) == 80
-    assert mosviz_helper.app.data_collection[0].label == "Image canucs F150W"
-    assert mosviz_helper.app.data_collection[-1].label == "MOS Table"
+
+    dc_0 = mosviz_helper.app.data_collection[0]
+    assert dc_0.label == "Image canucs F150W"
+    assert PRIHDR_KEY not in dc_0.meta
+    assert dc_0.meta['bunit_data'] == 'MJy/sr'  # ASDF metadata
+
+    dc_1 = mosviz_helper.app.data_collection[1]
+    assert dc_1.label == 'F150W Source 1 spec2d C'
+    assert PRIHDR_KEY not in dc_1.meta
+    assert dc_1.meta['SOURCEID'] == 1
+
+    dc_40 = mosviz_helper.app.data_collection[40]
+    assert dc_40.label == 'F150W Source 1 spec1d C'
+    assert PRIHDR_KEY not in dc_40.meta
+    assert 'header' not in dc_40.meta
+    assert dc_40.meta['FILTER'] == 'GR150C'
+
+    dc_tab = mosviz_helper.app.data_collection[-1]
+    assert dc_tab.label == "MOS Table"
+    assert len(dc_tab.meta) == 0

jdaviz/configs/specviz/tests/test_helper.py

@@ -26,7 +26,9 @@ def setup_class(self, specviz_helper, spectrum1d):
 
     def test_load_spectrum1d(self):
         assert len(self.spec_app.app.data_collection) == 1
-        assert self.spec_app.app.data_collection[0].label == self.label
+        dc_0 = self.spec_app.app.data_collection[0]
+        assert dc_0.label == self.label
+        assert dc_0.meta['uncertainty_type'] == 'std'
 
         data = self.spec_app.app.get_data_from_viewer('spectrum-viewer')
 
@@ -248,9 +250,12 @@ def test_load_spectrum_list_directory(tmpdir, specviz_helper):
     with pytest.warns(UserWarning, match='SRCTYPE is missing or UNKNOWN in JWST x1d loader'):
         specviz_helper.load_spectrum(data_path)
     assert len(specviz_helper.app.data_collection) == 3
-    for element in specviz_helper.app.data_collection:
-        assert element.data.main_components[0] in ['flux']
-        assert element.data.main_components[1] in ['uncertainty']
+    for data in specviz_helper.app.data_collection:
+        assert data.main_components[:2] == ['flux', 'uncertainty']
+
+    dc_0 = specviz_helper.app.data_collection[0]
+    assert 'header' not in dc_0.meta
+    assert dc_0.meta['SPORDER'] == 1
 
 
 def test_plot_uncertainties(specviz_helper, spectrum1d):

jdaviz/configs/specviz2d/tests/test_parsers.py

@@ -0,0 +1,33 @@
+import pytest
+from asdf.asdf import AsdfWarning
+from astropy.utils.data import download_file
+
+from jdaviz.utils import PRIHDR_KEY
+
+
+@pytest.mark.remote_data
+def test_2d_parser(specviz2d_helper):
+    fn = download_file('https://stsci.box.com/shared/static/exnkul627fcuhy5akf2gswytud5tazmw.fits', cache=True)  # noqa
+
+    with pytest.warns(AsdfWarning, match='jwextension'):
+        specviz2d_helper.load_data(spectrum_2d=fn)
+    assert len(specviz2d_helper.app.data_collection) == 2
+
+    dc_0 = specviz2d_helper.app.data_collection[0]
+    assert dc_0.label == 'Spectrum 2D'
+    assert PRIHDR_KEY not in dc_0.meta
+    assert 'header' not in dc_0.meta
+    assert dc_0.meta['DETECTOR'] == 'MIRIMAGE'
+
+    dc_1 = specviz2d_helper.app.data_collection[1]
+    assert dc_1.label == 'Spectrum 1D'
+    assert 'header' not in dc_1.meta
+    assert dc_1.meta['NAXIS'] == 2
+
+
+def test_1d_parser(specviz2d_helper, spectrum1d):
+    specviz2d_helper.load_data(spectrum_1d=spectrum1d)
+    assert len(specviz2d_helper.app.data_collection) == 1
+    dc_0 = specviz2d_helper.app.data_collection[0]
+    assert dc_0.label == 'Spectrum 1D'
+    assert dc_0.meta['uncertainty_type'] == 'std'

jdaviz/conftest.py

@@ -99,9 +99,7 @@ def spectrum1d_cube():
                 "CRPIX1": 0, "CRPIX2": 0, "CRPIX3": 0}
     w = WCS(wcs_dict)
 
-    spec = Spectrum1D(flux=flux, wcs=w)
-
-    return spec
+    return Spectrum1D(flux=flux, wcs=w)
 
 
 @pytest.fixture
@@ -116,6 +114,7 @@ def mos_spectrum1d():
     Unless linking the two is required, try to use the global spectrum1d fixture.
     '''
     spec_axis = np.linspace(6000, 8000, 1024) * u.AA
+    np.random.seed(42)
     flux = (np.random.randn(len(spec_axis.value)) +
             10*np.exp(-0.001*(spec_axis.value-6563)**2) +
             spec_axis.value/500) * u.Jy
@@ -132,78 +131,36 @@ def mos_spectrum2d():
     TODO: This should be reformed to match the global Spectrum1D defined above so that we may
     deprecate the mos-specific spectrum1d.
     '''
-    header = """
-WCSAXES =                    2 / Number of coordinate axes
-CRPIX1  =                  0.0 / Pixel coordinate of reference point
-CRPIX2  =               1024.5 / Pixel coordinate of reference point
-CDELT1  =                1E-06 / [m] Coordinate increment at reference point
-CDELT2  =  2.9256727777778E-05 / [deg] Coordinate increment at reference point
-CUNIT1  = 'm'                  / Units of coordinate increment and value
-CUNIT2  = 'deg'                / Units of coordinate increment and value
-CTYPE1  = 'WAVE'               / Vacuum wavelength (linear)
-CTYPE2  = 'OFFSET'             / Spatial offset
-CRVAL1  =                  0.0 / [m] Coordinate value at reference point
-CRVAL2  =                  5.0 / [deg] Coordinate value at reference point
-RADESYS = 'ICRS'               / Equatorial coordinate system
-SPECSYS = 'BARYCENT'           / Reference frame of spectral coordinates
-"""
-    new_hdr = {}
-
-    for line in header.split('\n'):
-        try:
-            key, value = line.split('=')
-            key = key.strip()
-            value, _ = value.split('/')
-            value = value.strip()
-            value = value.strip("'")
-        except ValueError:
-            continue
-
-        new_hdr[key] = value
-
-    wcs = WCS(new_hdr)
+    header = {
+        'WCSAXES': 2,
+        'CRPIX1': 0.0, 'CRPIX2': 1024.5,
+        'CDELT1': 1E-06, 'CDELT2': 2.9256727777778E-05,
+        'CUNIT1': 'm', 'CUNIT2': 'deg',
+        'CTYPE1': 'WAVE', 'CTYPE2': 'OFFSET',
+        'CRVAL1': 0.0, 'CRVAL2': 5.0,
+        'RADESYS': 'ICRS', 'SPECSYS': 'BARYCENT'}
+    wcs = WCS(header)
+    np.random.seed(42)
     data = np.random.sample((1024, 15)) * u.one
-    return Spectrum1D(data, wcs=wcs)
+    return Spectrum1D(data, wcs=wcs, meta=header)
 
 
 @pytest.fixture
 def mos_image():
-    header = """
-WCSAXES =                    2 / Number of coordinate axes
-CRPIX1  =                937.0 / Pixel coordinate of reference point
-CRPIX2  =                696.0 / Pixel coordinate of reference point
-CDELT1  = -1.5182221158397E-05 / [deg] Coordinate increment at reference point
-CDELT2  =  1.5182221158397E-05 / [deg] Coordinate increment at reference point
-CUNIT1  = 'deg'                / Units of coordinate increment and value
-CUNIT2  = 'deg'                / Units of coordinate increment and value
-CTYPE1  = 'RA---TAN'           / Right ascension, gnomonic projection
-CTYPE2  = 'DEC--TAN'           / Declination, gnomonic projection
-CRVAL1  =      5.0155198140981 / [deg] Coordinate value at reference point
-CRVAL2  =       5.002450989248 / [deg] Coordinate value at reference point
-LONPOLE =                180.0 / [deg] Native longitude of celestial pole
-LATPOLE =       5.002450989248 / [deg] Native latitude of celestial pole
-DATEREF = '1858-11-17'         / ISO-8601 fiducial time
-MJDREFI =                  0.0 / [d] MJD of fiducial time, integer part
-MJDREFF =                  0.0 / [d] MJD of fiducial time, fractional part
-RADESYS = 'ICRS'               / Equatorial coordinate system
-"""
-    new_hdr = {}
-
-    for line in header.split('\n'):
-        try:
-            key, value = line.split('=')
-            key = key.strip()
-            value, _ = value.split('/')
-            value = value.strip()
-            value = value.strip("'")
-        except ValueError:
-            continue
-
-        new_hdr[key] = value
-
-    wcs = WCS(new_hdr)
+    header = {
+        'WCSAXES': 2,
+        'CRPIX1': 937.0, 'CRPIX2': 696.0,
+        'CDELT1': -1.5182221158397e-05, 'CDELT2': 1.5182221158397e-05,
+        'CUNIT1': 'deg', 'CUNIT2': 'deg',
+        'CTYPE1': 'RA---TAN', 'CTYPE2': 'DEC--TAN',
+        'CRVAL1': 5.0155198140981, 'CRVAL2': 5.002450989248,
+        'LONPOLE': 180.0, 'LATPOLE': 5.002450989248,
+        'DATEREF': '1858-11-17', 'MJDREFI': 0.0, 'MJDREFF': 0.0,
+        'RADESYS': 'ICRS'}
+    wcs = WCS(header)
+    np.random.seed(42)
     data = np.random.sample((55, 55))
-    return CCDData(data, wcs=wcs, unit='Jy')
+    return CCDData(data, wcs=wcs, unit='Jy', meta=header)
 
 
 try: