def test_parse_nddata_with_one_only(self, imviz_helper, ndd, attributes):
parse_data(imviz_helper.app,
ndd,
data_label='some_data',
show_in_viewer=False)
for i, attrib in enumerate(attributes):
data = imviz_helper.app.data_collection[i]
comp = data.get_component(attrib)
assert data.label == f'some_data[{attrib}]'
assert data.shape == (2, 2)
assert comp.data.shape == (2, 2)
assert len(imviz_helper.app.data_collection) == 2
def test_parse_jwst_niriss_grism(self, imviz_app):
"""No valid image GWCS for Imviz, will fall back to FITS loading without WCS."""
filename = download_file(self.jwst_asdf_url_2, cache=True)
parse_data(imviz_app.app, filename, show_in_viewer=False)
data = imviz_app.app.data_collection[0]
comp = data.get_component('SCI,1')
assert data.label == 'contents[SCI,1]' # download_file returns cache loc
assert data.shape == (2048, 2048)
assert data.coords is None
assert comp.units == 'DN/s'
assert comp.data.shape == (2048, 2048)
def test_parse_rgba(self, imviz_helper, tmp_path, format):
if format == 'png': # Cross-test PNG with RGBA
a = np.zeros((10, 10, 4), dtype='uint8')
else: # Cross-test JPG with RGB only
a = np.zeros((10, 10, 3), dtype='uint8')
filename = str(tmp_path / f'myimage.{format}')
imsave(filename, a)
parse_data(imviz_helper.app, filename, show_in_viewer=False)
data = imviz_helper.app.data_collection[0]
assert data.label == 'myimage'
assert data.shape == (10, 10)
def test_parse_numpy_array(self, imviz_helper):
with pytest.raises(ValueError,
match='Imviz cannot load this array with ndim=1'):
parse_data(imviz_helper.app, np.zeros(2), show_in_viewer=False)
parse_data(imviz_helper.app,
np.zeros((2, 2)),
data_label='some_array',
show_in_viewer=False)
data = imviz_helper.app.data_collection[0]
comp = data.get_component('DATA')
assert data.label == 'some_array'
assert data.shape == (2, 2)
assert comp.data.shape == (2, 2)
def test_parse_nddata_simple(self, imviz_helper):
with pytest.raises(ValueError,
match='Imviz cannot load this NDData with ndim=1'):
parse_data(imviz_helper.app,
NDData([1, 2, 3, 4]),
show_in_viewer=False)
ndd = NDData([[1, 2], [3, 4]])
parse_data(imviz_helper.app,
ndd,
data_label='some_data',
show_in_viewer=False)
data = imviz_helper.app.data_collection[0]
comp = data.get_component('DATA')
assert data.label == 'some_data[DATA]'
assert data.shape == (2, 2)
assert comp.data.shape == (2, 2)
assert len(imviz_helper.app.data_collection) == 1
def test_parse_nddata_with_everything(self, imviz_app):
ndd = NDData([[1, 2], [3, 4]],
mask=[[True, False], [False, False]],
uncertainty=StdDevUncertainty([[0.1, 0.2], [0.3, 0.4]]),
unit=u.MJy / u.sr,
wcs=WCS(naxis=2))
parse_data(imviz_app.app,
ndd,
data_label='some_data',
show_in_viewer=False)
for i, attrib in enumerate(['DATA', 'MASK', 'UNCERTAINTY']):
data = imviz_app.app.data_collection[i]
comp = data.get_component(attrib)
assert data.label == f'some_data[{attrib}]'
assert data.shape == (2, 2)
assert isinstance(data.coords, WCS)
assert comp.data.shape == (2, 2)
if attrib == 'MASK':
assert comp.units == ''
else:
assert comp.units == 'MJy / sr'
assert len(imviz_app.app.data_collection) == 3
def test_invalid_file_obj(self, imviz_helper, some_obj):
with pytest.raises(NotImplementedError,
match='Imviz does not support'):
parse_data(imviz_helper.app, some_obj, show_in_viewer=False)
def test_hdulist_no_image(self, imviz_helper):
hdulist = fits.HDUList([fits.PrimaryHDU()])
with pytest.raises(ValueError, match='does not have any FITS image'):
parse_data(imviz_helper.app, hdulist, show_in_viewer=False)
def test_parse_hst_drz(self, imviz_helper):
url = 'https://mast.stsci.edu/api/v0.1/Download/file?bundle_name=MAST_2021-04-21T1828.sh&uri=mast:HST/product/jclj01010_drz.fits' # noqa: E501
filename = download_file(url, cache=True)
# Default behavior: Load first image
parse_data(imviz_helper.app, filename, show_in_viewer=True)
data = imviz_helper.app.data_collection[0]
comp = data.get_component('SCI,1')
assert data.label == 'contents[SCI,1]' # download_file returns cache loc
assert data.shape == (4300, 4219)
assert_allclose(data.meta['PHOTFLAM'], 7.8711728E-20)
assert isinstance(data.coords, WCS)
assert comp.units == 'electron/s'
assert comp.data.shape == (4300, 4219)
# --- Since download is expensive, we attach FITS WCS-specific tests here. ---
# Test simple aperture photometry plugin.
imviz_helper._apply_interactive_region('bqplot:ellipse', (1465, 2541),
(1512, 2611)) # Galaxy
phot_plugin = SimpleAperturePhotometry(app=imviz_helper.app)
phot_plugin._on_viewer_data_changed()
phot_plugin.vue_data_selected('contents[SCI,1]')
phot_plugin.vue_subset_selected('Subset 1')
phot_plugin.background_value = 0.0014 # Median on whole array
assert_allclose(phot_plugin.pixel_area,
0.0025) # Not used but still auto-populated
phot_plugin.vue_do_aper_phot()
tbl = imviz_helper.get_aperture_photometry_results()
assert_quantity_allclose(tbl[0]['xcenter'], 1488.5 * u.pix)
assert_quantity_allclose(tbl[0]['ycenter'], 2576 * u.pix)
sky = tbl[0]['sky_center']
assert_allclose(sky.ra.deg, 3.6840882015888323, rtol=1e-5)
assert_allclose(sky.dec.deg, 10.802065746813046, rtol=1e-5)
data_unit = u.electron / u.s
assert_quantity_allclose(tbl[0]['background'], 0.0014 * data_unit)
assert_quantity_allclose(tbl[0]['npix'], 645.98998939 * u.pix)
assert_quantity_allclose(tbl[0]['aperture_sum'], 78.352207 * data_unit)
assert_array_equal(tbl[0]['pixarea_tot'], None)
assert_array_equal(tbl[0]['aperture_sum_counts'], None)
assert_array_equal(tbl[0]['aperture_sum_counts_err'], None)
assert_array_equal(tbl[0]['counts_fac'], None)
assert_array_equal(tbl[0]['aperture_sum_mag'], None)
assert_array_equal(tbl[0]['flux_scaling'], None)
assert_quantity_allclose(tbl[0]['mean'],
0.120531 * data_unit,
rtol=1e-5)
assert_quantity_allclose(tbl[0]['stddev'],
0.174565 * data_unit,
rtol=1e-5)
assert_quantity_allclose(tbl[0]['median'],
0.068294 * data_unit,
rtol=1e-5)
assert_quantity_allclose(tbl[0]['min'],
-0.004208 * data_unit,
rtol=1e-3)
assert_quantity_allclose(tbl[0]['max'],
1.625122 * data_unit,
rtol=1e-5)
# Request specific extension (name only), use given label
parse_data(imviz_helper.app,
filename,
ext='CTX',
data_label='jclj01010_drz',
show_in_viewer=False)
data = imviz_helper.app.data_collection[1]
comp = data.get_component('CTX,1')
assert data.label == 'jclj01010_drz[CTX,1]'
assert data.meta['EXTNAME'] == 'CTX'
assert comp.units == '' # BUNIT is not set
# Request specific extension (name + ver), use given label
parse_data(imviz_helper.app,
filename,
ext=('WHT', 1),
data_label='jclj01010_drz',
show_in_viewer=False)
data = imviz_helper.app.data_collection[2]
comp = data.get_component('WHT,1')
assert data.label == 'jclj01010_drz[WHT,1]'
assert data.meta['EXTNAME'] == 'WHT'
assert comp.units == '' # BUNIT is not set
# Pass in file obj directly
with fits.open(filename) as pf:
# Default behavior: Load first image
parse_data(imviz_helper.app, pf, show_in_viewer=False)
data = imviz_helper.app.data_collection[3]
assert data.label.startswith(
'imviz_data|') and data.label.endswith('[SCI,1]')
assert_allclose(data.meta['PHOTFLAM'], 7.8711728E-20)
assert 'SCI,1' in data.components
# Request specific extension (name only), use given label
parse_data(imviz_helper.app, pf, ext='CTX', show_in_viewer=False)
data = imviz_helper.app.data_collection[4]
assert data.label.startswith(
'imviz_data|') and data.label.endswith('[CTX,1]')
assert data.meta['EXTNAME'] == 'CTX'
assert 'CTX,1' in data.components
# Pass in HDU directly, use given label
parse_data(imviz_helper.app,
pf[2],
data_label='foo',
show_in_viewer=False)
data = imviz_helper.app.data_collection[5]
assert data.label == 'foo[WHT,1]'
assert data.meta['EXTNAME'] == 'WHT'
assert 'WHT,1' in data.components
# Load all extensions
imviz_helper.app.data_collection.clear()
parse_data(imviz_helper.app,
filename,
ext='*',
show_in_viewer=False)
data = imviz_helper.app.data_collection
assert len(data.labels) == 3
assert data.labels[0].endswith('[SCI,1]')
assert data.labels[1].endswith('[WHT,1]')
assert data.labels[2].endswith('[CTX,1]')
# Cannot load non-image extension
with pytest.raises(ValueError, match='Imviz cannot load this HDU'):
parse_data(imviz_helper.app,
filename,
ext='HDRTAB',
show_in_viewer=False)
# Invalid FITS extension
with pytest.raises(KeyError, match='not found'):
parse_data(imviz_helper.app,
filename,
ext='DOES_NOT_EXIST',
data_label='foo',
show_in_viewer=False)
def test_parse_jwst_nircam_level2(self, imviz_helper):
filename = download_file(self.jwst_asdf_url_1, cache=True)
# Default behavior: Science image
parse_data(imviz_helper.app, filename, show_in_viewer=True)
data = imviz_helper.app.data_collection[0]
comp = data.get_component('DATA')
assert data.label == 'contents[DATA]' # download_file returns cache loc
assert data.shape == (2048, 2048)
assert isinstance(data.coords, GWCS)
assert comp.units == 'MJy/sr'
assert comp.data.shape == (2048, 2048)
# --- Since download is expensive, we attach GWCS-specific tests here. ---
# Ensure interactive region supports GWCS. Also see test_regions.py
imviz_helper._apply_interactive_region('bqplot:circle', (965, 1122),
(976.9, 1110.1)) # Star
subsets = imviz_helper.get_interactive_regions()
assert list(subsets.keys()) == ['Subset 1'], subsets
assert isinstance(subsets['Subset 1'], CirclePixelRegion)
# Test simple aperture photometry plugin.
phot_plugin = SimpleAperturePhotometry(app=imviz_helper.app)
phot_plugin._on_viewer_data_changed()
phot_plugin.vue_data_selected('contents[DATA]')
phot_plugin.vue_subset_selected('Subset 1')
phot_plugin.background_value = 0.22 # Median on whole array
# NOTE: jwst.datamodels.find_fits_keyword("PHOTMJSR")
phot_plugin.counts_factor = (
data.meta['photometry']['conversion_megajanskys'] /
data.meta['exposure']['exposure_time'])
assert_allclose(phot_plugin.counts_factor, 0.0036385915646798953)
phot_plugin.flux_scaling = 1 # Simple mag, no zeropoint
phot_plugin.vue_do_aper_phot()
tbl = imviz_helper.get_aperture_photometry_results()
assert_quantity_allclose(tbl[0]['xcenter'], 970.95 * u.pix)
assert_quantity_allclose(tbl[0]['ycenter'], 1116.05 * u.pix)
sky = tbl[0]['sky_center']
assert_allclose(sky.ra.deg, 80.48419863)
assert_allclose(sky.dec.deg, -69.49460838)
data_unit = u.MJy / u.sr
assert_quantity_allclose(tbl[0]['background'], 0.22 * data_unit)
assert_quantity_allclose(tbl[0]['npix'], 111.22023392 * u.pix)
assert_quantity_allclose(tbl[0]['aperture_sum'],
4.93689560e-09 * u.MJy)
assert_quantity_allclose(tbl[0]['pixarea_tot'],
1.0384377922763469e-11 * u.sr)
assert_quantity_allclose(tbl[0]['aperture_sum_counts'],
130659.2466386 * u.count)
assert_quantity_allclose(tbl[0]['aperture_sum_counts_err'],
361.46818205562715 * u.count)
assert_quantity_allclose(tbl[0]['counts_fac'],
0.0036385915646798953 * (data_unit / u.ct))
assert_quantity_allclose(tbl[0]['aperture_sum_mag'],
-6.692683645358997 * u.mag)
assert_quantity_allclose(tbl[0]['flux_scaling'], 1 * data_unit)
assert_quantity_allclose(tbl[0]['mean'], 4.34584047 * data_unit)
assert_quantity_allclose(tbl[0]['stddev'], 15.61862628 * data_unit)
assert_quantity_allclose(tbl[0]['median'], 0.43709442 * data_unit)
assert_quantity_allclose(tbl[0]['min'],
-0.00485992 * data_unit,
rtol=1e-5)
assert_quantity_allclose(tbl[0]['max'],
138.87786865 * data_unit,
rtol=1e-5)
# --- Back to parser testing below. ---
# Request specific extension (name + ver, but ver is not used), use given label
parse_data(imviz_helper.app,
filename,
ext=('DQ', 42),
data_label='jw01072001001_01101_00001_nrcb1_cal',
show_in_viewer=False)
data = imviz_helper.app.data_collection[1]
comp = data.get_component('DQ')
assert data.label == 'jw01072001001_01101_00001_nrcb1_cal[DQ]'
assert data.meta['aperture']['name'] == 'NRCB5_FULL'
assert comp.units == ''
# Pass in HDUList directly + ext (name only), use given label
with fits.open(filename) as pf:
parse_data(imviz_helper.app,
pf,
ext='SCI',
data_label='jw01072001001_01101_00001_nrcb1_cal',
show_in_viewer=False)
data = imviz_helper.app.data_collection[2]
comp = data.get_component('DATA') # SCI = DATA
assert data.label == 'jw01072001001_01101_00001_nrcb1_cal[DATA]'
assert isinstance(data.coords, GWCS)
assert comp.units == 'MJy/sr'
# Test duplicate label functionality
imviz_helper.app.data_collection.clear()
parse_data(imviz_helper.app,
pf,
ext='SCI',
show_in_viewer=False,
data_label='TEST')
data = imviz_helper.app.data_collection[0]
assert data.label.endswith('[DATA]')
parse_data(imviz_helper.app,
pf,
ext='SCI',
show_in_viewer=False,
data_label='TEST')
data = imviz_helper.app.data_collection[1]
assert data.label.endswith('[DATA]_2')
# Load all extensions
imviz_helper.app.data_collection.clear()
parse_data(imviz_helper.app, pf, ext='*', show_in_viewer=False)
data = imviz_helper.app.data_collection
assert len(data.labels) == 7
assert data.labels[0].endswith('[DATA]')
assert data.labels[1].endswith('[ERR]')
assert data.labels[2].endswith('[DQ]')
assert data.labels[3].endswith('[AREA]')
assert data.labels[4].endswith('[VAR_POISSON]')
assert data.labels[5].endswith('[VAR_RNOISE]')
assert data.labels[6].endswith('[VAR_FLAT]')
# Invalid ASDF attribute (extension)
with pytest.raises(KeyError, match='does_not_exist'):
parse_data(imviz_helper.app,
filename,
ext='DOES_NOT_EXIST',
data_label='foo',
show_in_viewer=False)
def test_parse_hst_drz(self, imviz_app):
url = 'https://mast.stsci.edu/api/v0.1/Download/file?bundle_name=MAST_2021-04-21T1828.sh&uri=mast:HST/product/jclj01010_drz.fits' # noqa: E501
filename = download_file(url, cache=True)
# Default behavior: Load first image
parse_data(imviz_app.app, filename, show_in_viewer=False)
data = imviz_app.app.data_collection[0]
comp = data.get_component('SCI,1')
assert data.label == 'contents[SCI,1]' # download_file returns cache loc
assert data.shape == (4300, 4219)
assert isinstance(data.coords, WCS)
assert comp.units == '' # "ELECTRONS/S" is not valid
assert comp.data.shape == (4300, 4219)
# Request specific extension (name only), use given label
parse_data(imviz_app.app,
filename,
ext='CTX',
data_label='jclj01010_drz',
show_in_viewer=False)
data = imviz_app.app.data_collection[1]
comp = data.get_component('CTX,1')
assert data.label == 'jclj01010_drz[CTX,1]'
assert comp.units == '' # BUNIT is not set
# Request specific extension (name + ver), use given label
parse_data(imviz_app.app,
filename,
ext=('WHT', 1),
data_label='jclj01010_drz',
show_in_viewer=False)
data = imviz_app.app.data_collection[2]
comp = data.get_component('WHT,1')
assert data.label == 'jclj01010_drz[WHT,1]'
assert comp.units == '' # BUNIT is not set
# Pass in file obj directly
with fits.open(filename) as pf:
# Default behavior: Load first image
parse_data(imviz_app.app, pf, show_in_viewer=False)
data = imviz_app.app.data_collection[3]
assert data.label.startswith(
'imviz_data|') and data.label.endswith('[SCI,1]')
assert 'SCI,1' in data.components
# Request specific extension (name only), use given label
parse_data(imviz_app.app, pf, ext='CTX', show_in_viewer=False)
data = imviz_app.app.data_collection[4]
assert data.label.startswith(
'imviz_data|') and data.label.endswith('[CTX,1]')
assert 'CTX,1' in data.components
# Pass in HDU directly, use given label
parse_data(imviz_app.app,
pf[2],
data_label='foo',
show_in_viewer=False)
data = imviz_app.app.data_collection[5]
assert data.label == 'foo[WHT,1]'
assert 'WHT,1' in data.components
# Load all extensions
imviz_app.app.data_collection.clear()
parse_data(imviz_app.app, filename, ext='*', show_in_viewer=False)
data = imviz_app.app.data_collection
assert len(data.labels) == 3
assert data.labels[0].endswith('[SCI,1]')
assert data.labels[1].endswith('[WHT,1]')
assert data.labels[2].endswith('[CTX,1]')
# Cannot load non-image extension
with pytest.raises(ValueError, match='Imviz cannot load this HDU'):
parse_data(imviz_app.app,
filename,
ext='HDRTAB',
show_in_viewer=False)
# Invalid FITS extension
with pytest.raises(KeyError, match='not found'):
parse_data(imviz_app.app,
filename,
ext='DOES_NOT_EXIST',
data_label='foo',
show_in_viewer=False)
def test_parse_jwst_nircam_level2(self, imviz_app):
from regions import CirclePixelRegion
filename = download_file(self.jwst_asdf_url_1, cache=True)
# Default behavior: Science image
parse_data(imviz_app.app, filename, show_in_viewer=True)
data = imviz_app.app.data_collection[0]
comp = data.get_component('DATA')
assert data.label == 'contents[DATA]' # download_file returns cache loc
assert data.shape == (2048, 2048)
assert isinstance(data.coords, GWCS)
assert comp.units == 'MJy/sr'
assert comp.data.shape == (2048, 2048)
# --- Since download is expensive, we attach GWCS-specific tests here. ---
# Ensure interactive region supports GWCS. Also see test_regions.py
imviz_app._apply_interactive_region('bqplot:circle', (0, 0),
(1000, 1000))
subsets = imviz_app.get_interactive_regions()
assert list(subsets.keys()) == ['Subset 1'], subsets
assert isinstance(subsets['Subset 1'], CirclePixelRegion)
# --- Back to parser testing below. ---
# Request specific extension (name + ver, but ver is not used), use given label
parse_data(imviz_app.app,
filename,
ext=('DQ', 42),
data_label='jw01072001001_01101_00001_nrcb1_cal',
show_in_viewer=False)
data = imviz_app.app.data_collection[1]
comp = data.get_component('DQ')
assert data.label == 'jw01072001001_01101_00001_nrcb1_cal[DQ]'
assert comp.units == ''
# Pass in HDUList directly + ext (name only), use given label
with fits.open(filename) as pf:
parse_data(imviz_app.app,
pf,
ext='SCI',
data_label='jw01072001001_01101_00001_nrcb1_cal',
show_in_viewer=False)
data = imviz_app.app.data_collection[2]
comp = data.get_component('DATA') # SCI = DATA
assert data.label == 'jw01072001001_01101_00001_nrcb1_cal[DATA]'
assert isinstance(data.coords, GWCS)
assert comp.units == 'MJy/sr'
# Test duplicate label functionality
imviz_app.app.data_collection.clear()
parse_data(imviz_app.app,
pf,
ext='SCI',
show_in_viewer=False,
data_label='TEST')
data = imviz_app.app.data_collection[0]
assert data.label.endswith('[DATA]')
parse_data(imviz_app.app,
pf,
ext='SCI',
show_in_viewer=False,
data_label='TEST')
data = imviz_app.app.data_collection[1]
assert data.label.endswith('[DATA]_2')
# Load all extensions
imviz_app.app.data_collection.clear()
parse_data(imviz_app.app, pf, ext='*', show_in_viewer=False)
data = imviz_app.app.data_collection
assert len(data.labels) == 7
assert data.labels[0].endswith('[DATA]')
assert data.labels[1].endswith('[ERR]')
assert data.labels[2].endswith('[DQ]')
assert data.labels[3].endswith('[AREA]')
assert data.labels[4].endswith('[VAR_POISSON]')
assert data.labels[5].endswith('[VAR_RNOISE]')
assert data.labels[6].endswith('[VAR_FLAT]')
# Invalid ASDF attribute (extension)
with pytest.raises(KeyError, match='does_not_exist'):
parse_data(imviz_app.app,
filename,
ext='DOES_NOT_EXIST',
data_label='foo',
show_in_viewer=False)