def test_plugins():
# Make sure that glue plugins are correctly loaded, by checking that the
# WCS autolinker works.
from astropy.wcs import WCS
app = gj.jglue()
data1 = Data(label='test1')
data1.coords = WCS(naxis=2)
data1.coords.wcs.ctype = 'RA---TAN', 'DEC--TAN'
data1.coords.wcs.set()
data1['x'] = np.ones((2, 3))
data2 = Data(label='test1')
data2.coords = WCS(naxis=2)
data2.coords.wcs.ctype = 'GLON-CAR', 'GLAT-CAR'
data2.coords.wcs.set()
data2['y'] = np.ones((2, 3))
app.add_data(data1=data1)
app.add_data(data2=data2)
links = find_possible_links(app.data_collection)
assert 'Astronomy WCS' in links
def __init__(self):
self._glue_app = gj.jglue()
self._history = []
self._3d_data = {}
self._2d_data = {}
self._1d_data = {}
self._3d_processing = {}
self.add_3d_processing("Median Collapse over Wavelenths", np.nanmedian,
'a', (('axis', 0), ))
self.add_3d_processing("Mean Collapse over Wavelenths", np.nanmean,
'a', (('axis', 0), ))
self.add_3d_processing("Median Collapse over Space", np.nanmedian, 'a',
(('axis', (1, 2)), ))
self.add_3d_processing("Mean Collapse over Space", np.nanmean, 'a',
(('axis', (1, 2)), ))
self._2d_processing = {}
self._1d_processing = {}
self.add_1d_processing("Median Smoothing", scipy.signal.medfilt,
'volume', (('kernel_size', 3), ))
self.add_1d_processing("Hanning Smoothing", np.convolve, 'a',
(('mode', 'valid'), ('w', np.hanning(3))))
self.add_1d_processing("Hamming Smoothing", np.convolve, 'a',
(('mode', 'valid'), ('w', np.hamming(3))))
self.add_1d_processing("Bartlett Smoothing", np.convolve, 'a',
(('mode', 'valid'), ('w', np.bartlett(3))))
self.add_1d_processing("Blackman Smoothing", np.convolve, 'a',
(('mode', 'valid'), ('w', np.blackman(3))))
def __init__(self, spec, rest_lines):
spec_data = gcore.Data(wl=spec.wavelength,
flux=spec.flux,
unc=spec.uncertainty.array)
self.app = app = gj.jglue(spec_data)
self.regions = {} # populated with spectral regions by frecord
line_selection = ipywidgets.Dropdown(options=rest_lines.keys(),
description='Line:')
record_button = ipywidgets.Button(description='Record line')
result_text = ipywidgets.Text(disabled=True, value='No line recorded')
record_box = ipywidgets.HBox(
[line_selection, record_button, result_text])
z_text = ipywidgets.FloatText(description='z guess:', value=0)
jump_button = ipywidgets.Button(description='Jump to line')
line_width_text = ipywidgets.FloatText(description='width(Ang):',
value=100)
jump_box = ipywidgets.HBox([z_text, jump_button, line_width_text])
def frecord(widget):
wls_selected = spec_data['wl'][
spec_data.subsets[0].to_index_list()]
reg = specutils.SpectralRegion(
np.min(wls_selected) * spec.wavelength.unit,
np.max(wls_selected) * spec.wavelength.unit)
result_text.value = 'Recorded {}: {} to {}'.format(
line_selection.value, reg.lower, reg.upper)
self.regions[line_selection.value] = reg
z_text.value = specutils.analysis.centroid(
spec, reg) / rest_lines[line_selection.value] - 1
record_button.on_click(frecord)
self.plot_to_jump = None
def fjump(widget):
if self.plot_to_jump is None:
return
rest_linecen = rest_lines[line_selection.value]
linecen = rest_linecen * (1 + z_text.value)
self.plot_to_jump.state.x_min = linecen.value + line_width_text.value / 2
self.plot_to_jump.state.x_max = linecen.value - line_width_text.value / 2
jump_button.on_click(fjump)
self.action_vbox = ipywidgets.VBox([record_box, jump_box])
def app(dataxyz, datax, dataxz, data_volume, data_image):
app = gj.jglue(dataxyz=dataxyz, dataxz=dataxz, datax=datax)
app.add_link(dataxyz, 'x', dataxz, 'x')
app.add_link(dataxyz, 'y', dataxz, 'z')
app.add_link(dataxyz, 'x', datax, 'x')
app.add_data(data_volume=data_volume)
app.add_data(data_image=data_image)
app.add_link(data_image, 'Pixel Axis 0 [y]', dataxyz, 'y')
app.add_link(data_image, 'Pixel Axis 1 [x]', dataxyz, 'x')
app.add_link(data_volume, 'Pixel Axis 0 [z]', dataxyz, 'z')
app.add_link(data_volume, 'Pixel Axis 1 [y]', dataxyz, 'y')
app.add_link(data_volume, 'Pixel Axis 2 [x]', dataxyz, 'x')
return app
def test_double_load_data(tmpdir):
# Regression test for a bug that caused a crash when adding two datasets
# with the same shape.
filename = tmpdir.join('data1.csv').strpath
with open(filename, 'w') as f:
f.write('a,b\n1,2\n3,4\n5.6\n')
app = gj.jglue()
app.load_data(filename)
app.load_data(filename)
def test_no_data(dataxz, dataxyz):
app = gj.jglue()
with pytest.raises(ValueError, match='No dataset is present'):
app.scatter2d()
app.add_data(dataxz)
app.scatter2d()
app.add_data(dataxyz)
with pytest.raises(ValueError, match='There is more than one dataset'):
app.scatter2d()
def app(dataxyz, datax, dataxz, data_volume, data_image):
link1 = ['dataxyz.x'], ['dataxz.x'], lambda x: x
link2 = ['dataxyz.y'], ['dataxz.z'], lambda y: y + 1, lambda z: z - 1
link3 = ['dataxyz.x'], ['datax.x'], lambda x: x
app = gj.jglue(dataxyz=dataxyz,
dataxz=dataxz,
datax=datax,
links=[link1, link2, link3])
app.add_data(data_volume=data_volume)
app.add_data(data_image=data_image)
app.add_link(data_image, 'Pixel Axis 0 [y]', dataxyz, 'y')
app.add_link(data_image, 'Pixel Axis 1 [x]', dataxyz, 'x')
app.add_link(data_volume, 'Pixel Axis 0 [z]', dataxyz, 'z')
app.add_link(data_volume, 'Pixel Axis 1 [y]', dataxyz, 'y')
app.add_link(data_volume, 'Pixel Axis 2 [x]', dataxyz, 'x')
return app
def app(dataxyz, dataxz, data_volume, data_image):
link1 = ['dataxyz.x'], ['dataxz.x'], lambda x: x
link2 = ['dataxyz.y'], ['dataxz.z'], lambda y: y + 1, lambda z: z - 1
app = gj.jglue(dataxyz=dataxyz, dataxz=dataxz, links=[link1, link2])
app.add_data(data_volume=data_volume)
app.add_data(data_image=data_image)
link1 = ComponentLink([data_image.id['Pixel Axis 0 [y]']], dataxyz.id['y'])
link2 = ComponentLink([data_image.id['Pixel Axis 1 [x]']], dataxyz.id['x'])
app.data_collection.add_link([link1, link2])
link1 = ComponentLink([data_volume.id['Pixel Axis 0 [z]']],
dataxyz.id['z'])
link2 = ComponentLink([data_volume.id['Pixel Axis 1 [y]']],
dataxyz.id['y'])
link3 = ComponentLink([data_volume.id['Pixel Axis 2 [x]']],
dataxyz.id['x'])
app.data_collection.add_link([link1, link2, link3])
return app
def __init__(self, vizapp):
self._app = gj.jglue()
