def test_session_cube_back_compat(self, protocol):
filename = os.path.join(DATA, 'image_cube_v{0}.glu'.format(protocol))
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
dc = ga.session.data_collection
assert len(dc) == 1
assert dc[0].label == 'array'
viewer1 = ga.viewers[0][0]
assert len(viewer1.state.layers) == 1
assert viewer1.state.x_att_world is dc[0].id['World 2']
assert viewer1.state.y_att_world is dc[0].id['World 1']
assert viewer1.state.slices == [2, 0, 0, 1]
ga.close()
def test_load_coordinate_link_helpers_013():
# This loads a session file made with Glue v0.13. In this session, we have
# two tables, and we use all the celestial link functions that were present
# in Glue v0.13. We now check that the paths are patched when loading the
# session (since the functions have been moved to a deprecated location)
with open(os.path.join(DATA, 'session_coordinate_links_013.glu'), 'r') as f:
content = f.read()
state = GlueUnSerializer.loads(content)
ga = state.object('__main__')
data1, data2 = ga.session.data_collection
print(data1)
print(data2)
# Check that the links works
data1[data2.id['x']]
data1[data2.id['y']]
data2[data1.id['x']]
data2[data1.id['y']]
ga.close()
def test_session_back_compat(self, protocol):
filename = os.path.join(DATA, 'scatter_v{0}.glu'.format(protocol))
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
dc = ga.session.data_collection
assert len(dc) == 1
assert dc[0].label == 'basic'
viewer1 = ga.viewers[0][0]
assert len(viewer1.state.layers) == 3
assert viewer1.state.x_att is dc[0].id['a']
assert viewer1.state.y_att is dc[0].id['b']
assert_allclose(viewer1.state.x_min, -1.04)
assert_allclose(viewer1.state.x_max, 1.04)
assert_allclose(viewer1.state.y_min, 1.98)
assert_allclose(viewer1.state.y_max, 3.02)
assert not viewer1.state.x_log
assert not viewer1.state.y_log
assert viewer1.state.layers[0].visible
assert viewer1.state.layers[1].visible
assert viewer1.state.layers[2].visible
viewer2 = ga.viewers[0][1]
assert len(viewer2.state.layers) == 3
assert viewer2.state.x_att is dc[0].id['a']
assert viewer2.state.y_att is dc[0].id['c']
assert_allclose(viewer2.state.x_min, 9.5e-6)
assert_allclose(viewer2.state.x_max, 1.05)
assert_allclose(viewer2.state.y_min, 0.38)
assert_allclose(viewer2.state.y_max, 5.25)
assert viewer2.state.x_log
assert viewer2.state.y_log
assert viewer2.state.layers[0].visible
assert not viewer2.state.layers[1].visible
assert viewer2.state.layers[2].visible
viewer3 = ga.viewers[0][2]
assert len(viewer3.state.layers) == 3
assert viewer3.state.x_att is dc[0].id['b']
assert viewer3.state.y_att is dc[0].id['a']
assert_allclose(viewer3.state.x_min, 0)
assert_allclose(viewer3.state.x_max, 5)
assert_allclose(viewer3.state.y_min, -5)
assert_allclose(viewer3.state.y_max, 5)
assert not viewer3.state.x_log
assert not viewer3.state.y_log
assert viewer3.state.layers[0].visible
assert viewer3.state.layers[1].visible
assert not viewer3.state.layers[2].visible
ga.close()
def test_session_line_back_compat(self):
# Backward-compatibility for v0.11 files in which the line and scatter
# plots were defined as separate styles.
filename = os.path.join(DATA, 'scatter_and_line_v1.glu')
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
dc = ga.session.data_collection
assert len(dc) == 1
assert dc[0].label == 'table'
viewer1 = ga.viewers[0][0]
assert len(viewer1.state.layers) == 1
assert viewer1.state.x_att is dc[0].id['a']
assert viewer1.state.y_att is dc[0].id['b']
assert viewer1.state.layers[0].markers_visible
assert not viewer1.state.layers[0].line_visible
viewer1 = ga.viewers[0][1]
assert len(viewer1.state.layers) == 1
assert viewer1.state.x_att is dc[0].id['a']
assert viewer1.state.y_att is dc[0].id['b']
assert not viewer1.state.layers[0].markers_visible
assert viewer1.state.layers[0].line_visible
ga.close()
def restore_session(path):
"""
Reload a previously-saved session
Parameters
----------
path : str
Path to the file to load
Returns
-------
app : :class:`Application`
The loaded application
"""
from glue.core.state import GlueUnSerializer
# In case relative paths are needed in the session file, we do the
# loading while setting the current directory to the directory
# in which the session file is so that relative paths are interpreted
# as relative to the session file.
start_dir = os.path.abspath('.')
session_dir = os.path.dirname(path) or '.'
session_file = os.path.basename(path)
try:
os.chdir(session_dir)
with open(session_file) as infile:
state = GlueUnSerializer.load(infile)
return state.object('__main__')
finally:
os.chdir(start_dir)
def test_session_back_compat(self, protocol):
filename = os.path.join(DATA, 'dendro_v{0}.glu'.format(protocol))
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
dc = ga.session.data_collection
assert len(dc) == 1
assert dc[0].label == 'data'
viewer1 = ga.viewers[0][0]
assert len(viewer1.state.layers) == 2
assert viewer1.state.parent_att is dc[0].id['parent']
assert viewer1.state.height_att is dc[0].id['height']
assert viewer1.state.order_att is dc[0].id['height']
layer_state = viewer1.state.layers[0]
assert layer_state.visible
assert layer_state.layer is dc[0]
layer_state = viewer1.state.layers[1]
assert layer_state.visible
assert layer_state.layer is dc[0].subsets[0]
ga.close()
def test_load_hdf5_grids_04():
# This loads a session file made with Glue v0.4. In this session, we have
# loaded two gridded datasets from an HDF5 datafile: the first one loaded
# via the auto loader and the other via the FITS/HDF5 loader.
with open(os.path.join(DATA, 'simple_hdf5_grid.glu'), 'r') as f:
template = f.read()
content = template.replace('{DATA_PATH}', (DATA + os.sep).replace('\\', '\\\\'))
state = GlueUnSerializer.loads(content)
ga = state.object('__main__')
dc = ga.session.data_collection
assert len(dc) == 2
assert dc[0].label == 'single_grid_auto'
assert dc[1].label == 'single_grid'
np.testing.assert_equal(dc[0]['/array1'], 1)
np.testing.assert_equal(dc[0]['/array1'].shape, (2, 3, 4))
ga.close()
def test_session_categorical(self, tmpdir):
def visible_xaxis_labels(ax):
# Due to a bug in Matplotlib the labels returned outside the field
# of view may be incorrect: https://github.com/matplotlib/matplotlib/issues/9397
pos = ax.xaxis.get_ticklocs()
labels = [tick.get_text() for tick in ax.xaxis.get_ticklabels()]
xmin, xmax = ax.get_xlim()
return [labels[i] for i in range(len(pos)) if pos[i] >= xmin and pos[i] <= xmax]
# Regression test for a bug that caused a restored scatter viewer
# with a categorical component to not show the categorical labels
# as tick labels.
filename = tmpdir.join('test_session_categorical.glu').strpath
self.viewer.add_data(self.data)
self.viewer.state.x_att = self.data.id['z']
assert visible_xaxis_labels(self.viewer.axes) == ['a', 'b', 'c']
self.session.application.save_session(filename)
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
dc = ga.session.data_collection
viewer = ga.viewers[0][0]
assert viewer.state.x_att is dc[0].id['z']
assert visible_xaxis_labels(self.viewer.axes) == ['a', 'b', 'c']
def test_load_link_helpers_04():
# This loads a session file made with Glue v0.4. In this session, we have
# two tables, and we use all the celestial link functions that were present
# in Glue v0.4. We now check that the paths are patched when loading the
# session (since the functions have been moved to a deprecated location)
with open(os.path.join(DATA, 'session_links.glu'), 'r') as f:
content = f.read()
state = GlueUnSerializer.loads(content)
ga = state.object('__main__')
def test_datetime64_support(self, tmpdir):
self.data.add_component(np.array([100, 200, 300, 400], dtype='M8[D]'), 't1')
self.viewer.add_data(self.data)
self.viewer.state.x_att = self.data.id['t1']
wait_for_layers(self.viewer)
# Matplotlib deals with dates by converting them to the number of days
# since 01-01-0001, so we can check that the limits are correctly
# converted (and not 100 to 400)
assert self.viewer.axes.get_xlim() == (719263.0, 719563.0)
# Apply an ROI selection in plotting coordinates
roi = XRangeROI(719313, 719513)
self.viewer.apply_roi(roi)
wait_for_layers(self.viewer)
# Check that the two middle elements are selected
assert_equal(self.data.subsets[0].to_mask(), [0, 1, 1, 0])
# Make sure that the Qt labels look ok
options = self.viewer.options_widget().ui
assert options.valuetext_x_min.text() == '1970-04-11'
assert options.valuetext_x_max.text() == '1971-02-05'
# Make sure that we can set the xmin/xmax to a string date
assert_equal(self.viewer.state.x_min, np.datetime64('1970-04-11', 'D'))
options.valuetext_x_min.setText('1970-04-14')
options.valuetext_x_min.editingFinished.emit()
assert self.viewer.axes.get_xlim() == (719266.0, 719563.0)
assert_equal(self.viewer.state.x_min, np.datetime64('1970-04-14', 'D'))
# Make sure that everything works fine after saving/reloading
filename = tmpdir.join('test_datetime64.glu').strpath
self.session.application.save_session(filename)
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
viewer = ga.viewers[0][0]
options = viewer.options_widget().ui
wait_for_layers(viewer)
assert_equal(self.viewer.state.x_min, np.datetime64('1970-04-14', 'D'))
assert options.valuetext_x_min.text() == '1970-04-14'
assert options.valuetext_x_max.text() == '1971-02-05'
def test_load_pixel_components_07():
# This loads a session file made with Glue v0.7. In 0.7 and before,
# PixelComponentID did not exist, so we need to make sure that when loading
# in such files, we transform the appropriate ComponentIDs to
# PixelComponentIDs.
with open(os.path.join(DATA, 'glue_v0.7_pixel_roi_selection.glu'), 'r') as f:
content = f.read()
state = GlueUnSerializer.loads(content)
ga = state.object('__main__')
assert isinstance(ga.data_collection[0].pixel_component_ids[0], PixelComponentID)
assert isinstance(ga.data_collection[0].pixel_component_ids[1], PixelComponentID)
def test_load_viewers_04():
# FIXME - for some reason this test with PySide2 causes a leftover reference
# to GlueApplication and appears to be due to x_log being True in the
# scatter plot. I suspect maybe there is some kind of circular reference
# This loads a session file made with Glue v0.4. In this session, we have
# three viewers: one scatter viewer, one image viewer, and one histogram
# viewer.
with open(os.path.join(DATA, 'simple_viewers.glu'), 'r') as f:
content = f.read()
state = GlueUnSerializer.loads(content)
ga = state.object('__main__')
assert len(ga.viewers[0]) == 3
labels = sorted([x.LABEL for x in ga.viewers[0]])
assert labels == ['1D Histogram', '2D Image', '2D Scatter']
viewers = {}
for x in ga.viewers[0]:
viewers[x.LABEL] = x
h = viewers['1D Histogram']
assert h.viewer_size == (1235, 531)
assert h.position == (0, 535)
assert h.state.x_att.label == 'b'
i = viewers['2D Image']
assert i.viewer_size == (562, 513)
assert i.position == (672, 0)
assert i.state.layers[0].attribute.label == "image"
s = viewers['2D Scatter']
assert s.viewer_size == (670, 512)
assert s.position == (0, 0)
assert s.state.x_att.label == 'b'
assert s.state.y_att.label == 'a'
assert s.state.x_log
assert not s.state.y_log
ga.close()
def test_load_log(protocol):
# Prior to Glue v0.13, components were added to the data as: first
# non-coordinate component, then coordinate components, then remaining non-
# coordinate components. In Glue v0.13, this changed to be coordinate
# components then non-coordinate components. The LoadLog functionality
# relies on an absolute component index, so we need to be careful - if the
# session file was created prior to Glue v0.13, we need to load the
# components in the log using the old order. The load_log_1.glu file was
# made with Glue v0.12.2, while the load_log_2.glu file was made with
# Glue v0.13.
with open(os.path.join(DATA, 'load_log_{0}.glu'.format(protocol)), 'r') as f:
template = f.read()
content = template.replace('{DATA_PATH}', (DATA + os.sep).replace('\\', '\\\\'))
state = GlueUnSerializer.loads(content)
ga = state.object('__main__')
dc = ga.session.data_collection
assert len(dc) == 1
data = dc[0]
assert data.label == 'simple'
np.testing.assert_equal(data['Pixel Axis 0 [x]'], [0, 1, 2])
np.testing.assert_equal(data['World 0'], [0, 1, 2])
np.testing.assert_equal(data['a'], [1, 3, 5])
np.testing.assert_equal(data['b'], [2, 2, 3])
if protocol == 0:
assert data.components == [data.id['a'], data.id['Pixel Axis 0 [x]'], data.id['World 0'], data.id['b']]
else:
assert data.components == [data.id['Pixel Axis 0 [x]'], data.id['World 0'], data.id['a'], data.id['b']]
assert type(data.get_component('Pixel Axis 0 [x]')) == CoordinateComponent
assert type(data.get_component('World 0')) == CoordinateComponent
assert type(data.get_component('a')) == Component
assert type(data.get_component('b')) == Component
ga.close()
def restore_session(path):
"""
Reload a previously-saved session
Parameters
----------
path : str
Path to the file to load
Returns
-------
app : :class:`Application`
The loaded application
"""
from glue.core.state import GlueUnSerializer
with open(path) as infile:
state = GlueUnSerializer.load(infile)
return state.object('__main__')
def test_load_viewers_04():
# This loads a session file made with Glue v0.4. In this session, we have
# three viewers: one scatter viewer, one image viewer, and one histogram
# viewer.
with open(os.path.join(DATA, 'simple_viewers.glu'), 'r') as f:
content = f.read()
state = GlueUnSerializer.loads(content)
ga = state.object('__main__')
assert len(ga.viewers[0]) == 3
labels = sorted([x.LABEL for x in ga.viewers[0]])
assert labels == ['1D Histogram', '2D Image Viewer', '2D Scatter Plot']
viewers = {}
for x in ga.viewers[0]:
viewers[x.LABEL] = x
h = viewers['1D Histogram']
assert h.viewer_size == (1235, 531)
assert h.position == (0, 535)
assert h.component.label == 'b'
i = viewers['2D Image Viewer']
assert i.viewer_size == (562, 513)
assert i.position == (672, 0)
assert i.attribute.label == "image"
s = viewers['2D Scatter Plot']
assert s.viewer_size == (670, 512)
assert s.position == (0, 0)
assert s.xatt.label == 'b'
assert s.yatt.label == 'a'
assert s.xlog
assert not s.ylog
assert not s.xflip
assert s.yflip
def test_load_simple_tables_04():
# This loads a session file made with Glue v0.4. In this session, we have
# loaded four tables. The first two are from the same file, but one loaded
# via the auto loader and the other via the Astropy FITS table loader. The
# second two were loaded similarly to the first two, but the file contains
# two HDUs this time. However, in Glue v0.4, only the first HDU was read so
# we shouldn't have access to columns c and d in ``double_tables.fits``.
with open(os.path.join(DATA, 'simple_tables.glu'), 'r') as f:
template = f.read()
content = template.replace('{DATA_PATH}',
(DATA + os.sep).replace('\\', '\\\\'))
state = GlueUnSerializer.loads(content)
ga = state.object('__main__')
dc = ga.session.data_collection
# All tables should actually be the same because the FITS reader back at
# 0.4 only read in the first HDU so the new reader is back-compatible
# since it preserves HDU order.
assert len(dc) == 4
assert dc[0].label == 'single_table_auto'
assert dc[1].label == 'single_table'
assert dc[2].label == 'double_tables_auto'
assert dc[3].label == 'double_tables'
np.testing.assert_equal(dc[0]['a'], [1, 2, 3])
np.testing.assert_equal(dc[0]['b'], [4, 5, 6])
np.testing.assert_equal(dc[0]['a'], dc[1]['a'])
np.testing.assert_equal(dc[0]['b'], dc[1]['b'])
np.testing.assert_equal(dc[0]['a'], dc[2]['a'])
np.testing.assert_equal(dc[0]['b'], dc[2]['b'])
np.testing.assert_equal(dc[0]['a'], dc[3]['a'])
np.testing.assert_equal(dc[0]['b'], dc[3]['b'])
ga.close()
def test_load_viewers_04():
# This loads a session file made with Glue v0.4. In this session, we have
# three viewers: one scatter viewer, one image viewer, and one histogram
# viewer.
with open(os.path.join(DATA, 'simple_viewers.glu'), 'r') as f:
content = f.read()
state = GlueUnSerializer.loads(content)
ga = state.object('__main__')
assert len(ga.viewers[0]) == 3
labels = sorted([x.LABEL for x in ga.viewers[0]])
assert labels == ['1D Histogram', '2D Image Viewer', '2D Scatter Plot']
viewers = {}
for x in ga.viewers[0]:
viewers[x.LABEL] = x
h = viewers['1D Histogram']
assert h.viewer_size == (1235, 531)
assert h.position == (0, 535)
assert h.component.label == 'b'
i = viewers['2D Image Viewer']
assert i.viewer_size == (562, 513)
assert i.position == (672, 0)
assert i.attribute.label == "image"
s = viewers['2D Scatter Plot']
assert s.viewer_size == (670, 512)
assert s.position == (0, 0)
assert s.xatt.label == 'b'
assert s.yatt.label == 'a'
assert s.xlog
assert not s.ylog
assert not s.xflip
assert s.yflip
def test_session_categorical(self, tmpdir):
def visible_xaxis_labels(ax):
# Due to a bug in Matplotlib the labels returned outside the field
# of view may be incorrect: https://github.com/matplotlib/matplotlib/issues/9397
pos = ax.xaxis.get_ticklocs()
labels = [tick.get_text() for tick in ax.xaxis.get_ticklabels()]
xmin, xmax = ax.get_xlim()
return [
labels[i] for i in range(len(pos))
if pos[i] >= xmin and pos[i] <= xmax
]
# Regression test for a bug that caused a restored scatter viewer
# with a categorical component to not show the categorical labels
# as tick labels.
filename = tmpdir.join('test_session_categorical.glu').strpath
self.viewer.add_data(self.data)
self.viewer.state.x_att = self.data.id['z']
process_events()
assert visible_xaxis_labels(self.viewer.axes) == ['a', 'b', 'c']
self.session.application.save_session(filename)
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
dc = ga.session.data_collection
viewer = ga.viewers[0][0]
assert viewer.state.x_att is dc[0].id['z']
assert visible_xaxis_labels(self.viewer.axes) == ['a', 'b', 'c']
ga.close()
def test_load_pixel_components_07():
# This loads a session file made with Glue v0.7. In 0.7 and before,
# PixelComponentID did not exist, so we need to make sure that when loading
# in such files, we transform the appropriate ComponentIDs to
# PixelComponentIDs.
with open(os.path.join(DATA, 'glue_v0.7_pixel_roi_selection.glu'),
'r') as f:
content = f.read()
state = GlueUnSerializer.loads(content)
ga = state.object('__main__')
assert isinstance(ga.data_collection[0].pixel_component_ids[0],
PixelComponentID)
assert isinstance(ga.data_collection[0].pixel_component_ids[1],
PixelComponentID)
ga.close()
def test_load_simple_tables_04():
# This loads a session file made with Glue v0.4. In this session, we have
# loaded four tables. The first two are from the same file, but one loaded
# via the auto loader and the other via the Astropy FITS table loader. The
# second two were loaded similarly to the first two, but the file contains
# two HDUs this time. However, in Glue v0.4, only the first HDU was read so
# we shouldn't have access to columns c and d in ``double_tables.fits``.
with open(os.path.join(DATA, 'simple_tables.glu'), 'r') as f:
template = f.read()
content = template.replace('{DATA_PATH}', (DATA + os.sep).replace('\\', '\\\\'))
state = GlueUnSerializer.loads(content)
ga = state.object('__main__')
dc = ga.session.data_collection
# All tables should actually be the same because the FITS reader back at
# 0.4 only read in the first HDU so the new reader is back-compatible
# since it preserves HDU order.
assert len(dc) == 4
assert dc[0].label == 'single_table_auto'
assert dc[1].label == 'single_table'
assert dc[2].label == 'double_tables_auto'
assert dc[3].label == 'double_tables'
np.testing.assert_equal(dc[0]['a'], [1, 2, 3])
np.testing.assert_equal(dc[0]['b'], [4, 5, 6])
np.testing.assert_equal(dc[0]['a'], dc[1]['a'])
np.testing.assert_equal(dc[0]['b'], dc[1]['b'])
np.testing.assert_equal(dc[0]['a'], dc[2]['a'])
np.testing.assert_equal(dc[0]['b'], dc[2]['b'])
np.testing.assert_equal(dc[0]['a'], dc[3]['a'])
np.testing.assert_equal(dc[0]['b'], dc[3]['b'])
ga.close()
def test_table_widget_010():
from glue.viewers.table.qt.tests.test_data_viewer import check_values_and_color
# This loads a session file made with Glue v0.10 that includes a table
# viewer. This is to make sure that loading table viewers from old files
# will always be backward-compatible.
with open(os.path.join(DATA, 'glue_v0.10_table.glu'), 'r') as f:
state = GlueUnSerializer.load(f)
ga = state.object('__main__')
viewer = ga.viewers[0][0]
data = {'x': [1, 2, 3], 'y': [4, 5, 6]}
colors = ['#e31a1c', '#6d7326', None]
check_values_and_color(viewer.model, data, colors)
ga.close()
def test_session_rgb_back_compat(self, protocol):
filename = os.path.join(DATA, 'image_rgb_v{0}.glu'.format(protocol))
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
dc = ga.session.data_collection
assert len(dc) == 1
assert dc[0].label == 'rgbcube'
viewer1 = ga.viewers[0][0]
assert len(viewer1.state.layers) == 3
assert viewer1.state.color_mode == 'One color per layer'
layer_state = viewer1.state.layers[0]
assert layer_state.visible
assert layer_state.attribute.label == 'a'
assert layer_state.color == 'r'
layer_state = viewer1.state.layers[1]
assert not layer_state.visible
assert layer_state.attribute.label == 'c'
assert layer_state.color == 'g'
layer_state = viewer1.state.layers[2]
assert layer_state.visible
assert layer_state.attribute.label == 'b'
assert layer_state.color == 'b'
ga.close()
def test_session_rgb_back_compat(self, protocol):
filename = os.path.join(DATA, 'image_rgb_v{0}.glu'.format(protocol))
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
dc = ga.session.data_collection
assert len(dc) == 1
assert dc[0].label == 'rgbcube'
viewer1 = ga.viewers[0][0]
assert len(viewer1.state.layers) == 3
assert viewer1.state.color_mode == 'One color per layer'
layer_state = viewer1.state.layers[0]
assert layer_state.visible
assert layer_state.attribute.label == 'a'
assert layer_state.color == 'r'
layer_state = viewer1.state.layers[1]
assert not layer_state.visible
assert layer_state.attribute.label == 'c'
assert layer_state.color == 'g'
layer_state = viewer1.state.layers[2]
assert layer_state.visible
assert layer_state.attribute.label == 'b'
assert layer_state.color == 'b'
ga.close()
def test_table_widget_010():
from glue.viewers.table.qt.tests.test_data_viewer import check_values_and_color
# This loads a session file made with Glue v0.10 that includes a table
# viewer. This is to make sure that loading table viewers from old files
# will always be backward-compatible.
with open(os.path.join(DATA, 'glue_v0.10_table.glu'), 'r') as f:
state = GlueUnSerializer.load(f)
ga = state.object('__main__')
viewer = ga.viewers[0][0]
data = {'x': [1, 2, 3],
'y': [4, 5, 6]}
colors = ['#e31a1c', '#6d7326', None]
check_values_and_color(viewer.model, data, colors)
ga.close()
def test_session_cube_back_compat(self, protocol):
filename = os.path.join(DATA, 'image_cube_v{0}.glu'.format(protocol))
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
dc = ga.session.data_collection
assert len(dc) == 1
assert dc[0].label == 'array'
viewer1 = ga.viewers[0][0]
assert len(viewer1.state.layers) == 1
assert viewer1.state.x_att_world is dc[0].id['World 2']
assert viewer1.state.y_att_world is dc[0].id['World 1']
assert viewer1.state.slices == [2, 0, 0, 1]
def test_datetime64_support(self, tmpdir):
self.data.add_component(np.array([100, 200, 300, 400], dtype='M8[D]'),
't1')
self.data.add_component(np.array([200, 300, 400, 500], dtype='M8[D]'),
't2')
self.viewer.add_data(self.data)
self.viewer.state.x_att = self.data.id['t1']
self.viewer.state.y_att = self.data.id['y']
# Matplotlib deals with dates by converting them to the number of days
# since 01-01-0001, so we can check that the limits are correctly
# converted (and not 100 to 400)
assert self.viewer.axes.get_xlim() == (719248.0, 719578.0)
assert self.viewer.axes.get_ylim() == (3.2 - 0.015, 3.5 + 0.015)
# Apply an ROI selection in plotting coordinates
roi = RectangularROI(xmin=719313, xmax=719513, ymin=3, ymax=4)
self.viewer.apply_roi(roi)
# Check that the two middle elements are selected
assert_equal(self.data.subsets[0].to_mask(), [0, 1, 1, 0])
# Now do the same with the y axis
self.viewer.state.y_att = self.data.id['t2']
assert self.viewer.axes.get_xlim() == (719248.0, 719578.0)
assert self.viewer.axes.get_ylim() == (719348.0, 719678.0)
# Apply an ROI selection in plotting coordinates
edit = self.session.edit_subset_mode
edit.edit_subset = []
roi = CircularROI(xc=719463, yc=719563, radius=200)
self.viewer.apply_roi(roi)
assert_equal(self.data.subsets[1].to_mask(), [0, 1, 1, 1])
# Make sure that the Qt labels look ok
self.viewer.state.y_att = self.data.id['y']
options = self.viewer.options_widget().ui
assert options.valuetext_x_min.text() == '1970-03-27'
assert options.valuetext_x_max.text() == '1971-02-20'
assert options.valuetext_y_min.text() == '3.185'
assert options.valuetext_y_max.text() == '3.515'
# Make sure that we can set the xmin/xmax to a string date
assert_equal(self.viewer.state.x_min, np.datetime64('1970-03-27', 'D'))
options.valuetext_x_min.setText('1970-04-14')
options.valuetext_x_min.editingFinished.emit()
assert self.viewer.axes.get_xlim() == (719266.0, 719578.0)
assert_equal(self.viewer.state.x_min, np.datetime64('1970-04-14', 'D'))
# Make sure that everything works fine after saving/reloading
filename = tmpdir.join('test_datetime64.glu').strpath
self.session.application.save_session(filename)
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
viewer = ga.viewers[0][0]
options = viewer.options_widget().ui
assert_equal(self.viewer.state.x_min, np.datetime64('1970-04-14', 'D'))
assert options.valuetext_x_min.text() == '1970-04-14'
assert options.valuetext_x_max.text() == '1971-02-20'
assert options.valuetext_y_min.text() == '3.185'
assert options.valuetext_y_max.text() == '3.515'
def test_session_back_compat(self, protocol):
filename = os.path.join(DATA, 'image_v{0}.glu'.format(protocol))
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
dc = ga.session.data_collection
assert len(dc) == 2
assert dc[0].label == 'data1'
assert dc[1].label == 'data2'
viewer1 = ga.viewers[0][0]
assert len(viewer1.state.layers) == 3
assert viewer1.state.x_att_world is dc[0].id['World 1']
assert viewer1.state.y_att_world is dc[0].id['World 0']
assert viewer1.state.x_min < -0.5
assert viewer1.state.x_max > 1.5
assert viewer1.state.y_min <= -0.5
assert viewer1.state.y_max >= 1.5
layer_state = viewer1.state.layers[0]
assert isinstance(layer_state, ImageLayerState)
assert layer_state.visible
assert layer_state.bias == 0.5
assert layer_state.contrast == 1.0
assert layer_state.stretch == 'sqrt'
assert layer_state.percentile == 99
layer_state = viewer1.state.layers[1]
assert isinstance(layer_state, ScatterLayerState)
assert layer_state.visible
layer_state = viewer1.state.layers[2]
assert isinstance(layer_state, ImageSubsetLayerState)
assert not layer_state.visible
viewer2 = ga.viewers[0][1]
assert len(viewer2.state.layers) == 2
assert viewer2.state.x_att_world is dc[0].id['World 1']
assert viewer2.state.y_att_world is dc[0].id['World 0']
assert viewer2.state.x_min < -0.5
assert viewer2.state.x_max > 1.5
assert viewer2.state.y_min <= -0.5
assert viewer2.state.y_max >= 1.5
layer_state = viewer2.state.layers[0]
assert layer_state.visible
assert layer_state.stretch == 'arcsinh'
assert layer_state.v_min == 1
assert layer_state.v_max == 4
layer_state = viewer2.state.layers[1]
assert layer_state.visible
viewer3 = ga.viewers[0][2]
assert len(viewer3.state.layers) == 2
assert viewer3.state.x_att_world is dc[0].id['World 1']
assert viewer3.state.y_att_world is dc[0].id['World 0']
assert viewer3.state.x_min < -0.5
assert viewer3.state.x_max > 1.5
assert viewer3.state.y_min <= -0.5
assert viewer3.state.y_max >= 1.5
layer_state = viewer3.state.layers[0]
assert layer_state.visible
assert layer_state.stretch == 'linear'
assert layer_state.v_min == -2
assert layer_state.v_max == 2
layer_state = viewer3.state.layers[1]
assert layer_state.visible
ga.close()
def test_session_back_compat(self, protocol):
filename = os.path.join(DATA, 'profile_v{0}.glu'.format(protocol))
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
dc = ga.session.data_collection
assert len(dc) == 1
assert dc[0].label == 'array'
viewer1 = ga.viewers[0][0]
assert len(viewer1.state.layers) == 3
assert viewer1.state.x_att_pixel is dc[0].pixel_component_ids[0]
assert_allclose(viewer1.state.x_min, -0.5)
assert_allclose(viewer1.state.x_max, 2.5)
assert_allclose(viewer1.state.y_min, 13)
assert_allclose(viewer1.state.y_max, 63)
assert viewer1.state.function == 'maximum'
assert not viewer1.state.normalize
assert viewer1.state.layers[0].visible
assert viewer1.state.layers[1].visible
assert viewer1.state.layers[2].visible
viewer2 = ga.viewers[0][1]
assert viewer2.state.x_att_pixel is dc[0].pixel_component_ids[1]
assert_allclose(viewer2.state.x_min, -0.5)
assert_allclose(viewer2.state.x_max, 3.5)
assert_allclose(viewer2.state.y_min, -0.1)
assert_allclose(viewer2.state.y_max, 1.1)
assert viewer2.state.function == 'maximum'
assert viewer2.state.normalize
assert viewer2.state.layers[0].visible
assert not viewer2.state.layers[1].visible
assert viewer2.state.layers[2].visible
viewer3 = ga.viewers[0][2]
assert viewer3.state.x_att_pixel is dc[0].pixel_component_ids[2]
assert_allclose(viewer3.state.x_min, -0.5)
assert_allclose(viewer3.state.x_max, 4.5)
assert_allclose(viewer3.state.y_min, -0.4)
assert_allclose(viewer3.state.y_max, 4.4)
assert viewer3.state.function == 'minimum'
assert not viewer3.state.normalize
assert viewer3.state.layers[0].visible
assert viewer3.state.layers[1].visible
assert not viewer3.state.layers[2].visible
viewer4 = ga.viewers[0][3]
assert viewer4.state.x_att_pixel is dc[0].pixel_component_ids[2]
assert_allclose(viewer4.state.x_min, -5.5)
assert_allclose(viewer4.state.x_max, 9.5)
assert_allclose(viewer4.state.y_min, 27.1)
assert_allclose(viewer4.state.y_max, 31.9)
assert viewer4.state.function == 'mean'
assert not viewer4.state.normalize
assert viewer4.state.layers[0].visible
assert not viewer4.state.layers[1].visible
assert not viewer4.state.layers[2].visible
ga.close()
def test_scatter_volume(protocol):
filename = os.path.join(DATA, 'scatter_volume_v{0}.glu'.format(protocol))
with open(filename, 'r') as f:
session = f.read()
with patch.object(QMessageBox, 'question') as question:
question.return_value = QMessageBox.Yes
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
dc = ga.session.data_collection
assert len(dc) == 2
assert dc[0].label == 'table'
assert dc[1].label == 'array'
# SCATTER VIEWER
scatter = ga.viewers[0][0]
viewer_state = scatter.state
assert viewer_state.x_att.label == 'b'
assert viewer_state.x_min == 8
assert viewer_state.x_max == 0
np.testing.assert_allclose(viewer_state.x_stretch, 0.4, rtol=1.e-3)
assert viewer_state.y_att.label == 'a'
assert viewer_state.y_min == 0.4
assert viewer_state.y_max == 4
np.testing.assert_allclose(viewer_state.y_stretch, 0.6, rtol=1.e-3)
assert viewer_state.z_att.label == 'c'
assert viewer_state.z_min == 2
assert viewer_state.z_max == 5.4
np.testing.assert_allclose(viewer_state.z_stretch, 1.4, rtol=1.e-3)
assert viewer_state.perspective_view
assert not viewer_state.visible_axes
if protocol >= 1:
assert not viewer_state.native_aspect
assert viewer_state.clip_data
layer_state = viewer_state.layers[0]
assert layer_state.size_mode == 'Linear'
assert layer_state.size_attribute.label == 'e'
assert layer_state.size_vmin == 3
assert layer_state.size_vmax == 4
np.testing.assert_allclose(layer_state.size_scaling, 1.51356, rtol=1.e-3)
assert layer_state.color_mode == 'Linear'
assert layer_state.cmap_attribute.label == 'd'
assert layer_state.cmap_vmin == 0
assert layer_state.cmap_vmax == 10
assert layer_state.alpha == 0.66
# VOLUME VIEWER
volume = ga.viewers[0][1]
viewer_state = volume.state
assert viewer_state.x_att.label == 'Pixel Axis 2 [x]'
assert viewer_state.x_min == 3.5
assert viewer_state.x_max == -0.5
np.testing.assert_allclose(viewer_state.x_stretch, 0.2, rtol=1.e-3)
assert viewer_state.y_att.label == 'Pixel Axis 1 [y]'
assert viewer_state.y_min == -0.5
assert viewer_state.y_max == 2.5
np.testing.assert_allclose(viewer_state.y_stretch, 1.2, rtol=1.e-3)
assert viewer_state.z_att.label == 'Pixel Axis 0 [z]'
assert viewer_state.z_min == -0.5
assert viewer_state.z_max == 1.5
np.testing.assert_allclose(viewer_state.z_stretch, 1.3, rtol=1.e-3)
assert not viewer_state.perspective_view
assert viewer_state.visible_axes
if protocol >= 1:
assert viewer_state.native_aspect
assert not viewer_state.clip_data
layer_state = viewer_state.layers[0]
assert layer_state.attribute == 'array'
assert layer_state.vmin == 0
assert layer_state.vmax == 23
assert layer_state.color == '#e60010'
assert layer_state.alpha == 0.36
ga.close()
def test_session_back_compat(self, protocol):
filename = os.path.join(DATA, 'histogram_v{0}.glu'.format(protocol))
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
dc = ga.session.data_collection
assert len(dc) == 1
assert dc[0].label == 'data'
viewer1 = ga.viewers[0][0]
assert len(viewer1.state.layers) == 2
assert viewer1.state.x_att is dc[0].id['a']
assert_allclose(viewer1.state.x_min, 0)
assert_allclose(viewer1.state.x_max, 9)
assert_allclose(viewer1.state.y_min, 0)
assert_allclose(viewer1.state.y_max, 2.4)
assert_allclose(viewer1.state.hist_x_min, 0)
assert_allclose(viewer1.state.hist_x_max, 9)
assert_allclose(viewer1.state.hist_n_bin, 6)
assert not viewer1.state.x_log
assert not viewer1.state.y_log
assert viewer1.state.layers[0].visible
assert not viewer1.state.layers[1].visible
assert not viewer1.state.cumulative
assert not viewer1.state.normalize
viewer2 = ga.viewers[0][1]
assert viewer2.state.x_att is dc[0].id['b']
assert_allclose(viewer2.state.x_min, 2)
assert_allclose(viewer2.state.x_max, 16)
assert_allclose(viewer2.state.y_min, 0)
assert_allclose(viewer2.state.y_max, 1.2)
assert_allclose(viewer2.state.hist_x_min, 2)
assert_allclose(viewer2.state.hist_x_max, 16)
assert_allclose(viewer2.state.hist_n_bin, 8)
assert not viewer2.state.x_log
assert not viewer2.state.y_log
assert viewer2.state.layers[0].visible
assert viewer2.state.layers[1].visible
assert not viewer2.state.cumulative
assert not viewer2.state.normalize
viewer3 = ga.viewers[0][2]
assert viewer3.state.x_att is dc[0].id['a']
assert_allclose(viewer3.state.x_min, 0)
assert_allclose(viewer3.state.x_max, 9)
assert_allclose(viewer3.state.y_min, 0.01111111111111111)
assert_allclose(viewer3.state.y_max, 0.7407407407407407)
assert_allclose(viewer3.state.hist_x_min, 0)
assert_allclose(viewer3.state.hist_x_max, 9)
assert_allclose(viewer3.state.hist_n_bin, 10)
assert not viewer3.state.x_log
assert viewer3.state.y_log
assert viewer3.state.layers[0].visible
assert viewer3.state.layers[1].visible
assert not viewer3.state.cumulative
assert viewer3.state.normalize
viewer4 = ga.viewers[0][3]
assert viewer4.state.x_att is dc[0].id['a']
assert_allclose(viewer4.state.x_min, -1)
assert_allclose(viewer4.state.x_max, 10)
assert_allclose(viewer4.state.y_min, 0)
assert_allclose(viewer4.state.y_max, 12)
assert_allclose(viewer4.state.hist_x_min, -1)
assert_allclose(viewer4.state.hist_x_max, 10)
assert_allclose(viewer4.state.hist_n_bin, 4)
assert not viewer4.state.x_log
assert not viewer4.state.y_log
assert viewer4.state.layers[0].visible
assert viewer4.state.layers[1].visible
assert viewer4.state.cumulative
assert not viewer4.state.normalize
def test_datetime64_support(self, tmpdir):
self.data.add_component(np.array([100, 200, 300, 400], dtype='M8[D]'), 't1')
self.data.add_component(np.array([200, 300, 400, 500], dtype='M8[D]'), 't2')
self.viewer.add_data(self.data)
self.viewer.state.x_att = self.data.id['t1']
self.viewer.state.y_att = self.data.id['y']
# Matplotlib deals with dates by converting them to the number of days
# since 01-01-0001, so we can check that the limits are correctly
# converted (and not 100 to 400)
assert self.viewer.axes.get_xlim() == (719251.0, 719575.0)
assert self.viewer.axes.get_ylim() == (3.2 - 0.012, 3.5 + 0.012)
# Apply an ROI selection in plotting coordinates
roi = RectangularROI(xmin=719313, xmax=719513, ymin=3, ymax=4)
self.viewer.apply_roi(roi)
# Check that the two middle elements are selected
assert_equal(self.data.subsets[0].to_mask(), [0, 1, 1, 0])
# Now do the same with the y axis
self.viewer.state.y_att = self.data.id['t2']
assert self.viewer.axes.get_xlim() == (719251.0, 719575.0)
assert self.viewer.axes.get_ylim() == (719351.0, 719675.0)
# Apply an ROI selection in plotting coordinates
edit = self.session.edit_subset_mode
edit.edit_subset = []
roi = CircularROI(xc=719463, yc=719563, radius=200)
self.viewer.apply_roi(roi)
assert_equal(self.data.subsets[1].to_mask(), [0, 1, 1, 1])
# Make sure that the Qt labels look ok
self.viewer.state.y_att = self.data.id['y']
options = self.viewer.options_widget().ui
assert options.valuetext_x_min.text() == '1970-03-30'
assert options.valuetext_x_max.text() == '1971-02-17'
assert options.valuetext_y_min.text() == '3.188'
assert options.valuetext_y_max.text() == '3.512'
# Make sure that we can set the xmin/xmax to a string date
assert_equal(self.viewer.state.x_min, np.datetime64('1970-03-30', 'D'))
options.valuetext_x_min.setText('1970-04-14')
options.valuetext_x_min.editingFinished.emit()
assert self.viewer.axes.get_xlim() == (719266.0, 719575.0)
assert_equal(self.viewer.state.x_min, np.datetime64('1970-04-14', 'D'))
# Make sure that everything works fine after saving/reloading
filename = tmpdir.join('test_datetime64.glu').strpath
self.session.application.save_session(filename)
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
viewer = ga.viewers[0][0]
options = viewer.options_widget().ui
assert_equal(self.viewer.state.x_min, np.datetime64('1970-04-14', 'D'))
assert options.valuetext_x_min.text() == '1970-04-14'
assert options.valuetext_x_max.text() == '1971-02-17'
assert options.valuetext_y_min.text() == '3.188'
assert options.valuetext_y_max.text() == '3.512'
ga.close()
def test_session_back_compat(self, protocol):
filename = os.path.join(DATA, 'image_v{0}.glu'.format(protocol))
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
dc = ga.session.data_collection
assert len(dc) == 2
assert dc[0].label == 'data1'
assert dc[1].label == 'data2'
viewer1 = ga.viewers[0][0]
assert len(viewer1.state.layers) == 3
assert viewer1.state.x_att_world is dc[0].id['World 1']
assert viewer1.state.y_att_world is dc[0].id['World 0']
assert viewer1.state.x_min < -0.5
assert viewer1.state.x_max > 1.5
assert viewer1.state.y_min <= -0.5
assert viewer1.state.y_max >= 1.5
layer_state = viewer1.state.layers[0]
assert isinstance(layer_state, ImageLayerState)
assert layer_state.visible
assert layer_state.bias == 0.5
assert layer_state.contrast == 1.0
assert layer_state.stretch == 'sqrt'
assert layer_state.percentile == 99
layer_state = viewer1.state.layers[1]
assert isinstance(layer_state, ScatterLayerState)
assert layer_state.visible
layer_state = viewer1.state.layers[2]
assert isinstance(layer_state, ImageSubsetLayerState)
assert not layer_state.visible
viewer2 = ga.viewers[0][1]
assert len(viewer2.state.layers) == 2
assert viewer2.state.x_att_world is dc[0].id['World 1']
assert viewer2.state.y_att_world is dc[0].id['World 0']
assert viewer2.state.x_min < -0.5
assert viewer2.state.x_max > 1.5
assert viewer2.state.y_min <= -0.5
assert viewer2.state.y_max >= 1.5
layer_state = viewer2.state.layers[0]
assert layer_state.visible
assert layer_state.stretch == 'arcsinh'
assert layer_state.v_min == 1
assert layer_state.v_max == 4
layer_state = viewer2.state.layers[1]
assert layer_state.visible
viewer3 = ga.viewers[0][2]
assert len(viewer3.state.layers) == 2
assert viewer3.state.x_att_world is dc[0].id['World 1']
assert viewer3.state.y_att_world is dc[0].id['World 0']
assert viewer3.state.x_min < -0.5
assert viewer3.state.x_max > 1.5
assert viewer3.state.y_min <= -0.5
assert viewer3.state.y_max >= 1.5
layer_state = viewer3.state.layers[0]
assert layer_state.visible
assert layer_state.stretch == 'linear'
assert layer_state.v_min == -2
assert layer_state.v_max == 2
layer_state = viewer3.state.layers[1]
assert layer_state.visible
ga.close()
def roundtrip_transform(transform):
gs = GlueSerializer(transform)
out_str = gs.dumps()
obj = GlueUnSerializer.loads(out_str)
return obj.object('__main__')
def test_session_back_compat(self, protocol):
filename = os.path.join(DATA, 'histogram_v{0}.glu'.format(protocol))
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
dc = ga.session.data_collection
assert len(dc) == 1
assert dc[0].label == 'data'
viewer1 = ga.viewers[0][0]
assert len(viewer1.state.layers) == 2
assert viewer1.state.x_att is dc[0].id['a']
assert_allclose(viewer1.state.x_min, 0)
assert_allclose(viewer1.state.x_max, 9)
assert_allclose(viewer1.state.y_min, 0)
assert_allclose(viewer1.state.y_max, 2.4)
assert_allclose(viewer1.state.hist_x_min, 0)
assert_allclose(viewer1.state.hist_x_max, 9)
assert_allclose(viewer1.state.hist_n_bin, 6)
assert not viewer1.state.x_log
assert not viewer1.state.y_log
assert viewer1.state.layers[0].visible
assert not viewer1.state.layers[1].visible
assert not viewer1.state.cumulative
assert not viewer1.state.normalize
viewer2 = ga.viewers[0][1]
assert viewer2.state.x_att is dc[0].id['b']
assert_allclose(viewer2.state.x_min, 2)
assert_allclose(viewer2.state.x_max, 16)
assert_allclose(viewer2.state.y_min, 0)
assert_allclose(viewer2.state.y_max, 1.2)
assert_allclose(viewer2.state.hist_x_min, 2)
assert_allclose(viewer2.state.hist_x_max, 16)
assert_allclose(viewer2.state.hist_n_bin, 8)
assert not viewer2.state.x_log
assert not viewer2.state.y_log
assert viewer2.state.layers[0].visible
assert viewer2.state.layers[1].visible
assert not viewer2.state.cumulative
assert not viewer2.state.normalize
viewer3 = ga.viewers[0][2]
assert viewer3.state.x_att is dc[0].id['a']
assert_allclose(viewer3.state.x_min, 0)
assert_allclose(viewer3.state.x_max, 9)
assert_allclose(viewer3.state.y_min, 0.037037037037037035)
assert_allclose(viewer3.state.y_max, 0.7407407407407407)
assert_allclose(viewer3.state.hist_x_min, 0)
assert_allclose(viewer3.state.hist_x_max, 9)
assert_allclose(viewer3.state.hist_n_bin, 10)
assert not viewer3.state.x_log
assert viewer3.state.y_log
assert viewer3.state.layers[0].visible
assert viewer3.state.layers[1].visible
assert not viewer3.state.cumulative
assert viewer3.state.normalize
viewer4 = ga.viewers[0][3]
assert viewer4.state.x_att is dc[0].id['a']
assert_allclose(viewer4.state.x_min, -1)
assert_allclose(viewer4.state.x_max, 10)
assert_allclose(viewer4.state.y_min, 0)
assert_allclose(viewer4.state.y_max, 12)
assert_allclose(viewer4.state.hist_x_min, -1)
assert_allclose(viewer4.state.hist_x_max, 10)
assert_allclose(viewer4.state.hist_n_bin, 4)
assert not viewer4.state.x_log
assert not viewer4.state.y_log
assert viewer4.state.layers[0].visible
assert viewer4.state.layers[1].visible
assert viewer4.state.cumulative
assert not viewer4.state.normalize
