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Fix export to Python script to correctly use Coordinates or WCS in reference_data #2335

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merged 5 commits into from
Oct 28, 2022
Merged

Fix export to Python script to correctly use Coordinates or WCS in reference_data #2335

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1477ebe
TST: add test for exporting data with WCS
dhomeier Oct 14, 2022
75a75b8
Fix mpl export `_script_header` to use WCS in data.coords
dhomeier Oct 14, 2022
b480316
Add more export tests with WCS
dhomeier Oct 14, 2022
a7dae6e
Simplify coords treatment; add tests for AffineCoordinates
dhomeier Oct 15, 2022
0cbfbd1
TST: use helper function to load alternative `Coordinates` datasets
dhomeier Oct 27, 2022
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75 changes: 57 additions & 18 deletions glue/viewers/image/qt/tests/test_python_export.py
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Original file line number Diff line number Diff line change
@@ -1,8 +1,11 @@
import pytest
import numpy as np
import matplotlib.pyplot as plt
from astropy.utils import NumpyRNGContext
from astropy.wcs import WCS

from glue.core import Data, DataCollection
from glue.core.coordinates import AffineCoordinates
from glue.app.qt.application import GlueApplication
from glue.viewers.image.qt import ImageViewer
from glue.viewers.matplotlib.qt.tests.test_python_export import BaseTestExportPython
Expand All @@ -14,7 +17,13 @@ def setup_method(self, method):

with NumpyRNGContext(12345):
self.data = Data(cube=np.random.random((30, 50, 20)))
self.data_collection = DataCollection([self.data])
# Create data versions with WCS and affine coordinates
matrix = np.array([[2, 3, 4, -1], [1, 2, 2, 2], [1, 1, 1, -2], [0, 0, 0, 1]])
affine = AffineCoordinates(matrix, units=['Mm', 'Mm', 'km'], labels=['xw', 'yw', 'zw'])

self.data_wcs = Data(label='cube', cube=self.data['cube'], coords=WCS(naxis=3))
self.data_affine = Data(label='cube', cube=self.data['cube'], coords=affine)
self.data_collection = DataCollection([self.data, self.data_wcs, self.data_affine])
self.app = GlueApplication(self.data_collection)
self.viewer = self.app.new_data_viewer(ImageViewer)
self.viewer.add_data(self.data)
Expand All @@ -34,19 +43,34 @@ def teardown_method(self, method):
def assert_same(self, tmpdir, tol=0.1):
BaseTestExportPython.assert_same(self, tmpdir, tol=tol)

def test_simple(self, tmpdir):
def viewer_load(self, coords):
if coords is not None:
self.viewer.add_data(getattr(self, f'data_{coords}'))
self.viewer.remove_data(self.data)

@pytest.mark.parametrize('coords', [None, 'wcs', 'affine'])
def test_simple(self, tmpdir, coords):
self.viewer_load(coords)
self.assert_same(tmpdir)

def test_simple_legend(self, tmpdir):
@pytest.mark.parametrize('coords', [None, 'wcs', 'affine'])
def test_simple_legend(self, tmpdir, coords):
self.viewer_load(coords)
self.viewer.state.show_legend = True
self.assert_same(tmpdir)

def test_simple_att(self, tmpdir):
self.viewer.state.x_att = self.data.pixel_component_ids[1]
self.viewer.state.y_att = self.data.pixel_component_ids[0]
@pytest.mark.parametrize('coords', [None, 'wcs', 'affine'])
def test_simple_att(self, tmpdir, coords):
self.viewer_load(coords)
self.viewer.state.x_att = self.viewer.state.reference_data.pixel_component_ids[1]
self.viewer.state.y_att = self.viewer.state.reference_data.pixel_component_ids[0]
if coords == 'affine':
pytest.xfail('Known issue with axis label rendering')
self.assert_same(tmpdir)

def test_simple_visual(self, tmpdir):
@pytest.mark.parametrize('coords', [None, 'wcs', 'affine'])
def test_simple_visual(self, tmpdir, coords):
self.viewer_load(coords)
self.viewer.state.legend.visible = True
self.viewer.state.layers[0].cmap = plt.cm.RdBu
self.viewer.state.layers[0].v_min = 0.2
Expand All @@ -57,31 +81,46 @@ def test_simple_visual(self, tmpdir):
self.viewer.state.layers[0].bias = 0.6
self.assert_same(tmpdir)

def test_slice(self, tmpdir):
self.viewer.state.x_att = self.data.pixel_component_ids[1]
self.viewer.state.y_att = self.data.pixel_component_ids[0]
@pytest.mark.parametrize('coords', [None, 'wcs', 'affine'])
def test_slice(self, tmpdir, coords):
self.viewer_load(coords)
self.viewer.state.x_att = self.viewer.state.reference_data.pixel_component_ids[1]
self.viewer.state.y_att = self.viewer.state.reference_data.pixel_component_ids[0]
self.viewer.state.slices = (2, 3, 4)
if coords == 'affine':
pytest.xfail('Known issue with axis label rendering')
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Can you open an issue in the repo to keep track of this?

self.assert_same(tmpdir)

def test_aspect(self, tmpdir):
@pytest.mark.parametrize('coords', [None, 'wcs', 'affine'])
def test_aspect(self, tmpdir, coords):
self.viewer_load(coords)
self.viewer.state.aspect = 'auto'
self.assert_same(tmpdir)

def test_subset(self, tmpdir):
@pytest.mark.parametrize('coords', [None, 'wcs', 'affine'])
def test_subset(self, tmpdir, coords):
self.viewer_load(coords)
self.data_collection.new_subset_group('mysubset', self.data.id['cube'] > 0.5)
self.assert_same(tmpdir)

def test_subset_legend(self, tmpdir):
@pytest.mark.parametrize('coords', [None, 'wcs', 'affine'])
def test_subset_legend(self, tmpdir, coords):
self.viewer_load(coords)
self.data_collection.new_subset_group('mysubset',
self.viewer.state.reference_data.id['cube'] > 0.5)
self.viewer.state.legend.visible = True
self.data_collection.new_subset_group('mysubset', self.data.id['cube'] > 0.5)
self.assert_same(tmpdir, tol=0.15) # transparency and such

def test_subset_slice(self, tmpdir):
@pytest.mark.parametrize('coords', [None, 'wcs', 'affine'])
def test_subset_slice(self, tmpdir, coords):
self.viewer_load(coords)
self.data_collection.new_subset_group('mysubset', self.data.id['cube'] > 0.5)
self.test_slice(tmpdir)
self.test_slice(tmpdir, coords)

def test_subset_transposed(self, tmpdir):
@pytest.mark.parametrize('coords', [None, 'wcs', 'affine'])
def test_subset_transposed(self, tmpdir, coords):
self.viewer_load(coords)
self.data_collection.new_subset_group('mysubset', self.data.id['cube'] > 0.5)
self.viewer.state.x_att = self.data.pixel_component_ids[0]
self.viewer.state.y_att = self.data.pixel_component_ids[1]
self.data_collection.new_subset_group('mysubset', self.data.id['cube'] > 0.5)
self.assert_same(tmpdir)
19 changes: 8 additions & 11 deletions glue/viewers/image/viewer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -214,24 +214,21 @@ def _script_header(self):

script = ""
script += "fig, ax = init_mpl(wcs=True)\n"
script += "ax.set_aspect('{0}')\n".format(self.state.aspect)
script += f"ax.set_aspect('{self.state.aspect}')\n"

script += '\ncomposite = CompositeArray()\n'
script += "image = imshow(ax, composite, origin='lower', interpolation='nearest', aspect='{0}')\n\n".format(self.state.aspect)
script += f"image = imshow(ax, composite, origin='lower', interpolation='nearest', aspect='{self.state.aspect}')\n\n"

dindex = self.session.data_collection.index(self.state.reference_data)

script += "ref_data = data_collection[{0}]\n".format(dindex)
script += f"ref_data = data_collection[{dindex}]\n"

ref_coords = self.state.reference_data.coords

if hasattr(ref_coords, 'wcs'):
script += "ax.reset_wcs(slices={0}, wcs=ref_data.coords.wcs)\n".format(self.state.wcsaxes_slice)
elif hasattr(ref_coords, 'wcsaxes_dict'):
raise NotImplementedError()
else:
if isinstance(self.state.reference_data.coords, (LegacyCoordinates, type(None))):
imports.append('from glue.viewers.image.viewer import get_identity_wcs')
script += "ax.reset_wcs(slices={0}, wcs=get_identity_wcs(ref_data.ndim))\n".format(self.state.wcsaxes_slice)
ref_wcs = "get_identity_wcs(ref_data.ndim)"
else:
ref_wcs = "ref_data.coords"
script += f"ax.reset_wcs(slices={self.state.wcsaxes_slice}, wcs={ref_wcs})\n"

script += "# for the legend\n"
script += "legend_handles = []\n"
Expand Down