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Merge pull request #2751 from pllim/wcs-pixels-wcs-ref
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Fix reference data for WCS to Pixels to WCS
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@pllim
pllim authored Mar 23, 2024
2 parents 31ef295 + f1ba4a6 commit d3dcfa5
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Showing 7 changed files with 264 additions and 283 deletions.
2 changes: 1 addition & 1 deletion jdaviz/app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2096,7 +2096,7 @@ def vue_data_item_remove(self, event):
data = self.data_collection[data_label]
orientation_plugin = self._jdaviz_helper.plugins.get("Orientation")
if orientation_plugin is not None:
from jdaviz.configs.imviz.helper import base_wcs_layer_label
from jdaviz.configs.imviz.plugins.orientation.orientation import base_wcs_layer_label
orient = orientation_plugin.orientation.selected
if orient == data_label:
orient = base_wcs_layer_label
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3 changes: 2 additions & 1 deletion jdaviz/configs/default/plugins/markers/tests/test_markers_plugin.py
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Expand Up @@ -20,7 +20,7 @@ def _assert_dict_allclose(dict1, dict2):
assert v == dict2.get(k)


def test_markers_cubeviz(cubeviz_helper, spectrum1d_cube):
def test_markers_cubeviz(tmp_path, cubeviz_helper, spectrum1d_cube):
cubeviz_helper.load_data(spectrum1d_cube, "test")
fv = cubeviz_helper.app.get_viewer('flux-viewer')
sv = cubeviz_helper.app.get_viewer('spectrum-viewer')
Expand Down Expand Up @@ -130,6 +130,7 @@ def test_markers_cubeviz(cubeviz_helper, spectrum1d_cube):

# appears as option in export plugin and exports successfully
assert "Markers:table" in exp.table.choices
exp.filename = str(tmp_path / "cubeviz_export.ecsv")
exp.table = "Markers:table"
exp.export()

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251 changes: 4 additions & 247 deletions jdaviz/configs/imviz/helper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,23 +4,15 @@
from copy import deepcopy

import numpy as np
import astropy.units as u
from astropy.wcs.wcsapi import BaseHighLevelWCS
from glue.core import BaseData
from glue.core.link_helpers import LinkSame
from glue.plugins.wcs_autolinking.wcs_autolinking import WCSLink, NoAffineApproximation

from jdaviz.core.events import SnackbarMessage, NewViewerMessage, LinkUpdatedMessage
from jdaviz.core.events import SnackbarMessage, NewViewerMessage
from jdaviz.core.helpers import ImageConfigHelper
from jdaviz.configs.imviz.wcs_utils import (
_get_rotated_nddata_from_label, get_compass_info
)
from jdaviz.utils import data_has_valid_wcs, _wcs_only_label

__all__ = ['Imviz']

base_wcs_layer_label = 'Default orientation'


class Imviz(ImageConfigHelper):
"""Imviz Helper class."""
Expand Down Expand Up @@ -436,7 +428,8 @@ def get_top_layer_index(viewer):

def get_reference_image_data(app, viewer_id=None):
"""
Return the reference data in the first image viewer and its index
Return the current reference data in the given image viewer and its index.
By default, the first viewer is used.
"""
if viewer_id is None:
refdata = app._jdaviz_helper.default_viewer._obj.state.reference_data
Expand All @@ -448,240 +441,4 @@ def get_reference_image_data(app, viewer_id=None):
iref = app.data_collection.index(refdata)
return refdata, iref

# if reference data not found above, fall back on old method:
for i, data in enumerate(app.data_collection):
if layer_is_image_data(data):
iref = i
refdata = data
break
if refdata is None:
raise ValueError(f'No valid reference data found in collection: {app.data_collection}')
return refdata, iref


# TODO: This is not really public API, so we can move what Orientation uses here into the plugin
# and remove this function from helper.py module in the future. Also move base_wcs_layer_label
# and remove update_plugin keyword when that happens.
def link_image_data(app, link_type='pixels', wcs_fallback_scheme=None, wcs_use_affine=True,
error_on_fail=False, update_plugin=True):
"""(Re)link loaded data in Imviz with the desired link type.
.. note::
Any markers added in Imviz will need to be removed manually before changing linking type.
You can add back the markers using
:meth:`~jdaviz.core.astrowidgets_api.AstrowidgetsImageViewerMixin.add_markers`
for the relevant viewer(s).
Parameters
----------
app : `~jdaviz.app.Application`
Application associated with Imviz, e.g., ``imviz.app``.
link_type : {'pixels', 'wcs'}
Choose to link by pixels or WCS.
wcs_fallback_scheme : {None, 'pixels'}
If WCS linking failed, choose to fall back to linking by pixels or not at all.
This is only used when ``link_type='wcs'``.
Choosing `None` may result in some Imviz functionality not working properly.
wcs_use_affine : bool
Use an affine transform to represent the offset between images if possible
(requires that the approximation is accurate to within 1 pixel with the
full WCS transformations). If approximation fails, it will automatically
fall back to full WCS transformation. This is only used when ``link_type='wcs'``.
Affine approximation is much more performant at the cost of accuracy.
error_on_fail : bool
If `True`, any failure in linking will raise an exception.
If `False`, warnings will be emitted as snackbar messages.
When only warnings are emitted and no links are assigned,
some Imviz functionality may not work properly.
update_plugin : bool
Whether to update the state of the "Orientation" plugin, if available.
Raises
------
ValueError
Invalid inputs or reference data.
"""
if len(app.data_collection) <= 1 and link_type != 'wcs': # No need to link, we are done.
return

if link_type not in ('pixels', 'wcs'):
raise ValueError(f"link_type must be 'pixels' or 'wcs', got {link_type}")
if link_type == 'wcs' and wcs_fallback_scheme not in (None, 'pixels'):
raise ValueError("wcs_fallback_scheme must be None or 'pixels', "
f"got {wcs_fallback_scheme}")
if link_type == 'wcs':
at_least_one_data_have_wcs = len([
hasattr(d, 'coords') and isinstance(d.coords, BaseHighLevelWCS)
for d in app.data_collection
]) > 0
if not at_least_one_data_have_wcs:
if wcs_fallback_scheme is None:
if error_on_fail:
raise ValueError("link_type can only be 'wcs' when wcs_fallback_scheme "
"is 'None' if all data have valid WCS.")
else:
return
else:
# fall back on pixel linking
link_type = 'pixels'

# default reference layer is the first-loaded image in default viewer:
default_reference_layer = app._jdaviz_helper.default_viewer._obj.first_loaded_data
if default_reference_layer is None: # No data in viewer, just use first in collection
default_reference_layer = app.data_collection[0]

# if the plugin exists, send a message so that the plugin's state is updated and spinner
# is shown (the plugin will make a call back here)
if 'imviz-orientation' in [item['name'] for item in app.state.tray_items]:
link_plugin = app.get_tray_item_from_name('imviz-orientation')
if update_plugin:
link_plugin.linking_in_progress = True
else:
link_plugin = None

data_already_linked = []
if link_type == app._link_type and wcs_use_affine == app._wcs_use_affine:
for link in app.data_collection.external_links:
if link.data1.label != _wcs_only_label:
data_already_linked.append(link.data2)
else:
for viewer in app._viewer_store.values():
if len(viewer._marktags):
raise ValueError(f"cannot change link_type (from '{app._link_type}' to "
f"'{link_type}') when markers are present. "
f" Clear markers with viewer.reset_markers() first")

old_link_type = getattr(app, '_link_type', None)

# if linking via WCS, add WCS-only reference data layer:
insert_base_wcs_layer = (
link_type == 'wcs' and
base_wcs_layer_label not in [d.label for d in app.data_collection]
)

if insert_base_wcs_layer:
degn = get_compass_info(default_reference_layer.coords, default_reference_layer.shape)[-3]
# Default rotation is the same orientation as the original reference data:
rotation_angle = -degn * u.deg
ndd = _get_rotated_nddata_from_label(
app, default_reference_layer.label, rotation_angle
)
app._jdaviz_helper.load_data(ndd, base_wcs_layer_label)

# set base layer to reference data in all viewers:
for viewer_id in app.get_viewer_ids():
app._change_reference_data(
base_wcs_layer_label, viewer_id=viewer_id
)

refdata, iref = get_reference_image_data(app)

# set internal tracking of link_type before changing reference data for anything that is
# subscribed to a change in reference data
app._link_type = link_type
app._wcs_use_affine = wcs_use_affine

if link_type == 'pixels' and old_link_type == 'wcs':
for viewer_id in app.get_viewer_ids():
app._change_reference_data(
default_reference_layer.label, viewer_id=viewer_id
)

links_list = []
ids0 = default_reference_layer.pixel_component_ids
ndim_range = range(default_reference_layer.ndim)

for i, data in enumerate(app.data_collection):
# Do not link with self
if i == iref:
continue

# We are not touching any existing Subsets. They keep their own links.
if not layer_is_2d(data):
continue

if data in data_already_linked:
# links already exist for this entry and we're not changing the type
continue

# We are not touching fake WCS layers in pixel linking.
if link_type == 'pixels' and data.meta.get('_WCS_ONLY'):
continue

ids1 = data.pixel_component_ids
new_links = []
try:
if link_type == 'pixels':
new_links = [LinkSame(ids0[i], ids1[i]) for i in ndim_range]
# otherwise if linking by WCS *and* this data entry has WCS:
elif hasattr(data.coords, 'pixel_to_world'):
wcslink = WCSLink(data1=refdata, data2=data, cids1=ids0, cids2=ids1)
if wcs_use_affine:
try:
new_links = [wcslink.as_affine_link()]
except NoAffineApproximation: # pragma: no cover
new_links = [wcslink]
else:
new_links = [wcslink]
except Exception as e:
if link_type == 'wcs' and wcs_fallback_scheme == 'pixels':
try:
new_links = [LinkSame(ids0[i], ids1[i]) for i in ndim_range]
except Exception as e: # pragma: no cover
if error_on_fail:
raise
else:
app.hub.broadcast(SnackbarMessage(
f"Error linking '{data.label}' to '{refdata.label}': "
f"{repr(e)}", color="warning", timeout=8000, sender=app))
continue
else:
if error_on_fail:
raise
else:
app.hub.broadcast(SnackbarMessage(
f"Error linking '{data.label}' to '{refdata.label}': "
f"{repr(e)}", color="warning", timeout=8000, sender=app))
continue
links_list += new_links

if len(links_list) > 0:
with app.data_collection.delay_link_manager_update():
if len(data_already_linked):
app.data_collection.add_link(links_list)
else:
app.data_collection.set_links(links_list)

app.hub.broadcast(SnackbarMessage(
'Images successfully relinked', color='success', timeout=8000, sender=app))

for viewer in app._viewer_store.values():
wcs_linked = link_type == 'wcs'
# viewer-state needs to know link type for reset_limits behavior
viewer.state.linked_by_wcs = wcs_linked
# also need to store a copy in the viewer item for the data dropdown to access
viewer_item = app._get_viewer_item(viewer.reference)

viewer_item['reference_data_label'] = refdata.label
viewer_item['linked_by_wcs'] = wcs_linked

# if changing from one link type to another, reset the limits:
if link_type != old_link_type:
viewer.state.reset_limits()

if link_plugin is not None:
# Only broadcast after success.
app.hub.broadcast(LinkUpdatedMessage(link_type,
wcs_fallback_scheme == 'pixels',
wcs_use_affine,
sender=app))

# reset the progress spinner
link_plugin.linking_in_progress = False
return None, -1
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