-
+
{{viewer.reference || viewer.id}}
-
+
diff --git a/jdaviz/core/astrowidgets_api.py b/jdaviz/core/astrowidgets_api.py
index da6639a3af..bd4504e6e9 100644
--- a/jdaviz/core/astrowidgets_api.py
+++ b/jdaviz/core/astrowidgets_api.py
@@ -9,8 +9,8 @@
from glue.config import colormaps
from glue.core import Data
-from jdaviz.configs.imviz.helper import get_top_layer_index
-from jdaviz.core.events import SnackbarMessage, MarkersChangedMessage
+from jdaviz.configs.imviz.helper import get_top_layer_index, get_reference_image_data
+from jdaviz.core.events import SnackbarMessage, AstrowidgetMarkersChangedMessage
from jdaviz.core.helpers import data_has_valid_wcs
__all__ = ['AstrowidgetsImageViewerMixin']
@@ -77,6 +77,9 @@ def center_on(self, point):
"""
i_top = get_top_layer_index(self)
+ if i_top is None:
+ return
+
image = self.layers[i_top].layer
if isinstance(point, SkyCoord):
@@ -131,8 +134,16 @@ def offset_by(self, dx, dy):
Sky offset has invalid unit.
"""
+ i_top = get_top_layer_index(self)
+ image = self.layers[i_top].layer
width = self.state.x_max - self.state.x_min
height = self.state.y_max - self.state.y_min
+ x_cen = self.state.x_min + (width * 0.5)
+ y_cen = self.state.y_min + (height * 0.5)
+ if hasattr(self, '_get_real_xy'):
+ real_cen = self._get_real_xy(image, x_cen, y_cen)
+ else:
+ real_cen = (x_cen, y_cen)
dx, dx_coord = _offset_is_pixel_or_sky(dx)
dy, dy_coord = _offset_is_pixel_or_sky(dy)
@@ -141,28 +152,26 @@ def offset_by(self, dx, dy):
raise ValueError(f'dx is of type {dx_coord} but dy is of type {dy_coord}')
if dx_coord == 'wcs':
- i_top = get_top_layer_index(self)
- image = self.layers[i_top].layer
if data_has_valid_wcs(image):
# To avoid distortion headache, assume offset is relative to
# displayed center.
- x_cen = self.state.x_min + (width * 0.5)
- y_cen = self.state.y_min + (height * 0.5)
- sky_cen = image.coords.pixel_to_world(x_cen, y_cen)
- new_sky_cen = sky_cen.spherical_offsets_by(dx, dy)
- self.center_on(new_sky_cen)
+ sky_cen = image.coords.pixel_to_world(real_cen[0], real_cen[1])
+ new_cen = sky_cen.spherical_offsets_by(dx, dy)
else:
raise AttributeError(f'{getattr(image, "label", None)} does not have a valid WCS')
else:
- with delay_callback(self.state, 'x_min', 'x_max', 'y_min', 'y_max'):
- self.state.x_min += dx
- self.state.y_min += dy
- self.state.x_max = self.state.x_min + width
- self.state.y_max = self.state.y_min + height
+ new_cen = (real_cen[0] + dx, real_cen[1] + dy)
+
+ self.center_on(new_cen)
@property
def zoom_level(self):
- """Zoom level:
+ """
+ The zoom level for an image viewer (not linked by WCS).
+
+ .. warning::
+ When a viewer is linked by WCS, the result corresponds
+ to the ``zoom_level`` of the reference data.
* 1 means real-pixel-size.
* 2 means zoomed in by a factor of 2.
@@ -173,10 +182,20 @@ def zoom_level(self):
if self.shape is None: # pragma: no cover
raise ValueError('Viewer is still loading, try again later')
+ if hasattr(self, '_get_real_xy'):
+ image, i_ref = get_reference_image_data(self.jdaviz_app, self.reference)
+ # TODO: Do we want top layer instead?
+ # i_top = get_top_layer_index(self)
+ # image = self.layers[i_top].layer
+ real_min = self._get_real_xy(image, self.state.x_min, self.state.y_min)
+ real_max = self._get_real_xy(image, self.state.x_max, self.state.y_max)
+ else:
+ real_min = (self.state.x_min, self.state.y_min)
+ real_max = (self.state.x_max, self.state.y_max)
screenx = self.shape[1]
screeny = self.shape[0]
- zoom_x = screenx / (self.state.x_max - self.state.x_min)
- zoom_y = screeny / (self.state.y_max - self.state.y_min)
+ zoom_x = screenx / abs(real_max[0] - real_min[0])
+ zoom_y = screeny / abs(real_max[1] - real_min[1])
return max(zoom_x, zoom_y) # Similar to Ginga get_scale()
@@ -187,8 +206,7 @@ def zoom_level(self, val):
(isinstance(val, (int, float)) and val <= 0)):
raise ValueError(f'Unsupported zoom level: {val}')
- image = self.state.reference_data
- if (image is None or self.shape is None or
+ if (self.shape is None or
self.state.x_att is None or self.state.y_att is None): # pragma: no cover
return
@@ -196,15 +214,26 @@ def zoom_level(self, val):
if val == 'fit':
self.state.reset_limits()
return
+
+ new_dx = self.shape[1] * 0.5 / val
+ if hasattr(self, '_get_real_xy'):
+ image, i_ref = get_reference_image_data(self.jdaviz_app, self.reference)
+ # TODO: Do we want top layer instead?
+ # i_top = get_top_layer_index(self)
+ # image = self.layers[i_top].layer
+ real_min = self._get_real_xy(image, self.state.x_min, self.state.y_min)
+ real_max = self._get_real_xy(image, self.state.x_max, self.state.y_max)
+ cur_xcen = (real_min[0] + real_max[0]) * 0.5
+ new_x_min = self._get_real_xy(image, cur_xcen - new_dx - 0.5, real_min[1], reverse=True)[0] # noqa: E501
+ new_x_max = self._get_real_xy(image, cur_xcen + new_dx - 0.5, real_max[1], reverse=True)[0] # noqa: E501
else:
cur_xcen = (self.state.x_min + self.state.x_max) * 0.5
- new_dx = self.shape[1] * 0.5 / val
- new_x_min = cur_xcen - new_dx
- new_x_max = cur_xcen + new_dx
+ new_x_min = cur_xcen - new_dx - 0.5
+ new_x_max = cur_xcen + new_dx - 0.5
with delay_callback(self.state, 'x_min', 'x_max'):
- self.state.x_min = new_x_min - 0.5
- self.state.x_max = new_x_max - 0.5
+ self.state.x_min = new_x_min
+ self.state.x_max = new_x_max
# We need to adjust the limits in here to avoid triggering all
# the update events then changing the limits again.
@@ -215,6 +244,10 @@ def zoom_level(self, val):
def zoom(self, val):
"""Zoom in or out by the given factor.
+ .. warning::
+ When a viewer is linked by WCS, this method accidentally
+ changes the center also; see the warning in ``zoom_level``.
+
Parameters
----------
val : int or float
@@ -451,8 +484,12 @@ def add_markers(self, table, x_colname='x', y_colname='y',
self._validate_marker_name(marker_name)
jglue = self.session.application
- # Link markers to reference image data.
- image = self.state.reference_data
+ # Link markers to top visible image data or reference data.
+ if not use_skycoord and hasattr(self, '_get_real_xy'):
+ i_top = get_top_layer_index(self)
+ image = self.layers[i_top].layer
+ else:
+ image = self.state.reference_data
# TODO: Is Glue smart enough to no-op if link already there?
if use_skycoord:
@@ -500,7 +537,7 @@ def add_markers(self, table, x_colname='x', y_colname='y',
self._marktags.add(marker_name)
- self.session.hub.broadcast(MarkersChangedMessage(True, sender=self))
+ self.session.hub.broadcast(AstrowidgetMarkersChangedMessage(True, sender=self))
def remove_markers(self, marker_name=None):
"""Remove some but not all of the markers by name used when
@@ -535,7 +572,8 @@ def remove_markers(self, marker_name=None):
self.session.application.data_collection.remove(data)
self._marktags.remove(marker_name)
- self.session.hub.broadcast(MarkersChangedMessage(len(self._marktags) > 0, sender=self))
+ self.session.hub.broadcast(AstrowidgetMarkersChangedMessage(len(self._marktags) > 0,
+ sender=self))
def reset_markers(self):
"""Delete all markers."""
diff --git a/jdaviz/core/events.py b/jdaviz/core/events.py
index a69332acae..7e4440ebed 100644
--- a/jdaviz/core/events.py
+++ b/jdaviz/core/events.py
@@ -7,8 +7,9 @@
'SliceSelectSliceMessage',
'SliceToolStateMessage',
'TableClickMessage', 'LinkUpdatedMessage', 'ExitBatchLoadMessage',
- 'MarkersChangedMessage', 'CanvasRotationChangedMessage',
- 'GlobalDisplayUnitChanged']
+ 'AstrowidgetMarkersChangedMessage', 'MarkersPluginUpdate',
+ 'CanvasRotationChangedMessage',
+ 'GlobalDisplayUnitChanged', 'ChangeRefDataMessage']
class NewViewerMessage(Message):
@@ -129,6 +130,32 @@ def viewer_id(self):
return self._viewer_id
+class ChangeRefDataMessage(Message):
+ def __init__(self, data, viewer, viewer_id=None, old=None, *args, **kwargs):
+ super().__init__(*args, **kwargs)
+
+ self._data = data
+ self._viewer = viewer
+ self._viewer_id = viewer_id
+ self._old = old
+
+ @property
+ def data(self):
+ return self._data
+
+ @property
+ def viewer(self):
+ return self._viewer
+
+ @property
+ def viewer_id(self):
+ return self._viewer_id
+
+ @property
+ def old(self):
+ return self._old
+
+
class SnackbarMessage(Message):
def __init__(self, text, color=None, timeout=5000, loading=False,
*args, **kwargs):
@@ -326,8 +353,8 @@ def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
-class MarkersChangedMessage(Message):
- '''Message generated when markers are added/removed from an image viewer'''
+class AstrowidgetMarkersChangedMessage(Message):
+ '''Message generated when markers are added/removed from an image viewer via astrowidgets API'''
def __init__(self, has_markers, *args, **kwargs):
super().__init__(*args, **kwargs)
self._has_markers = has_markers
@@ -337,6 +364,13 @@ def has_markers(self):
return self._has_markers
+class MarkersPluginUpdate(Message):
+ '''Message when the length of the markers plugin table changes'''
+ def __init__(self, table_length, *args, **kwargs):
+ super().__init__(*args, **kwargs)
+ self.table_length = table_length
+
+
class CanvasRotationChangedMessage(Message):
'''Message generated by canvas rotation plugin'''
def __init__(self, viewer_id, angle, flip_horizontal, *args, **kwargs):
diff --git a/jdaviz/core/freezable_state.py b/jdaviz/core/freezable_state.py
index 6405bf035b..eb6bdf7b38 100644
--- a/jdaviz/core/freezable_state.py
+++ b/jdaviz/core/freezable_state.py
@@ -56,6 +56,7 @@ class FreezableBqplotImageViewerState(BqplotImageViewerState, FreezableState):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
+ self.wcs_only_layers = [] # For Imviz rotation use.
def reset_limits(self, *event):
if self.reference_data is None: # Nothing to do
diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index 43a6df1f88..07b9417b6a 100644
--- a/jdaviz/core/helpers.py
+++ b/jdaviz/core/helpers.py
@@ -13,7 +13,6 @@
import numpy as np
import astropy.units as u
-from astropy.wcs.wcsapi import BaseHighLevelWCS
from astropy.nddata import CCDData, StdDevUncertainty
from regions.core.core import Region
from glue.core import HubListener
@@ -28,6 +27,7 @@
from jdaviz.app import Application
from jdaviz.core.events import SnackbarMessage, ExitBatchLoadMessage
from jdaviz.core.template_mixin import show_widget
+from jdaviz.utils import data_has_valid_wcs
__all__ = ['ConfigHelper', 'ImageConfigHelper']
@@ -131,8 +131,17 @@ def plugins(self):
plugins : dict
dict of plugin objects
"""
- return {item['label']: widget_serialization['from_json'](item['widget'], None).user_api
- for item in self.app.state.tray_items}
+ plugins = {item['label']: widget_serialization['from_json'](item['widget'], None).user_api
+ for item in self.app.state.tray_items}
+
+ # handle renamed plugins during deprecation
+ if 'Orientation' in plugins:
+ plugins['Links Control'] = plugins['Orientation']._obj.user_api
+ plugins['Links Control']._deprecation_msg = 'in the future, the formerly named \"Links Control\" plugin will only be available by its new name: \"Orientation\".' # noqa
+ if 'Canvas Rotation' in plugins:
+ plugins['Canvas Rotation']._deprecation_msg = 'this functionality will be removed in favor of the implementation for rotation in the \"Orientation\" plugin.' # noqa
+
+ return plugins
@property
def viewers(self):
@@ -769,6 +778,14 @@ def load_regions(self, regions, max_num_regions=None, refdata_label=None,
bad_regions.append((region, 'Sky region provided but data has no valid WCS'))
continue
+ if (isinstance(region, (CircularAperture, EllipticalAperture,
+ RectangularAperture, CircularAnnulus,
+ CirclePixelRegion, EllipsePixelRegion,
+ RectanglePixelRegion, CircleAnnulusPixelRegion))
+ and self.app._link_type == "wcs"):
+ bad_regions.append((region, 'Pixel region provided by data is linked by WCS'))
+ continue
+
# photutils: Convert to regions shape first
if isinstance(region, (CircularAperture, SkyCircularAperture,
EllipticalAperture, SkyEllipticalAperture,
@@ -862,8 +879,11 @@ def get_interactive_regions(self):
``regions`` objects.
"""
+ from glue_astronomy.translators.regions import roi_subset_state_to_region
+
regions = {}
failed_regs = set()
+ to_sky = self.app._link_type == 'wcs'
# Subset is global, so we just use default viewer.
for lyr in self.default_viewer._obj.layers:
@@ -880,8 +900,11 @@ def get_interactive_regions(self):
continue
try:
- region = subset_data.data.get_selection_definition(
- subset_id=subset_label, format='astropy-regions')
+ if self.app.config == "imviz" and to_sky:
+ region = roi_subset_state_to_region(subset_data.subset_state, to_sky=to_sky)
+ else:
+ region = subset_data.data.get_selection_definition(
+ subset_id=subset_label, format='astropy-regions')
except (NotImplementedError, ValueError):
failed_regs.add(subset_label)
else:
@@ -924,14 +947,6 @@ def _delete_all_regions(self):
self.app.data_collection.remove_subset_group(subset_grp)
-def data_has_valid_wcs(data, ndim=None):
- """Check if given glue Data has WCS that is compatible with APE 14."""
- status = hasattr(data, 'coords') and isinstance(data.coords, BaseHighLevelWCS)
- if ndim is not None:
- status = status and data.coords.world_n_dim == ndim
- return status
-
-
def _next_subset_num(label_prefix, subset_groups):
"""Assumes ``prefix i`` format.
Does not go back and fill in lower but available numbers. This is consistent with Glue.
diff --git a/jdaviz/core/region_translators.py b/jdaviz/core/region_translators.py
index a9e4a07b90..ee2026dc72 100644
--- a/jdaviz/core/region_translators.py
+++ b/jdaviz/core/region_translators.py
@@ -20,7 +20,7 @@
__all__ = ['regions2roi', 'regions2aperture', 'aperture2regions']
-def _get_region_from_spatial_subset(plugin_obj, subset_state, dataset=None):
+def _get_region_from_spatial_subset(plugin_obj, subset_state):
"""Convert the given ``glue`` ROI subset state to ``regions`` shape.
.. note:: This is for internal use only in Imviz plugins.
@@ -30,16 +30,11 @@ def _get_region_from_spatial_subset(plugin_obj, subset_state, dataset=None):
plugin_obj : obj
Plugin instance that needs this translation.
The plugin is assumed to have a special setup that gives
- it access to these attributes: ``app`` and ``dataset_selected``.
- The ``app._jdaviz_helper.get_link_type`` method must also
- exist.
+ it access to these attributes: ``app`` and ``app._link_type``.
subset_state : obj
ROI subset state to translate.
- dataset : string, optional
- Name of the dataset. If not provided, will look for ``plugin_obj.dataset_selected``.
-
Returns
-------
reg : `regions.Region`
@@ -56,12 +51,8 @@ def _get_region_from_spatial_subset(plugin_obj, subset_state, dataset=None):
# Subset is defined against its parent. This is not necessarily
# the current viewer reference data, which can be changed.
- if dataset is None:
- dataset = plugin_obj.dataset_selected
-
- # See https://github.com/spacetelescope/jdaviz/issues/2230
- link_type = plugin_obj.app._jdaviz_helper.get_link_type(
- subset_state.xatt.parent.label, dataset)
+ # Mixed link types no longer allowed, so just check app setting.
+ link_type = plugin_obj.app._link_type
return roi_subset_state_to_region(subset_state, to_sky=(link_type == 'wcs'))
diff --git a/jdaviz/core/template_mixin.py b/jdaviz/core/template_mixin.py
index cc04dbf7ec..61761de605 100644
--- a/jdaviz/core/template_mixin.py
+++ b/jdaviz/core/template_mixin.py
@@ -1244,7 +1244,7 @@ class LayerSelect(SelectPluginComponent):
* register with all the automatic logic in the plugin's init by passing the string names
of the respective traitlets.
* use component in plugin template (see below)
- * refer to properties above based on the interally stored reference to the
+ * refer to properties above based on the internally stored reference to the
instantiated object of this component
* observe the traitlets created and defined in the plugin, as necessary
@@ -1262,7 +1262,8 @@ class LayerSelect(SelectPluginComponent):
def __init__(self, plugin, items, selected, viewer,
multiselect=None,
default_text=None, manual_options=[],
- default_mode='first'):
+ default_mode='first',
+ only_wcs_layers=False):
"""
Parameters
----------
@@ -1310,6 +1311,7 @@ def __init__(self, plugin, items, selected, viewer,
self.add_observe(viewer, self._on_viewer_selected_changed)
self.add_observe(selected, self._update_layer_items)
self._update_layer_items()
+ self.update_wcs_only_filter(only_wcs_layers)
def _get_viewer(self, viewer):
# newer will likely be the viewer name in most cases, but viewer id in the case
@@ -1437,23 +1439,64 @@ def _update_layer_items(self, msg={}):
# NOTE: _on_layers_changed is passed without a msg object during init
# TODO: Handle changes to just one item without recompiling the whole thing
manual_items = [{'label': label} for label in self.manual_options]
- all_layers = [layer for viewer in self.viewer_objs
- for layer in getattr(viewer, 'layers', [])]
+ # use getattr so the super() call above doesn't try to access the attr before
+ # it is initialized:
+
+ all_layers = [
+ layer for viewer in self.viewer_objs
+ for layer in getattr(viewer, 'layers', [])
+ if self._is_valid_item(layer)
+ ]
+
# remove duplicates - we'll loop back through all selected viewers to get a list of colors
# and visibilities later within _layer_to_dict
- layer_labels = [layer.layer.label for layer in all_layers if self.app.state.layer_icons.get(layer.layer.label)] # noqa
+ layer_labels = [
+ layer.layer.label for layer in all_layers
+ if self.app.state.layer_icons.get(layer.layer.label) or
+ self.only_wcs_layers
+ ]
unique_layer_labels = list(set(layer_labels))
-
layer_items = [self._layer_to_dict(layer_label) for layer_label in unique_layer_labels]
def _sort_by_icon(items_dict):
- return items_dict['icon']
+ icon = items_dict['icon']
+ return icon if icon is not None else ''
+
layer_items.sort(key=_sort_by_icon)
self.items = manual_items + layer_items
self._apply_default_selection()
+ def update_wcs_only_filter(self, wcs_only):
+ """
+ The layers that are populated in LayerSelect.choices
+ will be either WCS-only layers (for setting viewer orientation)
+ or non-WCS-only layers (for "real data"). This method toggles
+ the layer choices by adjusting the layer filters on this
+ LayerSelect instance.
+
+ Parameters
+ ----------
+ wcs_only : bool
+ `True` will filter only the WCS-only layers, `False` will
+ give the non-WCS-only layers.
+ """
+ def is_wcs_only(layer):
+ return getattr(layer.layer, 'meta', {}).get(self.app._wcs_only_label, False)
+
+ filter_names = [getattr(filt, '__name__', '') for filt in self.filters]
+
+ if not wcs_only and 'is_wcs_only' in filter_names:
+ self.filters.remove(*[filt for filt in self.filters
+ if getattr(filt, '__name__', '') == 'is_wcs_only'])
+ elif wcs_only and 'is_wcs_only' not in filter_names:
+ self.add_filter(is_wcs_only)
+
+ @property
+ def only_wcs_layers(self):
+ return 'is_wcs_only' in [getattr(filt, '__name__', '') for filt in self.filters]
+
@cached_property
def selected_obj(self):
viewer_names = self.viewer
@@ -1782,9 +1825,7 @@ def _get_spatial_region(self, dataset, subset=None):
subset_state = self.selected_subset_state
else:
subset_state = self._get_subset_state(subset)
- region = _get_region_from_spatial_subset(self.plugin,
- subset_state,
- dataset=dataset)
+ region = _get_region_from_spatial_subset(self.plugin, subset_state)
region.meta['label'] = subset
return region
@@ -2458,7 +2499,7 @@ class DatasetSelect(SelectPluginComponent):
def __init__(self, plugin, items, selected,
multiselect=None,
- filters=['not_from_plugin_model_fitting', 'layer_in_viewers'],
+ filters=['not_from_plugin_model_fitting', 'layer_in_viewers', 'is_not_wcs_only'],
default_text=None, manual_options=[],
default_mode='first'):
"""
@@ -2615,6 +2656,9 @@ def is_image(data):
def is_cube(data):
return len(data.shape) == 3
+ def is_not_wcs_only(data):
+ return not data.meta.get(self.app._wcs_only_label, False)
+
return super()._is_valid_item(data, locals())
@observe('filters')
diff --git a/jdaviz/core/tools.py b/jdaviz/core/tools.py
index 8ce84647e3..adc553129e 100644
--- a/jdaviz/core/tools.py
+++ b/jdaviz/core/tools.py
@@ -58,9 +58,6 @@ def _iter_matched_viewers(self, include_self=False):
def _map_limits(self, from_viewer, to_viewer, limits={}):
return limits
- def _post_activate(self):
- return
-
@property
def match_keys(self):
keys = []
@@ -80,8 +77,6 @@ def activate(self):
for k in self.match_keys:
self.viewer.state.add_callback(k, self.on_limits_change)
- self._post_activate()
-
# Trigger a sync so the initial limits match
self.on_limits_change()
@@ -94,29 +89,49 @@ def deactivate(self):
def on_limits_change(self, *args):
# from_lims: limits in the viewer belonging to the tool
from_lims = {k: getattr(self.viewer.state, k) for k in self.match_keys}
+ orig_refdata = self.viewer.state.reference_data
+ if hasattr(self.viewer, '_get_fov') and orig_refdata and orig_refdata.coords:
+ orig_fov_sky = self.viewer._get_fov(wcs=orig_refdata.coords)
+ sky_cen = self.viewer._get_center_skycoord()
+ else:
+ orig_fov_sky = sky_cen = None
for viewer in self._iter_matched_viewers(include_self=False):
# orig_lims: limits in this "matched" viewer
# to_lims: proposed new limits for this "matched" viewer
orig_lims = {k: getattr(viewer.state, k) for k in self.match_keys}
to_lims = self._map_limits(self.viewer, viewer, from_lims)
- with delay_callback(viewer.state, *self.match_keys):
- for ax in self.match_axes:
- # to avoid recursion we'll only update the state if there is a change
- # outside a tolerance set by some fraction of the limits range
- if None in orig_lims.values():
- orig_range = np.inf
- else:
- orig_range = abs(orig_lims.get(f'{ax}_max') - orig_lims.get(f'{ax}_min'))
- to_range = abs(to_lims.get(f'{ax}_max') - to_lims.get(f'{ax}_min'))
- tol = 1e-6 * min(orig_range, to_range)
-
- for k in (f'{ax}_min', f'{ax}_max'):
- value = to_lims.get(k)
- orig_value = orig_lims.get(k)
- if not np.isnan(value) and (orig_value is None or
- abs(value-orig_lims.get(k, np.inf)) > tol):
- setattr(viewer.state, k, value)
+ matched_refdata = viewer.state.reference_data
+
+ if hasattr(viewer, '_get_fov'):
+ to_fov_sky = viewer._get_fov(wcs=matched_refdata.coords)
+ else:
+ to_fov_sky = None
+
+ if to_fov_sky is not None and orig_fov_sky is not None:
+ old_level = viewer.zoom_level
+ viewer.zoom_level = old_level * float(to_fov_sky / orig_fov_sky)
+ viewer.center_on(sky_cen)
+
+ else:
+ with delay_callback(viewer.state, *self.match_keys):
+ for ax in self.match_axes:
+ if None in orig_lims.values():
+ orig_range = np.inf
+ else:
+ orig_range = abs(orig_lims.get(f'{ax}_max') -
+ orig_lims.get(f'{ax}_min'))
+ to_range = abs(to_lims.get(f'{ax}_max') -
+ to_lims.get(f'{ax}_min'))
+ tol = 1e-6 * min(orig_range, to_range)
+
+ for k in (f'{ax}_min', f'{ax}_max'):
+ value = to_lims.get(k)
+ orig_value = orig_lims.get(k)
+
+ if not np.isnan(value) and (orig_value is None or
+ abs(value-orig_lims.get(k, np.inf)) > tol):
+ setattr(viewer.state, k, value)
def is_visible(self):
return len(self.viewer.jdaviz_app._viewer_store) > 1
diff --git a/jdaviz/core/user_api.py b/jdaviz/core/user_api.py
index 848e5da5c1..7f70045e36 100644
--- a/jdaviz/core/user_api.py
+++ b/jdaviz/core/user_api.py
@@ -1,8 +1,9 @@
+import logging
import astropy.units as u
__all__ = ['UserApiWrapper', 'PluginUserApi', 'ViewerUserApi']
-_internal_attrs = ('_obj', '_expose', '_readonly', '__doc__')
+_internal_attrs = ('_obj', '_expose', '_readonly', '__doc__', '_deprecation_msg')
class UserApiWrapper:
@@ -14,6 +15,7 @@ def __init__(self, obj, expose=[], readonly=[]):
self._obj = obj
self._expose = list(expose) + list(readonly)
self._readonly = readonly
+ self._deprecation_msg = None
if obj.__doc__ is not None:
self.__doc__ = self.__doc__ + "\n\n\n" + obj.__doc__
@@ -94,9 +96,13 @@ def __init__(self, plugin, expose=[], readonly=[]):
expose = list(set(list(expose) + ['open_in_tray', 'close_in_tray', 'show']))
if plugin.uses_active_status:
expose += ['keep_active', 'as_active']
+ self._deprecation_msg = None
super().__init__(plugin, expose, readonly)
def __repr__(self):
+ if self._deprecation_msg:
+ logging.warning("DeprecationWarning: %s" % self._deprecation_msg)
+ super().__setattr__('_deprecation_msg', None)
return f'<{self._obj._registry_label} API>'
@@ -114,4 +120,16 @@ def __init__(self, viewer, expose=[], readonly=[]):
super().__init__(viewer, expose, readonly)
def __repr__(self):
- return f'<{self._obj._ref_or_id} API>'
+ return f'<{self._obj.reference} API>'
+
+ def __getattr__(self, *args, **kwargs):
+ if super().__getattr__('_deprecation_msg'):
+ logging.warning(f"DeprecationWarning: {self._deprecation_msg}")
+ super().__setattr__('_deprecation_msg', None)
+ return super().__getattr__(*args, **kwargs)
+
+ def __setattr__(self, *args, **kwargs):
+ if hasattr(self, '_deprecation_msg') and self._deprecation_msg:
+ logging.warning(f"DeprecationWarning: {self._deprecation_msg}")
+ super().__setattr__('_deprecation_msg', None)
+ return super().__setattr__(*args, **kwargs)
diff --git a/jdaviz/tests/test_subsets.py b/jdaviz/tests/test_subsets.py
index d258006ad3..63cccdf374 100644
--- a/jdaviz/tests/test_subsets.py
+++ b/jdaviz/tests/test_subsets.py
@@ -43,10 +43,10 @@ def test_region_from_subset_2d(cubeviz_helper):
assert subset_plugin.subset_types == ["EllipticalROI"]
assert subset_plugin.is_centerable
for key in ("orig", "value"):
- assert subset_plugin._get_value_from_subset_definition(0, "X Center", key) == 1
- assert subset_plugin._get_value_from_subset_definition(0, "Y Center", key) == 3.5
- assert subset_plugin._get_value_from_subset_definition(0, "X Radius", key) == 1.2
- assert subset_plugin._get_value_from_subset_definition(0, "Y Radius", key) == 3.3
+ assert subset_plugin._get_value_from_subset_definition(0, "X Center (pixels)", key) == 1
+ assert subset_plugin._get_value_from_subset_definition(0, "Y Center (pixels)", key) == 3.5
+ assert subset_plugin._get_value_from_subset_definition(0, "X Radius (pixels)", key) == 1.2
+ assert subset_plugin._get_value_from_subset_definition(0, "Y Radius (pixels)", key) == 3.3
assert subset_plugin._get_value_from_subset_definition(0, "Angle", key) == 0
# Recenter GUI should not be exposed, but API call would raise exception.
@@ -82,26 +82,26 @@ def test_region_from_subset_3d(cubeviz_helper):
assert subset_plugin.is_centerable
assert subset_plugin.get_center() == (2.25, 1.55)
for key in ("orig", "value"):
- assert subset_plugin._get_value_from_subset_definition(0, "Xmin", key) == 1
- assert subset_plugin._get_value_from_subset_definition(0, "Xmax", key) == 3.5
- assert subset_plugin._get_value_from_subset_definition(0, "Ymin", key) == -0.2
- assert subset_plugin._get_value_from_subset_definition(0, "Ymax", key) == 3.3
+ assert subset_plugin._get_value_from_subset_definition(0, "Xmin (pixels)", key) == 1
+ assert subset_plugin._get_value_from_subset_definition(0, "Xmax (pixels)", key) == 3.5
+ assert subset_plugin._get_value_from_subset_definition(0, "Ymin (pixels)", key) == -0.2
+ assert subset_plugin._get_value_from_subset_definition(0, "Ymax (pixels)", key) == 3.3
assert subset_plugin._get_value_from_subset_definition(0, "Angle", key) == 0
# Mimic user changing something in Subset Tool GUI.
- subset_plugin._set_value_in_subset_definition(0, "Xmin", "value", 2)
- subset_plugin._set_value_in_subset_definition(0, "Ymin", "value", 0)
+ subset_plugin._set_value_in_subset_definition(0, "Xmin (pixels)", "value", 2)
+ subset_plugin._set_value_in_subset_definition(0, "Ymin (pixels)", "value", 0)
subset_plugin._set_value_in_subset_definition(0, "Angle", "value", 45) # ccw deg
# "orig" is unchanged until user clicks Update button.
- assert subset_plugin._get_value_from_subset_definition(0, "Xmin", "orig") == 1
- assert subset_plugin._get_value_from_subset_definition(0, "Ymin", "orig") == -0.2
+ assert subset_plugin._get_value_from_subset_definition(0, "Xmin (pixels)", "orig") == 1
+ assert subset_plugin._get_value_from_subset_definition(0, "Ymin (pixels)", "orig") == -0.2
assert subset_plugin._get_value_from_subset_definition(0, "Angle", "orig") == 0
subset_plugin.vue_update_subset()
for key in ("orig", "value"):
- assert subset_plugin._get_value_from_subset_definition(0, "Xmin", key) == 2
- assert subset_plugin._get_value_from_subset_definition(0, "Xmax", key) == 3.5
- assert subset_plugin._get_value_from_subset_definition(0, "Ymin", key) == 0
- assert subset_plugin._get_value_from_subset_definition(0, "Ymax", key) == 3.3
+ assert subset_plugin._get_value_from_subset_definition(0, "Xmin (pixels)", key) == 2
+ assert subset_plugin._get_value_from_subset_definition(0, "Xmax (pixels)", key) == 3.5
+ assert subset_plugin._get_value_from_subset_definition(0, "Ymin (pixels)", key) == 0
+ assert subset_plugin._get_value_from_subset_definition(0, "Ymax (pixels)", key) == 3.3
assert subset_plugin._get_value_from_subset_definition(0, "Angle", key) == 45
subsets = cubeviz_helper.app.get_subsets()
@@ -132,9 +132,9 @@ def test_region_from_subset_3d(cubeviz_helper):
assert subset_plugin.subset_types == ["CircularROI"]
assert subset_plugin.is_centerable
for key in ("orig", "value"):
- assert subset_plugin._get_value_from_subset_definition(0, "X Center", key) == 3
- assert subset_plugin._get_value_from_subset_definition(0, "Y Center", key) == 4
- assert subset_plugin._get_value_from_subset_definition(0, "Radius", key) == 2.4
+ assert subset_plugin._get_value_from_subset_definition(0, "X Center (pixels)", key) == 3
+ assert subset_plugin._get_value_from_subset_definition(0, "Y Center (pixels)", key) == 4
+ assert subset_plugin._get_value_from_subset_definition(0, "Radius (pixels)", key) == 2.4
# Circular Annulus Subset
flux_viewer = cubeviz_helper.app.get_viewer("flux-viewer")
@@ -147,10 +147,10 @@ def test_region_from_subset_3d(cubeviz_helper):
assert subset_plugin.subset_selected == "Subset 3"
assert subset_plugin.subset_types == ["CircularAnnulusROI"]
for key in ("orig", "value"):
- assert subset_plugin._get_value_from_subset_definition(0, "X Center", key) == 5
- assert subset_plugin._get_value_from_subset_definition(0, "Y Center", key) == 6
- assert subset_plugin._get_value_from_subset_definition(0, "Inner radius", key) == 2
- assert subset_plugin._get_value_from_subset_definition(0, "Outer radius", key) == 4
+ assert subset_plugin._get_value_from_subset_definition(0, "X Center (pixels)", key) == 5
+ assert subset_plugin._get_value_from_subset_definition(0, "Y Center (pixels)", key) == 6
+ assert subset_plugin._get_value_from_subset_definition(0, "Inner Radius (pixels)", key) == 2
+ assert subset_plugin._get_value_from_subset_definition(0, "Outer Radius (pixels)", key) == 4
def test_region_from_subset_profile(cubeviz_helper, spectral_cube_wcs):
@@ -486,7 +486,7 @@ def test_composite_region_with_consecutive_and_not_states(cubeviz_helper):
def test_composite_region_with_imviz(imviz_helper, image_2d_wcs):
- arr = np.ones((10, 10))
+ arr = NDData(np.ones((10, 10)), wcs=image_2d_wcs)
data_label = 'image-data'
viewer = imviz_helper.default_viewer._obj
@@ -540,11 +540,12 @@ def test_recenter_linked_by_wcs(imviz_helper):
# Link them by WCS
imviz_helper.link_data(link_type='wcs')
+ w = imviz_helper.app.data_collection[0].coords
# This rectangle is over a real object in reference image but
# only the last row in the second image if linked by pixel.
imviz_helper.load_regions(
- RectanglePixelRegion(center=PixCoord(x=229, y=152), width=17, height=7))
+ RectanglePixelRegion(center=PixCoord(x=229, y=152), width=17, height=7).to_sky(w))
subset_plugin = imviz_helper.plugins["Subset Tools"]._obj
subset_plugin.subset_selected = "Subset 1"
@@ -556,13 +557,15 @@ def test_recenter_linked_by_wcs(imviz_helper):
# If handled correctly, it won't change much.
# But if not, it move down by 7 pix or so (229.05, 145.92) and fails the test.
- assert_allclose(subset_plugin.get_center(), (229.067822, 152.371943))
+ xy = imviz_helper.default_viewer._obj._get_real_xy(
+ imviz_helper.app.data_collection[0], *subset_plugin.get_center())[:2]
+ assert_allclose(xy, (229.067822, 152.371943))
# Now create a new subset that has a source in the corner and test
# recentering with multiselect.
imviz_helper.load_regions(
- CirclePixelRegion(center=PixCoord(x=145, y=175), radius=17))
+ CirclePixelRegion(center=PixCoord(x=145, y=175), radius=17).to_sky(w))
subset_plugin.multiselect = True
subset_plugin.subset_selected = ["Subset 1", "Subset 2"]
@@ -570,7 +573,9 @@ def test_recenter_linked_by_wcs(imviz_helper):
for _ in range(5):
subset_plugin.vue_recenter_subset()
- assert_allclose(subset_plugin.get_center("Subset 2"), (145.593022, 172.515541))
+ xy = imviz_helper.default_viewer._obj._get_real_xy(
+ imviz_helper.app.data_collection[0], *subset_plugin.get_center("Subset 2"))[:2]
+ assert_allclose(xy, (145.593022, 172.515541))
with pytest.raises(ValueError, match="Please include subset_name in"):
subset_plugin.get_center()
diff --git a/jdaviz/utils.py b/jdaviz/utils.py
index 9be5230092..30aa315b8d 100644
--- a/jdaviz/utils.py
+++ b/jdaviz/utils.py
@@ -2,15 +2,16 @@
import time
import threading
from collections import deque
-import numpy as np
+import numpy as np
from astropy.io import fits
from astropy.utils import minversion
-from ipyvue import watch
-from glue.core.exceptions import IncompatibleAttribute
+from astropy.wcs.wcsapi import BaseHighLevelWCS
from glue.config import settings
+from glue.core import BaseData
+from glue.core.exceptions import IncompatibleAttribute
from glue.core.subset import SubsetState, RangeSubsetState, RoiSubsetState
-
+from ipyvue import watch
__all__ = ['SnackbarQueue', 'enable_hot_reloading', 'bqplot_clear_figure',
'standardize_metadata', 'ColorCycler', 'alpha_index', 'get_subset_type']
@@ -216,6 +217,18 @@ def alpha_index(index):
return chr(97 + index//26 - 1) + chr(97 + index % 26)
+def data_has_valid_wcs(data, ndim=None):
+ """Check if given glue Data has WCS that is compatible with APE 14."""
+ status = hasattr(data, 'coords') and isinstance(data.coords, BaseHighLevelWCS)
+ if ndim is not None:
+ status = status and data.coords.world_n_dim == ndim
+ return status
+
+
+def layer_is_table_data(layer):
+ return isinstance(layer, BaseData) and layer.ndim == 1
+
+
def standardize_metadata(metadata):
"""Standardize given metadata so it can be viewed in
Metadata Viewer plugin. The input can be plain
diff --git a/notebooks/concepts/imviz_dithered_gwcs.ipynb b/notebooks/concepts/imviz_dithered_gwcs.ipynb
index 7e716ef3bf..00f1b9122d 100644
--- a/notebooks/concepts/imviz_dithered_gwcs.ipynb
+++ b/notebooks/concepts/imviz_dithered_gwcs.ipynb
@@ -101,8 +101,8 @@
"outputs": [],
"source": [
"# Link by WCS\n",
- "imviz.plugins['Links Control'].link_type = 'WCS'\n",
- "imviz.plugins['Links Control'].wcs_use_affine = True"
+ "imviz.plugins['Orientation'].link_type = 'WCS'\n",
+ "imviz.plugins['Orientation'].wcs_use_affine = True"
]
},
{