Merge pull request #311 from astrofrog/profile-viewer-units

Initial support for unit conversion in profile viewer

.github/workflows/ci_workflows.yml

@@ -28,13 +28,11 @@ jobs:
           - libhdf5-dev
 
       envs: |
-        - linux: py37-test
         - linux: py38-test
         - linux: py39-test
         - linux: py310-test
         - linux: py311-test
 
-        - macos: py37-test
         - macos: py38-test
         - macos: py39-test
         # One of these to be switched to arm64 running natively once the PLAT var is supported.
@@ -52,12 +50,11 @@ jobs:
       pytest: false
 
       envs: |
-        - linux: py37-notebooks
-        - windows: py37-notebooks
+        - windows: py39-notebooks
         - macos: py38-notebooks
         - linux: py310-notebooks
 
-        - linux: py37-docs
+        - linux: py311-docs
         - macos: py39-docs
         - windows: py38-docs
 

docs/conf.py

@@ -178,7 +178,7 @@
 intersphinx_cache_limit = 10     # days to keep the cached inventories
 intersphinx_mapping = {
     # 'sphinx': ('https://www.sphinx-doc.org/en/latest/', None),
-    'python': ('https://docs.python.org/3.7', None),
+    'python': ('https://docs.python.org/3.11', None),
     # 'matplotlib': ('https://matplotlib.org', None),
     # 'numpy': ('https://docs.scipy.org/doc/numpy', None),
     # 'astropy': ('http://docs.astropy.org/en/stable/', None),

docs/installing.rst

@@ -10,7 +10,7 @@ installing it in an isolated Python environment for now. If you are using conda,
 you can create an environment and install the latest version of glue-jupyter in
 it using::
 
-    conda create -n glue-jupyter -c glueviz/label/dev python=3.7 glue-jupyter
+    conda create -n glue-jupyter -c glueviz/label/dev python=3.11 glue-jupyter
 
 To switch to the environment, use::
 
@@ -27,7 +27,7 @@ latest version of glue-jupyter, or if you find conda too slow to install all the
 dependencies, you can also create the environment with conda (or another Python
 environment manager)::
 
-    conda create -n glue-jupyter python=3.7
+    conda create -n glue-jupyter python=3.11
 
 then switch to the environment as above and install glue-jupyter and all its
 dependencies with::

glue_jupyter/app.py

@@ -67,19 +67,24 @@ def __init__(self, data_collection=None, session=None, settings=None):
             REQUIRED_PLUGINS.clear()
             load_plugins()
 
-        self.output = widgets.Output()
-        self.widget_data_collection = widgets.SelectMultiple()
-        self.widget_subset_select = SubsetSelect(session=self.session)
-        self.widget_subset_mode = SelectionModeMenu(session=self.session)
-        self.widget = widgets.VBox(children=[self.widget_subset_mode, self.output])
-
         self._settings['new_subset_on_selection_tool_change'] = [False, bool]
         self._settings['single_global_active_tool'] = [True, bool]
+        self._settings['disable_output_widget'] = [False, bool]
 
         if settings is not None:
             for key, value in settings.items():
                 self.set_setting(key, value)
 
+        self.output = None if self.get_setting('disable_output_widget') else widgets.Output()
+        self.widget_data_collection = widgets.SelectMultiple()
+        self.widget_subset_select = SubsetSelect(session=self.session)
+        self.widget_subset_mode = SelectionModeMenu(session=self.session)
+
+        if self.output is None:
+            self.widget = widgets.VBox(children=[self.widget_subset_mode])
+        else:
+            self.widget = widgets.VBox(children=[self.widget_subset_mode, self.output])
+
         self._viewer_refs = []
 
     def _ipython_display_(self):

glue_jupyter/bqplot/common/tools.py

@@ -1,3 +1,5 @@
+from contextlib import nullcontext
+
 import os
 from bqplot import PanZoom
 from bqplot.interacts import BrushSelector, BrushIntervalSelector
@@ -132,7 +134,7 @@ def __init__(self, viewer, roi=None, finalize_callback=None, **kwargs):
     def update_selection(self, *args):
         if self.interact.brushing:
             return
-        with self.viewer._output_widget:
+        with self.viewer._output_widget or nullcontext():
             if self.interact.selected_x is not None and self.interact.selected_y is not None:
                 x = self.interact.selected_x
                 y = self.interact.selected_y
@@ -142,7 +144,7 @@ def update_selection(self, *args):
                     self.finalize_callback()
 
     def update_from_roi(self, roi):
-        with self.viewer._output_widget:
+        with self.viewer._output_widget or nullcontext():
             if isinstance(roi, RectangularROI):
                 self.interact.selected_x = [roi.xmin, roi.xmax]
                 self.interact.selected_y = [roi.ymin, roi.ymax]
@@ -161,7 +163,7 @@ def on_selection_change(self, *args):
                 self.finalize_callback()
 
     def activate(self):
-        with self.viewer._output_widget:
+        with self.viewer._output_widget or nullcontext():
             self.interact.selected_x = None
             self.interact.selected_y = None
         super().activate()
@@ -203,7 +205,7 @@ def __init__(self, viewer, roi=None, finalize_callback=None, **kwargs):
     def update_selection(self, *args):
         if self.interact.brushing:
             return
-        with self.viewer._output_widget:
+        with self.viewer._output_widget or nullcontext():
             if self.interact.selected_x is not None and self.interact.selected_y is not None:
                 x = self.interact.selected_x
                 y = self.interact.selected_y
@@ -242,7 +244,7 @@ def on_selection_change(self, *args):
                 self.finalize_callback()
 
     def activate(self):
-        with self.viewer._output_widget:
+        with self.viewer._output_widget or nullcontext():
             self.interact.selected_x = None
             self.interact.selected_y = None
         super().activate()
@@ -299,15 +301,15 @@ def __init__(self, viewer, **kwargs):
         self.interact.observe(self.update_selection, "brushing")
 
     def update_selection(self, *args):
-        with self.viewer._output_widget:
+        with self.viewer._output_widget or nullcontext():
             if self.interact.selected is not None:
                 x = self.interact.selected
                 if x is not None and len(x):
                     roi = RangeROI(min=min(x), max=max(x), orientation='x')
                     self.viewer.apply_roi(roi)
 
     def activate(self):
-        with self.viewer._output_widget:
+        with self.viewer._output_widget or nullcontext():
             self.interact.selected = None
         super().activate()
 
@@ -331,15 +333,15 @@ def __init__(self, viewer, **kwargs):
         self.interact.observe(self.update_selection, "brushing")
 
     def update_selection(self, *args):
-        with self.viewer._output_widget:
+        with self.viewer._output_widget or nullcontext():
             if self.interact.selected is not None:
                 y = self.interact.selected
                 if y is not None and len(y):
                     roi = RangeROI(min=min(y), max=max(y), orientation='y')
                     self.viewer.apply_roi(roi)
 
     def activate(self):
-        with self.viewer._output_widget:
+        with self.viewer._output_widget or nullcontext():
             self.interact.selected = None
         super().activate()
 

glue_jupyter/bqplot/common/viewer.py

@@ -1,5 +1,6 @@
 import bqplot
 from functools import partial
+from contextlib import nullcontext
 
 from glue.core.subset import roi_to_subset_state
 from glue.core.command import ApplySubsetState
@@ -65,28 +66,13 @@ def __init__(self, session, state=None):
         self.state.remove_callback('layers', self._sync_layer_artist_container)
         self.state.add_callback('layers', self._sync_layer_artist_container, priority=10000)
 
-        def update_axes(*ignore):
-            try:
-                # Extract units from data
-                x_unit = self.state.reference_data.get_component(self.state.x_att_world).units
-            except AttributeError:
-                # If no data loaded yet, ignore units
-                x_unit = ""
-            finally:
-                # Append units to axis label
-                self.axis_x.label = str(self.state.x_att) + " " + str(x_unit)
-            if self.is2d:
-                self.axis_y.label = str(self.state.y_att)
-                try:
-                    y_unit = self.state.reference_data.get_component(self.state.y_att_world).units
-                except AttributeError:
-                    y_unit = ""
-                finally:
-                    self.axis_y.label = str(self.state.y_att) + " " + str(y_unit)
-
-        self.state.add_callback('x_att', update_axes)
-        if self.is2d:
-            self.state.add_callback('y_att', update_axes)
+        self.state.add_callback('x_axislabel', self.update_x_axislabel)
+        # self.state.add_callback('x_axislabel_weight', self.update_x_axislabel)
+        # self.state.add_callback('x_axislabel_size', self.update_x_axislabel)
+
+        self.state.add_callback('y_axislabel', self.update_y_axislabel)
+        # self.state.add_callback('y_axislabel_weight', self.update_y_axislabel)
+        # self.state.add_callback('y_axislabel_size', self.update_y_axislabel)
 
         self.scale_x.observe(self.update_glue_scales, names=['min', 'max'])
         self.scale_y.observe(self.update_glue_scales, names=['min', 'max'])
@@ -103,6 +89,12 @@ def update_axes(*ignore):
 
         self.create_layout()
 
+    def update_x_axislabel(self, *event):
+        self.axis_x.label = self.state.x_axislabel
+
+    def update_y_axislabel(self, *event):
+        self.axis_y.label = self.state.y_axislabel
+
     def _update_bqplot_limits(self, *args):
 
         if self._last_limits == (self.state.x_min, self.state.x_max,
@@ -224,7 +216,7 @@ def _sync_show_axes(self):
 
     def apply_roi(self, roi, use_current=False):
         # TODO: partial copy paste from glue/viewers/matplotlib/qt/data_viewer.py
-        with self._output_widget:
+        with self._output_widget or nullcontext():
             if len(self.layers) > 0:
                 subset_state = self._roi_to_subset_state(roi)
                 cmd = ApplySubsetState(data_collection=self._data,

glue_jupyter/bqplot/histogram/viewer.py

@@ -26,6 +26,23 @@ class BqplotHistogramView(BqplotBaseView):
 
     tools = ['bqplot:home', 'bqplot:panzoom', 'bqplot:xrange']
 
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.state.add_callback('x_att', self._update_axes)
+        self.state.add_callback('x_log', self._update_axes)
+        self.state.add_callback('normalize', self._update_axes)
+        self._update_axes()
+
+    def _update_axes(self, *args):
+
+        if self.state.x_att is not None:
+            self.state.x_axislabel = str(self.state.x_att)
+
+        if self.state.normalize:
+            self.state.y_axislabel = 'Normalized number'
+        else:
+            self.state.y_axislabel = 'Number'
+
     def _roi_to_subset_state(self, roi):
         # TODO: copy paste from glue/viewers/histogram/qt/data_viewer.py
         # TODO Does subset get applied to all data or just visible data?

glue_jupyter/bqplot/image/viewer.py

@@ -44,12 +44,22 @@ def __init__(self, session):
         self.state.add_callback('reference_data', self._reset_limits, echo_old=True)
         self.state.add_callback('x_att', self._reset_limits, echo_old=True)
         self.state.add_callback('y_att', self._reset_limits, echo_old=True)
+        self.state.add_callback('x_att_world', self._update_axes)
+        self.state.add_callback('y_att_world', self._update_axes)
 
         self._setup_view_listener()
 
         on_change([(self.state, 'aspect')])(self._sync_figure_aspect)
         self._sync_figure_aspect()
 
+    def _update_axes(self, *args):
+
+        if self.state.x_att_world is not None:
+            self.state.x_axislabel = str(self.state.x_att_world)
+
+        if self.state.y_att_world is not None:
+            self.state.y_axislabel = str(self.state.y_att_world)
+
     def _setup_view_listener(self):
         self._vl = ViewListener(widget=self.figure,
                                 css_selector=".plotarea_events")

glue_jupyter/bqplot/profile/layer_artist.py

@@ -153,7 +153,8 @@ def _update_profile(self, force=False, **kwargs):
         if force or any(prop in changed for prop in ('layer', 'x_att', 'attribute',
                                                      'function', 'normalize',
                                                      'v_min', 'v_max',
-                                                     'as_steps')):
+                                                     'as_steps',
+                                                     'x_display_unit', 'y_display_unit')):
             self._calculate_profile(reset=force)
             force = True
 

glue_jupyter/bqplot/profile/tests/test_viewer.py

@@ -1,3 +1,13 @@
+from astropy.wcs import WCS
+
+import numpy as np
+from numpy.testing import assert_allclose, assert_equal
+
+from glue.core import Data
+from glue.core.roi import XRangeROI
+from glue.plugins.wcs_autolinking.wcs_autolinking import WCSLink
+
+
 def test_non_hex_colors(app, dataxyz):
 
     # Make sure non-hex colors such as '0.4' and 'red', which are valid
@@ -22,3 +32,88 @@ def test_remove(app, data_image, data_volume):
     assert len(s.figure.marks) == 2
     s.remove_data(data_volume)
     assert len(s.figure.marks) == 0
+
+
+def test_unit_conversion(app):
+
+    wcs1 = WCS(naxis=1)
+    wcs1.wcs.ctype = ['FREQ']
+    wcs1.wcs.crval = [1]
+    wcs1.wcs.cdelt = [1]
+    wcs1.wcs.crpix = [1]
+    wcs1.wcs.cunit = ['GHz']
+
+    d1 = Data(f1=[1, 2, 3])
+    d1.get_component('f1').units = 'Jy'
+    d1.coords = wcs1
+
+    wcs2 = WCS(naxis=1)
+    wcs2.wcs.ctype = ['WAVE']
+    wcs2.wcs.crval = [10]
+    wcs2.wcs.cdelt = [10]
+    wcs2.wcs.crpix = [1]
+    wcs2.wcs.cunit = ['cm']
+
+    d2 = Data(f2=[2000, 1000, 3000])
+    d2.get_component('f2').units = 'mJy'
+    d2.coords = wcs2
+
+    session = app.session
+
+    data_collection = session.data_collection
+    data_collection.append(d1)
+    data_collection.append(d2)
+    data_collection.add_link(WCSLink(d1, d2))
+
+    viewer = app.profile1d(data=d1)
+    viewer.add_data(d2)
+
+    assert viewer.layers[0].enabled
+    assert viewer.layers[1].enabled
+
+    x, y = viewer.state.layers[0].profile
+    assert_allclose(x, [1.e9, 2.e9, 3.e9])
+    assert_allclose(y, [1, 2, 3])
+
+    x, y = viewer.state.layers[1].profile
+    assert_allclose(x, 299792458 / np.array([0.1, 0.2, 0.3]))
+    assert_allclose(y, [2000, 1000, 3000])
+
+    assert viewer.state.x_min == 1.e9
+    assert viewer.state.x_max == 3.e9
+    assert viewer.state.y_min == 1.
+    assert viewer.state.y_max == 3.
+
+    roi = XRangeROI(1.4e9, 2.1e9)
+    viewer.apply_roi(roi)
+
+    assert len(d1.subsets) == 1
+    assert_equal(d1.subsets[0].to_mask(), [0, 1, 0])
+
+    assert len(d2.subsets) == 1
+    assert_equal(d2.subsets[0].to_mask(), [0, 1, 0])
+
+    viewer.state.x_display_unit = 'GHz'
+    viewer.state.y_display_unit = 'mJy'
+
+    x, y = viewer.state.layers[0].profile
+    assert_allclose(x, [1, 2, 3])
+    assert_allclose(y, [1000, 2000, 3000])
+
+    x, y = viewer.state.layers[1].profile
+    assert_allclose(x, 2.99792458 / np.array([1, 2, 3]))
+    assert_allclose(y, [2000, 1000, 3000])
+
+    assert viewer.state.x_min == 1.
+    assert viewer.state.x_max == 3.
+    assert viewer.state.y_min == 1000.
+    assert viewer.state.y_max == 3000.
+
+    roi = XRangeROI(0.5, 1.2)
+    viewer.apply_roi(roi)
+
+    assert len(d1.subsets) == 1
+    assert_equal(d1.subsets[0].to_mask(), [1, 0, 0])
+
+    assert len(d2.subsets) == 1
+    assert_equal(d2.subsets[0].to_mask(), [0, 0, 1])