Merge pull request #92 from Carifio24/ipyvolume

Add support for ipyvolume viewers

glue_plotly/__init__.py

@@ -90,6 +90,16 @@ def setup_jupyter():
     from glue_jupyter.bqplot.image import BqplotImageView
     from glue_jupyter.bqplot.profile import BqplotProfileView
     from glue_jupyter.bqplot.scatter import BqplotScatterView
+    from glue_jupyter.ipyvolume import IpyvolumeScatterView, IpyvolumeVolumeView
+
+    from glue_jupyter.ipyvolume.common.viewer import IpyvolumeBaseView
+    print(IpyvolumeBaseView.tools)
+    BqplotHistogramView.tools += ['save:bqplot_plotlyhist']
+    BqplotImageView.tools += ['save:bqplot_plotlyimage2d']
+    BqplotProfileView.tools += ['save:bqplot_plotlyprofile']
+    BqplotScatterView.tools += ['save:bqplot_plotly2d']
+    IpyvolumeScatterView.tools = [tool for tool in IpyvolumeScatterView.tools] + ['save:jupyter_plotly3dscatter']
+    IpyvolumeVolumeView.tools = [tool for tool in IpyvolumeVolumeView.tools] + ['save:jupyter_plotlyvolume']
 
     try:
         from glue_vispy_viewers.scatter.jupyter import JupyterVispyScatterViewer
@@ -99,8 +109,3 @@ def setup_jupyter():
     else:
         JupyterVispyScatterViewer.tools += ['save:jupyter_plotly3dscatter']
         JupyterVispyVolumeViewer.tools += ['save:jupyter_plotlyvolume']
-
-    BqplotHistogramView.tools += ['save:bqplot_plotlyhist']
-    BqplotImageView.tools += ['save:bqplot_plotlyimage2d']
-    BqplotProfileView.tools += ['save:bqplot_plotlyprofile']
-    BqplotScatterView.tools += ['save:bqplot_plotly2d']

glue_plotly/common/base_3d.py

@@ -21,7 +21,38 @@ def dimensions(viewer_state):
 
 
 def projection_type(viewer_state):
-    return "perspective" if viewer_state.perspective_view else "orthographic"
+    return "perspective" if getattr(viewer_state, "perspective_view", True) else "orthographic"
+
+
+def get_resolution(viewer_state):
+    try:
+        from glue_vispy_viewers.volume.viewer_state import Vispy3DVolumeViewerState
+        if isinstance(viewer_state, Vispy3DVolumeViewerState):
+            return viewer_state.resolution
+    except ImportError:
+        pass
+
+    try:
+        from glue_jupyter.common.state3d import VolumeViewerState
+        if isinstance(viewer_state, VolumeViewerState):
+            resolutions = tuple(getattr(state, 'max_resolution', None) for state in viewer_state.layers)
+            return max((res for res in resolutions if res is not None), default=256)
+    except ImportError:
+        pass
+
+    return 256
+
+
+# TODO: Update other methods to not rely on these being reversed
+def bounds(viewer_state, with_resolution=False):
+    bds = [(viewer_state.z_min, viewer_state.z_max),
+           (viewer_state.y_min, viewer_state.y_max),
+           (viewer_state.x_min, viewer_state.x_max)]
+    if with_resolution:
+        resolution = get_resolution(viewer_state)
+        return [(*b, resolution) for b in bds]
+
+    return bds
 
 
 def axis(viewer_state, ax):
@@ -84,6 +115,9 @@ def plotly_up_from_vispy(vispy_up):
 
 def layout_config(viewer_state):
     width, height, depth = dimensions(viewer_state)
+    x_stretch = getattr(viewer_state, "x_stretch", 1.)
+    y_stretch = getattr(viewer_state, "y_stretch", 1.)
+    z_stretch = getattr(viewer_state, "z_stretch", 1.)
     return dict(
         margin=dict(r=50, l=50, b=50, t=50),  # noqa
         width=1200,
@@ -99,9 +133,9 @@ def layout_config(viewer_state):
                 # Currently there's no way to change this in glue
                 up=plotly_up_from_vispy("+z")
             ),
-            aspectratio=dict(x=1 * viewer_state.x_stretch,
-                             y=height / width * viewer_state.y_stretch,
-                             z=depth / width * viewer_state.z_stretch),
+            aspectratio=dict(x=1 * x_stretch,
+                             y=height / width * y_stretch,
+                             z=depth / width * z_stretch),
             aspectmode='manual'
         )
     )

glue_plotly/common/scatter3d.py

@@ -93,6 +93,21 @@ def error_bar_info(layer_state, mask):
     return errs
 
 
+_IPYVOLUME_GEOMETRY_SYMBOLS = {
+    "sphere": "circle",
+    "box": "square",
+    "diamond": "diamond",
+    "circle2d": "circle",
+}
+
+
+def symbol_for_geometry(geometry: str) -> str:
+    symbol = _IPYVOLUME_GEOMETRY_SYMBOLS.get(geometry)
+    if symbol is not None:
+        return symbol
+    raise ValueError(f"Invalid geometry: {geometry}")
+
+
 def traces_for_layer(viewer_state, layer_state, hover_data=None, add_data_label=True):
 
     x, y, z, mask = clipped_data(viewer_state, layer_state)
@@ -103,6 +118,10 @@ def traces_for_layer(viewer_state, layer_state, hover_data=None, add_data_label=
                   opacity=layer_state.alpha,
                   line=dict(width=0))
 
+    if hasattr(layer_state, "geo"):
+        symbol = symbol_for_geometry(layer_state.geo)
+        marker["symbol"] = symbol
+
     if hover_data is None or np.sum(hover_data) == 0:
         hoverinfo = 'skip'
         hovertext = None

glue_plotly/common/volume.py

@@ -1,4 +1,4 @@
-from glue_plotly.utils import rgba_components
+from glue_plotly.utils import frb_for_layer, rgba_components
 from numpy import linspace, meshgrid, nan_to_num, nanmin
 
 from glue.core import BaseData
@@ -30,23 +30,9 @@ def values(viewer_state, layer_state, bounds, precomputed=None):
     parent = layer_state.layer.data if subset_layer else layer_state.layer
     parent_label = parent.label
     if precomputed is not None and parent_label in precomputed:
-        data = precomputed[parent_label]
+        values = precomputed[parent_label]
     else:
-        data = parent.compute_fixed_resolution_buffer(
-                   target_data=viewer_state.reference_data,
-                   bounds=bounds,
-                   target_cid=layer_state.attribute
-               )
-
-    if subset_layer:
-        subcube = parent.compute_fixed_resolution_buffer(
-            target_data=viewer_state.reference_data,
-            bounds=bounds,
-            subset_state=layer_state.layer.subset_state
-        )
-        values = subcube * data
-    else:
-        values = data
+        values = frb_for_layer(viewer_state, layer_state, bounds)
 
     # This accounts for two transformations: the fact that the viewer bounds are in reverse order,
     # plus a need to change R -> L handedness for Plotly

glue_plotly/html_exporters/jupyter/__init__.py

@@ -2,5 +2,5 @@
 from . import image  # noqa
 from . import profile  # noqa
 from . import scatter2d  # noqa
-from . import vispy_scatter  # noqa
-from . import vispy_volume  # noqa
+from . import scatter3d # noqa
+from . import volume  # noqa

glue_plotly/html_exporters/jupyter/tests/test_base.py

@@ -1,7 +1,7 @@
 from glue_jupyter import jglue
 
 
-class TestBqplotExporter:
+class BaseTestJupyterExporter:
 
     viewer_type = None
     tool_id = None

glue_plotly/html_exporters/jupyter/tests/test_histogram.py

@@ -6,12 +6,12 @@
 
 importorskip('glue_jupyter')
 
-from glue_jupyter.bqplot.histogram import BqplotHistogramView  # noqa
+from glue_jupyter.bqplot.histogram import BqplotHistogramView  # noqa: E402
 
-from .test_base import TestBqplotExporter  # noqa
+from .test_base import BaseTestJupyterExporter  # noqa: E402
 
 
-class TestHistogram(TestBqplotExporter):
+class TestHistogram(BaseTestJupyterExporter):
 
     viewer_type = BqplotHistogramView
     tool_id = 'save:bqplot_plotlyhist'

glue_plotly/html_exporters/jupyter/tests/test_image.py

@@ -6,14 +6,14 @@
 
 importorskip('glue_jupyter')
 
-from glue_jupyter.bqplot.image import BqplotImageView  # noqa
+from glue_jupyter.bqplot.image import BqplotImageView  # noqa: E402
 
-from numpy import arange, ones  # noqa
+from numpy import arange, ones  # noqa: E402
 
-from .test_base import TestBqplotExporter  # noqa
+from .test_base import BaseTestJupyterExporter  # noqa: E402
 
 
-class TestImage(TestBqplotExporter):
+class TestImage(BaseTestJupyterExporter):
 
     viewer_type = BqplotImageView
     tool_id = 'save:bqplot_plotlyimage2d'

glue_plotly/html_exporters/jupyter/tests/test_ipyvolume_scatter3d.py

@@ -0,0 +1,23 @@
+import os
+
+from glue.core import Data
+from glue_plotly.html_exporters.jupyter.tests.test_base import BaseTestJupyterExporter
+
+from pytest import importorskip
+
+importorskip('glue_jupyter')
+
+from glue_jupyter.ipyvolume import IpyvolumeScatterView  # noqa: E402
+
+
+class TestScatter3D(BaseTestJupyterExporter):
+
+    viewer_type = IpyvolumeScatterView
+    tool_id = 'save:jupyter_plotly3dscatter'
+
+    def make_data(self):
+        return Data(x=[1, 2, 3], y=[4, 5, 6], z=[7, 8, 9], label='d1')
+
+    def test_default(self, tmpdir):
+        output_path = self.export_figure(tmpdir, 'test_default.html')
+        assert os.path.exists(output_path)

glue_plotly/html_exporters/jupyter/tests/test_ipyvolume_volume.py

@@ -0,0 +1,28 @@
+import os
+
+from glue.core import Data
+from glue_plotly.html_exporters.jupyter.tests.test_base import BaseTestJupyterExporter
+
+from pytest import importorskip
+
+importorskip('glue_jupyter')
+
+from glue_jupyter.ipyvolume import IpyvolumeVolumeView  # noqa: E402
+
+from numpy import arange, ones  # noqa: E402
+
+
+class TestVolume(BaseTestJupyterExporter):
+
+    viewer_type = IpyvolumeVolumeView
+    tool_id = 'save:jupyter_plotlyvolume'
+
+    def make_data(self):
+        return Data(label='d1',
+                    x=arange(24).reshape((2, 3, 4)),
+                    y=ones((2, 3, 4)),
+                    z=arange(100, 124).reshape((2, 3, 4)))
+
+    def test_default(self, tmpdir):
+        output_path = self.export_figure(tmpdir, 'test_default.html')
+        assert os.path.exists(output_path)

glue_plotly/html_exporters/jupyter/tests/test_profile.py

@@ -6,12 +6,12 @@
 
 importorskip('glue_jupyter')
 
-from glue_jupyter.bqplot.profile import BqplotProfileView  # noqa
+from glue_jupyter.bqplot.profile import BqplotProfileView  # noqa: E402
 
-from .test_base import TestBqplotExporter  # noqa
+from .test_base import BaseTestJupyterExporter  # noqa: E402
 
 
-class TestProfile(TestBqplotExporter):
+class TestProfile(BaseTestJupyterExporter):
 
     viewer_type = BqplotProfileView
     tool_id = 'save:bqplot_plotlyprofile'

glue_plotly/html_exporters/jupyter/tests/test_scatter2d.py

@@ -6,12 +6,12 @@
 
 importorskip('glue_jupyter')
 
-from glue_jupyter.bqplot.scatter import BqplotScatterView  # noqa
+from glue_jupyter.bqplot.scatter import BqplotScatterView  # noqa: E402
 
-from .test_base import TestBqplotExporter  # noqa
+from .test_base import BaseTestJupyterExporter  # noqa: E402
 
 
-class TestScatter2D(TestBqplotExporter):
+class TestScatter2D(BaseTestJupyterExporter):
 
     viewer_type = BqplotScatterView
     tool_id = 'save:bqplot_plotly2d'

glue_plotly/html_exporters/jupyter/tests/test_scatter3d.py → glue_plotly/html_exporters/jupyter/tests/test_vispy_scatter3d.py

@@ -1,7 +1,7 @@
 import os
 
 from glue.core import Data
-from glue_plotly.html_exporters.jupyter.tests.test_base import TestBqplotExporter
+from glue_plotly.html_exporters.jupyter.tests.test_base import BaseTestJupyterExporter
 
 from pytest import importorskip
 
@@ -11,7 +11,7 @@
 from glue_vispy_viewers.scatter.jupyter import JupyterVispyScatterViewer  # noqa: E402
 
 
-class TestScatter3D(TestBqplotExporter):
+class TestScatter3D(BaseTestJupyterExporter):
 
     viewer_type = JupyterVispyScatterViewer
     tool_id = 'save:jupyter_plotly3dscatter'

glue_plotly/html_exporters/jupyter/tests/test_volume.py → glue_plotly/html_exporters/jupyter/tests/test_vispy_volume.py

@@ -1,7 +1,7 @@
 import os
 
 from glue.core import Data
-from glue_plotly.html_exporters.jupyter.tests.test_base import TestBqplotExporter
+from glue_plotly.html_exporters.jupyter.tests.test_base import BaseTestJupyterExporter
 
 from pytest import importorskip
 
@@ -13,7 +13,7 @@
 from numpy import arange, ones  # noqa: E402
 
 
-class TestVolume(TestBqplotExporter):
+class TestVolume(BaseTestJupyterExporter):
 
     viewer_type = JupyterVispyVolumeViewer
     tool_id = 'save:jupyter_plotlyvolume'

glue_plotly/html_exporters/jupyter/vispy_volume.py → glue_plotly/html_exporters/jupyter/volume.py

@@ -1,7 +1,7 @@
 from glue.config import viewer_tool
 from glue_vispy_viewers.scatter.layer_artist import ScatterLayerArtist
 
-from glue_plotly.common.base_3d import layout_config
+from glue_plotly.common.base_3d import bounds, layout_config
 from glue_plotly.common.common import data_count, layers_to_export
 from glue_plotly.common.scatter3d import traces_for_layer as scatter3d_traces_for_layer
 from glue_plotly.common.volume import traces_for_layer as volume_traces_for_layer
@@ -26,14 +26,14 @@ def save_figure(self, filepath):
 
         layers = layers_to_export(self.viewer)
         add_data_label = data_count(layers) > 1
-        bounds = self.viewer._vispy_widget._multivol._data_bounds
+        bds = bounds(self.viewer.state, with_resolution=True)
         count = 5
         for layer in layers:
             if isinstance(layer, ScatterLayerArtist):
                 traces = scatter3d_traces_for_layer(self.viewer.state, layer.state,
                                                     add_data_label=add_data_label)
             else:
-                traces = volume_traces_for_layer(self.viewer.state, layer.state, bounds,
+                traces = volume_traces_for_layer(self.viewer.state, layer.state, bds,
                                                  isosurface_count=count,
                                                  add_data_label=add_data_label)
 

glue_plotly/utils.py

@@ -1,5 +1,8 @@
 from re import match, sub
 
+from glue.core import BaseData
+from glue.viewers.common.state import LayerState
+
 __all__ = [
     'cleaned_labels',
     'mpl_ticks_values',
@@ -93,3 +96,35 @@ def rgba_components(color):
 def components_to_hex(r, g, b, a=None):
     components = [hex_string(t) for t in (r, g, b, a) if t is not None]
     return f"#{''.join(components)}"
+
+
+def data_for_layer(layer_or_state):
+    if isinstance(layer_or_state.layer, BaseData):
+        return layer_or_state.layer
+    else:
+        return layer_or_state.layer.data
+
+
+def frb_for_layer(viewer_state,
+                  layer_or_state,
+                  bounds):
+
+    data = data_for_layer(layer_or_state)
+    layer_state = layer_or_state if isinstance(layer_or_state, LayerState) else layer_or_state.state
+    is_data_layer = data is layer_or_state.layer
+    target_data = getattr(viewer_state, 'reference_data', data)
+    data_frb = data.compute_fixed_resolution_buffer(
+        target_data=target_data,
+        bounds=bounds,
+        target_cid=layer_state.attribute
+    )
+
+    if is_data_layer:
+        return data_frb
+    else:
+        subcube = data.compute_fixed_resolution_buffer(
+            target_data=target_data,
+            bounds=bounds,
+            subset_state=layer_state.layer.subset_state
+        )
+        return subcube * data_frb