Merge pull request #70 from Carifio24/volume

Add exporter for volume viewer

glue_plotly/__init__.py

@@ -70,10 +70,18 @@ def setup_qt():
 
     try:
         from glue_vispy_viewers.scatter.scatter_viewer import VispyScatterViewer
+        from glue_vispy_viewers.volume.volume_viewer import VispyVolumeViewer
     except ImportError:
         pass
     else:
-        VispyScatterViewer.subtools['save'] = VispyScatterViewer.subtools['save'] + ['save:plotly3d']
+        VispyScatterViewer.subtools = {
+            **VispyScatterViewer.subtools,
+            "save": VispyScatterViewer.subtools["save"] + ["save:plotly3d"]
+        }
+        VispyVolumeViewer.subtools = {
+            **VispyVolumeViewer.subtools,
+            "save": VispyVolumeViewer.subtools["save"] + ["save:plotlyvolume"]
+        }
 
 
 def setup_jupyter():

glue_plotly/common/base_3d.py

@@ -0,0 +1,107 @@
+import re
+
+from glue.config import settings
+from glue_plotly.common import DEFAULT_FONT
+
+
+def dimensions(viewer_state):
+    # when vispy viewer is in "native aspect ratio" mode, scale axes size by data
+    if viewer_state.native_aspect:
+        width = viewer_state.x_max - viewer_state.x_min
+        height = viewer_state.y_max - viewer_state.y_min
+        depth = viewer_state.z_max - viewer_state.z_min
+
+    # otherwise, set all axes to be equal size
+    else:
+        width = 1200  # this 1200 size is arbitrary, could change to any width; just need to scale rest accordingly
+        height = 1200
+        depth = 1200
+
+    return [width, height, depth]
+
+
+def projection_type(viewer_state):
+    return "perspective" if viewer_state.perspective_view else "orthographic"
+
+
+def axis(viewer_state, ax):
+    title = getattr(viewer_state, f'{ax}_att').label
+    range = [getattr(viewer_state, f'{ax}_min'), getattr(viewer_state, f'{ax}_max')]
+    return dict(
+        title=title,
+        titlefont=dict(
+            family=DEFAULT_FONT,
+            size=20,
+            color=settings.FOREGROUND_COLOR
+        ),
+        backgroundcolor=settings.BACKGROUND_COLOR,
+        showspikes=False,
+        linecolor=settings.FOREGROUND_COLOR,
+        tickcolor=settings.FOREGROUND_COLOR,
+        zeroline=False,
+        mirror=True,
+        ticks='outside',
+        showline=True,
+        showgrid=False,
+        showticklabels=True,
+        tickfont=dict(
+            family=DEFAULT_FONT,
+            size=12,
+            color=settings.FOREGROUND_COLOR),
+        range=range,
+        type='linear',
+        rangemode='normal',
+        visible=viewer_state.visible_axes
+    )
+
+
+def bbox_mask(viewer_state, x, y, z):
+    return (x >= viewer_state.x_min) & (x <= viewer_state.x_max) & \
+           (y >= viewer_state.y_min) & (y <= viewer_state.y_max) & \
+           (z >= viewer_state.z_min) & (z <= viewer_state.z_max)
+
+
+def clipped_data(viewer_state, layer_state):
+    x = layer_state.layer[viewer_state.x_att]
+    y = layer_state.layer[viewer_state.y_att]
+    z = layer_state.layer[viewer_state.z_att]
+
+    # Plotly doesn't show anything outside the bounding box
+    mask = bbox_mask(viewer_state, x, y, z)
+
+    return x[mask], y[mask], z[mask], mask
+
+
+def plotly_up_from_vispy(vispy_up):
+    regex = re.compile("(\\+|-)(x|y|z)")
+    up = {"x": 0, "y": 0, "z": 0}
+    m = regex.match(vispy_up)
+    if m is not None and len(m.groups()) == 2:
+        sign = 1 if m.group(1) == "+" else -1
+        up[m.group(2)] = sign
+    return up
+
+
+def layout_config(viewer_state):
+    width, height, depth = dimensions(viewer_state)
+    return dict(
+        margin=dict(r=50, l=50, b=50, t=50),  # noqa
+        width=1200,
+        paper_bgcolor=settings.BACKGROUND_COLOR,
+        scene=dict(
+            xaxis=axis(viewer_state, 'x'),
+            yaxis=axis(viewer_state, 'y'),
+            zaxis=axis(viewer_state, 'z'),
+            camera=dict(
+                projection=dict(
+                    type=projection_type(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),
+            aspectmode='manual'
+        )
+    )

glue_plotly/common/common.py

@@ -108,7 +108,7 @@ def sanitize(*arrays):
 def fixed_color(layer_state):
     layer_color = layer_state.color
     if layer_color == '0.35' or layer_color == '0.75':
-        layer_color = 'gray'
+        layer_color = '#808080'
     if is_rgba_hex(layer_color):
         layer_color = rgba_hex_to_rgb_hex(layer_color)
     return layer_color

glue_plotly/common/scatter3d.py

@@ -1,77 +1,13 @@
 import numpy as np
-from glue.config import settings
 from glue.core import BaseData
 from glue.utils import ensure_numerical
 from matplotlib.colors import to_rgb
 from numpy import clip
 from plotly.graph_objs import Cone, Scatter3d
 from uuid import uuid4
 
-from glue_plotly.common import DEFAULT_FONT, color_info
-
-
-def dimensions(viewer_state):
-    # when vispy viewer is in "native aspect ratio" mode, scale axes size by data
-    if viewer_state.native_aspect:
-        width = viewer_state.x_max - viewer_state.x_min
-        height = viewer_state.y_max - viewer_state.y_min
-        depth = viewer_state.z_max - viewer_state.z_min
-
-    # otherwise, set all axes to be equal size
-    else:
-        width = 1200  # this 1200 size is arbitrary, could change to any width; just need to scale rest accordingly
-        height = 1200
-        depth = 1200
-
-    return [width, height, depth]
-
-
-def projection_type(viewer_state):
-    return "perspective" if viewer_state.perspective_view else "orthographic"
-
-
-def axis(viewer_state, ax):
-    title = getattr(viewer_state, f'{ax}_att').label
-    range = [getattr(viewer_state, f'{ax}_min'), getattr(viewer_state, f'{ax}_max')]
-    return dict(
-        title=title,
-        titlefont=dict(
-            family=DEFAULT_FONT,
-            size=20,
-            color=settings.FOREGROUND_COLOR
-        ),
-        backgroundcolor=settings.BACKGROUND_COLOR,
-        showspikes=False,
-        linecolor=settings.FOREGROUND_COLOR,
-        tickcolor=settings.FOREGROUND_COLOR,
-        zeroline=False,
-        mirror=True,
-        ticks='outside',
-        showline=True,
-        showgrid=False,
-        showticklabels=True,
-        tickfont=dict(
-            family=DEFAULT_FONT,
-            size=12,
-            color=settings.FOREGROUND_COLOR),
-        range=range,
-        type='linear',
-        rangemode='normal',
-        visible=viewer_state.visible_axes
-    )
-
-
-def clipped_data(viewer_state, layer_state):
-    x = layer_state.layer[viewer_state.x_att]
-    y = layer_state.layer[viewer_state.y_att]
-    z = layer_state.layer[viewer_state.z_att]
-
-    # Plotly doesn't show anything outside the bounding box
-    mask = (x >= viewer_state.x_min) & (x <= viewer_state.x_max) & \
-           (y >= viewer_state.y_min) & (y <= viewer_state.y_max) & \
-           (z >= viewer_state.z_min) & (z <= viewer_state.z_max)
-
-    return x[mask], y[mask], z[mask], mask
+from glue_plotly.common import color_info
+from glue_plotly.common.base_3d import clipped_data
 
 
 def size_info(layer_state, mask):
@@ -157,29 +93,6 @@ def error_bar_info(layer_state, mask):
     return errs
 
 
-def layout_config(viewer_state):
-    width, height, depth = dimensions(viewer_state)
-    return dict(
-        margin=dict(r=50, l=50, b=50, t=50),  # noqa
-        width=1200,
-        paper_bgcolor=settings.BACKGROUND_COLOR,
-        scene=dict(
-            xaxis=axis(viewer_state, 'x'),
-            yaxis=axis(viewer_state, 'y'),
-            zaxis=axis(viewer_state, 'z'),
-            camera=dict(
-                projection=dict(
-                    type=projection_type(viewer_state)
-                )
-            ),
-            aspectratio=dict(x=1 * viewer_state.x_stretch,
-                             y=height / width * viewer_state.y_stretch,
-                             z=depth / width * viewer_state.z_stretch),
-            aspectmode='manual'
-        )
-    )
-
-
 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)

glue_plotly/common/volume.py

@@ -0,0 +1,119 @@
+from glue_plotly.utils import rgba_components
+from numpy import linspace, meshgrid, nan_to_num, nanmin
+
+from glue.core import BaseData
+from glue.core.state_objects import State
+from glue.core.subset_group import GroupedSubset
+
+from glue_plotly.common import color_info
+from glue_plotly.common.base_3d import bbox_mask
+
+import plotly.graph_objects as go
+
+
+def positions(bounds):
+    # The viewer bounds are in reverse order
+    coord_arrays = [linspace(b[0], b[1], num=b[2]) for b in reversed(bounds)]
+    return meshgrid(*coord_arrays)
+
+
+def parent_layer(viewer_or_state, subset):
+    data = subset.data
+    for layer in viewer_or_state.layers:
+        if layer.layer is data:
+            return layer
+    return None
+
+
+def values(viewer_state, layer_state, bounds, precomputed=None):
+    subset_layer = isinstance(layer_state.layer, GroupedSubset)
+    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]
+    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
+
+    # 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
+    values = values.transpose(1, 2, 0)
+    min_value = nanmin(values)
+    replacement = min_value - 1
+    replaced = nan_to_num(values, replacement)
+    return replaced
+
+
+def colorscale(layer_state, size=10):
+    color = color_info(layer_state)
+    r, g, b, a = rgba_components(color)
+    fractions = [(i / size) ** 0.25 for i in range(size + 1)]
+    return [f"rgba({f*r},{f*g},{f*b},{f*a})" for f in fractions]
+
+
+def opacity_scale(layer_state):
+    return [[0, 0], [1, 1]]
+
+
+def isomin_for_layer(viewer_or_state, layer):
+    if isinstance(layer.layer, GroupedSubset):
+        parent = parent_layer(viewer_or_state, layer.layer)
+        if parent is not None:
+            parent_state = parent if isinstance(parent, State) else parent.state
+            return parent_state.vmin
+
+    state = layer if isinstance(layer, State) else layer
+    return state.vmin
+
+
+def isomax_for_layer(viewer_or_state, layer):
+    if isinstance(layer.layer, GroupedSubset):
+        parent = parent_layer(viewer_or_state, layer.layer)
+        if parent is not None:
+            parent_state = parent if isinstance(parent, State) else parent.state
+            return parent_state.vmax
+
+    state = layer if isinstance(layer, State) else layer
+    return state.vmax
+
+
+def traces_for_layer(viewer_state, layer_state, bounds,
+                     isosurface_count=5, add_data_label=True):
+
+    xyz = positions(bounds)
+    mask = bbox_mask(viewer_state, *xyz)
+    clipped_xyz = [c[mask] for c in xyz]
+    clipped_values = values(viewer_state, layer_state, bounds)[mask]
+    name = layer_state.layer.label
+    if add_data_label and not isinstance(layer_state.layer, BaseData):
+        name += " ({0})".format(layer_state.layer.data.label)
+
+    return [go.Volume(
+       name=name,
+       hoverinfo="skip",
+       hovertext=None,
+       x=clipped_xyz[0],
+       y=clipped_xyz[1],
+       z=clipped_xyz[2],
+       value=clipped_values,
+       colorscale=colorscale(layer_state),
+       opacityscale=opacity_scale(layer_state),
+       isomin=isomin_for_layer(viewer_state, layer_state),
+       isomax=isomax_for_layer(viewer_state, layer_state),
+       opacity=layer_state.alpha,
+       surface_count=isosurface_count,
+       showscale=False
+    )]

glue_plotly/html_exporters/qt/__init__.py

@@ -5,3 +5,5 @@
 from . import profile  # noqa
 from . import table  # noqa
 from . import dendrogram  # noqa
+from . import volume  # noqa
+from .options_state import *  # noqa