Implement indicators

Author: almarklein

dash_3d_viewer/slicer.py

@@ -1,18 +1,47 @@
 import numpy as np
-from plotly.graph_objects import Figure, Image
+from plotly.graph_objects import Figure, Image, Scatter
 from dash import Dash
-from dash.dependencies import Input, Output, State
+from dash.dependencies import Input, Output, State, ALL
 from dash_core_components import Graph, Slider, Store
 
-from .utils import gen_random_id, img_array_to_uri
+from .utils import img_array_to_uri, get_thumbnail_size_from_shape
 
 
 class DashVolumeSlicer:
-    """A slicer to show 3D image data in Dash."""
+    """A slicer to show 3D image data in Dash.
 
-    def __init__(self, app, volume, axis=0, id=None):
+    Parameters:
+      app (dash.Dash): the Dash application instance.
+      volume (ndarray): the 3D numpy array to slice through.
+      axis (int): the dimension to slice in. Default 0.
+      volume_id (str): the id to use for the volume. By default this is a
+        hash of ``id(volume)``. Slicers that have the same volume-id show
+        each-other's positions with line indicators.
+
+    This is a placeholder object, not a Dash component. The components
+    that make up the slicer can be accessed as attributes:
+
+    * ``graph``: the Graph object.
+    * ``slider``: the Slider object.
+    * ``stores``: a list of Store objects. Some are "public" values, others
+      used internally. Make sure to put them somewhere in the layout.
+
+    Each component is given a dict-id with the following keys:
+
+    * "context": a unique string id for this slicer instance.
+    * "volume": the volume_id.
+    * "axis": the int axis.
+    * "name": the name of the component.
+
+    TODO: iron out these details, list the stores that are public
+    """
+
+    _global_slicer_counter = 0
+
+    def __init__(self, app, volume, axis=0, volume_id=None):
         if not isinstance(app, Dash):
             raise TypeError("Expect first arg to be a Dash app.")
+        self._app = app
         # Check and store volume
         if not (isinstance(volume, np.ndarray) and volume.ndim == 3):
             raise TypeError("Expected volume to be a 3D numpy array")
@@ -22,29 +51,36 @@ def __init__(self, app, volume, axis=0, id=None):
             raise ValueError("The given axis must be 0, 1, or 2.")
         self._axis = int(axis)
         # Check and store id
-        if id is None:
-            id = gen_random_id()
-        elif not isinstance(id, str):
-            raise TypeError("Id must be a string")
-        self._id = id
+        if volume_id is None:
+            volume_id = hex(id(volume))
+        elif not isinstance(volume_id, str):
+            raise TypeError("volume_id must be a string")
+        self.volume_id = volume_id
+        # Get unique id scoped to this slicer object
+        DashVolumeSlicer._global_slicer_counter += 1
+        self.context_id = "slicer" + str(DashVolumeSlicer._global_slicer_counter)
 
         # Get the slice size (width, height), and max index
-        # arr_shape = list(volume.shape)
-        # arr_shape.pop(self._axis)
-        # slice_size = list(reversed(arr_shape))
+        arr_shape = list(volume.shape)
+        arr_shape.pop(self._axis)
+        self._slice_size = tuple(reversed(arr_shape))
         self._max_index = self._volume.shape[self._axis] - 1
 
         # Prep low-res slices
+        thumbnail_size = get_thumbnail_size_from_shape(arr_shape, 32)
         thumbnails = [
-            img_array_to_uri(self._slice(i), (32, 32))
+            img_array_to_uri(self._slice(i), thumbnail_size)
             for i in range(self._max_index + 1)
         ]
 
         # Create a placeholder trace
         # todo: can add "%{z[0]}", but that would be the scaled value ...
-        trace = Image(source="", hovertemplate="(%{x}, %{y})<extra></extra>")
+        image_trace = Image(
+            source="", dx=1, dy=1, hovertemplate="(%{x}, %{y})<extra></extra>"
+        )
+        scatter_trace = Scatter(x=[], y=[])  # placeholder
         # Create the figure object
-        fig = Figure(data=[trace])
+        self._fig = fig = Figure(data=[image_trace, scatter_trace])
         fig.update_layout(
             template=None,
             margin=dict(l=0, r=0, b=0, t=0, pad=4),
@@ -70,6 +106,7 @@ def __init__(self, app, volume, axis=0, id=None):
             config={"scrollZoom": True},
         )
         # Create a slider object that the user can put in the layout (or not)
+        # todo: use tooltip to show current value?
         self.slider = Slider(
             id=self._subid("slider"),
             min=0,
@@ -80,18 +117,29 @@ def __init__(self, app, volume, axis=0, id=None):
         )
         # Create the stores that we need (these must be present in the layout)
         self.stores = [
-            Store(id=self._subid("slice-index"), data=volume.shape[self._axis] // 2),
+            Store(
+                id=self._subid("_slice-size"), data=self._slice_size + thumbnail_size
+            ),
+            Store(id=self._subid("index"), data=volume.shape[self._axis] // 2),
             Store(id=self._subid("_requested-slice-index"), data=0),
             Store(id=self._subid("_slice-data"), data=""),
             Store(id=self._subid("_slice-data-lowres"), data=thumbnails),
+            Store(id=self._subid("_indicators"), data=[]),
         ]
 
-        self._create_server_callbacks(app)
-        self._create_client_callbacks(app)
+        self._create_server_callbacks()
+        self._create_client_callbacks()
 
-    def _subid(self, subid):
+    def _subid(self, name):
         """Given a subid, get the full id including the slicer's prefix."""
-        return self._id + "-" + subid
+        # return self.context_id + "-" + name
+        # todo: is there a penalty for using a dict-id vs a string-id?
+        return {
+            "context": self.context_id,
+            "volume-id": self.volume_id,
+            "axis": self._axis,
+            "name": name,
+        }
 
     def _slice(self, index):
         """Sample a slice from the volume."""
@@ -100,8 +148,9 @@ def _slice(self, index):
         im = self._volume[tuple(indices)]
         return (im.astype(np.float32) * (255 / im.max())).astype(np.uint8)
 
-    def _create_server_callbacks(self, app):
+    def _create_server_callbacks(self):
         """Create the callbacks that run server-side."""
+        app = self._app
 
         @app.callback(
             Output(self._subid("_slice-data"), "data"),
@@ -111,16 +160,17 @@ def upload_requested_slice(slice_index):
             slice = self._slice(slice_index)
             return [slice_index, img_array_to_uri(slice)]
 
-    def _create_client_callbacks(self, app):
+    def _create_client_callbacks(self):
         """Create the callbacks that run client-side."""
+        app = self._app
 
         app.clientside_callback(
             """
         function handle_slider_move(index) {
             return index;
         }
         """,
-            Output(self._subid("slice-index"), "data"),
+            Output(self._subid("index"), "data"),
             [Input(self._subid("slider"), "value")],
         )
 
@@ -137,24 +187,24 @@ def _create_client_callbacks(self, app):
             }
         }
         """.replace(
-                "{{ID}}", self._id
+                "{{ID}}", self.context_id
             ),
             Output(self._subid("_requested-slice-index"), "data"),
-            [Input(self._subid("slice-index"), "data")],
+            [Input(self._subid("index"), "data")],
         )
 
         # app.clientside_callback("""
         # function update_slider_pos(index) {
         #     return index;
         # }
         # """,
-        #     [Output("slice-index", "data")],
+        #     [Output("index", "data")],
         #     [State("slider", "value")],
         # )
 
         app.clientside_callback(
             """
-        function handle_incoming_slice(index, index_and_data, ori_figure, lowres) {
+        function handle_incoming_slice(index, index_and_data, indicators, ori_figure, lowres, slice_size) {
             let new_index = index_and_data[0];
             let new_data = index_and_data[1];
             // Store data in cache
@@ -163,30 +213,98 @@ def _create_client_callbacks(self, app):
             slice_cache[new_index] = new_data;
             // Get the data we need *now*
             let data = slice_cache[index];
+            let x0 = 0, y0 = 0, dx = 1, dy = 1;
             //slice_cache[new_index] = undefined;  // todo: disabled cache for now!
             // Maybe we do not need an update
+            console.log(slice_size)
             if (!data) {
                 data = lowres[index];
+                // Scale the image to take the exact same space as the full-res
+                // version. It's not correct, but it looks better ...
+                // slice_size = full_w, full_h, low_w, low_h
+                dx = slice_size[0] / slice_size[2];
+                dy = slice_size[1] / slice_size[3];
+                x0 = 0.5 * dx - 0.5;
+                y0 = 0.5 * dy - 0.5;
             }
-            if (data == ori_figure.data[0].source) {
+            if (data == ori_figure.data[0].source && indicators.version == ori_figure.data[1].version) {
                 return window.dash_clientside.no_update;
             }
             // Otherwise, perform update
             console.log("updating figure");
             let figure = {...ori_figure};
             figure.data[0].source = data;
+            figure.data[0].x0 = x0;
+            figure.data[0].y0 = y0;
+            figure.data[0].dx = dx;
+            figure.data[0].dy = dy;
+            figure.data[1] = indicators;
             return figure;
         }
         """.replace(
-                "{{ID}}", self._id
+                "{{ID}}", self.context_id
             ),
             Output(self._subid("graph"), "figure"),
             [
-                Input(self._subid("slice-index"), "data"),
+                Input(self._subid("index"), "data"),
                 Input(self._subid("_slice-data"), "data"),
+                Input(self._subid("_indicators"), "data"),
             ],
             [
                 State(self._subid("graph"), "figure"),
                 State(self._subid("_slice-data-lowres"), "data"),
+                State(self._subid("_slice-size"), "data"),
+            ],
+        )
+
+        # Select the *other* axii
+        axii = [0, 1, 2]
+        axii.pop(self._axis)
+
+        # Create a callback to create a trace representing all slice-indices that:
+        # * corresponding to the same volume data
+        # * match any of the selected axii
+        app.clientside_callback(
+            """
+        function handle_indicator(indices1, indices2, slice_size, current) {
+            let w = slice_size[0], h = slice_size[1];
+            let dx = w / 20, dy = h / 20;
+            let version = (current.version || 0) + 1;
+            let x = [], y = [];
+            for (let index of indices1) {
+                x.push(...[-dx, -1, null, w, w + dx, null]);
+                y.push(...[index, index, index, index, index, index]);
+            }
+            for (let index of indices2) {
+                x.push(...[index, index, index, index, index, index]);
+                y.push(...[-dy, -1, null, h, h + dy, null]);
+            }
+            return {
+                type: 'scatter',
+                mode: 'lines',
+                line: {color: '#ff00aa'},
+                x: x,
+                y: y,
+                hoverinfo: 'skip',
+                version: version
+            }
+        }
+        """,
+            Output(self._subid("_indicators"), "data"),
+            [
+                Input(
+                    {
+                        "volume-id": self.volume_id,
+                        "context": ALL,
+                        "name": "index",
+                        "axis": axis,
+                    },
+                    "data",
+                )
+                for axis in axii
+            ],
+            [
+                State(self._subid("_slice-size"), "data"),
+                State(self._subid("_indicators"), "data"),
             ],
         )

dash_3d_viewer/utils.py

@@ -2,6 +2,7 @@
 import random
 import base64
 
+import numpy as np
 import PIL.Image
 import skimage
 
@@ -23,3 +24,11 @@ def img_array_to_uri(img_array, new_size=None):
     img_pil.save(f, format="PNG")
     base64_str = base64.b64encode(f.getvalue()).decode()
     return "data:image/png;base64," + base64_str
+
+
+def get_thumbnail_size_from_shape(shape, base_size):
+    base_size = int(base_size)
+    img_array = np.zeros(shape, np.uint8)
+    img_pil = PIL.Image.fromarray(img_array)
+    img_pil.thumbnail((base_size, base_size))
+    return img_pil.size

examples/slicer_with_2_views.py

@@ -11,8 +11,8 @@
 app = dash.Dash(__name__)
 
 vol = imageio.volread("imageio:stent.npz")
-slicer1 = DashVolumeSlicer(app, vol, axis=1, id="slicer1")
-slicer2 = DashVolumeSlicer(app, vol, axis=2, id="slicer2")
+slicer1 = DashVolumeSlicer(app, vol, axis=1)
+slicer2 = DashVolumeSlicer(app, vol, axis=2)
 
 app.layout = html.Div(
     style={

examples/slicer_with_3_views.py

@@ -15,9 +15,9 @@
 
 # Read volumes and create slicer objects
 vol = imageio.volread("imageio:stent.npz")
-slicer1 = DashVolumeSlicer(app, vol, axis=0, id="slicer1")
-slicer2 = DashVolumeSlicer(app, vol, axis=1, id="slicer2")
-slicer3 = DashVolumeSlicer(app, vol, axis=2, id="slicer3")
+slicer1 = DashVolumeSlicer(app, vol, axis=0)
+slicer2 = DashVolumeSlicer(app, vol, axis=1)
+slicer3 = DashVolumeSlicer(app, vol, axis=2)
 
 # Calculate isosurface and create a figure with a mesh object
 verts, faces, _, _ = marching_cubes(vol, 300, step_size=2)