Support for anisotropic data. (#8)

almarklein · web-flow · commit 88e2e7b56d99 · 2020-11-05T13:29:23.000+01:00
* Support for anisotropic data.

* add support/comments for swapping/reversing axes
diff --git a/dash_3d_viewer/slicer.py b/dash_3d_viewer/slicer.py
@@ -4,16 +4,25 @@
 from dash.dependencies import Input, Output, State, ALL
 from dash_core_components import Graph, Slider, Store
 
-from .utils import img_array_to_uri, get_thumbnail_size_from_shape
+from .utils import img_array_to_uri, get_thumbnail_size_from_shape, shape3d_to_size2d
 
 
 class DashVolumeSlicer:
     """A slicer to show 3D image data in Dash.
 
     Parameters:
       app (dash.Dash): the Dash application instance.
-      volume (ndarray): the 3D numpy array to slice through.
+      volume (ndarray): the 3D numpy array to slice through. The dimensions
+        are assumed to be in zyx order. If this is not the case, you can
+        use ``np.swapaxes`` to make it so.
+      spacing (tuple of floats): The distance between voxels for each dimension (zyx).
+        The spacing and origin are applied to make the slice drawn in
+        "scene space" rather than "voxel space".
+      origin (tuple of floats): The offset for each dimension (zyx).
       axis (int): the dimension to slice in. Default 0.
+      reverse_y (bool): Whether to reverse the y-axis, so that the origin of
+        the slice is in the top-left, rather than bottom-left. Default True.
+        (This sets the figure's yaxes ``autorange`` to either "reversed" or True.)
       scene_id (str): the scene that this slicer is part of. Slicers
         that have the same scene-id show each-other's positions with
         line indicators. By default this is a hash of ``id(volume)``.
@@ -38,14 +47,29 @@ class DashVolumeSlicer:
 
     _global_slicer_counter = 0
 
-    def __init__(self, app, volume, axis=0, scene_id=None):
+    def __init__(
+        self,
+        app,
+        volume,
+        *,
+        spacing=None,
+        origin=None,
+        axis=0,
+        reverse_y=True,
+        scene_id=None
+    ):
+        # todo: also implement xyz dim order?
         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")
         self._volume = volume
+        spacing = (1, 1, 1) if spacing is None else spacing
+        spacing = float(spacing[0]), float(spacing[1]), float(spacing[2])
+        origin = (0, 0, 0) if origin is None else origin
+        origin = float(origin[0]), float(origin[1]), float(origin[2])
         # Check and store axis
         if not (isinstance(axis, int) and 0 <= axis <= 2):
             raise ValueError("The given axis must be 0, 1, or 2.")
@@ -60,20 +84,26 @@ def __init__(self, app, volume, axis=0, scene_id=None):
         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)
-        self._slice_size = tuple(reversed(arr_shape))
-        self._max_index = self._volume.shape[self._axis] - 1
+        # Prepare slice info
+        info = {
+            "shape": tuple(volume.shape),
+            "axis": self._axis,
+            "size": shape3d_to_size2d(volume.shape, axis),
+            "origin": shape3d_to_size2d(origin, axis),
+            "spacing": shape3d_to_size2d(spacing, axis),
+        }
 
         # Prep low-res slices
-        thumbnail_size = get_thumbnail_size_from_shape(arr_shape, 32)
+        thumbnail_size = get_thumbnail_size_from_shape(
+            (info["size"][1], info["size"][0]), 32
+        )
         thumbnails = [
             img_array_to_uri(self._slice(i), thumbnail_size)
-            for i in range(self._max_index + 1)
+            for i in range(info["size"][2])
         ]
+        info["lowres_size"] = thumbnail_size
 
-        # Create a placeholder trace
+        # Create traces
         # todo: can add "%{z[0]}", but that would be the scaled value ...
         image_trace = Image(
             source="", dx=1, dy=1, hovertemplate="(%{x}, %{y})<extra></extra>"
@@ -97,6 +127,7 @@ def __init__(self, app, volume, axis=0, scene_id=None):
             scaleanchor="x",
             showticklabels=False,
             zeroline=False,
+            autorange="reversed" if reverse_y else True,
         )
         # Wrap the figure in a graph
         # todo: or should the user provide this?
@@ -106,22 +137,20 @@ def __init__(self, app, volume, axis=0, scene_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,
-            max=self._max_index,
+            max=info["size"][2] - 1,
             step=1,
-            value=self._max_index // 2,
+            value=info["size"][2] // 2,
             tooltip={"always_visible": False, "placement": "left"},
             updatemode="drag",
         )
         # Create the stores that we need (these must be present in the layout)
         self.stores = [
-            Store(
-                id=self._subid("_slice-size"), data=self._slice_size + thumbnail_size
-            ),
+            Store(id=self._subid("info"), data=info),
             Store(id=self._subid("index"), data=volume.shape[self._axis] // 2),
+            Store(id=self._subid("position"), data=0),
             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),
@@ -175,6 +204,17 @@ def _create_client_callbacks(self):
             [Input(self._subid("slider"), "value")],
         )
 
+        app.clientside_callback(
+            """
+        function update_position(index, info) {
+            return info.origin[2] + index * info.spacing[2];
+        }
+        """,
+            Output(self._subid("position"), "data"),
+            [Input(self._subid("index"), "data")],
+            [State(self._subid("info"), "data")],
+        )
+
         app.clientside_callback(
             """
         function handle_slice_index(index) {
@@ -205,7 +245,7 @@ def _create_client_callbacks(self):
 
         app.clientside_callback(
             """
-        function handle_incoming_slice(index, index_and_data, indicators, ori_figure, lowres, slice_size) {
+        function handle_incoming_slice(index, index_and_data, indicators, ori_figure, lowres, info) {
             let new_index = index_and_data[0];
             let new_data = index_and_data[1];
             // Store data in cache
@@ -214,18 +254,18 @@ def _create_client_callbacks(self):
             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;
+            let x0 = info.origin[0], y0 = info.origin[1];
+            let dx = info.spacing[0], dy = info.spacing[1];
             //slice_cache[new_index] = undefined;  // todo: disabled cache for now!
             // Maybe we do not need an update
             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;
+                dx *= info.size[0] / info.lowres_size[0];
+                dy *= info.size[1] / info.lowres_size[1];
+                x0 += 0.5 * dx - 0.5 * info.spacing[0];
+                y0 += 0.5 * dy - 0.5 * info.spacing[1];
             }
             if (data == ori_figure.data[0].source && indicators.version == ori_figure.data[1].version) {
                 return window.dash_clientside.no_update;
@@ -253,7 +293,7 @@ def _create_client_callbacks(self):
             [
                 State(self._subid("graph"), "figure"),
                 State(self._subid("_slice-data-lowres"), "data"),
-                State(self._subid("_slice-size"), "data"),
+                State(self._subid("info"), "data"),
             ],
         )
 
@@ -266,18 +306,22 @@ def _create_client_callbacks(self):
         # * 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;
+        function handle_indicator(positions1, positions2, info, current) {
+            let x0 = info.origin[0], y0 = info.origin[1];
+            let x1 = x0 + info.size[0] * info.spacing[0], y1 = y0 + info.size[1] * info.spacing[1];
+            x0 = x0 - info.spacing[0], y0 = y0 - info.spacing[1];
+            let d = ((x1 - x0) + (y1 - y0)) * 0.5 * 0.05;
             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 pos of positions1) {
+                // x relative to our slice, y in scene-coords
+                x.push(...[x0 - d, x0, null, x1, x1 + d, null]);
+                y.push(...[pos, pos, pos, pos, pos, pos]);
             }
-            for (let index of indices2) {
-                x.push(...[index, index, index, index, index, index]);
-                y.push(...[-dy, -1, null, h, h + dy, null]);
+            for (let pos of positions2) {
+                // x in scene-coords, y relative to our slice
+                x.push(...[pos, pos, pos, pos, pos, pos]);
+                y.push(...[y0 - d, y0, null, y1, y1 + d, null]);
             }
             return {
                 type: 'scatter',
@@ -296,15 +340,15 @@ def _create_client_callbacks(self):
                     {
                         "scene": self.scene_id,
                         "context": ALL,
-                        "name": "index",
+                        "name": "position",
                         "axis": axis,
                     },
                     "data",
                 )
                 for axis in axii
             ],
             [
-                State(self._subid("_slice-size"), "data"),
+                State(self._subid("info"), "data"),
                 State(self._subid("_indicators"), "data"),
             ],
         )
diff --git a/dash_3d_viewer/utils.py b/dash_3d_viewer/utils.py
@@ -32,3 +32,14 @@ def get_thumbnail_size_from_shape(shape, base_size):
     img_pil = PIL.Image.fromarray(img_array)
     img_pil.thumbnail((base_size, base_size))
     return img_pil.size
+
+
+def shape3d_to_size2d(shape, axis):
+    """Turn a 3d shape (z, y, x) into a local (x', y', z'),
+    where z' represents the dimension indicated by axis.
+    """
+    shape = list(shape)
+    axis_value = shape.pop(axis)
+    size = list(reversed(shape))
+    size.append(axis_value)
+    return tuple(size)
diff --git a/examples/slicer_with_1_plus_2_views.py b/examples/slicer_with_1_plus_2_views.py
@@ -3,10 +3,14 @@
 This demonstrates how multiple indicators can be shown per axis.
 
 Sharing the same scene_id is enough for the slicers to show each-others
-position. If the same volume object is given, it works by default,
+position. If the same volume object would be given, it works by default,
 because the default scene_id is a hash of the volume object. Specifying
 a scene_id provides slice position indicators even when slicing through
 different volumes.
+
+Further, this example has one slider showing data with different spacing.
+Note how the indicators represent the actual position in "scene coordinates".
+
 """
 
 import dash
@@ -17,22 +21,33 @@
 
 app = dash.Dash(__name__)
 
-vol = imageio.volread("imageio:stent.npz")
-slicer1 = DashVolumeSlicer(app, vol, axis=1, scene_id="myscene")
-slicer2 = DashVolumeSlicer(app, vol, axis=0, scene_id="myscene")
-slicer3 = DashVolumeSlicer(app, vol, axis=0, scene_id="myscene")
+vol1 = imageio.volread("imageio:stent.npz")
+
+vol2 = vol1[::3, ::2, :]
+spacing = 3, 2, 1
+ori = 110, 120, 140
+
+
+slicer1 = DashVolumeSlicer(
+    app, vol1, axis=1, origin=ori, reverse_y=False, scene_id="scene1"
+)
+slicer2 = DashVolumeSlicer(
+    app, vol1, axis=0, origin=ori, reverse_y=False, scene_id="scene1"
+)
+slicer3 = DashVolumeSlicer(
+    app, vol2, axis=0, origin=ori, spacing=spacing, reverse_y=False, scene_id="scene1"
+)
 
 app.layout = html.Div(
     style={
         "display": "grid",
-        "grid-template-columns": "40% 40%",
+        "gridTemplateColumns": "40% 40%",
     },
     children=[
         html.Div(
             [
                 html.H1("Coronal"),
                 slicer1.graph,
-                html.Br(),
                 slicer1.slider,
                 *slicer1.stores,
             ]
@@ -41,7 +56,6 @@
             [
                 html.H1("Transversal 1"),
                 slicer2.graph,
-                html.Br(),
                 slicer2.slider,
                 *slicer2.stores,
             ]
@@ -51,7 +65,6 @@
             [
                 html.H1("Transversal 2"),
                 slicer3.graph,
-                html.Br(),
                 slicer3.slider,
                 *slicer3.stores,
             ]
diff --git a/examples/slicer_with_2_views.py b/examples/slicer_with_2_views.py
@@ -17,7 +17,7 @@
 app.layout = html.Div(
     style={
         "display": "grid",
-        "grid-template-columns": "40% 40%",
+        "gridTemplateColumns": "40% 40%",
     },
     children=[
         html.Div(
diff --git a/examples/slicer_with_3_views.py b/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)
-slicer2 = DashVolumeSlicer(app, vol, axis=1)
-slicer3 = DashVolumeSlicer(app, vol, axis=2)
+slicer1 = DashVolumeSlicer(app, vol, reverse_y=False, axis=0)
+slicer2 = DashVolumeSlicer(app, vol, reverse_y=False, axis=1)
+slicer3 = DashVolumeSlicer(app, vol, reverse_y=False, axis=2)
 
 # Calculate isosurface and create a figure with a mesh object
 verts, faces, _, _ = marching_cubes(vol, 300, step_size=2)
@@ -30,7 +30,7 @@
 app.layout = html.Div(
     style={
         "display": "grid",
-        "grid-template-columns": "40% 40%",
+        "gridTemplateColumns": "40% 40%",
     },
     children=[
         html.Div(
diff --git a/tests/test_utils.py b/tests/test_utils.py
@@ -0,0 +1,14 @@
+from dash_3d_viewer.utils import shape3d_to_size2d
+
+from pytest import raises
+
+
+def test_shape3d_to_size2d():
+    # shape -> z, y, x
+    # size -> x, y, out-of-plane
+    assert shape3d_to_size2d((12, 13, 14), 0) == (14, 13, 12)
+    assert shape3d_to_size2d((12, 13, 14), 1) == (14, 12, 13)
+    assert shape3d_to_size2d((12, 13, 14), 2) == (13, 12, 14)
+
+    with raises(IndexError):
+        shape3d_to_size2d((12, 13, 14), 3)
