Add volume slice plugin (#81)

README.md

@@ -202,6 +202,23 @@ viewer.avr.lp.build_plane()
 
 <img src="docs/source/_static/images/lattice_plane.png"  width="300px"/>
 
+### Slice 2D
+```python
+from ase.build import molecule
+from weas_widget import WeasWidget
+from ase.io.cube import read_cube_data
+volume, atoms = read_cube_data("h2o-homo.cube")
+viewer = WeasWidget()
+viewer.from_ase(atoms)
+viewer.avr.model_style = 1
+viewer.avr.volume_slice.volumetric_data = {"values": volume}
+viewer.avr.volume_slice.settings = {"Slice 1": {"h": 0, "k": 1, "l": 0, "distance": 5.5, "samplingDistance": 0.1 },
+                                    "Slice 2": {"h": 1, "k": 1, "l": 0, "distance": 5.5, "samplingDistance": 0.1 },
+                                   }
+viewer.camera.setting = {"direction": [0.5, 1, 2], "zoom": 1.5}
+viewer
+```
+<img src="docs/source/_static/images/example-volume-slice.png"  width="300px"/>
 
 
 ## Test

docs/source/index.rst

@@ -29,6 +29,7 @@ A widget to visualize and interact with atomic structures in Jupyter Notebook. I
    boundary
    measurement
    isosurface
+   volume_slice
    vector_field
    lattice_plane
    highlight

docs/source/volume_slice.rst

@@ -0,0 +1,40 @@
+Volume Slice
+=================
+
+The volume slice is a 2D cross-sectional visualization of 3D volumetric data. It is an effective method for analyzing volumetric properties, such as molecular orbitals or charge densities, by slicing through the data at specified orientations and distances.
+
+Usage Example
+-------------
+Here is an example of drawing volume slices for the HOMO of the H2O molecule.
+
+.. code-block:: python
+
+   from ase.build import molecule
+   from weas_widget import WeasWidget
+   from ase.io.cube import read_cube_data
+   volume, atoms = read_cube_data("h2o-homo.cube")
+   viewer = WeasWidget()
+   viewer.from_ase(atoms)
+   viewer.avr.model_style = 1
+   viewer.avr.volume_slice.volumetric_data = {"values": volume}
+   viewer.avr.volume_slice.settings = {
+       "Slice 1": {"h": 0, "k": 1, "l": 0, "distance": 5.5, "samplingDistance": 0.1},
+       "Slice 2": {"h": 1, "k": 1, "l": 0, "distance": 5.5, "samplingDistance": 0.1},
+   }
+   viewer.camera.setting = {"direction": [0.5, 1, 2], "zoom": 1.5}
+   viewer
+
+.. figure:: _static/images/example-volume-slice.png
+   :width: 40%
+   :align: center
+
+
+For the ``settings``:
+
+- **h, k, l**: Miller indices defining the orientation of the slice.
+- **distance**: The distance of the slice from the origin, in Ångstroms.
+- **samplingDistance**: The sampling distance for rendering the slice, affecting resolution.
+
+.. tip::
+
+   Support for multiple slices with individual settings, allowing analysis from different orientations and depths.

js/widget.js

@@ -74,9 +74,11 @@ function render({ model, el }) {
         // console.log("highlightSettings: ", model.get("highlightSettings"));
         editor.avr.highlightManager.fromSettings(model.get("highlightSettings"));
         // volumetric data
-        editor.avr.isosurfaceManager.volumetricData = createVolumeData(model.get("volumetricData"), atoms.cell);
-        console.log("isosettings: ", model.get("isoSettings"));
+        editor.avr.volumetricData = createVolumeData(model.get("volumetricData"), atoms.cell);
+        // isosurface
         editor.avr.isosurfaceManager.fromSettings(model.get("isoSettings"));
+        // volume slice
+        editor.avr.volumeSliceManager.fromSettings(model.get("sliceSettings"));
         // vector field
         editor.avr.VFManager.fromSettings(model.get("vectorField"));
         editor.avr.showVectorField = model.get("showVectorField");

package.json

@@ -7,7 +7,7 @@
 	"dependencies": {
 		"dat.gui": "^0.7.9",
 		"three": "^0.161.0",
-		"weas": ">=0.1.33"
+		"weas": ">=0.1.34"
 	},
 	"devDependencies": {
 		"esbuild": "^0.20.0"

src/weas_widget/atoms_viewer.py

@@ -1,6 +1,7 @@
 from .base_class import WidgetWrapper
 from .plugins.vector_field import VectorField
 from .plugins.isosurface import Isosurface
+from .plugins.volume_slice import VolumeSlice
 from .plugins.lattice_plane import LatticePlane
 from .plugins.bond import BondManager
 from .plugins.species import SpeciesManager
@@ -36,6 +37,7 @@ class AtomsViewer(WidgetWrapper):
         "species",
         "vf",
         "iso",
+        "volume_slice",
         "lp",
         "atoms",
         "bond",
@@ -53,6 +55,7 @@ def __init__(self, _widget):
         setattr(self, "bond", BondManager(_widget))
         setattr(self, "species", SpeciesManager(_widget))
         setattr(self, "highlight", HighlightManager(_widget))
+        setattr(self, "volume_slice", VolumeSlice(_widget))
 
     @property
     def atoms(self):

src/weas_widget/base_widget.py

@@ -38,7 +38,6 @@ class BaseWidget(anywidget.AnyWidget):
     modelSticks = tl.List([]).tag(sync=True)
     modelPolyhedras = tl.List([]).tag(sync=True)
     volumetricData = tl.Dict({"values": [[[]]]}).tag(sync=True)
-    isoSettings = tl.Dict([]).tag(sync=True)
     imageData = tl.Unicode("").tag(sync=True)
     vectorField = tl.Dict().tag(sync=True)
     showVectorField = tl.Bool(True).tag(sync=True)
@@ -65,6 +64,10 @@ class BaseWidget(anywidget.AnyWidget):
     speciesSettings = tl.Dict({}).tag(sync=True)
     # bond
     bondSettings = tl.Dict({}).tag(sync=True)
+    # isosurface
+    isoSettings = tl.Dict({}).tag(sync=True)
+    # volume slice
+    sliceSettings = tl.Dict({}).tag(sync=True)
     # phonon
     phonon = tl.Dict({}).tag(sync=True)
     # highlight

src/weas_widget/plugins/volume_slice.py

@@ -0,0 +1,16 @@
+from ..base_class import WidgetWrapper
+
+
+class VolumeSlice(WidgetWrapper):
+
+    catalog = "VolumeSlice"
+
+    _attribute_map = {
+        "volumetric_data": "volumetricData",
+        "settings": "sliceSettings",
+    }
+
+    _extra_allowed_attrs = []
+
+    def __init__(self, _widget):
+        super().__init__(_widget)

tests/notebooks/tests/notebooks/plugins.ipynb

@@ -128,6 +128,33 @@
     "viewer.avr.highlight.settings[\"fixed\"][\"indices\"] = [0, 1, 2]\n",
     "viewer"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from weas_widget import WeasWidget\n",
+    "import requests\n",
+    "from io import StringIO\n",
+    "from ase.io.cube import read_cube_data\n",
+    "url = \"https://raw.githubusercontent.com/superstar54/weas/main/demo/datas/h2o-homo.cube\"\n",
+    "response = requests.get(url)\n",
+    "file_content = response.text\n",
+    "# Use StringIO to simulate a file-like object for ASE to read from\n",
+    "file_like_object = StringIO(file_content)\n",
+    "volume, atoms = read_cube_data(file_like_object)\n",
+    "viewer = WeasWidget()\n",
+    "viewer.from_ase(atoms)\n",
+    "viewer.avr.model_style = 1\n",
+    "viewer.avr.volume_slice.volumetric_data = {\"values\": volume}\n",
+    "viewer.avr.volume_slice.settings = {\"Slice 1\": {\"h\": 0, \"k\": 1, \"l\": 0, \"distance\": 5.5, \"samplingDistance\": 0.1 },\n",
+    "                                    \"Slice 2\": {\"h\": 1, \"k\": 1, \"l\": 0, \"distance\": 5.5, \"samplingDistance\": 0.1 },\n",
+    "                                   }\n",
+    "viewer.camera.setting = {\"direction\": [0.5, 1, 2], \"zoom\": 1.5}\n",
+    "viewer"
+   ]
   }
  ],
  "metadata": {