Atom color picker options

GoVizzy/gv_ui/gv_ui/DisplayUI.py

@@ -1,15 +1,17 @@
 import ipywidgets as widgets
-from ipywidgets import Dropdown, VBox, HBox, Output, ColorPicker, AppLayout, Layout, Label, Button
+from ipywidgets import Dropdown, VBox, HBox, Output, ColorPicker, AppLayout, Layout, Label, Button, Checkbox, link, Accordion
 import ipyvolume as ipv
 import matplotlib.pyplot as plt
 from gv_ui import plotting, meshes, gvWidgets
+from gv_ui.gvWidgets import mesh_visibility_toggle, atom_color_picker
+from IPython.display import display
 
 # Define globals
 selected_option ='Slice Options'
-options = ['Slice Options', 'Mesh Options', 'Color Options']
+options = ['Slice Options', 'Mesh Options'] #, 'Color Options']
 dropdown = Dropdown(options=options, value=options[0], layout=Layout(margin='5px 0 0 5px'));
 large_box = Output(layout=Layout(width="70%", height="100%"))
-selected_view_options = Output(layout=Layout(width="200px", height="300px"))
+selected_view_options = Output(layout=Layout(width="auto", height="300px"))
 slice_picker = Output(layout=Layout(flex= '1',border='1px solid black'))
 slice_picker_descr = widgets.Label(value="Slice Picker", layout=Layout(margin='5px 0 0 5px'))
 exit_button = widgets.Button(description='[X]', button_style='danger',border='1px solid black')
@@ -18,6 +20,11 @@
 
 newCube_button = Button(description='New Cube', layout=Layout(flex= '1',  border='1px solid black'))
 save_button = Button(description='Save', layout=Layout(flex= '1',  border='1px solid black'))
+
+
+# atom mesh globals
+atom_meshes = []
+
 # Displays logo and hides the app output
 def show_menu():
     exit_button.layout.visibility = 'visible'
@@ -49,7 +56,9 @@ def show_ui():
     newCube_button.layout.visibility = 'visible'
 
 def display_cube(cube):
+    global atom_meshes
     visualizer = plotting.Visualizer(cube)
+    global atom_meshes
     with large_box:  # Capture output within large_box
         # Clear previous content
         large_box.clear_output()
@@ -62,10 +71,8 @@ def display_cube(cube):
         # Mesh View
         elif selected_option == 'Mesh Options':
             visualizer.display_cell()
-            origin = (50, 50, 50)
-            radius = 10
-            meshes.plot_sphere_surface(origin, radius)
-
+            atom_meshes = meshes.plot_atoms(cube)
+
         # Additional View   
         elif selected_option == 'Color Options':
             visualizer.display_cell()
@@ -78,7 +85,7 @@ def display_cube(cube):
 def display_app():
 
     # Containers for right menu 
-
+    global atom_meshes
 
     top_container = HBox([dropdown, in_app_exit])
 
@@ -96,12 +103,18 @@ def display_app():
 
 
     elif selected_option == 'Mesh Options':
-        #display Mesh TO DO 
+        #display Mesh TO DO
+        atom_controls = []
+        for mesh in atom_meshes:
+            controls = [mesh_visibility_toggle(mesh, 'Visible'),
+                    atom_color_picker(mesh, 'Color')]
+            atom_controls.append(VBox(children=controls))
+        titles = tuple(f'Atom {idx}' for idx in range(len(atom_controls)))
         with selected_view_options:
             selected_view_options.clear_output()
-
-
-
+            accordion = Accordion(children=atom_controls, titles=titles)
+            mesh_box = VBox([accordion])
+            display(mesh_box)
 
 
 

GoVizzy/gv_ui/gv_ui/gvWidgets.py

@@ -3,7 +3,8 @@
     Documentation for widget library: https://ipywidgets.readthedocs.io/en/latest/examples/Widget%20List.html#file-upload
 '''
 from IPython.display import display
-from ipywidgets import Layout, Button, Box, Textarea, Label, ColorPicker, FloatSlider, Checkbox
+from ipywidgets import Layout, Button, Box, Textarea, Label, ColorPicker, FloatSlider, Checkbox, link
+from ipyvolume.widgets import Mesh
 
 # Input form
 # Layout for Input form
@@ -65,8 +66,17 @@
     indent=True
 )
 
+def mesh_visibility_toggle(mesh: Mesh, description: str="Atom"):
+    toggle = Checkbox(value=True, description=description)
+    link((toggle, 'value'), (mesh, 'visible'))
+    return toggle
+
 color = ColorPicker(concise=True, value='white', description='Color', disabled=False, layout=Layout(flex='1 1 0%', width='auto'))
 
+def atom_color_picker(atom: Mesh, description: str="Color"):
+    picker = ColorPicker(value=str(atom.color), description=description)
+    link((picker, 'value'), (atom, 'color'))
+    return picker
 
 # Input form items
 form_items = [

GoVizzy/gv_ui/gv_ui/meshes.py

@@ -71,7 +71,7 @@ def sphere_surface(phi: float, theta: float):
         return (x, y, z)
 
     x, y, z = np.array(list(sphere_surface(gridx, gridy)))
-    ipv.plot_surface(x, z, y, color=color)
+    return ipv.plot_surface(x, z, y, color=color)
 
 def plot_atoms(cube: Cube, sizes: dict[int, int]=vanderwaals, colors: dict[int, str]=default_colors):
     '''
@@ -80,8 +80,11 @@ def plot_atoms(cube: Cube, sizes: dict[int, int]=vanderwaals, colors: dict[int,
     '''
     default_color = "red"
     default_size = 10
+    atom_meshes = []
     for atom in range(len(cube.atoms)):
         position = cube.atoms.get_scaled_positions()[atom]
         number = cube.atoms.get_atomic_numbers()[atom]
         x, z, y = tuple(p * cube.data3D.shape[idx] / Bohr for idx, p in enumerate(position))
-        plot_sphere_surface((x, y, z), sizes[number] or default_size, colors[number] or default_color)
+        mesh = plot_sphere_surface((x, y, z), sizes.get(number, default_size), colors.get(number, default_color))
+        atom_meshes.append(mesh)
+    return atom_meshes