Change name into tetradymite_PRM2020

Trainign set reduced

metainfo.json

@@ -6,9 +6,9 @@
   "email": "ghiringhelli@fhi-berlin.mpg.de",
   "title": "Artificial intelligence for high-throughput discovery of topological insulators",
   "description": "In this tutorial... ",
-  "url": "https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-topological-insulators",
-  "link": "https://analytics-toolkit.nomad-coe.eu/hub/user-redirect/notebooks/tutorials/topological_insulators.ipynb",
-  "link_public": "https://analytics-toolkit.nomad-coe.eu/public/user-redirect/notebooks/tutorials/topological_insulators.ipynb",
+  "url": "https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-tetradymite-PRM2020",
+  "link": "https://analytics-toolkit.nomad-coe.eu/hub/user-redirect/notebooks/tutorials/tetradymite_PRM2020.ipynb",
+  "link_public": "https://analytics-toolkit.nomad-coe.eu/public/user-redirect/notebooks/tutorials/tetradymite_PRM2020.ipynb",
   "updated": "2020-26-08",
   "flags":{
     "featured": true,

setup.py

@@ -5,7 +5,7 @@ with open('metainfo.json') as file:
     metainfo = json.load(file)
 
 setup(
-    name='topological_insulators',
+    name='tetradymite_PRM2020',
     version='1.0',
     author=', '.join(metainfo['authors']),
     author_email=metainfo['email'],

topological_insulators/visualizer.py → tetradymite_PRM2020/visualizer.py

@@ -74,19 +74,18 @@ class Visualizer:
         self.viewer_l = JsmolView()
         self.viewer_r = JsmolView()
         self.instantiate_widgets()
+
+        x_cls0 = df[self.features[0]][self.df_cls0]
+        y_cls0 = df[self.features[1]][self.df_cls0]
+        x_cls1 = df[self.features[0]][self.df_cls1]
+        y_cls1 = df[self.features[1]][self.df_cls1]
         line_x, line_y = self.f_x(self.features[0], self.features[1])
         hullx_cls0, hully_cls0, hullx_cls1, hully_cls1 = self.make_hull(self.features[0], self.features[1])
-
         # custom_cls0 = np.dstack((self.target_train[self.df_cls0],
         #                          self.target_predict[self.df_cls0]))[0]
         # custom_cls1 = np.dstack((self.target_train[self.df_cls1],
         #                          self.target_predict[self.df_cls1]))[0]
 
-        # the final plot is the sum of two traces, respectively containing the RS vs ZB materials
-        x_cls0 = df[self.features[0]][self.df_cls0]
-        y_cls0 = df[self.features[1]][self.df_cls0]
-        x_cls1 = df[self.features[0]][self.df_cls1]
-        y_cls1 = df[self.features[1]][self.df_cls1]
         self.fig.add_trace(
             (
                 go.Scatter(
@@ -129,7 +128,7 @@ class Visualizer:
                 y=hully_cls0,
                 line=dict(color='Grey', width=1, dash=self.line_styles[0]),
                 name=r'Convex' + '<br>' + 'hull 0',
-                visible=True
+                visible=False
             ),
         )
         self.fig.add_trace(
@@ -138,7 +137,7 @@ class Visualizer:
                 y=hully_cls1,
                 line=dict(color='Grey', width=1, dash=self.line_styles[0]),
                 name=r'Convex' + '<br>' + 'hull 1',
-                visible=True
+                visible=False
             ),
 
         )
@@ -148,7 +147,7 @@ class Visualizer:
                 y=line_y,
                 line=dict(color='Black', width=1, dash='solid'),
                 name=r'Classification' + '<br>' + 'line',
-                visible=True
+                visible=False
             ),
 
         )
@@ -193,6 +192,7 @@ class Visualizer:
         if self.total_features == 2:
             self.scatter_hull0.visible = True
             self.scatter_hull1.visible = True
+            self.scatter_clsline.visible = True
         else:
             self.widg_hullslinewidth.disabled = True
             self.widg_hullslinestyle.disabled = True
@@ -417,7 +417,6 @@ class Visualizer:
                 self.scatter_hull1['x'] = hullx_cls1
                 self.scatter_hull1['y'] = hully_cls1
 
-
     def handle_yfeat_change(self, change):
         # changes the feature plotted on the x-axis
         # separating line is modified accordingly
@@ -450,8 +449,6 @@ class Visualizer:
                 self.scatter_hull1['x'] = hullx_cls1
                 self.scatter_hull1['y'] = hully_cls1
 
-
-
     def handle_markerfeat_change(self, change):
         self.set_markers_size(feature=change.new)
         self.update_markers()
@@ -477,7 +474,7 @@ class Visualizer:
             structure_l = self.df[self.df['Chem Formula'] ==
                                   self.widg_compound_text_l.value]['Structure'].values[0]
             self.viewer_l.script(
-                "load data/topological_insulators/structures/" + structure_l + "_structures/"
+                "load data/tetradymite_PRM2020/structures/" + structure_l + "_structures/"
                 + self.widg_compound_text_l.value + ".xyz")
 
             symbols_cls0 = self.symbols_cls0
@@ -511,7 +508,7 @@ class Visualizer:
             structure_r = self.df[self.df['Chem Formula'] ==
                                   self.widg_compound_text_r.value]['Structure'].values[0]
             self.viewer_r.script(
-                "load data/topological_insulators/structures/" + structure_r + "_structures/"
+                "load data/tetradymite_PRM2020/structures/" + structure_r + "_structures/"
                 + self.widg_compound_text_r.value + ".xyz")
 
             symbols_cls0 = self.symbols_cls0
@@ -648,7 +645,7 @@ class Visualizer:
         text = "A download link will appear soon."
         with self.widg_print_out:
             print(text)
-        path = "./data/topological_insulators/plots/"
+        path = "./data/tetradymite_PRM2020/plots/"
         try:
             os.mkdir(path)
         except:
@@ -693,16 +690,16 @@ class Visualizer:
             self.widg_checkbox_l.value = True
 
     def view_structure_cls0_l(self, formula):
-        self.viewer_l.script("load data/topological_insulators/structures/RS_structures/" + formula + ".xyz")
+        self.viewer_l.script("load data/tetradymite_PRM2020/structures/RS_structures/" + formula + ".xyz")
 
     def view_structure_cls0_r(self, formula):
-        self.viewer_r.script("load data/topological_insulators/structures/RS_structures/" + formula + ".xyz")
+        self.viewer_r.script("load data/tetradymite_PRM2020/structures/RS_structures/" + formula + ".xyz")
 
     def view_structure_cls1_l(self, formula):
-        self.viewer_l.script("load data/topological_insulators/structures/ZB_structures/" + formula + ".xyz")
+        self.viewer_l.script("load data/tetradymite_PRM2020/structures/ZB_structures/" + formula + ".xyz")
 
     def view_structure_cls1_r(self, formula):
-        self.viewer_r.script("load data/topological_insulators/structures/ZB_structures/" + formula + ".xyz")
+        self.viewer_r.script("load data/tetradymite_PRM2020/structures/ZB_structures/" + formula + ".xyz")
 
     def update_point_cls0(self, trace, points, selector):
         # changes the points labeled with a cross on the map.
@@ -1078,7 +1075,7 @@ class Visualizer:
                                             self.widg_print_button, self.widg_print_out,
                                             ])
 
-        file1 = open("./assets/topological_insulators/cross.png", "rb")
+        file1 = open("./assets/tetradymite_PRM2020/cross.png", "rb")
         image1 = file1.read()
         self.widg_img1 = widgets.Image(
             value=image1,
@@ -1086,7 +1083,7 @@ class Visualizer:
             width=30,
             height=30,
         )
-        file2 = open("./assets/topological_insulators/cross2.png", "rb")
+        file2 = open("./assets/tetradymite_PRM2020/cross2.png", "rb")
         image2 = file2.read()
         self.widg_img2 = widgets.Image(
             value=image2,