Merge pull request #844 from dianna-ai/838-create-tabular-tab-to-dashboard

838 create tabular tab to dashboard and redesign loaded data results #819

Author: laurasootes

dianna/dashboard/Home.py

@@ -1,12 +1,11 @@
 import importlib
 import streamlit as st
-from _shared import add_sidebar_logo
 from _shared import data_directory
 from streamlit_option_menu import option_menu
 
 st.set_page_config(page_title="Dianna's dashboard",
                    page_icon='📊',
-                   layout='centered',
+                   layout='wide',
                    initial_sidebar_state='auto',
                    menu_items={
                        'Get help':
@@ -22,6 +21,7 @@
 pages = {
     "Home": "home",
     "Images": "pages.Images",
+    "Tabular": "pages.Tabular",
     "Text": "pages.Text",
     "Time series": "pages.Time_series"
 }
@@ -30,16 +30,14 @@
 selected = option_menu(
     menu_title=None,
     options=list(pages.keys()),
-    icons=["house", "camera", "alphabet", "clock"],
+    icons=["house", "camera", "table", "alphabet", "clock"],
     menu_icon="cast",
     default_index=0,
     orientation="horizontal"
 )
 
 # Display the content of the selected page
 if selected == "Home":
-    add_sidebar_logo()
-
     st.image(str(data_directory / 'logo.png'))
 
     st.markdown("""
@@ -50,9 +48,10 @@
 
     ### Pages
 
-    - <a href="/Images" target="_parent">Images</a>
-    - <a href="/Text" target="_parent">Text</a>
-    - <a href="/Time_series" target="_parent">Time series</a>
+    - <a href="/Images" target="_parent">Image data</a>
+    - <a href="/Tabular" target="_parent">Tabular data</a>
+    - <a href="/Text" target="_parent">Text data</a>
+    - <a href="/Time_series" target="_parent">Time series data</a>
 
 
     ### More information
@@ -70,6 +69,10 @@
         for k in st.session_state.keys():
             if 'Image' in k:
                 st.session_state.pop(k, None)
+    if selected != 'Tabular':
+        for k in st.session_state.keys():
+            if 'Tabular' in k:
+                st.session_state.pop(k, None)
     if selected != 'Text':
         for k in st.session_state.keys():
             if 'Text' in k:

dianna/dashboard/_model_utils.py

@@ -1,6 +1,15 @@
 from pathlib import Path
 import numpy as np
 import onnx
+import pandas as pd
+
+
+def load_data(file):
+    """Open data from a file and returns it as pandas DataFrame."""
+    df = pd.read_csv(file, parse_dates=True)
+    # Add index column
+    df.insert(0, 'Index', df.index)
+    return df
 
 
 def preprocess_function(image):
@@ -29,3 +38,7 @@ def load_labels(file):
     if labels is None or labels == ['']:
         raise ValueError(labels)
     return labels
+
+
+def load_training_data(file):
+    return np.float32(np.load(file, allow_pickle=False))

dianna/dashboard/_models_tabular.py

@@ -0,0 +1,57 @@
+import tempfile
+import numpy as np
+import streamlit as st
+from dianna import explain_tabular
+from dianna.utils.onnx_runner import SimpleModelRunner
+
+
+@st.cache_data
+def predict(*, model, tabular_input):
+    model_runner = SimpleModelRunner(model)
+    predictions = model_runner(tabular_input.reshape(1,-1).astype(np.float32))
+    return predictions
+
+
+@st.cache_data
+def _run_rise_tabular(_model, table, training_data, **kwargs):
+    relevances = explain_tabular(
+        _model,
+        table,
+        method='RISE',
+        training_data=training_data,
+        **kwargs,
+    )
+    return relevances
+
+
+@st.cache_data
+def _run_lime_tabular(_model, table, training_data, _feature_names, **kwargs):
+    relevances = explain_tabular(
+        _model,
+        table,
+        method='LIME',
+        training_data=training_data,
+        feature_names=_feature_names,
+        **kwargs,
+    )
+    return relevances
+
+@st.cache_data
+def _run_kernelshap_tabular(model, table, training_data, **kwargs):
+    # Kernelshap interface is different. Write model to temporary file.
+    with tempfile.NamedTemporaryFile() as f:
+        f.write(model)
+        f.flush()
+        relevances = explain_tabular(f.name,
+                table,
+                method='KernelSHAP',
+                training_data=training_data,
+                **kwargs)
+    return relevances[0]
+
+
+explain_tabular_dispatcher = {
+    'RISE': _run_rise_tabular,
+    'LIME': _run_lime_tabular,
+    'KernelSHAP': _run_kernelshap_tabular
+}

dianna/dashboard/_shared.py

@@ -1,7 +1,5 @@
 import base64
 import sys
-from typing import Any
-from typing import Dict
 from typing import Sequence
 import numpy as np
 import streamlit as st
@@ -46,71 +44,67 @@ def build_markup_for_logo(
 
 
 def add_sidebar_logo():
-    """Based on: https://stackoverflow.com/a/73278825."""
-    png_file = data_directory / 'logo.png'
-    logo_markup = build_markup_for_logo(png_file)
-    st.markdown(
-        logo_markup,
-        unsafe_allow_html=True,
-    )
+    """Upload DIANNA logo to sidebar element."""
+    st.sidebar.image(str(data_directory / 'logo.png'))
 
 
 def _methods_checkboxes(*, choices: Sequence, key):
-    """Get methods from a horizontal row of checkboxes."""
+    """Get methods from a horizontal row of checkboxes and the corresponding parameters."""
     n_choices = len(choices)
     methods = []
+    method_params = {}
+
+    # Create a container for the message
+    message_container = st.empty()
+
     for col, method in zip(st.columns(n_choices), choices):
         with col:
-            if st.checkbox(method, key=key + method):
+            if st.checkbox(method, key=f'{key}_{method}'):
                 methods.append(method)
+                with st.expander(f'Click to modify {method} parameters'):
+                    method_params[method] = _get_params(method, key=f'{key}_param')
 
     if not methods:
-        st.info('Select a method to continue')
+        # Put the message in the container above
+        message_container.info('Select a method to continue')
         st.stop()
 
-    return methods
+    return methods, method_params
 
 
 def _get_params(method: str, key):
     if method == 'RISE':
         return {
             'n_masks':
-            st.number_input('Number of masks', value=1000, key=key + method + 'nmasks'),
+            st.number_input('Number of masks', value=1000, key=f'{key}_{method}_nmasks'),
             'feature_res':
-            st.number_input('Feature resolution', value=6, key=key + method + 'fr'),
+            st.number_input('Feature resolution', value=6, key=f'{key}_{method}_fr'),
             'p_keep':
-            st.number_input('Probability to be kept unmasked', value=0.1, key=key + method + 'pkeep'),
+            st.number_input('Probability to be kept unmasked', value=0.1, key=f'{key}_{method}_pkeep'),
         }
 
     elif method == 'KernelSHAP':
-        return {
-            'nsamples': st.number_input('Number of samples', value=1000, key=key + method + 'nsamp'),
-            'background': st.number_input('Background', value=0, key=key + method + 'background'),
-            'n_segments': st.number_input('Number of segments', value=200, key=key + method + 'nseg'),
-            'sigma': st.number_input('σ', value=0, key=key + method + 'sigma'),
-        }
+        if 'Tabular' in key:
+            return {'training_data_kmeans': st.number_input('Training data kmeans', value=5,
+                                                            key=f'{key}_{method}_training_data_kmeans'),
+            }
+        else:
+            return {
+                'nsamples': st.number_input('Number of samples', value=1000, key=f'{key}_{method}_nsamp'),
+                'background': st.number_input('Background', value=0, key=f'{key}_{method}_background'),
+                'n_segments': st.number_input('Number of segments', value=200, key=f'{key}_{method}_nseg'),
+                'sigma': st.number_input('σ', value=0, key=f'{key}_{method}_sigma'),
+            }
 
     elif method == 'LIME':
         return {
-            'random_state': st.number_input('Random state', value=2, key=key + method + 'rs'),
+            'random_state': st.number_input('Random state', value=2, key=f'{key}_{method}_rs'),
         }
 
     else:
         raise ValueError(f'No such method: {method}')
 
 
-def _get_method_params(methods: Sequence[str], key) -> Dict[str, Dict[str, Any]]:
-    method_params = {}
-
-    with st.expander('Click to modify method parameters'):
-        for method, col in zip(methods, st.columns(len(methods))):
-            with col:
-                st.header(method)
-                method_params[method] = _get_params(method, key=key)
-
-    return method_params
-
-
 def _get_top_indices(predictions, n_top):
     indices = np.array(np.argpartition(predictions, -n_top)[-n_top:])
     indices = indices[np.argsort(predictions[indices])]
@@ -119,29 +113,35 @@ def _get_top_indices(predictions, n_top):
 
 
 def _get_top_indices_and_labels(*, predictions, labels):
-    c1, c2 = st.columns(2)
+    cols = st.columns(4)
 
-    with c2:
-        n_top = st.number_input('Number of top results to show',
-                                value=2,
-                                min_value=1,
-                                max_value=len(labels))
+    if labels is not None:
+        with cols[-1]:
+            n_top = st.number_input('Number of top classes to show',
+                                    value=1,
+                                    min_value=1,
+                                    max_value=len(labels))
 
-    top_indices = _get_top_indices(predictions, n_top)
-    top_labels = [labels[i] for i in top_indices]
+        top_indices = _get_top_indices(predictions, n_top)
+        top_labels = [labels[i] for i in top_indices]
 
-    with c1:
-        st.metric('Predicted class', top_labels[0])
+        with cols[0]:
+            st.metric('Predicted class:', top_labels[0])
+    else:
+        # If not a classifier, only return the predicted value
+        top_indices = top_labels = " "
+        with cols[0]:
+            st.metric('Predicted value:', f"{predictions[0]:.2f}")
 
     return top_indices, top_labels
 
 def reset_method():
     # Clear selection
     for k in st.session_state.keys():
-        if '_cb_' in k:
-            st.session_state[k] = False
-        if 'params' in k:
+        if '_param' in k:
             st.session_state.pop(k)
+        elif '_cb' in k:
+            st.session_state[k] = False
 
 def reset_example():
     # Clear selection

dianna/dashboard/pages/Images.py

@@ -4,7 +4,6 @@
 from _model_utils import load_model
 from _models_image import explain_image_dispatcher
 from _models_image import predict
-from _shared import _get_method_params
 from _shared import _get_top_indices_and_labels
 from _shared import _methods_checkboxes
 from _shared import add_sidebar_logo
@@ -88,15 +87,23 @@
 labels = load_labels(image_label_file)
 
 choices = ('RISE', 'KernelSHAP', 'LIME')
-methods = _methods_checkboxes(choices=choices, key='Image_cb_')
 
-method_params = _get_method_params(methods, key='Image_params_')
+st.text("")
+st.text("")
 
-with st.spinner('Predicting class'):
-    predictions = predict(model=model, image=image)
+with st.container(border=True):
+    prediction_placeholder = st.empty()
+    methods, method_params = _methods_checkboxes(choices=choices, key='Image_cb')
 
-top_indices, top_labels = _get_top_indices_and_labels(predictions=predictions,
-                                                      labels=labels)
+    with st.spinner('Predicting class'):
+        predictions = predict(model=model, image=image)
+
+    with prediction_placeholder:
+        top_indices, top_labels = _get_top_indices_and_labels(
+            predictions=predictions,labels=labels)
+
+st.text("")
+st.text("")
 
 # check which axis is color channel
 original_data = image[:, :, 0] if image.shape[2] <= 3 else image[1, :, :]
@@ -107,11 +114,11 @@
 
 _, *columns = st.columns(column_spec)
 for col, method in zip(columns, methods):
-    col.header(method)
+    col.markdown(f"<h4 style='text-align: center; '>{method}</h4>", unsafe_allow_html=True)
 
 for index, label in zip(top_indices, top_labels):
     index_col, *columns = st.columns(column_spec)
-    index_col.markdown(f'##### {label}')
+    index_col.markdown(f'##### Class: {label}')
 
     for col, method in zip(columns, methods):
         kwargs = method_params[method].copy()