add biomat application file

app.py

@@ -1,4 +1,122 @@
 import streamlit as st
 
 x = st.slider('Select a value')
-st.write(x, 'squared is', x * x)
+st.write(x, 'squared is', x * x)
+
+import streamlit as st
+import os
+import torch
+
+from torch.utils.data import DataLoader
+from config import get_config_universal
+from dataset import DataSet
+from datasetbuilder import DataSetBuilder
+from test import Test
+from visualization.steamlit_plot import plot_kinematic_predictions
+
+dataset_name = 'camargo'
+config = get_config_universal(dataset_name)
+
+# model_file = 'transformertsai_g1g2rardsasd_g1g2rardsasd.pt'
+# model = torch.load(os.path.join('./caches/trained_model/v05', model_file))
+sensor_options = {'Thigh & Shank & Foot': ['foot', 'shank', 'thigh'],
+                  'Thigh & Shank': ['thigh', 'shank'],
+                  'Thigh & Foot': ['thigh', 'foot'],
+                  'Shank & Foot': ['shank', 'foot'],
+                  'Thigh': ['thigh'],
+                  'Shank': ['shank'],
+                  'Foot': ['foot']}
+
+@st.cache
+def fetch_data(config):
+    dataset_handler = DataSet(config, load_dataset=True)
+    kihadataset_train, kihadataset_test = dataset_handler.run_dataset_split_loop()
+    kihadataset_train['x'], kihadataset_train['y'], kihadataset_train['labels'] = dataset_handler.run_segmentation(
+        kihadataset_train['x'],
+        kihadataset_train['y'], kihadataset_train['labels'])
+    kihadataset_test['x'], kihadataset_test['y'], kihadataset_test['labels'] = dataset_handler.run_segmentation(
+        kihadataset_test['x'],
+        kihadataset_test['y'], kihadataset_test['labels'])
+    train_dataset = DataSetBuilder(kihadataset_train['x'], kihadataset_train['y'], kihadataset_train['labels'],
+                                   transform_method=config['data_transformer'], scaler=None, noise=None)
+    test_dataset = DataSetBuilder(kihadataset_test['x'], kihadataset_test['y'], kihadataset_test['labels'],
+                                  transform_method=config['data_transformer'], scaler=train_dataset.scaler,
+                                  noise=None)
+    test_dataloader = DataLoader(dataset=test_dataset, batch_size=config['batch_size'], shuffle=False)
+    return test_dataloader, kihadataset_test
+
+# @st.cache()
+def fetch_model(sensor_name, model_name):
+    device = torch.device('cpu')
+    model_names = {'CNNLSTM':'hernandez2021cnnlstm', 'BiLSTM':'bilstm', 'BioMAT': 'transformertsai'}
+    sensor_names = {'Thigh & Shank & Foot':'thighshankfoot',
+                    'Thigh & Shank':'thighshank',
+                   'Thigh & Foot':'thighfoot',
+                   'Shank & Foot':'shankfoot',
+                   'Thigh':'thigh',
+                   'Shank':'shank',
+                   'Foot':'foot'}
+    if sensor_names[sensor_name]=='thighshankfoot':
+        model_file = model_names[model_name] + '_g1g2rardsasd_g1g2rardsasd.pt'
+    else:
+        model_file = sensor_names[sensor_name] + '_' + model_names[model_name]+'_g1g2rardsasd_g1g2rardsasd.pt'
+    st.write(model_file)
+    model = torch.load(os.path.join('./caches/trained_model/v05', model_file))
+    return model
+
+# @st.cache
+def fetch_predictions(model):
+    test_handler = Test()
+    y_pred, y_true, loss = test_handler.run_testing(config, model, test_dataloader=test_dataloader)
+    y_true = y_true.detach().cpu().clone().numpy()
+    y_pred = y_pred.detach().cpu().clone().numpy()
+    return y_pred, y_true, loss
+
+st.set_page_config(layout="wide")
+st.title('BioMAT:Biomechanical Multi-Activity Transformer Model for Joint Kinematic Prediction From IMUs')
+st.info('If you change the sensor configuration, press rerun', icon="ℹ️")
+
+st.sidebar.title('Sensor Configuration')
+selected_sensor = st.sidebar.selectbox('Pick one', ['Thigh & Shank & Foot',
+                                                    'Thigh & Shank',
+                                                    'Thigh & Foot',
+                                                    'Shank & Foot',
+                                                    'Thigh',
+                                                    'Shank',
+                                                    'Foot'])
+
+config['selected_sensors'] = sensor_options[selected_sensor]
+
+st.sidebar.title('Model Configuration')
+selected_model = st.sidebar.selectbox('Pick one', ['CNNLSTM',
+                                                    'BiLSTM',
+                                                   'BioMAT'])
+
+st.sidebar.title('Subject')
+selected_subject = st.sidebar.slider('Pick a Subject Number', min_value=23, max_value=25, step=1)
+
+st.sidebar.title('Activity')
+selected_activities = st.sidebar.multiselect('Pick Output Activities',
+                                           ['LevelGround Walking', 'Ramp Ascent', 'Ramp Descent', 'Stair Ascent', 'Stair Descent'])
+
+index_to_plot = st.sidebar.number_input('Enter a number between 0 and 5', min_value=0, max_value=5)
+
+if st.sidebar.button('Predict'):
+    with st.spinner('Data is loading...'):
+        test_dataloader, kihadataset_test = fetch_data(config)
+    st.success('Data is loaded!')
+    with st.spinner('Model is loading...'):
+        model = fetch_model(selected_sensor, selected_model)
+    st.success('Model is loaded!')
+    with st.spinner('Prediction ...'):
+        y_pred, y_true, loss = fetch_predictions(model)
+    st.success('Prediction is Completed!')
+    st.write('plot ...')
+    subject = 'AB' + str(selected_subject)
+    fig = plot_kinematic_predictions(y_true, y_pred, kihadataset_test['labels'], subject,
+                                 selected_activities=selected_activities, selected_index_to_plot=index_to_plot)
+    st.plotly_chart(fig, use_container_width=True)
+
+
+
+