Code and data release

Author: Zackory

.gitignore

@@ -3,6 +3,11 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+*.DS_Store
+*.h5
+*.csv
+*.zip
+
 # C extensions
 *.so
 

3d_models/scio_camera_holder.stl

@@ -1,4 +1,42 @@
 # SpectroVision
 The SpectroVision dataset and associated code for the paper "Multimodal Material Classification for Robots using Spectroscopy and High Resolution Texture Imaging"
 
-Full code release and dataset will become public in the next few days.
+![SpectroVision](images/spectrovision.jpg "SpectroVision")
+
+## Install
+```bash
+git clone https://github.com/Healthcare-Robotics/spectrovision.git
+cd spectrovision
+# Setup a virtual python environment to install requirements
+python3 -m pip install --user virtualenv
+python3 -m venv env
+source env/bin/activate
+pip3 install -r requirements.txt
+```
+
+## Download SpectroVision Dataset
+Download the processed image and spectral data used for training neural network models:
+```bash
+wget -O dataset/spectrovision_dataset.zip https://github.com/Healthcare-Robotics/spectrovision/releases/download/1.0/spectrovision_dataset.zip
+unzip dataset/spectrovision_dataset.zip -d dataset
+```
+Download the raw images and spectral measurements:
+```bash
+wget -O dataset/spectrovision_raw_dataset.zip https://github.com/Healthcare-Robotics/spectrovision/releases/download/1.0/spectrovision_raw_dataset.zip
+unzip dataset/spectrovision_raw_dataset.zip -d dataset
+```
+
+## Retrain Networks (recompute results from paper)
+Note: These computations will take a long time. Computing leave-one-object-out results for a training set of 104 material objects requires training 104 neural networks.
+```bash
+python3 main.py
+```
+Results are currently averaged over 10 seeds (which takes 10 times as long). If you wish to use only a single seed to speed up result computations (at the risk of large variation in results), you can use the following command:
+```bash
+python3 main.py --seed 8000
+```
+You may also run the script in the background using nohup. This is especially helpful when computing results on a remote machine.
+```bash
+nohup python3 main.py > results.out &
+```
+

README.md

@@ -0,0 +1,280 @@
+import os, random, warnings, argparse
+warnings.filterwarnings('ignore')
+os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
+import torch
+import numpy as np
+
+seed_value = 1000
+os.environ['PYTHONHASHSEED'] = str(seed_value)
+torch.manual_seed(seed_value)
+torch.cuda.manual_seed(seed_value)
+torch.cuda.manual_seed_all(seed_value)
+np.random.seed(seed_value)
+random.seed(seed_value)
+torch.manual_seed(seed_value)
+torch.backends.cudnn.benchmark = False
+torch.backends.cudnn.deterministic = True
+torch.set_num_threads(1)
+
+import sys, pickle, time, gc
+from poutyne.framework import Model
+import multiprocessing
+from functools import partial
+from multiprocessing.pool import Pool
+import util
+
+from sklearn.utils import shuffle
+from sklearn import preprocessing
+from sklearn.model_selection import StratifiedKFold
+from sklearn.metrics import confusion_matrix
+
+def first_deriv(x, wavelengths):
+    # First derivative of measurements with respect to wavelength
+    x = np.copy(x)
+    for i, xx in enumerate(x):
+        dx = np.zeros(xx.shape, np.float)
+        dx[0:-1] = np.diff(xx)/np.diff(wavelengths)
+        dx[-1] = (xx[-1] - xx[-2])/(wavelengths[-1] - wavelengths[-2])
+        x[i] = dx
+    return x
+
+def prepare_data(x_spectral_train, x_image_train, y_train, x_spectral_test, x_image_test, y_test, wavelengths, deriv=True, data_type='spectral_image', image_preprocess='resnet', objs=None):
+    if deriv:
+        # Finite difference (Numerical differentiation)
+        x_spectral_train = np.concatenate([x_spectral_train, first_deriv(x_spectral_train, wavelengths)], axis=-1)
+        x_spectral_test = np.concatenate([x_spectral_test, first_deriv(x_spectral_test, wavelengths)], axis=-1)
+
+    if data_type == 'spectral':
+        # Zero mean unit variance
+        scaler_spectral = preprocessing.StandardScaler()
+        x_spectral_train = scaler_spectral.fit_transform(x_spectral_train)
+        x_spectral_test = scaler_spectral.transform(x_spectral_test)
+    elif data_type == 'image':
+        if 'none' in image_preprocess:
+            scaler_image = preprocessing.StandardScaler()
+            x_image_train = np.reshape(scaler_image.fit_transform(np.reshape(x_image_train, (len(x_image_train), -1))), np.shape(x_image_train))
+            x_image_test = np.reshape(scaler_image.transform(np.reshape(x_image_test, (len(x_image_test), -1))), np.shape(x_image_test))
+        else:
+            scaler_image = preprocessing.StandardScaler()
+            x_image_train = scaler_image.fit_transform(x_image_train)
+            x_image_test = scaler_image.transform(x_image_test)
+    elif data_type == 'spectral_image':
+        scaler_image = preprocessing.StandardScaler()
+        x = scaler_image.fit_transform(np.concatenate([x_spectral_train, x_image_train], axis=-1))
+        x_spectral_train = x[:, :np.shape(x_spectral_train)[-1]]
+        x_image_train = x[:, np.shape(x_spectral_train)[-1]:]
+        x = scaler_image.transform(np.concatenate([x_spectral_test, x_image_test], axis=-1))
+        x_spectral_test = x[:, :np.shape(x_spectral_test)[-1]]
+        x_image_test = x[:, np.shape(x_spectral_test)[-1]:]
+
+    return x_spectral_train, x_image_train, y_train, x_spectral_test, x_image_test, y_test
+
+def nn(input_size, layers, dropout, material_count=None, batchnorm=True):
+    modules = []
+    for i in range(len(layers)-1):
+        modules.append(torch.nn.Linear(input_size if i == 0 else layers[i-1], layers[i]))
+        if batchnorm:
+            modules.append(torch.nn.BatchNorm1d(layers[i]))
+        modules.append(torch.nn.LeakyReLU())
+        if dropout > 0:
+            modules.append(torch.nn.Dropout(dropout))
+    modules.append(torch.nn.Linear(layers[-2], layers[-1]) if len(layers) > 1 else torch.nn.Linear(input_size, layers[-1]))
+    if batchnorm:
+        modules.append(torch.nn.BatchNorm1d(layers[-1]))
+    modules.append(torch.nn.LeakyReLU())
+    if material_count is not None:
+        modules.append(torch.nn.Linear(layers[-1], material_count))
+    return torch.nn.Sequential(*modules)
+
+def learn(o, X_spectral, X_image, y, objs, wavelengths, data_type='spectral_image', image_preprocess='resnet', epochs=50, batch_size=128, material_count=8, layers=[64]*2, dropout=0.0, lr=0.0005, seed=1000, test='looo', verbose=False):
+    torch.manual_seed(seed)
+    np.random.seed(seed)
+    random.seed(seed)
+    torch.set_num_threads(1)
+
+    if 'test' in test:
+        train_idx, test_idx = o
+        X_spectral_train = X_spectral[train_idx]
+        X_image_train = X_image[train_idx]
+        y_train = y[train_idx]
+        X_spectral_test = X_spectral[test_idx]
+        X_image_test = X_image[test_idx]
+        y_test = y[test_idx]
+        objs_train = objs[train_idx]
+    elif 'looo' in test:
+        _, obj = o
+        # Set up leave-one-object-out training and test sets
+        X_spectral_train = X_spectral[objs != obj]
+        X_image_train = X_image[objs != obj]
+        y_train = y[objs != obj]
+        X_spectral_test = X_spectral[objs == obj]
+        X_image_test = X_image[objs == obj]
+        y_test = y[objs == obj]
+        objs_train = objs[objs != obj]
+
+    X_spectral_train, X_image_train, y_train, X_spectral_test, X_image_test, y_test = prepare_data(X_spectral_train, X_image_train, y_train, X_spectral_test, X_image_test, y_test, wavelengths, deriv=True, data_type=data_type, image_preprocess=image_preprocess, objs=objs)
+
+    if data_type == 'spectral':
+        X_spectral_train, y_train = shuffle(X_spectral_train, y_train)
+    elif data_type == 'image':
+        X_image_train, y_train = shuffle(X_image_train, y_train)
+    elif data_type == 'spectral_image':
+        X_spectral_train, X_image_train, y_train = shuffle(X_spectral_train, X_image_train, y_train)
+
+    y_train = torch.tensor(y_train, dtype=torch.long)
+    y_test = torch.tensor(y_test, dtype=torch.long)
+
+    # Image layers
+    if data_type == 'spectral_image':
+        spectral_layers = [64, 64, 32, 32]
+        spectral_dropout = 0.25
+        spectral_epochs = 50
+        image_layers = [128, 64, 32]
+        image_dropout = 0.1
+        image_epochs = 50
+
+        class ConcatPretrainedNetwork(torch.nn.Module):
+            def __init__(self):
+                # global spectral_accuracy, image_accuracy
+                super().__init__()
+                spectral_net = nn(np.shape(X_spectral_train)[-1], spectral_layers, spectral_dropout, material_count)
+                opt = torch.optim.Adam(spectral_net.parameters(), lr=lr)
+                spectral_model = Model(spectral_net, opt, 'cross_entropy', batch_metrics=['accuracy'])
+                spectral_model.fit(X_spectral_train, y_train, epochs=spectral_epochs, batch_size=batch_size, verbose=False)
+
+                image_net = nn(np.shape(X_image_train)[-1], image_layers, image_dropout, material_count)
+                opt = torch.optim.Adam(image_net.parameters(), lr=lr)
+                image_model = Model(image_net, opt, 'cross_entropy', batch_metrics=['accuracy'])
+                image_model.fit(X_image_train, y_train, epochs=image_epochs, batch_size=batch_size, verbose=False)
+
+                # Disable dropout, remove last layer and freeze network
+                self.trained_spectral_model = torch.nn.Sequential(*(list(spectral_net.children())[:-1]))
+                for p in self.trained_spectral_model.parameters():
+                    p.requires_grad = False
+                self.trained_image_model = torch.nn.Sequential(*(list(image_net.children())[:-1]))
+                for p in self.trained_image_model.parameters():
+                    p.requires_grad = False
+
+                self.concat_net = nn(spectral_layers[-1] + image_layers[-1], layers, dropout, material_count, batchnorm=False)
+            def forward(self, x_spectral, x_image):
+                y1 = self.trained_spectral_model(x_spectral)
+                y2 = self.trained_image_model(x_image)
+                concat = torch.cat((y1, y2), -1)
+                return self.concat_net(concat)
+        net = ConcatPretrainedNetwork()
+        X_train = [X_spectral_train, X_image_train]
+        X_test = [X_spectral_test, X_image_test]
+    elif data_type == 'image':
+        net = nn(np.shape(X_image_train)[-1], layers, dropout, material_count)
+        X_train = X_image_train
+        X_test = X_image_test
+    elif data_type == 'spectral':
+        net = nn(np.shape(X_spectral_train)[-1], layers, dropout, material_count)
+        X_train = X_spectral_train
+        X_test = X_spectral_test
+
+    opt = torch.optim.Adam(net.parameters(), lr=lr)
+    model = Model(net, opt, 'cross_entropy', batch_metrics=['accuracy'])
+
+    model.fit(X_train, y_train, validation_data=(X_test, y_test), epochs=epochs, batch_size=batch_size, verbose=False)
+    cm = confusion_matrix(y_test, model.predict(X_test).argmax(axis=-1), labels=range(material_count))
+    # Return accuracy and confusion matrices
+    if 'backprop' in test:
+        return {'accuracy': model.evaluate(X_test, y_test)[-1], 'cm': cm, 'obj_cm': np.copy(cm[y_test[0]]), 'model': model, 'net': net, 'X_test': X_test, 'y_test': y_test}
+    else:
+        if verbose:
+            print(obj, model.evaluate(X_test, y_test)[-1])
+        return {'accuracy': model.evaluate(X_test, y_test)[-1], 'cm': cm, 'obj_cm': np.copy(cm[y_test[0]])}
+
+# NOTE: Leave-one-object-out cross-validation.
+
+def looo_cv(X_spectral, X_image, y, objs, wavelengths, data_type, image_preprocess, layers, dropout, epochs, batch_size, lr, seeds, material_count, jobs, test='looo', verbose=False):
+    objs_set = []
+    for o in objs:
+        if o not in objs_set:
+            objs_set.append(o)
+    accuracies = []
+    confusion_mat = None
+    object_confusion_matrix = []
+    for s in seeds:
+        pool = Pool(processes=jobs)
+        results = pool.imap(partial(learn, X_spectral=X_spectral, X_image=X_image, y=y, objs=objs, wavelengths=wavelengths, data_type=data_type, image_preprocess=image_preprocess, epochs=epochs, batch_size=batch_size, material_count=material_count, layers=layers, dropout=dropout, lr=lr, seed=s, test=test, verbose=verbose), list(enumerate(objs_set)))
+        pool.close()
+        pool.join()
+
+        seed_accuracy = []
+        for result in list(results):
+            accuracies.append(result['accuracy'])
+            seed_accuracy.append(result['accuracy'])
+            if confusion_mat is None:
+                confusion_mat = result['cm']
+            else:
+                confusion_mat += result['cm']
+            object_confusion_matrix.append(result['obj_cm'])
+        print('Accuracy with seed', s, ':', np.mean(seed_accuracy))
+    print('Results for:', data_type, '5 materials' if five_mats else '8 materials', image_preprocess, '- Accuracy:', np.mean(accuracies))
+    # print(confusion_mat.astype('float') / confusion_mat.sum(axis=1)[:, np.newaxis], '\n')
+    sys.stdout.flush()
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Training and Evaluation for SpectroVision')
+    parser.add_argument('-s', '--seed', default=-1, help='Seed used for random number generators. (default -1) for averaging of 10 seeds', type=int)
+    parser.add_argument('-v', '--verbose', help='Verbose', action='store_true')
+    args = parser.parse_args()
+
+    verbose = args.verbose
+    jobs = multiprocessing.cpu_count()
+    layers = {'spectral': [64, 64, 32, 32], 'image': [128, 64, 32], 'spectral_image': [32]}
+    dropout = {'spectral': 0.25, 'image': 0.1, 'spectral_image': 0.0}
+    epochs = {'spectral': 50, 'image': 50, 'spectral_image': 10}
+    lr = 0.0005
+    batch_size = 128
+    seeds = range(8000, 8010) if args.seed == -1 else [args.seed]
+    parent_directory = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'dataset')
+
+    # Table I, Leave-one-object-out
+    print('Table I: leave-one-object-out')
+    for five_mats in [True, False]:
+        for data_type in ['spectral', 'image', 'spectral_image']:
+            X_spectral, X_image, y, objs, wavelengths = util.load_data(parent_directory, data_type, 'densenet201_240_320', (240, 320), five_mats)
+            # print(np.shape(X_spectral), np.shape(X_image))
+            print('Computing results for:', data_type, '5 materials' if five_mats else '8 materials')
+            looo_cv(X_spectral, X_image, y, objs, wavelengths, data_type, 'densenet201_240_320', layers[data_type], dropout[data_type], epochs[data_type], batch_size, lr, seeds, 5 if five_mats else 8, jobs, 'looo', verbose)
+
+    # Table II, Test set
+    print('Table II: test set')
+    for five_mats in [True, False]:
+        for data_type in ['spectral', 'image', 'spectral_image']:
+            X_spectral, X_image, y, objs, wavelengths = util.load_data(parent_directory, data_type, 'densenet201_240_320', (240, 320), five_mats)
+            X_spectral_test, X_image_test, y_test, objs_test, wavelengths_test = util.load_data(parent_directory, data_type, 'densenet201_240_320', (240, 320), five_mats, test_set=True)
+            accuracies = []
+            confusion_mat = None
+            for seed in seeds:
+                results = learn([list(range(len(y))), list(range(len(y), len(y)+len(y_test)))], np.concatenate([X_spectral, X_spectral_test], axis=0), np.concatenate([X_image, X_image_test], axis=0), np.concatenate([y, y_test], axis=0), np.concatenate([objs, objs_test], axis=0), wavelengths, data_type, 'densenet201_240_320', epochs[data_type], batch_size, 5 if five_mats else 8, layers[data_type], dropout[data_type], lr, seed, 'test', verbose)
+                accuracies.append(results['accuracy'])
+                if confusion_mat is None:
+                    confusion_mat = results['cm']
+                else:
+                    confusion_mat += results['cm']
+            print(data_type, '5 materials' if five_mats else '8 materials', '- Accuracy:', np.mean(accuracies))
+            # print(confusion_mat.astype('float') / confusion_mat.sum(axis=1)[:, np.newaxis], '\n')
+            sys.stdout.flush()
+
+    # Table IV, Resizing and cropping images
+    print('Table IV: resizing and cropping images')
+    for image_shape, crop in [((240, 320), False), ((240, 320), True), ((480, 640), False), ((480, 640), True), ((960, 1280), False)]:
+        five_mats = False
+        data_type = 'image'
+        image_preprocess = 'densenet201_%d_%d%s' % (image_shape[0], image_shape[1], '_crop' if crop else '')
+        X_spectral, X_image, y, objs, wavelengths = util.load_data(parent_directory, data_type, image_preprocess, (240, 320), five_mats)
+        looo_cv(X_spectral, X_image, y, objs, wavelengths, data_type, image_preprocess, layers[data_type], dropout[data_type], epochs[data_type], batch_size, lr, seeds, 5 if five_mats else 8, jobs, 'looo', verbose)
+
+    # Table V, ImageNet models
+    print('Table V: ImageNet models')
+    for model in ['vgg19', 'resnet50', 'resnet101', 'resnet152', 'densenet201', 'resnext101', 'efficientnet-b5']:
+        five_mats = False
+        data_type = 'image'
+        image_preprocess = ('%s_240_320' % model) if 'efficient' not in model else ('%s_456_608' % model)
+        X_spectral, X_image, y, objs, wavelengths = util.load_data(parent_directory, data_type, image_preprocess, (240, 320), five_mats)
+        looo_cv(X_spectral, X_image, y, objs, wavelengths, data_type, image_preprocess, layers[data_type], dropout[data_type], epochs[data_type], batch_size, lr, seeds, 5 if five_mats else 8, jobs, 'looo', verbose)
+

dataset/__init__.py

@@ -0,0 +1,15 @@
+cycler==0.10.0
+h5py==2.10.0
+joblib==0.14.1
+kiwisolver==1.2.0
+matplotlib==3.2.1
+numpy==1.18.2
+Pillow==7.1.1
+Poutyne==0.7.2
+pyparsing==2.4.6
+python-dateutil==2.8.1
+scikit-learn==0.22.2.post1
+scipy==1.4.1
+six==1.14.0
+torch==1.4.0
+torchvision==0.5.0