Merge pull request #1228 from npcmaci/dev-postgresql

create the application folder for the healthcare model zoo

Author: chrishkchris

examples/healthcare/application/Malaria_Detection/train_cnn.py

@@ -0,0 +1,318 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+from singa import singa_wrap as singa
+from singa import device
+from singa import tensor
+from singa import opt
+import numpy as np
+import time
+import argparse
+import sys
+sys.path.append("../../..")
+
+from PIL import Image
+
+from healthcare.data import malaria
+from healthcare.models import malaria_net
+
+np_dtype = {"float16": np.float16, "float32": np.float32}
+
+singa_dtype = {"float16": tensor.float16, "float32": tensor.float32}
+
+
+# Data augmentation
+def augmentation(x, batch_size):
+    xpad = np.pad(x, [[0, 0], [0, 0], [4, 4], [4, 4]], 'symmetric')
+    for data_num in range(0, batch_size):
+        offset = np.random.randint(8, size=2)
+        x[data_num, :, :, :] = xpad[data_num, :,
+                               offset[0]:offset[0] + x.shape[2],
+                               offset[1]:offset[1] + x.shape[2]]
+        if_flip = np.random.randint(2)
+        if (if_flip):
+            x[data_num, :, :, :] = x[data_num, :, :, ::-1]
+    return x
+
+
+# Calculate accuracy
+def accuracy(pred, target):
+    # y is network output to be compared with ground truth (int)
+    y = np.argmax(pred, axis=1)
+    a = y == target
+    correct = np.array(a, "int").sum()
+    return correct
+
+
+# Data partition according to the rank
+def partition(global_rank, world_size, train_x, train_y, val_x, val_y):
+    # Partition training data
+    data_per_rank = train_x.shape[0] // world_size
+    idx_start = global_rank * data_per_rank
+    idx_end = (global_rank + 1) * data_per_rank
+    train_x = train_x[idx_start:idx_end]
+    train_y = train_y[idx_start:idx_end]
+
+    # Partition evaluation data
+    data_per_rank = val_x.shape[0] // world_size
+    idx_start = global_rank * data_per_rank
+    idx_end = (global_rank + 1) * data_per_rank
+    val_x = val_x[idx_start:idx_end]
+    val_y = val_y[idx_start:idx_end]
+    return train_x, train_y, val_x, val_y
+
+
+# Function to all reduce NUMPY accuracy and loss from multiple devices
+def reduce_variable(variable, dist_opt, reducer):
+    reducer.copy_from_numpy(variable)
+    dist_opt.all_reduce(reducer.data)
+    dist_opt.wait()
+    output = tensor.to_numpy(reducer)
+    return output
+
+
+def resize_dataset(x, image_size):
+    num_data = x.shape[0]
+    dim = x.shape[1]
+    X = np.zeros(shape=(num_data, dim, image_size, image_size),
+                 dtype=np.float32)
+    for n in range(0, num_data):
+        for d in range(0, dim):
+            X[n, d, :, :] = np.array(Image.fromarray(x[n, d, :, :]).resize(
+                (image_size, image_size), Image.BILINEAR),
+                dtype=np.float32)
+    return X
+
+
+def run(global_rank,
+        world_size,
+        dir_path,
+        max_epoch,
+        batch_size,
+        model,
+        data,
+        sgd,
+        graph,
+        verbosity,
+        dist_option='plain',
+        spars=None,
+        precision='float32'):
+    # now CPU version only, could change to GPU device for GPU-support machines
+    dev = device.get_default_device()
+    dev.SetRandSeed(0)
+    np.random.seed(0)
+    if data == 'malaria':
+
+        train_x, train_y, val_x, val_y = malaria.load(dir_path=dir_path)
+    else:
+        print(
+            'Wrong dataset!'
+        )
+        sys.exit(0)
+
+    num_channels = train_x.shape[1]
+    image_size = train_x.shape[2]
+    data_size = np.prod(train_x.shape[1:train_x.ndim]).item()
+    num_classes = (np.max(train_y) + 1).item()
+
+    if model == 'cnn':
+        model = malaria_net.create_model(model_option='cnn', num_channels=num_channels,
+                                         num_classes=num_classes)
+    else:
+        print(
+            'Wrong model!'
+        )
+        sys.exit(0)
+
+    # For distributed training, sequential has better performance
+    if hasattr(sgd, "communicator"):
+        DIST = True
+        sequential = True
+    else:
+        DIST = False
+        sequential = False
+
+    if DIST:
+        train_x, train_y, val_x, val_y = partition(global_rank, world_size,
+                                                   train_x, train_y, val_x,
+                                                   val_y)
+
+    if model.dimension == 4:
+        tx = tensor.Tensor(
+            (batch_size, num_channels, model.input_size, model.input_size), dev,
+            singa_dtype[precision])
+    elif model.dimension == 2:
+        tx = tensor.Tensor((batch_size, data_size),
+                           dev, singa_dtype[precision])
+        np.reshape(train_x, (train_x.shape[0], -1))
+        np.reshape(val_x, (val_x.shape[0], -1))
+
+    ty = tensor.Tensor((batch_size,), dev, tensor.int32)
+    num_train_batch = train_x.shape[0] // batch_size
+    num_val_batch = val_x.shape[0] // batch_size
+    idx = np.arange(train_x.shape[0], dtype=np.int32)
+
+    # Attach model to graph
+    model.set_optimizer(sgd)
+    model.compile([tx], is_train=True, use_graph=graph, sequential=sequential)
+    dev.SetVerbosity(verbosity)
+
+    # Training and evaluation loop
+    for epoch in range(max_epoch):
+        start_time = time.time()
+        np.random.shuffle(idx)
+
+        if global_rank == 0:
+            print('Starting Epoch %d:' % (epoch))
+
+        # Training phase
+        train_correct = np.zeros(shape=[1], dtype=np.float32)
+        test_correct = np.zeros(shape=[1], dtype=np.float32)
+        train_loss = np.zeros(shape=[1], dtype=np.float32)
+
+        model.train()
+        for b in range(num_train_batch):
+            # if b % 100 == 0:
+            #     print ("b: \n", b)
+            # Generate the patch data in this iteration
+            x = train_x[idx[b * batch_size:(b + 1) * batch_size]]
+            if model.dimension == 4:
+                x = augmentation(x, batch_size)
+                if (image_size != model.input_size):
+                    x = resize_dataset(x, model.input_size)
+            x = x.astype(np_dtype[precision])
+            y = train_y[idx[b * batch_size:(b + 1) * batch_size]]
+
+            # Copy the patch data into input tensors
+            tx.copy_from_numpy(x)
+            ty.copy_from_numpy(y)
+
+            # Train the model
+            out, loss = model(tx, ty, dist_option, spars)
+            train_correct += accuracy(tensor.to_numpy(out), y)
+            train_loss += tensor.to_numpy(loss)[0]
+
+            # print('batch training loss = %f' % train_loss, flush=True)
+
+        if DIST:
+            # Reduce the evaluation accuracy and loss from multiple devices
+            reducer = tensor.Tensor((1,), dev, tensor.float32)
+            train_correct = reduce_variable(train_correct, sgd, reducer)
+            train_loss = reduce_variable(train_loss, sgd, reducer)
+
+        if global_rank == 0:
+            print('Training loss = %f, training accuracy = %f' %
+                  (train_loss, train_correct /
+                   (num_train_batch * batch_size * world_size)),
+                  flush=True)
+
+        # Evaluation phase
+        model.eval()
+        for b in range(num_val_batch):
+            x = val_x[b * batch_size:(b + 1) * batch_size]
+            if model.dimension == 4:
+                if (image_size != model.input_size):
+                    x = resize_dataset(x, model.input_size)
+            x = x.astype(np_dtype[precision])
+            y = val_y[b * batch_size:(b + 1) * batch_size]
+            tx.copy_from_numpy(x)
+            ty.copy_from_numpy(y)
+            out_test = model(tx)
+            test_correct += accuracy(tensor.to_numpy(out_test), y)
+
+        if DIST:
+            # Reduce the evaulation accuracy from multiple devices
+            test_correct = reduce_variable(test_correct, sgd, reducer)
+
+        # Output the evaluation accuracy
+        if global_rank == 0:
+            print('Evaluation accuracy = %f, Elapsed Time = %fs' %
+                  (test_correct / (num_val_batch * batch_size * world_size),
+                   time.time() - start_time),
+                  flush=True)
+
+    dev.PrintTimeProfiling()
+
+
+if __name__ == '__main__':
+    # Use argparse to get command config: max_epoch, model, data, etc., for single gpu training
+    parser = argparse.ArgumentParser(
+        description='Training using the autograd and graph.')
+    parser.add_argument(
+        'model',
+        choices=['cnn'],
+        default='cnn')
+    parser.add_argument('data',
+                        choices=['malaria'],
+                        default='malaria')
+    parser.add_argument('-p',
+                        choices=['float32', 'float16'],
+                        default='float32',
+                        dest='precision')
+    parser.add_argument('-dir',
+                        '--dir-path',
+                        default="/tmp/malaria",
+                        type=str,
+                        help='the directory to store the malaria dataset',
+                        dest='dir_path')
+    parser.add_argument('-m',
+                        '--max-epoch',
+                        default=100,
+                        type=int,
+                        help='maximum epochs',
+                        dest='max_epoch')
+    parser.add_argument('-b',
+                        '--batch-size',
+                        default=64,
+                        type=int,
+                        help='batch size',
+                        dest='batch_size')
+    parser.add_argument('-l',
+                        '--learning-rate',
+                        default=0.005,
+                        type=float,
+                        help='initial learning rate',
+                        dest='lr')
+    parser.add_argument('-g',
+                        '--disable-graph',
+                        default='True',
+                        action='store_false',
+                        help='disable graph',
+                        dest='graph')
+    parser.add_argument('-v',
+                        '--log-verbosity',
+                        default=0,
+                        type=int,
+                        help='logging verbosity',
+                        dest='verbosity')
+
+    args = parser.parse_args()
+
+    sgd = opt.SGD(lr=args.lr, momentum=0.9, weight_decay=1e-5,
+                  dtype=singa_dtype[args.precision])
+    run(0,
+        1,
+        args.dir_path,
+        args.max_epoch,
+        args.batch_size,
+        args.model,
+        args.data,
+        sgd,
+        args.graph,
+        args.verbosity,
+        precision=args.precision);