Merge branch 'master' of https://github.com/chm123/examples into feat…

…ure/metrics

image_detection/retinanet_svhn.py

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+from fastestimator.pipeline.dynamic.preprocess import AbstractPreprocessing as AbstractPreprocessingD
+from fastestimator.architecture.retinanet import RetinaNet, get_fpn_anchor_box, get_target
+from fastestimator.pipeline.dynamic.preprocess import ImageReader
+from fastestimator.pipeline.static.preprocess import Minmax
+from fastestimator.estimator.estimator import Estimator
+from fastestimator.pipeline.pipeline import Pipeline
+from fastestimator.estimator.trace import Accuracy, Trace
+import tensorflow as tf
+import numpy as np
+import svhn_data
+import cv2
+
+class Network:
+    def __init__(self):
+        self.model = RetinaNet(input_shape=(64, 128, 3), num_classes=10)
+        self.optimizer = tf.optimizers.Adam(learning_rate=0.0001)
+        self.loss = MyLoss()
+        self.anchorbox = tf.convert_to_tensor(get_fpn_anchor_box(input_shape=(64, 128, 3)))
+        self.anchor_w_h = tf.tile(self.anchorbox[:,2:], [1, 2]) - tf.tile(self.anchorbox[:, :2], [1, 2])
+
+    def train_op(self, batch):
+        with tf.GradientTape() as tape:
+            predictions = self.model(batch["image"])
+            loss = self.loss((batch["target_cls"], batch["target_loc"]), predictions)
+        gradients = tape.gradient(loss, self.model.trainable_variables)
+        self.optimizer.apply_gradients(zip(gradients, self.model.trainable_variables))
+        return predictions, loss
+
+    def eval_op(self, batch):
+        top_n = 10
+        score_threshold = 0.2
+        predictions = self.model(batch["image"], training=False)
+        loss = self.loss((batch["target_cls"], batch["target_loc"]), predictions)
+        cls_pred, loc_pred = tuple(predictions)
+        #convert the residual prediction to absolute prediction in (x1, y1, x2, y2)
+        loc_pred = tf.map_fn(lambda x: x * self.anchor_w_h + self.anchorbox, elems=loc_pred, dtype=tf.float32, back_prop=False)
+        num_batch, num_anchor, _ = loc_pred.shape
+        cls_best_score = tf.reduce_max(cls_pred, axis=-1)
+        cls_best_class = tf.argmax(cls_pred, axis=-1)
+        #select top n anchor boxes to proceed 
+        sorted_score = tf.sort(cls_best_score,  direction='DESCENDING')
+        top_n = tf.minimum(top_n, num_anchor)
+        cls_best_score = tf.cond(tf.greater(num_anchor, top_n),
+                                lambda: tf.where(tf.greater_equal(cls_best_score, tf.tile(sorted_score[:,top_n-1:top_n],[1, num_anchor])), cls_best_score, 0.0),
+                                lambda: cls_best_score)
+        #Padded Nonmax suppression with threshold
+        selected_indices_padded = tf.map_fn(lambda x: tf.image.non_max_suppression_padded(x[0], x[1], top_n, pad_to_max_output_size=True, score_threshold=score_threshold).selected_indices, (loc_pred, cls_best_score), dtype=tf.int32, back_prop=False)
+        valid_outputs = tf.map_fn(lambda x: tf.image.non_max_suppression_padded(x[0], x[1], top_n, pad_to_max_output_size=True, score_threshold=score_threshold).valid_outputs, (loc_pred, cls_best_score), dtype=tf.int32, back_prop=False)
+        #select output anchors after the NMS
+        batch_index = tf.tile(tf.reshape(tf.range(num_batch),[-1, 1]), [1, top_n])
+        selected_indices_padded = tf.stack([batch_index, selected_indices_padded], axis=-1)
+        select_mask = tf.sequence_mask(valid_outputs, top_n)
+        selected_anchors = tf.boolean_mask(selected_indices_padded, select_mask)
+        #get the class and coordinates or output anchor
+        loc_selected = tf.gather_nd(loc_pred, selected_anchors)
+        cls_selected = tf.gather_nd(cls_best_class, selected_anchors)
+        output = (cls_selected, loc_selected, valid_outputs)
+        return output, loss
+
+class MyPipeline(Pipeline):
+    def edit_feature(self, feature):
+        height, width = feature["image"].shape[0], feature["image"].shape[1]
+        feature["x1"], feature["y1"], feature["x2"], feature["y2"] = feature["x1"]/width, feature["y1"]/height, feature["x2"]/width, feature["y2"]/height
+        feature["image"] = cv2.resize(feature["image"], (128, 64)) #cv2 requires (width, height)
+        anchorbox = get_fpn_anchor_box(input_shape=feature["image"].shape)
+        target_cls, target_loc = get_target(anchorbox, feature["label"], feature["x1"], feature["y1"], feature["x2"], feature["y2"], num_classes=10)
+        feature["target_cls"], feature["target_loc"] = target_cls, target_loc
+        return feature
+
+class String2List(AbstractPreprocessingD):
+    #this thing converts '[1, 2, 3]' into np.array([1, 2, 3])
+    def transform(self, data):
+        data = np.array([int(x) for x in data[1:-1].split(',')])
+        return data
+
+class MyLoss(tf.losses.Loss):
+    def call(self, y_true, y_pred):
+        cls_gt, loc_gt = tuple(y_true)
+        cls_pred, loc_pred = tuple(y_pred)
+        focal_loss, obj_idx = self.focal_loss(cls_gt, cls_pred, num_classes=10)
+        smooth_l1_loss = self.smooth_l1(loc_gt, loc_pred, obj_idx)
+        return 40000*focal_loss+smooth_l1_loss
+
+    def focal_loss(self, cls_gt, cls_pred, num_classes, alpha=0.25, gamma=2.0):
+        #cls_gt has shape [B, A], cls_pred is in [B, A, K]
+        obj_idx = tf.where(tf.greater_equal(cls_gt, 0)) #index of object
+        obj_bg_idx = tf.where(tf.greater_equal(cls_gt, -1)) #index of object and background
+        cls_gt = tf.one_hot(cls_gt, num_classes)
+        cls_gt = tf.gather_nd(cls_gt, obj_bg_idx)
+        cls_pred = tf.gather_nd(cls_pred, obj_bg_idx)
+        #getting the object count for each image in batch
+        _, idx, count = tf.unique_with_counts(obj_bg_idx[:,0])
+        object_count = tf.gather_nd(count, tf.reshape(idx, (-1, 1)))
+        object_count = tf.tile(tf.reshape(object_count,(-1, 1)), [1,num_classes])
+        object_count = tf.cast(object_count, tf.float32)
+        #reshape to the correct shape
+        cls_gt = tf.reshape(cls_gt, (-1, 1))
+        cls_pred = tf.reshape(cls_pred, (-1, 1))
+        object_count = tf.reshape(object_count, (-1, 1))
+        # compute the focal weight on each selected anchor box
+        alpha_factor = tf.ones_like(cls_gt) * alpha
+        alpha_factor = tf.where(tf.equal(cls_gt, 1), alpha_factor, 1 - alpha_factor)
+        focal_weight = tf.where(tf.equal(cls_gt, 1), 1 - cls_pred, cls_pred)
+        focal_weight = alpha_factor * focal_weight ** gamma / object_count
+        focal_loss =  tf.losses.BinaryCrossentropy()(cls_gt, cls_pred, sample_weight=focal_weight)
+        return focal_loss, obj_idx
+
+    def smooth_l1(self, loc_gt, loc_pred, obj_idx):
+        #loc_gt anf loc_pred has shape [B, A, 4]
+        loc_gt = tf.gather_nd(loc_gt, obj_idx)
+        loc_pred = tf.gather_nd(loc_pred, obj_idx)
+        loc_gt = tf.reshape(loc_gt, (-1, 1))
+        loc_pred = tf.reshape(loc_pred, (-1, 1))
+        loc_diff = tf.abs(loc_gt - loc_pred)
+        smooth_l1_loss = tf.where(tf.less(loc_diff,1), 0.5 * loc_diff**2, loc_diff-0.5)
+        smooth_l1_loss = tf.reduce_mean(smooth_l1_loss)
+        return smooth_l1_loss
+
+def get_estimator():
+    train_csv, test_csv, path = svhn_data.load_data()
+
+    pipeline = MyPipeline(batch_size=256,
+                          feature_name=["image", "label", "x1", "y1", "x2", "y2", "target_cls", "target_loc"],
+                          train_data=train_csv,
+                          validation_data=test_csv,
+                          transform_dataset=[[ImageReader(parent_path=path)], [String2List()], [String2List()], [String2List()], [String2List()], [String2List()], [],[]],
+                          transform_train= [[Minmax()], [], [], [],[],[],[],[]],
+                          padded_batch=True)
+
+    estimator = Estimator(network= Network(),
+                          pipeline=pipeline,
+                          epochs= 15,
+                          log_steps=20,
+                          traces=[SaveBoundingImage()])
+    return estimator

image_detection/svhn_data.py

@@ -0,0 +1,71 @@
+import os
+import tarfile
+import tempfile
+from operator import add
+
+import h5py
+import numpy as np
+import pandas as pd
+import wget
+
+
+def get_name(index, hdf5_data):
+    name = hdf5_data['/digitStruct/name']
+    return ''.join([chr(v[0]) for v in hdf5_data[name[index][0]].value])
+
+def get_bbox(index, hdf5_data):
+    attrs = {}
+    item = hdf5_data['digitStruct']['bbox'][index].item()
+    for key in ['label', 'left', 'top', 'width', 'height']:
+        attr = hdf5_data[item][key]
+        values = [int(hdf5_data[attr.value[i].item()].value[0][0]) for i in range(len(attr))] if len(attr) > 1 else [int(attr.value[0][0])]
+        attrs[key] = values
+    return attrs
+
+def img_boundingbox_data_constructor(data_folder, mode, csv_path):
+    f = h5py.File(os.path.join(data_folder, "digitStruct.mat"),'r')     
+    row_list = []
+    num_example = f['/digitStruct/bbox'].shape[0]
+    logging_interval = num_example // 10
+    print("found %d number of examples for %s" % (num_example, mode))
+    for j in range(num_example):
+        if j % logging_interval == 0:
+            print("retrieving bounding box for %s: %f%%" % (mode, j/num_example*100))
+        img_name = get_name(j, f)
+        bbox = get_bbox(j, f)
+        row_dict = {'image': os.path.join(mode, img_name),
+                    'label': bbox["label"],
+                    'x1': bbox["left"],
+                    'y1': bbox["top"],
+                    'x2': list(map(add, bbox["left"], bbox["width"])),
+                    'y2': list(map(add, bbox["top"], bbox["height"]))}
+        row_list.append(row_dict)
+    bbox_df = pd.DataFrame(row_list, columns=['image','label','x1','y1','x2','y2'])
+    bbox_df.to_csv(csv_path, index=False)
+    return bbox_df
+
+def load_data(path=None):
+    if path is None:
+        path = os.path.join(tempfile.gettempdir(), "FE_SVHN")
+    if not os.path.exists(path):
+        os.mkdir(path)
+    train_csv = os.path.join(path, "train_data.csv")
+    test_csv = os.path.join(path, "test_data.csv")
+    if not (os.path.exists(os.path.join(path, "train.tar.gz")) and os.path.exists(os.path.join(path, "test.tar.gz"))):
+        print("downloading data to %s" % path)
+        wget.download('http://ufldl.stanford.edu/housenumbers/train.tar.gz', path)
+        wget.download("http://ufldl.stanford.edu/housenumbers/test.tar.gz", path)
+    if not (os.path.exists(os.path.join(path, "train")) and os.path.exists(os.path.join(path, "test"))):
+        print(" ")
+        print("extracting data...")
+        test_file = tarfile.open(os.path.join(path, "test.tar.gz"))
+        train_file = tarfile.open(os.path.join(path, "train.tar.gz"))
+        test_file.extractall(path=path)
+        train_file.extractall(path=path)
+    if not (os.path.exists(train_csv) and os.path.exists(test_csv)):
+        print("constructing bounding box data...")
+        train_folder = os.path.join(path, "train")
+        test_folder = os.path.join(path, "test")
+        img_boundingbox_data_constructor(train_folder, "train", train_csv)
+        img_boundingbox_data_constructor(test_folder, "test", test_csv)
+    return train_csv, test_csv, path