コード例 #1
0
def main(_):
    resized_width = 128
    resized_height = 128

    model = build_CNN()

    opt = Adam(lr=FLAGS.learning_rate)
    model.compile(loss="categorical_crossentropy",
                  optimizer=opt,
                  metrics=["accuracy"])

    model.load_weights(os.path.join(FLAGS.path, "save_model", "CNN.h5df"))

    image_lists = data_process.create_image_lists(FLAGS.images_dir)

    test_datas, test_labels = data_process.get_batch_of_data(
        image_lists, -1, FLAGS.images_dir, "test", resized_width,
        resized_height)

    test_loss, test_acc = model.evaluate(test_datas, test_labels)

    print("Test accuracy:{0:.4f}, test loss:{1:.4f}".format(
        test_acc, test_loss))

    prediction = model.predict(test_datas)

    pre_data_dir = "../../predictData/CNN"

    if not os.path.exists(pre_data_dir):
        os.makedirs(pre_data_dir)

    with h5py.File(os.path.join(pre_data_dir, "prediction_and_labels.h5"),
                   "w") as f:
        f["prediction"] = prediction
        f["truth"] = test_labels
コード例 #2
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def main(_):
    path = FLAGS.path
    image_name = "random"

    # Generate a random image
    img = np.random.random((128, 128, 3))
    # cv2.imwrite(os.path.join(path,"visualization/filter_sample","random_image.jpg"),img*255)
    img = np.array([img])

    model = build_CNN()

    model.load_weights(os.path.join(path, "weights/weights", "model.h5df"))

    # Select the corresponding conv_block
    layer_names = ["max_pool1", "max_pool2", "max_pool3", "max_pool4"]
    #layer_names = ["max_pool1"]

    for layer_name in layer_names:
        save_path = os.path.join(path + "visualization/filter_sample",
                                 image_name)
        if not os.path.exists(save_path):
            os.makedirs(save_path)

        filters = conv_filter(model, layer_name, img)

        filters_show(filters, FLAGS.filter_num, save_path, layer_name + ".jpg")
コード例 #3
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def main(_):
    path = FLAGS.path
    images_dir = FLAGS.images.dir
    category = "test"

    image_lists = data_process.create_image_lists(images_dir)

    model = build_CNN()

    model.load_weights(os.path.join(path, "weights/weights", "model.h5df"))

    # Select a different intermediate layer and change the output figure size in "image_show".
    #layer_names=["max_pool1","max_pool2","max_pool3","max_pool4"]
    layer_names = ["max_pool4"]

    image_num = 120

    images = []
    file_names = []
    for label_index, label_name in enumerate(image_lists.keys()):
        image_list = image_lists[label_name][category]
        minlist = image_list[0:image_num]
        for image_index, image_name in enumerate(minlist):
            image_path = os.path.join(images_dir, category, label_name,
                                      image_name)
            image_data = cv2.imread(image_path)
            images.append(
                data_process.image_normalization(image_data, 128, 128))
            file_names.append(image_name)
    images = np.array(images)
    file_names = np.array(file_names)

    print(images.shape)
    print(file_names.shape)

    for layer_name in layer_names:
        for label_index, label_name in enumerate(image_lists.keys()):
            img_inputs = images[image_num * label_index:image_num *
                                (label_index + 1)]
            img_names = file_names[image_num * label_index:image_num *
                                   (label_index + 1)]
            feature_map = conv_output(model, layer_name, img_inputs)

            # If you want to save the channel with maximum activation, please comment the next 2 lines.
            save_path = os.path.join(path, "visualization/Hidden_layer",
                                     layer_name, label_name)

            # If you want to save the channel with maximum activation, please uncomment the next 2 lines.
            # save_path = os.path.join(
            #    path, "visualization/Hidden_layer/activation_max", layer_name, label_name)

            if not os.path.exists(save_path):
                os.makedirs(save_path)

            for i in range(image_num):
                image = feature_map[i]
                image_name = img_names[i]
                # If you want to save the channel with maximum activation, please comment the next lines.
                image_show(image, image.shape[-1], save_path, image_name)
コード例 #4
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ファイル: Grad-CAM.py プロジェクト: JinghaoPeng/DeepOrganelle
def main(_):
    path = FLAGS.path
    images_dir = FLAGS.images_dir
    category = "test"

    image_lists = data_process.create_image_lists(images_dir)

    model = build_CNN()

    model.load_weights(os.path.join(path + "weights/weights", "model.h5df"))

    layer_names = ["max_pool1", "max_pool2", "max_pool3", "max_pool4"]
    #layer_names = ["max_pool4"]

    # Different conv_block with different resolutions
    for layer_name in layer_names:
        if (layer_name == "max_pool1"):
            resolution = "63"
        elif (layer_name == "max_pool2"):
            resolution = "30"
        elif (layer_name == "max_pool3"):
            resolution = "14"
        elif (layer_name == "max_pool4"):
            resolution = "6"

        for label_index, label_name in enumerate(image_lists.keys()):
            image_list = image_lists[label_name][category]
            minlist = image_list[0:120]
            for image_index, image_name in enumerate(minlist):
                image_path = os.path.join(images_dir, category, label_name,
                                          image_name)

                # If you want to save "heatmap", please comment the next 2 lines.
                save_path = os.path.join(path, "visualization/CAM", resolution,
                                         label_name)

                # If you want to save "heatmap", please uncomment the following.
                # save_path = os.path.join(
                #    path, "visualization/CAM/heatmap", resolution, label_name)

                if not os.path.exists(save_path):
                    os.makedirs(save_path)

                Visualizing_heatmaps(model, layer_name, image_path, save_path,
                                     image_name)
コード例 #5
0
ファイル: predict.py プロジェクト: JinghaoPeng/DeepOrganelle
def main(_):
    resized_width = 128
    resized_height = 128

    model = build_CNN()

    opt = Adam(lr=FLAGS.learning_rate)
    model.compile(loss="categorical_crossentropy",
                  optimizer=opt,
                  metrics=["accuracy"])

    model.load_weights(os.path.join(FLAGS.path,"weights/weights/", "model.h5df"))

    image_lists = data_process.create_image_lists(FLAGS.images_dir)

    test_datas, test_labels = data_process.get_batch_of_data(
        image_lists, -1, FLAGS.images_dir, "test", resized_width, resized_height)

    test_loss, test_acc = model.evaluate(test_datas, test_labels)

    print("Test accuracy:{0:.4f}, test loss:{1:.4f}".format(test_acc, test_loss))
コード例 #6
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def main(_):
    resized_width = 128
    resized_height = 128

    since = time.time()

    model = build_CNN()
    model.summary()

    opt = Adam(lr=FLAGS.learning_rate)
    model.compile(loss="categorical_crossentropy",
                  optimizer=opt,
                  metrics=["accuracy"])

    result = get_result()

    checkpoint_path = os.path.join(FLAGS.path, "save_model", "CNN.h5df")
    checkpoint = ModelCheckpoint(filepath=checkpoint_path,
                                 save_best_only=True,
                                 save_weights_only=True,
                                 monitor="val_acc",
                                 mode=max)

    tb = TensorBoard(log_dir=os.path.join(FLAGS.path, "results/results/logs"))

    callbacks = [result, checkpoint, tb]

    image_lists = data_process.create_image_lists(FLAGS.images_dir)

    with gfile.FastGFile(os.path.join(FLAGS.path, "results/output_labels.txt"),
                         "w") as f:
        f.write("\n".join(image_lists.keys()) + "\n")

    val_datas, val_labels = data_process.get_batch_of_data(
        image_lists, -1, FLAGS.images_dir, "val", resized_width,
        resized_height)

    model.fit_generator(generate_train_data(image_lists, FLAGS.images_dir,
                                            FLAGS.batch_size, resized_width,
                                            resized_height),
                        epochs=FLAGS.epochs,
                        steps_per_epoch=100,
                        validation_data=(val_datas, val_labels),
                        callbacks=callbacks)

    test_datas, test_labels = data_process.get_batch_of_data(
        image_lists, -1, FLAGS.images_dir, "test", resized_width,
        resized_height)

    test_loss1, test_acc1 = model.evaluate(test_datas, test_labels)

    print("Test accuracy:{0:.4f}, test loss:{1:.4f}".format(
        test_acc1, test_loss1))

    model.load_weights(os.path.join(FLAGS.path, "save_model", "CNN.h5df"))
    test_loss2, test_acc2 = model.evaluate(test_datas, test_labels)

    time_elapsed = time.time() - since

    print("Test accuracy with best validation =  {}".format(test_acc2 * 100))
    print("Final test accuracy =  {}".format(test_acc1 * 100))
    print("Total Model Runtime: {}min, {:0.2f}sec".format(
        int(time_elapsed // 60), time_elapsed % 60))

    with open(os.path.join(FLAGS.path, "results/results/results.txt"),
              "w") as f:
        f.write("Test accuracy with best validation:" + str(test_acc2) + "\n")
        f.write("Final test accuracy: " + str(test_acc1) + "\n")
        f.write("Total Model Runtime: " + str(int(time_elapsed // 60)) +
                "min," + str(time_elapsed % 60) + "sec")