convnet_model.py

@@ -18,7 +18,7 @@ IMAGE_SIZE = 64   # i.e. IMAGE_SIZExIMAGE_SIZE pixels
 NUM_CHANNELS = 1  # i.e. number of colour channels (gray images have 1)
 NUM_LABELS = 19   # Number of labels in the data
 SEED = 66478      # Set to None for random seed.
-IFIND_ROOT = '/vol/medic01/users/cbaumgar/data/iFind1/iFind1_300/iFind1_simple/stillframes_testtrain'
+IFIND_ROOT = '/vol/bitbucket/cts12/data/bylabels_manual_one_other/'
 
 ### DEFINE THE FREE PARAMETER VARIABLES OF THE MODEL
 # In particular this includes the weights (W) and biases (b) of the convolutional and fully connected layers
@@ -178,6 +178,10 @@ def _process_folder(folder, use_existing_label_numbers=False, label_numbers=None
             path = os.path.join(root, fn)
             label_name = root.split('/')[-1]
 
+            for other_label_name in (root.split('/')):
+                if other_label_name == 'OTHER':
+                    label_name = other_label_name
+
             if label_name not in done_labels:
                 label_counter += 1
                 if not use_existing_label_numbers:
@@ -260,4 +264,4 @@ def _dense_to_one_hot(labels_dense, num_classes):
         index_offset = np.arange(num_labels) * num_classes
         labels_one_hot = np.zeros((num_labels, num_classes))
         labels_one_hot.flat[index_offset + labels_dense.ravel()] = 1
-        return labels_one_hot
\ No newline at end of file
+        return labels_one_hot

convnet_train.py

@@ -23,9 +23,9 @@ NUM_EPOCHS = 10
 EVAL_BATCH_SIZE = 64
 EVAL_FREQUENCY = 100  # Number of steps between evaluations.
 FLAGS = tf.app.flags.FLAGS
-FLAGS.checkpoint_dir = '.'
+FLAGS.checkpoint_dir = '/vol/bitbucket/cts12/data/bylabels_manual_one_other/'
 VALIDATION_SET_PERCENTAGE = 0.2
-PROCESSED_DATA_DIR = '.'
+PROCESSED_DATA_DIR = '/vol/bitbucket/cts12/data/bylabels_manual_one_other/'
 
 def error_rate(predictions, labels):
     """

ifind_data.py

+"""
+Code for reading image in a folder structure and sorting them into labels based on the folder names on the lowest
+hirarchy level.
+
+The data then gets stored as 2 *.npz arrays for easier access later on.
+"""
+
+import os
+import numpy as np
+import cv2
+
+SIZE_TOPBOTTOM = 64
+SIZE_LEFTRIGHT = 79  #int((float(im.shape[1])/float(im.shape[0]))*64)
+NUM_CHANNELS = 1  # i.e. number of colour channels (gray images have 1)
+IFIND_ROOT = '/vol/medic01/users/cbaumgar/data/iFind1/iFind1_1200/simple/images/bylabels_manual_one_other/'
+DATA_POSTFIX = 'rectangular'
+
+def read_npz(filename):
+    """
+    Helper function for reading out all arrays in an npz archive
+    """
+    with np.load(filename) as f:
+        values = [f['arr_%d' % i] for i in range(len(f.files))]
+        return values
+
+def read_labels(filename):
+    """
+    Helper function for reading the label data
+    """
+    values = read_npz(filename)
+    y_train = values[0]
+    y_test = values[1]
+    label_names = values[2].item()
+    label_numbers = values[3].item()
+    return y_train, y_test, label_names, label_numbers
+
+def read_data(filename):
+    """
+    Helper function for reading the image data
+    """
+    values = read_npz(filename)
+    X_train = values[0]
+    X_test = values[1]
+    return X_train, X_test
+
+def load_ifind_data(path):
+    """
+    This function tries to load the preprocessed training and testing data
+    located in `path`
+    If it cannot find the data it preprocesses the data if finds in
+    the folder IFIND_ROOT
+    It returns training and testing data plus two dictionaries for going from label numbers to label names
+    and back.
+    """
+    expected_label_path = os.path.join(path, 'ifind1_scanplane_labels_' + DATA_POSTFIX + '.npz')
+    expected_data_path = os.path.join(path, 'ifind1_scanplane_data_' + DATA_POSTFIX + '.npz')
+
+    if os.path.exists(expected_data_path) and os.path.exists(expected_label_path):
+
+        y_train, y_test, label_names, label_numbers = read_labels(expected_label_path)
+        X_train, X_test = read_data(expected_data_path)
+
+    else:
+        print "Dataset is being created from %s" % IFIND_ROOT
+        X_train, y_train, X_test, y_test, label_names, label_numbers = _preprocess_dataset(path)
+
+    return X_train, y_train, X_test, y_test, label_names, label_numbers
+
+"""
+ Helper functions for the data loader
+"""
+
+def _preprocess_dataset(path):
+    """
+    Starts the proprocessing
+    """
+    test_folder = os.path.join(IFIND_ROOT, 'test')
+    train_folder = os.path.join(IFIND_ROOT, 'train')
+
+    print "Doing test folder: "
+    X_test, y_test, label_numbers = _process_folder(test_folder) # don't augment test dataset (we want to test on original data)
+    print X_test.shape
+    print y_test.shape
+    print X_test.dtype
+    print y_test.dtype
+    print "Doing train folder: "
+    X_train, y_train, dmy = _process_folder(train_folder, True, label_numbers, augment_dataset=True)
+    print X_train.shape
+    print y_train.shape
+    print X_train.dtype
+    print y_train.dtype
+
+    label_names = _invert_dictionary(label_numbers)
+
+    # Convert into a format suitable for tensorflow
+    X_train = _whiten_images(X_train)
+    X_test = _whiten_images(X_test)
+
+    # MAY HAVE TO UNCOMMENT THIS FOR TENSORFLOW CODE!!!!!!!!!!!!!!!!!!
+    #y_train = _dense_to_one_hot(y_train, len(label_names))
+    #y_test = _dense_to_one_hot(y_test, len(label_names))
+
+    # saving
+    labels_path = os.path.join(path, 'ifind1_scanplane_labels_' + DATA_POSTFIX + '.npz')
+    print "Saving labels to %s..." % labels_path
+    np.savez(labels_path, y_train, y_test, label_names, label_numbers)
+
+    data_path = os.path.join(path, 'ifind1_scanplane_data_' + DATA_POSTFIX + '.npz')
+    print "Saving data to %s..." % data_path
+    np.savez(data_path, X_train, X_test)
+
+    return X_train, y_train, X_test, y_test, label_names, label_numbers
+
+
+def _process_folder(folder, use_existing_label_numbers=False, label_numbers=None, augment_dataset=False):
+    """
+    Goes into a specific folder and preprocess the data it finds there
+    :param folder: The folder
+    :param use_existing_label_numbers: Use a label dictionary found in a previous run of this function?
+    :param label_numbers: If use_existing_label_numbers, give it the label numbers
+    :param augment_dataset: Augment the dataset? I.e., from each image create multiple versions
+    :return: the preprocessed data, the labels, and the label dictionary
+    """
+
+    if not use_existing_label_numbers:
+        label_numbers = {}
+
+    label_counter = -1
+    labels = []
+    data = []
+    done_labels = []
+
+    for directory in next(os.walk(folder))[1]:
+
+        label_name = directory.split('/')[-1]
+        directory_path = os.path.join(folder, directory)
+
+        for root, dir_list, file_list in os.walk(directory_path):
+
+            for file_name in file_list:
+
+                image_path = os.path.join(root, file_name)
+
+                # Sort out the labels
+                if label_name not in done_labels:
+                    label_counter += 1
+                    if not use_existing_label_numbers:
+                        label_number = label_counter
+                        label_numbers[label_name] = label_number
+                        print "added label %d which is %s" % (label_number, label_name)
+                    else:
+                        label_number = label_numbers[label_name]
+                        print "Doing label %s which has label %d" % (label_name, label_number)
+
+                    done_labels.append(label_name)
+                else:
+                    #print "! Going back to label %s" % label_name
+                    label_number = label_numbers[label_name]
+
+                # Load image
+                im = cv2.imread(image_path)
+
+                # figure out if video frame or still-frame image
+                is_highres = True if im.shape[1] > 850 else False
+
+                # the crop ranges are square regions from [center, left, right]
+                if is_highres:
+                    crop_range = (106, 106, 853, 713)
+                else:
+                    crop_range = (98, 80, 652, 530)
+
+                im_array = _crop_and_preprocess(im, crop_range, is_highres)
+                data.append(im_array)
+                labels.append(label_number)
+
+    data = np.asarray(data)
+    labels = np.asarray(labels, dtype=np.int32)
+
+    return data, labels, label_numbers
+
+def _crop_and_preprocess(im, crop_range, is_highres):
+    """
+    Helper for cropping images. I determined the constants for contrast, brightness, and the
+    Gaussian manually to match the appearance of the video frames
+    (using find_image_to_video_mapping.py)
+    """
+    # crop image
+    im_cropped = im.copy()[crop_range[1]:crop_range[3], crop_range[0]:crop_range[2], :]
+    # change to gray levels
+    im_cropped = cv2.cvtColor(im_cropped, cv2.COLOR_BGR2GRAY)
+
+    # cv2.imshow('debug2', im_cropped)
+    # cv2.waitKey(0)
+
+    if is_highres:
+        # contrast
+        im_adjusted = _adjust_contrast(im_cropped, 0.92)
+        # brightness
+        im_adjusted = _adjust_brightness(im_adjusted, 13)
+        # gaussian blur
+        im_adjusted = _blur_gaussian(im_adjusted, 7)
+        # resize
+    else:
+        # if the frame comes from a video then there is no need for adjustment
+        im_adjusted = im_cropped
+
+    im_resized = cv2.resize(im_adjusted, (SIZE_LEFTRIGHT, SIZE_TOPBOTTOM))
+
+    # debugging
+    # cv2.imshow('debug', im_resized)
+    # cv2.waitKey(0)
+
+    # change type
+    im_array = im_resized.astype(np.float32)
+    # add a dummy dimensions where usually the color channels would be
+    im_array = np.reshape(im_array, (1, SIZE_TOPBOTTOM, SIZE_LEFTRIGHT))
+
+    # debugging
+    # plt.imshow(np.squeeze(im_array[0,:,:]))
+    # plt.show()
+
+    return im_array
+
+def _invert_dictionary(dictionary):
+    """
+    Helper for inverting a dictionary
+    """
+    return {v: k for k, v in dictionary.items()}
+
+
+def _whiten_images(X):
+    """
+    Helper for making the images zero mean and unit standard deviation i.e. `white`
+    """
+
+    X_white = np.zeros(X.shape, dtype=np.float32)
+
+    for ii in xrange(X.shape[0]):
+
+        Xc = X[ii,:,:,:]
+        mc = Xc.mean()
+        sc = Xc.std()
+
+        Xc_white = np.divide((Xc - mc), sc)
+
+        X_white[ii,:,:,:] = Xc_white
+
+    return X_white
+
+
+def _dense_to_one_hot(labels_dense, num_classes):
+        """
+        Convert class labels from scalars to one-hot vectors.
+        This means if there are 10 possible labels
+        1 -> [1,0,0,0,0,0,0,0,0,0]
+        4 -> [0,0,0,1,0,0,0,0,0,0]
+         etc...
+        """
+        num_labels = labels_dense.shape[0]
+        index_offset = np.arange(num_labels) * num_classes
+        labels_one_hot = np.zeros((num_labels, num_classes))
+        labels_one_hot.flat[index_offset + labels_dense.ravel()] = 1
+        return labels_one_hot
+
+def _adjust_contrast(image, contrast_factor):
+    """
+    Helper function for adjusting the contrast of an image using simple multiplication and rebinning into [0,255]
+    """
+    max_value = image.max()
+    min_value = image.min()
+    new_image = contrast_factor * image.copy().astype(np.float32)
+    new_image[new_image>max_value] = max_value
+    new_image[new_image<min_value] = min_value
+    return new_image.astype(np.uint8)
+
+def _adjust_brightness(image, brightness_factor):
+    """
+    Helper function for adjusting the brightness of an image by adding a constant and rebinning into [0,255]
+    """
+    max_value = image.max()
+    min_value = image.min()
+    new_image = image.copy().astype(np.uint16) + brightness_factor
+    new_image[new_image > max_value] = max_value
+    new_image[new_image < min_value] = min_value
+    return new_image.astype(np.uint8)
+
+def _blur_average(image, blur_kernel_size):
+    """
+    Helper function for blurring a square average filter (sliding window)
+    """
+    blur_kernel = (blur_kernel_size, blur_kernel_size)
+    kernel = np.ones(blur_kernel,np.float32)/(blur_kernel_size**2)
+    new_image = cv2.filter2D(image.copy().astype(np.float32),-1,kernel)
+    return new_image.astype(np.uint8)
+
+def _blur_gaussian(image, blur_kernel_size):
+    """
+    Helper function for blurring an image with a Gaussian
+    """
+    blur_kernel = (blur_kernel_size, blur_kernel_size)
+    new_image = cv2.GaussianBlur(image.copy().astype(np.float32),blur_kernel,0)
+    return new_image.astype(np.uint8)
+
+def _blur_billateral(image, param1, param2):
+    """
+    Helper function for applying the billateral smoothing filter to an image
+    """
+    new_image = cv2.bilateralFilter(image.copy().astype(np.float32),param1,param2,param2)
+    return new_image.astype(np.uint8)