Source code for tf_unet.image_util

# tf_unet is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# tf_unet is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with tf_unet.  If not, see <>.

author: jakeret
from __future__ import print_function, division, absolute_import, unicode_literals

import glob
import numpy as np
from PIL import Image

[docs]class BaseDataProvider(object): """ Abstract base class for DataProvider implementation. Subclasses have to overwrite the `_next_data` method that load the next data and label array. This implementation automatically clips the data with the given min/max and normalizes the values to (0,1]. To change this behavoir the `_process_data` method can be overwritten. To enable some post processing such as data augmentation the `_post_process` method can be overwritten. :param a_min: (optional) min value used for clipping :param a_max: (optional) max value used for clipping """ channels = 1 n_class = 2 def __init__(self, a_min=None, a_max=None): self.a_min = a_min if a_min is not None else -np.inf self.a_max = a_max if a_min is not None else np.inf def _load_data_and_label(self): data, label = self._next_data() train_data = self._process_data(data) labels = self._process_labels(label) train_data, labels = self._post_process(train_data, labels) nx = train_data.shape[1] ny = train_data.shape[0] return train_data.reshape(1, ny, nx, self.channels), labels.reshape(1, ny, nx, self.n_class), def _process_labels(self, label): if self.n_class == 2: nx = label.shape[1] ny = label.shape[0] labels = np.zeros((ny, nx, self.n_class), dtype=np.float32) # It is the responsibility of the child class to make sure that the label # is a boolean array, but we a chech here just in case. if label.dtype != 'bool': label = label.astype(np.bool) labels[..., 1] = label labels[..., 0] = ~label return labels return label def _process_data(self, data): # normalization data = np.clip(np.fabs(data), self.a_min, self.a_max) data -= np.amin(data) if np.amax(data) != 0: data /= np.amax(data) return data def _post_process(self, data, labels): """ Post processing hook that can be used for data augmentation :param data: the data array :param labels: the label array """ return data, labels def __call__(self, n): train_data, labels = self._load_data_and_label() nx = train_data.shape[1] ny = train_data.shape[2] X = np.zeros((n, nx, ny, self.channels)) Y = np.zeros((n, nx, ny, self.n_class)) X[0] = train_data Y[0] = labels for i in range(1, n): train_data, labels = self._load_data_and_label() X[i] = train_data Y[i] = labels return X, Y
[docs]class SimpleDataProvider(BaseDataProvider): """ A simple data provider for numpy arrays. Assumes that the data and label are numpy array with the dimensions data `[n, X, Y, channels]`, label `[n, X, Y, classes]`. Where `n` is the number of images, `X`, `Y` the size of the image. :param data: data numpy array. Shape=[n, X, Y, channels] :param label: label numpy array. Shape=[n, X, Y, classes] :param a_min: (optional) min value used for clipping :param a_max: (optional) max value used for clipping """ def __init__(self, data, label, a_min=None, a_max=None): super(SimpleDataProvider, self).__init__(a_min, a_max) = data self.label = label self.file_count = data.shape[0] self.n_class = label.shape[-1] self.channels = data.shape[-1] def _next_data(self): idx = np.random.choice(self.file_count) return[idx], self.label[idx]
[docs]class ImageDataProvider(BaseDataProvider): """ Generic data provider for images, supports gray scale and colored images. Assumes that the data images and label images are stored in the same folder and that the labels have a different file suffix e.g. 'train/fish_1.tif' and 'train/fish_1_mask.tif' Number of pixels in x and y of the images and masks should be even. Usage: data_provider = ImageDataProvider("..fishes/train/*.tif") :param search_path: a glob search pattern to find all data and label images :param a_min: (optional) min value used for clipping :param a_max: (optional) max value used for clipping :param data_suffix: suffix pattern for the data images. Default '.tif' :param mask_suffix: suffix pattern for the label images. Default '_mask.tif' :param shuffle_data: if the order of the loaded file path should be randomized. Default 'True' """ def __init__(self, search_path, a_min=None, a_max=None, data_suffix=".tif", mask_suffix='_mask.tif', shuffle_data=True): super(ImageDataProvider, self).__init__(a_min, a_max) self.data_suffix = data_suffix self.mask_suffix = mask_suffix self.file_idx = -1 self.shuffle_data = shuffle_data self.data_files = self._find_data_files(search_path) if self.shuffle_data: np.random.shuffle(self.data_files) assert len(self.data_files) > 0, "No training files" print("Number of files used: %s" % len(self.data_files)) image_path = self.data_files[0] label_path = image_path.replace(self.data_suffix, self.mask_suffix) img = self._load_file(image_path) mask = self._load_file(label_path) self.channels = 1 if len(img.shape) == 2 else img.shape[-1] self.n_class = 2 if len(mask.shape) == 2 else mask.shape[-1] print("Number of channels: %s"%self.channels) print("Number of classes: %s"%self.n_class) def _find_data_files(self, search_path): all_files = glob.glob(search_path) return [name for name in all_files if self.data_suffix in name and not self.mask_suffix in name] def _load_file(self, path, dtype=np.float32): return np.array(, dtype) def _cylce_file(self): self.file_idx += 1 if self.file_idx >= len(self.data_files): self.file_idx = 0 if self.shuffle_data: np.random.shuffle(self.data_files) def _next_data(self): self._cylce_file() image_name = self.data_files[self.file_idx] label_name = image_name.replace(self.data_suffix, self.mask_suffix) img = self._load_file(image_name, np.float32) label = self._load_file(label_name, np.bool) return img,label