Add pipeline for numpy

Augmentor/NumpyPipeline.py

@@ -0,0 +1,119 @@
+# NumpyPipeline.py
+# Author: vugia.truong <https://github.com/gachiemchiep>
+# Licensed under the terms of the MIT Licence.
+"""
+The Pipeline module is the user facing API for the Augmentor package. It
+contains the :class:`~Augmentor.Pipeline.Pipeline` class which is used to
+create pipeline objects, which can be used to build an augmentation pipeline
+by adding operations to the pipeline object.
+
+For a good overview of how to use Augmentor, along with code samples and
+example images, can be seen in the :ref:`mainfeatures` section.
+"""
+from __future__ import (absolute_import, division,
+                        print_function, unicode_literals)
+
+from builtins import *
+
+from .Operations import *
+from .ImageUtilities import scan_directory, scan, AugmentorImage
+from .Pipeline import Pipeline
+
+import os
+import sys
+import random
+import uuid
+import warnings
+import numbers
+import numpy as np
+
+from tqdm import tqdm
+from PIL import Image
+
+
+class NumpyPipeline(Pipeline):
+    """
+    The NumpyPipeline class handles the creation of augmentation pipelines
+    and the generation of augmented data by applying operations to
+    this pipeline.
+    """
+
+    # Some class variables we use often
+    _probability_error_text = "The probability argument must be between 0 and 1."
+    _threshold_error_text = "The value of threshold must be between 0 and 255."
+    _valid_formats = ["PNG", "BMP", "GIF", "JPEG"]
+    _legal_filters = ["NEAREST", "BICUBIC", "ANTIALIAS", "BILINEAR"]
+
+    def __init__(self, images=None, labels=None):
+        """
+        Init NumpyPipeline
+        :param images: List of numpy array of image
+        :param labels: List of correspoding label of image
+        """
+
+        images_count = len(images)
+        labels_count = len(labels)
+
+        # Check input image depth
+        for idx, image in enumerate(images):
+            channel = np.shape(image)[2]
+            if channel != 3:
+                sys.stdout.write("Channel of %d sample does not match : %d instead of %d . Remove it " %
+                     (idx, channel, 3))
+                images.pop(idx)
+                labels.pop(idx)
+
+        if images_count != labels_count:
+            raise Exception("Number of input images and labels does not match : %d vs %d" % (images_count, labels_count))
+
+        self.images = images
+        self.labels = labels
+        self.operations = []
+
+    def sample(self, n):
+        """
+        Generate :attr:`n` number of samples from the current pipeline.
+
+        This function generate samples from the NumpyPipeline, 
+        using a list of image (numpy array) and a corresponding list of label which 
+        were defined during instantiation. 
+        For each image with size (w, h, d) a new n*(w, h, d) image is generated.
+
+        :param n: The number of new samples to produce.
+        :type n: Integer
+        :return: image_samples_all: rendered images
+        :type n: List
+        :return: label_samples_all: list of image's label
+        :type n: List
+        """
+        if len(self.operations) == 0:
+            raise IndexError("There are no operations associated with this pipeline.")
+
+        labels_count = len(self.labels)
+        samples_total = n * labels_count
+        progress_bar = tqdm(total=samples_total, desc="Executing Pipeline", unit=' Samples', leave=False)
+
+        image_samples_all = []
+        label_samples_all = []
+
+        for idx, image in enumerate(self.images):
+            sample_count = 0
+
+            width, height, depth = np.shape(image)
+            image_samples = np.zeros((width, height, depth, n), dtype=np.uint8)
+            while sample_count < n:
+                image_sample = self._execute_with_array(image)
+                sample_count += 1
+                progress = idx * labels_count + sample_count
+                progress_bar.set_description("Processing %d in total %d" % (progress, samples_total))
+                progress_bar.update(1)
+
+                image_samples_all.append(image_sample)
+                label_samples_all.append(self.labels[idx])
+
+        progress_bar.close()
+        return image_samples_all, label_samples_all
+
+
+
+

Augmentor/Operations.py

@@ -29,12 +29,12 @@
 from math import floor, ceil
 
 import numpy as np
-# from skimage import img_as_ubyte
-# from skimage import transform
 
 import os
 import random
 import warnings
+import cv2
+from skimage.draw import line
 
 # Python 2-3 compatibility - not currently needed.
 # try:
@@ -735,6 +735,135 @@ def do(image):
         return augmented_images
 
 
+class LinearMotion(Operation):
+    """
+    This class is used to perform linear motion on images.
+    The algorithm is heavily based on https://github.com/lospooky/pyblur/tree/master/pyblur
+    """
+
+    def __init__(self, probability, size, angle, linetype):
+        """
+        :param probability: Controls the probability that the operation is
+         performed when it is invoked in the pipeline.
+        :param size: size of linear motion kernel
+        :param angle: angle of linear motion
+        :param linetype: type of linear motion line
+
+        """
+        Operation.__init__(self, probability)
+        self.size = size
+        self.angle = angle
+        self.line_dict = self.gen_motion_lines()
+        self.kernel = self.get_kernel(size, angle, linetype)
+
+    def get_kernel(self, size, angle, linetype):
+        kernel_width = size
+        kernel_center = int(math.floor(size / 2))
+        angle = self.get_sanitize_angle_value(kernel_center, angle)
+        kernel = np.zeros((kernel_width, kernel_width), dtype=np.float32)
+        line_anchors = self.line_dict[size][angle]
+        if (linetype == 'right'):
+            line_anchors[0] = kernel_center
+            line_anchors[1] = kernel_center
+        if (linetype == 'left'):
+            line_anchors[2] = kernel_center
+            line_anchors[3] = kernel_center
+        rr, cc = line(line_anchors[0], line_anchors[1], line_anchors[2], line_anchors[3])
+        kernel[rr, cc] = 1
+        normalization_factor = np.count_nonzero(kernel)
+        kernel = kernel / normalization_factor
+        return kernel
+
+    def get_nearest_value(self, theta, valid_angles):
+        idx = (np.abs(valid_angles - theta)).argmin()
+        return valid_angles[idx]
+
+    def get_sanitize_angle_value(self, kernel_center, angle):
+        num_distinct_lines = kernel_center * 4
+        angle = math.fmod(angle, 180.0)
+        valid_line_angles = np.linspace(0, 180, num_distinct_lines, endpoint=False)
+        angle = self.get_nearest_value(angle, valid_line_angles)
+        return angle
+
+    def gen_motion_lines(self):
+
+        ret = {}
+        # 3x3 lines
+        lines = {}
+        lines[0] = [1, 0, 1, 2]
+        lines[45] = [2, 0, 0, 2]
+        lines[90] = [0, 1, 2, 1]
+        lines[135] = [0, 0, 2, 2]
+        ret[3] = lines
+
+        # 5x5 lines
+        lines = {}
+        lines[0] = [2, 0, 2, 4]
+        lines[22.5] = [3, 0, 1, 4]
+        lines[45] = [0, 4, 4, 0]
+        lines[67.5] = [0, 3, 4, 1]
+        lines[90] = [0, 2, 4, 2]
+        lines[112.5] = [0, 1, 4, 3]
+        lines[135] = [0, 0, 4, 4]
+        lines[157.5] = [1, 0, 3, 4]
+        ret[5] = lines
+
+        # 7x7 lines
+        lines = {}
+        lines[0] = [3, 0, 3, 6]
+        lines[15] = [4, 0, 2, 6]
+        lines[30] = [5, 0, 1, 6]
+        lines[45] = [6, 0, 0, 6]
+        lines[60] = [6, 1, 0, 5]
+        lines[75] = [6, 2, 0, 4]
+        lines[90] = [0, 3, 6, 3]
+        lines[105] = [0, 2, 6, 4]
+        lines[120] = [0, 1, 6, 5]
+        lines[135] = [0, 0, 6, 6]
+        lines[150] = [1, 0, 5, 6]
+        lines[165] = [2, 0, 4, 6]
+        ret[7] = lines
+
+        # 9x9 lines
+        lines = {}
+        lines[0] = [4, 0, 4, 8]
+        lines[11.25] = [5, 0, 3, 8]
+        lines[22.5] = [6, 0, 2, 8]
+        lines[33.75] = [7, 0, 1, 8]
+        lines[45] = [8, 0, 0, 8]
+        lines[56.25] = [8, 1, 0, 7]
+        lines[67.5] = [8, 2, 0, 6]
+        lines[78.75] = [8, 3, 0, 5]
+        lines[90] = [8, 4, 0, 4]
+        lines[101.25] = [0, 3, 8, 5]
+        lines[112.5] = [0, 2, 8, 6]
+        lines[123.75] = [0, 1, 8, 7]
+        lines[135] = [0, 0, 8, 8]
+        lines[146.25] = [1, 0, 7, 8]
+        lines[157.5] = [2, 0, 6, 8]
+        lines[168.75] = [3, 0, 5, 8]
+        ret[9] = lines
+
+        return ret
+
+    def perform_operation(self, images):
+        """
+        """
+
+        def do(image):
+            img_np = np.array(image)
+            img_np_filtered = cv2.filter2D(img_np, -1, self.kernel)
+
+            return Image.fromarray(img_np_filtered)
+
+        augmented_images = []
+
+        for image in images:
+            augmented_images.append(do(image))
+
+        return augmented_images
+
+
 class RotateRange(Operation):
     """
     This class is used to perform rotations on images by arbitrary numbers of
@@ -1832,7 +1961,6 @@ def __init__(self, probability, hue_shift, saturation_scale, saturation_shift, v
         self.value_shift = value_shift
 
     def perform_operation(self, images):
-
         def do(image):
             hsv = np.array(image.convert("HSV"), 'float64')
             hsv /= 255.

Augmentor/Pipeline.py

@@ -236,7 +236,8 @@ def _execute(self, augmentor_image, save_to_disk=True, multi_threaded=True):
         # save_to_disk = False
 
         if save_to_disk:
-            file_name = str(uuid.uuid4())
+            filename, ext = os.path.splitext(os.path.basename(augmentor_image.image_path))
+            file_name = "{}_{}.{}".format(filename, str(uuid.uuid4()), self.save_format)
             try:
                 for i in range(len(images)):
                     if i == 0:
@@ -1010,6 +1011,21 @@ def flip_top_bottom(self, probability):
         else:
             self.add_operation(Flip(probability=probability, top_bottom_left_right="TOP_BOTTOM"))
 
+    def linear_motion(self, probability, size, angle, linetype="left"):
+        """
+        Perform linear motion blurring
+
+        :param probability: A value between 0 and 1 representing the
+         probability that the operation should be performed.
+        :param size: size of kernel
+        :param angle: motion angle3
+        :param linetype: type of line (left, right or full (both left and right))
+        """
+        if not 0 < probability <= 1:
+            raise ValueError(Pipeline._probability_error_text)
+        else:
+            self.add_operation(LinearMotion(probability=probability, size=size, angle=angle, linetype=linetype))
+
     def flip_left_right(self, probability):
         """
         Flip (mirror) the image along its horizontal axis, i.e. from left to

Augmentor/__init__.py

@@ -11,10 +11,12 @@
 
 """
 
+from .Pipeline import Pipeline
+from .NumpyPipeline import NumpyPipeline
 from .Pipeline import Pipeline, DataFramePipeline, DataPipeline
 
 __author__ = """Marcus D. Bloice"""
 __email__ = 'marcus.bloice@medunigraz.at'
 __version__ = '0.2.7'
 
-__all__ = ['Pipeline', 'DataFramePipeline', 'DataPipeline']
+__all__ = ['Pipeline', 'DataFramePipeline', 'DataPipeline', 'NumpyPipeline']

README.md

@@ -55,6 +55,34 @@ p.sample(10000)
 
 which will generate 10,000 augmented images based on your specifications. By default these will be written to the disk in a directory named `output` relative to the path specified when initialising the `p` pipeline object above.
 
+### Numpy
+
+If you want to work with numpy array, you can use the NumpyPipeline:
+
+```python
+
+# Read examples image
+img1 = cv2.imread("tmp/000.jpg", 1)
+img2 = cv2.imread("tmp/000.jpg", 1)
+label1 = "1"
+label2 = "2"
+
+# Create list of images
+imgs = [img1, img2]
+labels = [label1, label2]
+
+# Create numpy pipline
+np_p = Augmentor.NumpyPipeline(imgs, labels)
+
+# Add operations
+np_p.flip_top_bottom(probability=0.5)
+
+# generate 10 samples
+imgs_, labels_ = np_p.sample(10)
+
+```
+
+### Keras and PyTorch
 If you wish to process each image in the pipeline exactly once, use `process()`:
 
 ```python