Axis Error

[Pranjal-Jadhav]

What is wrong with my code?

I am using smooth windowing for autoencoder

test_img = cv2.imread("a.jpg")
test_img = cv2.resize(test_img, (768, 1024))
test_img = np.array(test_img)
test_img = test_img.astype('float32')
test_img /= 255

test_img.shape
(1024, 768, 3)

predictions_smooth = predict_img_with_smooth_windowing(
test_img,
window_size=64,
subdivisions=2, # Minimal amount of overlap for windowing. Must be an even number.
nb_classes=3,
pred_func=(
lambda img_batch_subdiv: autoencoder.predict((img_batch_subdiv))
)
)

0%| | 0/8 [00:00<?, ?it/s]

---

AxisError Traceback (most recent call last)

in ()
5 nb_classes=3,
6 pred_func=(
----> 7 lambda img_batch_subdiv: autoencoder.predict((img_batch_subdiv))
8 )
9 )

5 frames

/content/smooth_tiled_predictions.py in predict_img_with_smooth_windowing(input_img, window_size, subdivisions, nb_classes, pred_func)
251 # possible to fake a full-size window which would in fact just have a narrow
252 # non-zero dommain. This may require to augment the subdivisions argument
--> 253 # to 4 rather than 2.
254
255 res = []

/content/smooth_tiled_predictions.py in _windowed_subdivs(padded_img, window_size, subdivisions, nb_classes, pred_func)
163 nb_patches_along_Y,
164 patches_resolution_along_X,
--> 165 patches_resolution_along_Y,
166 nb_output_channels
167 )

/content/smooth_tiled_predictions.py in _window_2D(window_size, power)
57 """
58 Make a 1D window function, then infer and return a 2D window function.
---> 59 Done with an augmentation, and self multiplication with its transpose.
60 Could be generalized to more dimensions.
61 """

<array_function internals> in expand_dims(*args, **kwargs)

/usr/local/lib/python3.7/dist-packages/numpy/lib/shape_base.py in expand_dims(a, axis)
595
596 out_ndim = len(axis) + a.ndim
--> 597 axis = normalize_axis_tuple(axis, out_ndim)
598
599 shape_it = iter(a.shape)

/usr/local/lib/python3.7/dist-packages/numpy/core/numeric.py in normalize_axis_tuple(axis, ndim, argname, allow_duplicate)
1356 pass
1357 # Going via an iterator directly is slower than via list comprehension.
-> 1358 axis = tuple([normalize_axis_index(ax, ndim, argname) for ax in axis])
1359 if not allow_duplicate and len(set(axis)) != len(axis):
1360 if argname:

/usr/local/lib/python3.7/dist-packages/numpy/core/numeric.py in (.0)
1356 pass
1357 # Going via an iterator directly is slower than via list comprehension.
-> 1358 axis = tuple([normalize_axis_index(ax, ndim, argname) for ax in axis])
1359 if not allow_duplicate and len(set(axis)) != len(axis):
1360 if argname:

AxisError: axis 3 is out of bounds for array of dimension 2

[davodogster]

@Pranjal-Jadhav I am getting a similar error with the expand dims function, were you able to fix it?

[guillaume-chevalier]

Could be related to this:
https://github.com/Vooban/Smoothly-Blend-Image-Patches/pull/6/files

[MadsLorentzen]

This solved my issue (I changed 'np.expand_dims' function input in the 'get_dummy_img' function, as well as the modifications highlighted by @guillaume-chevalier.

I've copied the full content of my modified 'smooth_tiled_predictions.py' here (it runs for me without any errors)

# MIT License
# Copyright (c) 2017 Vooban Inc.
# Coded by: Guillaume Chevalier
# Source to original code and license:
#     https://github.com/Vooban/Smoothly-Blend-Image-Patches
#     https://github.com/Vooban/Smoothly-Blend-Image-Patches/blob/master/LICENSE


"""Do smooth predictions on an image from tiled prediction patches."""


import numpy as np
import scipy.signal
from tqdm import tqdm

import gc


if __name__ == '__main__':
    import matplotlib.pyplot as plt
    PLOT_PROGRESS = True
    # See end of file for the rest of the __main__.
else:
    PLOT_PROGRESS = False


def _spline_window(window_size, power=2):
    """
    Squared spline (power=2) window function:
    https://www.wolframalpha.com/input/?i=y%3Dx**2,+y%3D-(x-2)**2+%2B2,+y%3D(x-4)**2,+from+y+%3D+0+to+2
    """
    intersection = int(window_size/4)
    wind_outer = (abs(2*(scipy.signal.triang(window_size))) ** power)/2
    wind_outer[intersection:-intersection] = 0

    wind_inner = 1 - (abs(2*(scipy.signal.triang(window_size) - 1)) ** power)/2
    wind_inner[:intersection] = 0
    wind_inner[-intersection:] = 0

    wind = wind_inner + wind_outer
    wind = wind / np.average(wind)
    return wind


cached_2d_windows = dict()
def _window_2D(window_size, power=2):
    """
    Make a 1D window function, then infer and return a 2D window function.
    Done with an augmentation, and self multiplication with its transpose.
    Could be generalized to more dimensions.
    """
    # Memoization
    global cached_2d_windows
    key = "{}_{}".format(window_size, power)
    if key in cached_2d_windows:
        wind = cached_2d_windows[key]
    else:
        wind = _spline_window(window_size, power)
        wind = np.expand_dims(np.expand_dims(wind, 1), 1)
        wind = wind * wind.transpose(1, 0, 2)
        if PLOT_PROGRESS:
            # For demo purpose, let's look once at the window:
            plt.imshow(wind[:, :, 0], cmap="viridis")
            plt.title("2D Windowing Function for a Smooth Blending of "
                      "Overlapping Patches")
            plt.show()
        cached_2d_windows[key] = wind
    return wind


def _pad_img(img, window_size, subdivisions):
    """
    Add borders to img for a "valid" border pattern according to "window_size" and
    "subdivisions".
    Image is an np array of shape (x, y, nb_channels).
    """
    aug = int(round(window_size * (1 - 1.0/subdivisions)))
    more_borders = ((aug, aug), (aug, aug), (0, 0))
    ret = np.pad(img, pad_width=more_borders, mode='reflect')
    # gc.collect()

    if PLOT_PROGRESS:
        # For demo purpose, let's look once at the window:
        plt.imshow(ret)
        plt.title("Padded Image for Using Tiled Prediction Patches\n"
                  "(notice the reflection effect on the padded borders)")
        plt.show()
    return ret


def _unpad_img(padded_img, window_size, subdivisions):
    """
    Undo what's done in the `_pad_img` function.
    Image is an np array of shape (x, y, nb_channels).
    """
    aug = int(round(window_size * (1 - 1.0/subdivisions)))
    ret = padded_img[
        aug:-aug,
        aug:-aug,
        :
    ]
    # gc.collect()
    return ret


def _rotate_mirror_do(im):
    """
    Duplicate an np array (image) of shape (x, y, nb_channels) 8 times, in order
    to have all the possible rotations and mirrors of that image that fits the
    possible 90 degrees rotations.

    It is the D_4 (D4) Dihedral group:
    https://en.wikipedia.org/wiki/Dihedral_group
    """
    mirrs = []
    mirrs.append(np.array(im))
    mirrs.append(np.rot90(np.array(im), axes=(0, 1), k=1))
    mirrs.append(np.rot90(np.array(im), axes=(0, 1), k=2))
    mirrs.append(np.rot90(np.array(im), axes=(0, 1), k=3))
    im = np.array(im)[:, ::-1]
    mirrs.append(np.array(im))
    mirrs.append(np.rot90(np.array(im), axes=(0, 1), k=1))
    mirrs.append(np.rot90(np.array(im), axes=(0, 1), k=2))
    mirrs.append(np.rot90(np.array(im), axes=(0, 1), k=3))
    return mirrs


def _rotate_mirror_undo(im_mirrs):
    """
    merges a list of 8 np arrays (images) of shape (x, y, nb_channels) generated
    from the `_rotate_mirror_do` function. Each images might have changed and
    merging them implies to rotated them back in order and average things out.

    It is the D_4 (D4) Dihedral group:
    https://en.wikipedia.org/wiki/Dihedral_group
    """
    origs = []
    origs.append(np.array(im_mirrs[0]))
    origs.append(np.rot90(np.array(im_mirrs[1]), axes=(0, 1), k=3))
    origs.append(np.rot90(np.array(im_mirrs[2]), axes=(0, 1), k=2))
    origs.append(np.rot90(np.array(im_mirrs[3]), axes=(0, 1), k=1))
    origs.append(np.array(im_mirrs[4])[:, ::-1])
    origs.append(np.rot90(np.array(im_mirrs[5]), axes=(0, 1), k=3)[:, ::-1])
    origs.append(np.rot90(np.array(im_mirrs[6]), axes=(0, 1), k=2)[:, ::-1])
    origs.append(np.rot90(np.array(im_mirrs[7]), axes=(0, 1), k=1)[:, ::-1])
    return np.mean(origs, axis=0)


def _windowed_subdivs(padded_img, window_size, subdivisions, nb_classes, pred_func):
    """
    Create tiled overlapping patches.

    Returns:
        5D numpy array of shape = (
            nb_patches_along_X,
            nb_patches_along_Y,
            patches_resolution_along_X,
            patches_resolution_along_Y,
            nb_output_channels
        )

    Note:
        patches_resolution_along_X == patches_resolution_along_Y == window_size
    """
    WINDOW_SPLINE_2D = _window_2D(window_size=window_size, power=2)

    step = int(window_size/subdivisions)
    padx_len = padded_img.shape[0]
    pady_len = padded_img.shape[1]
    subdivs = []

    for i in range(0, padx_len-window_size+1, step):
        subdivs.append([])
        for j in range(0, pady_len-window_size+1, step):
            patch = padded_img[i:i+window_size, j:j+window_size, :]
            subdivs[-1].append(patch)

    # Here, `gc.collect()` clears RAM between operations.
    # It should run faster if they are removed, if enough memory is available.
    gc.collect()
    subdivs = np.array(subdivs)
    gc.collect()
    a, b, c, d, e = subdivs.shape
    subdivs = subdivs.reshape(a * b, c, d, e)
    gc.collect()

    subdivs = pred_func(subdivs)
    gc.collect()
    subdivs = np.array([patch * WINDOW_SPLINE_2D for patch in subdivs])
    gc.collect()

    # Such 5D array:
    subdivs = subdivs.reshape(a, b, c, d, nb_classes)
    gc.collect()

    return subdivs


def _recreate_from_subdivs(subdivs, window_size, subdivisions, padded_out_shape):
    """
    Merge tiled overlapping patches smoothly.
    """
    step = int(window_size/subdivisions)
    padx_len = padded_out_shape[0]
    pady_len = padded_out_shape[1]

    y = np.zeros(padded_out_shape)

    a = 0
    for i in range(0, padx_len-window_size+1, step):
        b = 0
        for j in range(0, pady_len-window_size+1, step):
            windowed_patch = subdivs[a, b]
            y[i:i+window_size, j:j+window_size] = y[i:i+window_size, j:j+window_size] + windowed_patch
            b += 1
        a += 1
    return y / (subdivisions ** 2)


def predict_img_with_smooth_windowing(input_img, window_size, subdivisions, nb_classes, pred_func):
    """
    Apply the `pred_func` function to square patches of the image, and overlap
    the predictions to merge them smoothly.

    See 6th, 7th and 8th idea here:
    http://blog.kaggle.com/2017/05/09/dstl-satellite-imagery-competition-3rd-place-winners-interview-vladimir-sergey/
    """
    pad = _pad_img(input_img, window_size, subdivisions)
    pads = _rotate_mirror_do(pad)

    # Note that the implementation could be more memory-efficient by merging
    # the behavior of `_windowed_subdivs` and `_recreate_from_subdivs` into
    # one loop doing in-place assignments to the new image matrix, rather than
    # using a temporary 5D array.

    # It would also be possible to allow different (and impure) window functions
    # that might not tile well. Adding their weighting to another matrix could
    # be done to later normalize the predictions correctly by dividing the whole
    # reconstructed thing by this matrix of weightings - to normalize things
    # back from an impure windowing function that would have badly weighted
    # windows.

    # For example, since the U-net of Kaggle's DSTL satellite imagery feature
    # prediction challenge's 3rd place winners use a different window size for
    # the input and output of the neural net's patches predictions, it would be
    # possible to fake a full-size window which would in fact just have a narrow
    # non-zero dommain. This may require to augment the `subdivisions` argument
    # to 4 rather than 2.

    res = []
    for pad in tqdm(pads):
        # For every rotation:
        sd = _windowed_subdivs(pad, window_size, subdivisions, nb_classes, pred_func)
        one_padded_result = _recreate_from_subdivs(
            sd, window_size, subdivisions,
            padded_out_shape=list(pad.shape[:-1])+[nb_classes])

        res.append(one_padded_result)

    # Merge after rotations:
    padded_results = _rotate_mirror_undo(res)

    prd = _unpad_img(padded_results, window_size, subdivisions)

    prd = prd[:input_img.shape[0], :input_img.shape[1], :]

    if PLOT_PROGRESS:
        plt.imshow(prd)
        plt.title("Smoothly Merged Patches that were Tiled Tighter")
        plt.show()
    return prd


def cheap_tiling_prediction(img, window_size, nb_classes, pred_func):
    """
    Does predictions on an image without tiling.
    """
    original_shape = img.shape
    full_border = img.shape[0] + (window_size - (img.shape[0] % window_size))
    prd = np.zeros((full_border, full_border, nb_classes))
    tmp = np.zeros((full_border, full_border, original_shape[-1]))
    tmp[:original_shape[0], :original_shape[1], :] = img
    img = tmp
    print(img.shape, tmp.shape, prd.shape)
    for i in tqdm(range(0, prd.shape[0], window_size)):
        for j in range(0, prd.shape[0], window_size):
            im = img[i:i+window_size, j:j+window_size]
            prd[i:i+window_size, j:j+window_size] = pred_func([im])
    prd = prd[:original_shape[0], :original_shape[1]]
    if PLOT_PROGRESS:
        plt.imshow(prd)
        plt.title("Cheaply Merged Patches")
        plt.show()
    return prd


def get_dummy_img(xy_size=128, nb_channels=3):
    """
    Create a random image with different luminosity in the corners.

    Returns an array of shape (xy_size, xy_size, nb_channels).
    """
    x = np.random.random((xy_size, xy_size, nb_channels))
    x = x + np.ones((xy_size, xy_size, 1))
    lin = np.expand_dims(
        np.expand_dims(
            np.linspace(0, 1, xy_size),
            1),
        2)
    x = x * lin
    x = x * lin.transpose(1, 0, 2)
    x = x + x[::-1, ::-1, :]
    x = x - np.min(x)
    x = x / np.max(x) / 2
    gc.collect()
    if PLOT_PROGRESS:
        plt.imshow(x)
        plt.title("Random image for a test")
        plt.show()
    return x


def round_predictions(prd, nb_channels_out, thresholds):
    """
    From a threshold list `thresholds` containing one threshold per output
    channel for comparison, the predictions are converted to a binary mask.
    """
    assert (nb_channels_out == len(thresholds))
    prd = np.array(prd)
    for i in range(nb_channels_out):
        # Per-pixel and per-channel comparison on a threshold to
        # binarize prediction masks:
        prd[:, :, i] = prd[:, :, i] > thresholds[i]
    return prd


if __name__ == '__main__':
    ###
    # Image:
    ###

    img_resolution = 600
    # 3 such as RGB, but there could be more in other cases:
    nb_channels_in = 3

    # Get an image
    input_img = get_dummy_img(img_resolution, nb_channels_in)
    # Normally, preprocess the image for input in the neural net:
    # input_img = to_neural_input(input_img)

    ###
    # Neural Net predictions params:
    ###

    # Number of output channels. E.g. a U-Net may output 10 classes, per pixel:
    nb_channels_out = 3
    # U-Net's receptive field border size, it does not absolutely
    # need to be a divisor of "img_resolution":
    window_size = 128

    # This here would be the neural network's predict function, to used below:
    def predict_for_patches(small_img_patches):
        """
        Apply prediction on images arranged in a 4D array as a batch.

        Here, we use a random color filter for each patch so as to see how it
        will blend.

        Note that the np array shape of "small_img_patches" is:
            (nb_images, x, y, nb_channels_in)
        The returned arra should be of the same shape, except for the last
        dimension which will go from nb_channels_in to nb_channels_out
        """
        small_img_patches = np.array(small_img_patches)
        rand_channel_color = np.random.random(size=(
            small_img_patches.shape[0],
            1,
            1,
            small_img_patches.shape[-1])
        )
        return small_img_patches * rand_channel_color * 2

    ###
    # Doing cheap tiled prediction:
    ###

    # Predictions, blending the patches:
    cheaply_predicted_img = cheap_tiling_prediction(
        input_img, window_size, nb_channels_out, pred_func=predict_for_patches
    )

    ###
    # Doing smooth tiled prediction:
    ###

    # The amount of overlap (extra tiling) between windows. A power of 2, and is >= 2:
    subdivisions = 2

    # Predictions, blending the patches:
    smoothly_predicted_img = predict_img_with_smooth_windowing(
        input_img, window_size, subdivisions,
        nb_classes=nb_channels_out, pred_func=predict_for_patches
    )

    ###
    # Demonstrating that the reconstruction is correct:
    ###

    # No more plots from now on
    PLOT_PROGRESS = False

    # useful stats to get a feel on how high will be the error relatively
    print(
        "Image's min and max pixels' color values:",
        np.min(input_img),
        np.max(input_img))

    # First, defining a prediction function that just returns the patch without
    # any modification:
    def predict_same(small_img_patches):
        """
        Apply NO prediction on images arranged in a 4D array as a batch.
        This implies that nb_channels_in == nb_channels_out: dimensions
        and contained values are unchanged.
        """
        return small_img_patches

    same_image_reconstructed = predict_img_with_smooth_windowing(
        input_img, window_size, subdivisions,
        nb_classes=nb_channels_out, pred_func=predict_same
    )

    diff = np.mean(np.abs(same_image_reconstructed - input_img))
    print(
        "Mean absolute reconstruction difference on pixels' color values:",
        diff)
    print(
        "Relative absolute mean error on pixels' color values:",
        100*diff/(np.max(input_img)) - np.min(input_img),
        "%")
    print(
        "A low error (e.g.: 0.28 %) confirms that the image is still "
        "the same before and after reconstruction if no changes are "
        "made by the passed prediction function.")