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@Westerby, try to replace WindowData layer to the following values:
input: "data"
input_dim: 1
input_dim: 3
input_dim: 227
input_dim: 227
Also, remove the last Accuracy layer.
To achieve similar quality, you need to subtract the values stored at imagenet_mean.binaryproto from input images. Here is a serialized .npy array: https://github.com/BVLC/caffe/blob/master/python/caffe/imagenet/ilsvrc_2012_mean.npy.
However I don't know how to process crop to 227x227 because I have no text_file_accroding_to_window_data_layer_formatting.txt file and I can't compare Caffe and OpenCV implementations. Can you share it?