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evaluate.py in branch pytorch-1.1
line 134 and line 135
you only use the prediction result of the first image, but treat it as the result of the remaining images in the same batch, in line 136. so something goes wrong when evaluate with batch size larger than 1.
you should modify it with
prediction = padded_prediction[:, 0:img.shape[2], 0:img.shape[3], :]
and
count_predictions[:, y1:y2, x1:x2] += 1
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