EXA: batching. 99.99% of issue #1

Author: anwarnunez

examples/introduction/demo_batching.py

@@ -0,0 +1,83 @@
+'''
+===========================================
+ Extracting features from stimulus batches
+===========================================
+
+This example shows how to use batches to extract motion-energy features from a video.
+
+When the stimulus is very high-resolution (e.g. 4K) or is multiple hours long, it might not be possible to fit the data in memory. In such situations, it is useful to load a small number of video frames and extract motion-energy features from that subset of frames alone. In order to do this properly, one must avoid edge effects. In this example we show how to batch
+'''
+
+
+# %%
+# First, we'll specify the stimulus we want to load.
+
+import moten
+import numpy as np
+import matplotlib.pyplot as plt
+stimulus_fps = 24
+video_file = 'http://anwarnunez.github.io/downloads/avsnr150s24fps_tiny.mp4'
+
+# %%
+# Load the first 300 images and spatially downsample the video.
+small_vhsize = (72, 128)        # height x width
+luminance_images = moten.io.video2luminance(video_file, size=small_vhsize, nimages=300)
+nimages, vdim, hdim = luminance_images.shape
+print(vdim, hdim)
+
+fig, ax = plt.subplots()
+ax.matshow(luminance_images[200], vmin=0, vmax=100, cmap='inferno')
+ax.set_xticks([])
+ax.set_yticks([])
+
+# %%
+# Next we need to construct the pyramid and extract the motion-energy features from the full stimulus.
+
+pyramid = moten.pyramids.MotionEnergyPyramid(stimulus_vhsize=(vdim, hdim),
+                                             stimulus_fps=stimulus_fps,
+                                             filter_temporal_width=16)
+
+moten_features = pyramid.project_stimulus(luminance_images)
+print(moten_features.shape)
+
+# %%
+# We have to include some padding to the batches in order to avoid convolution edge effects. The padding is determined by the temporal width of the motion-energy filter. By default, the temporal width is 2/3 of the stimulus frame rate (`int(fps*(2/3))`). This parameter can be specified when instantating a pyramid by passing e.g. ``filter_temporal_width=16``. Once the pyramid is defined, the parameter can also be accessed from the ``pyramid.definition`` dictionary.
+
+filter_temporal_width = pyramid.definition['filter_temporal_width']
+
+# %%
+# Finally, we define the padding window as half the temporal filter width.
+
+window = int(np.ceil((filter_temporal_width/2)))
+print(filter_temporal_width, window)
+
+# %%
+# Now we are ready to extract motion-energy features in batches:
+
+nbatches = 5
+batch_size = int(np.ceil(nimages/nbatches))
+batched_data = []
+for bdx in range(nbatches):
+    start_frame, end_frame = batch_size*bdx, batch_size*(bdx + 1)
+    print('Batch %i/%i [%i:%i]'%(bdx+1, nbatches, start_frame, end_frame))
+
+    # Padding
+    batch_start = max(start_frame - window, 0)
+    batch_end = end_frame + window
+    batched_responses = pyramid.project_stimulus(
+        luminance_images[batch_start:batch_end])
+
+    # Trim edges
+    if bdx == 0:
+        batched_responses = batched_responses[:-window]
+    elif bdx + 1 == nbatches:
+        batched_responses = batched_responses[window:]
+    else:
+        batched_responses = batched_responses[window:-window]
+    batched_data.append(batched_responses)
+
+batched_data = np.vstack(batched_data)
+
+# %%
+# They are exactly the same.
+assert np.allclose(moten_features, batched_data)