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Feature: support epoch shapes and ABF1 in the ABF protocol reconstruction - #1963
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h-mayorquin wants to merge 1 commit into
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h-mayorquin wants to merge 1 commit into
h-mayorquin wants to merge 1 commit into
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Draw ramps and pulse, triangle, cosine and biphasic trains, start each sweep at the last epoch level when the protocol asks for it, read the protocol of ABF1 files from version 1.6 on, and warn when a file uses user lists, alternating outputs, stimulus-file waveforms or conditioning trains, which are not reconstructed yet.
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ABF files do not store the command that the amplifier played as samples. They store a protocol: a holding level plus a table of up to ten epochs per output, each with a shape, a level, a duration and how these change from sweep to sweep.
read_raw_protocolrebuilds the command from that table, and right now it has these problems:This PR draws all six epoch shapes with their train period and width, keeps the level and duration increments, follows the "use last epoch level" option and reads the protocol of ABF1 files from version 1.6 on. Files with user lists, stimulus files, alternating outputs or conditioning trains are not reconstructed yet, and the reader now warns about them. Before the first epoch the output stays at the holding level for 1/64 of the sweep. The old code used that value with a
# TODO guess for first holdingcomment and #1305 asked about it. It is right (the recorded responses start right after it), so it stays. The test files were added to gin in https://gin.g-node.org/NeuralEnsemble/ephy_testing_data/pulls/197.This should close #1305.