h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = ["numpy"]
# ///
"""Write the PL2 fixtures of the gin `plexon/pl2/` folder from their source recordings.

Usage::

    uv run stub_pl2.py [fixture_name ...]     # no names: every fixture in FIXTURES

h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = ["numpy"]
# ///
"""Write the PLX fixtures of the gin `plexon/plx/` folder from their source recordings.

The fixture `plx/timestamp_clock/one_megahertz_forty_bit_timestamps/` is written by a separate script with
the same machinery, `stub_plx_forty_bit_timestamps.py`, because its source file is not public.

Usage::

h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = [
#     "numpy",
#     "load-heka-python @ git+https://github.com/easy-electrophysiology/load-heka-python",
# ]
# ///
"""Shrink a HEKA PatchMaster bundled .dat by keeping whole sweeps of truncated traces.

Source: any DAT2 bundle (see the per-fixture calls in stubs/README.md)

h-mayorquin

#!/usr/bin/env -S uv run --script
# /// script
# requires-python = ">=3.10,<3.12"
# dependencies = [
#     "keypoint-moseq==0.6.10",
#     "h5py",
#     "pandas",
#     "tables",
# ]
# ///

h-mayorquin

#!/usr/bin/env -S uv run --script
# /// script
# requires-python = ">=3.10,<3.12"
# dependencies = [
#     "keypoint-moseq==0.6.10",
#     "h5py",
#     "pandas",
#     "tables",
#     "requests",
# ]

h-mayorquin

# /// script
# requires-python = ">=3.11"
# dependencies = [
#     "neo>=0.14.3",
#     "numpy",
# ]
# ///
"""Stub a split Intan Traditional (header-attached) recording that carries digital and aux lines.

Source: ~/data/nelson_lab/Intan files/64 site example 2 camera example/pm231213a_240205_240205_120954

h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = []
# ///
"""Cut RWD Life Science fiber photometry sessions down to test-fixture size.

Source: ~/data/rwd/zenodo_21842013_laing/session_R2 (1 channel, 410+470, 10 fps)
        ~/data/rwd/zenodo_17645091_cjdae8/20241004_DAL01_..._AirPuff (2 channels, 50 fps, marked)
        ~/data/rwd/zenodo_17645091_cjdae8/20240920_DAL01_... (2 channels, 50 fps, unmarked)
Output: ~/data/rwd/stubs/{fiber_photometry_datasets,events_datasets}/rwd/...

h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = [
#     "numpy",
# ]
# ///
"""Cut pyPhotometry ``.ppd`` windows for the digital lines they carry, keeping the header untouched.

A ``.ppd`` word holds fifteen bits of an analog sample and one bit of a digital line, so the lines cannot
be cut out of a recording: a window carries the fluorescence with them. What can be chosen is which shape

h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = []
# ///
"""Cut a pyPhotometry ``.ppd`` recording down to its first seconds, keeping the header untouched.

Source: an hour-and-a-half recording from the Blanco-Pozo, Akam and Walton OSF deposit (CC BY 4.0),
        header version 0.2, mode ``2 colour time div.``, 130 Hz, about 2.9 MB.
Output: the same header and the leading whole cycles of samples, about 20 KB.

h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = [
#     "pyedflib",
#     "numpy",
# ]
# ///
"""
Generate a synthetic BDF+ file carrying a trigger stream at realistic length.