Giorgio Gilestro
28b7a227c0
For every session (training and testing alike), the loader now looks
up the corresponding row in barrier_opening.csv and:
- drops the read if the ROI is in bad_rois (barrier never opened
for that fly so its tracking has no biological meaning)
- drops the read if the session is flagged unusable
- stamps the session's opening_s onto every sample so downstream
code can compute t_from_opening = t - opening_s
Tested against ETHOSCOPE_082 2024-09-17: training (bad_rois=1,3,5)
correctly drops ROIs 1/3/5; testing keeps all six; opening_s differs
between sessions as expected (646.8 vs 154.7).
Opt out with apply_barrier_filter=False if you need raw data.
42 lines
1.9 KiB
Python
42 lines
1.9 KiB
Python
"""Shared path constants for the Cupido tracking project."""
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import os
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from pathlib import Path
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# Where this code repository lives (the directory containing scripts/, notebooks/, ...).
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PROJECT_ROOT = Path(__file__).resolve().parent.parent
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DATA_METADATA = PROJECT_ROOT / "data" / "metadata"
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DATA_PROCESSED = PROJECT_ROOT / "data" / "processed"
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FIGURES = PROJECT_ROOT / "figures"
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LOGS_DIR = PROJECT_ROOT / "data" / "logs"
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# Where the source videos live (read-only NFS mount).
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VIDEOS_ROOT = Path("/mnt/ethoscope_data/videos")
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# Where the project's bulky data lives — outside the cloud-synced repo so
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# it doesn't churn the sync. This single root holds everything that's big
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# or regenerable: tracking DBs, target-point JSONs, and the metadata
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# spreadsheet (xlsx + TSV).
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DATA_VOLUME = Path("/mnt/data/projects/cupido")
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TARGETS_DIR = DATA_VOLUME / "targets"
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TRACKING_OUTPUT_DIR = DATA_VOLUME / "tracked"
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VIDEO_INFO_XLSX = DATA_VOLUME / "all_video_info_merged.xlsx"
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VIDEO_INFO_TSV = DATA_VOLUME / "all_video_info_merged.tsv"
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# A small CSV listing every video file we know about (built locally).
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INVENTORY_CSV = DATA_METADATA / "video_inventory.csv"
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# Hand-annotated barrier-opening times (output of the picker app). One
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# row per testing session; columns: machine_name, session_date,
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# session_time, opening_s, trim_first_s, bad_rois, analyst, notes.
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BARRIER_OPENING_CSV = DATA_METADATA / "barrier_opening.csv"
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# Where the ethoscope source tree is checked out (used by track_videos.py
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# and auto_detect_targets.py — host-side scripts that import ethoscope
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# from a local clone rather than from pip). Default assumes the standard
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# layout `~/Code/ethoscope_project/ethoscope/src/ethoscope`; override with
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# the ETHOSCOPE_SRC environment variable if your clone lives elsewhere.
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ETHOSCOPE_SRC = Path(os.environ.get(
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"ETHOSCOPE_SRC",
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str(Path.home() / "Code" / "ethoscope_project" / "ethoscope" / "src" / "ethoscope"),
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))
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