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Remove hardcoded /home/gg paths so the project is portable

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Notebooks now use Path.home() / "cupido" for the repo root (works for
any user inside the JupyterLab container), and the offline-tracking
scripts read the ethoscope source-tree location from the new
ETHOSCOPE_SRC config constant — defaulting to ~/Code/ethoscope_project/...
and overridable via the ETHOSCOPE_SRC environment variable.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
This commit is contained in:
Giorgio Gilestro 2026-05-01 08:55:44 +01:00
parent 5934dce21e
commit 231c7a437f
8 changed files with 25 additions and 14 deletions
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2
README.md
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@ -53,7 +53,7 @@ is split in two stages so you can sit at the screen and click for an hour, then
let the tracker grind through overnight. let the tracker grind through overnight.
```bash ```bash
# extra deps (ethoscope src must be at /home/gg/Code/ethoscope_project/...) # extra deps (set ETHOSCOPE_SRC env var if your ethoscope clone isn't at ~/Code/ethoscope_project/...)
pip install -r requirements-tracking.txt pip install -r requirements-tracking.txt
# 1) build the inventory (xlsx ↔ /mnt/ethoscope_data/videos/) # 1) build the inventory (xlsx ↔ /mnt/ethoscope_data/videos/)

2
notebooks/flies_analysis.ipynb
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@ -14,7 +14,7 @@
"execution_count": null, "execution_count": null,
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": "import sys\nfrom pathlib import Path\n\nimport pandas as pd\nimport numpy as np\nimport sqlite3\nimport glob\nimport re\nimport matplotlib.pyplot as plt\nimport seaborn as sns\nfrom scipy.spatial.distance import euclidean\nfrom scipy import stats\n\n# Two locations to know about:\n# - DATA_DIR : where the project's bulky data lives (data volume)\n# - REPO_ROOT : where the code repository lives (this notebook is inside it)\nDATA_DIR = Path(\"/mnt/data/projects/cupido\")\nREPO_ROOT = Path(\"/home/gg/ownCloud/Work/Projects/coding/cupido/tracking\")\n\n# Pull every other path constant from scripts/config.py so this notebook\n# stays in sync with the rest of the codebase. (Reason: avoids drift when\n# paths change — config.py is the single source of truth.)\nsys.path.insert(0, str(REPO_ROOT / \"scripts\"))\nfrom config import DATA_RAW, DATA_METADATA, DATA_PROCESSED, FIGURES\n\n# Plotting style\nplt.style.use('seaborn-v0_8')\nsns.set_palette(\"husl\")\n" "source": "import sys\nfrom pathlib import Path\n\nimport pandas as pd\nimport numpy as np\nimport sqlite3\nimport glob\nimport re\nimport matplotlib.pyplot as plt\nimport seaborn as sns\nfrom scipy.spatial.distance import euclidean\nfrom scipy import stats\n\n# Two locations to know about:\n# - DATA_DIR : where the project's bulky data lives (mounted into the container)\n# - REPO_ROOT : where the code repository is checked out (your home directory)\n# Path.home() expands to the current user's home, so this works for any\n# user running the container (no hard-coded usernames).\nDATA_DIR = Path(\"/mnt/data/projects/cupido\")\nREPO_ROOT = Path.home() / \"cupido\"\n\n# Pull every other path constant from scripts/config.py so this notebook\n# stays in sync with the rest of the codebase. (Reason: avoids drift when\n# paths change — config.py is the single source of truth.)\nsys.path.insert(0, str(REPO_ROOT / \"scripts\"))\nfrom config import DATA_RAW, DATA_METADATA, DATA_PROCESSED, FIGURES\n\n# Plotting style\nplt.style.use('seaborn-v0_8')\nsns.set_palette(\"husl\")\n"
}, },
{ {
"cell_type": "markdown", "cell_type": "markdown",

2
notebooks/flies_analysis_simple.ipynb
View file

@ -14,7 +14,7 @@
"execution_count": null, "execution_count": null,
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": "import sys\nfrom pathlib import Path\n\nimport pandas as pd\nimport numpy as np\nimport matplotlib.pyplot as plt\nimport seaborn as sns\nfrom scipy.spatial.distance import euclidean\nfrom scipy import stats\n\n# Two locations to know about:\n# - DATA_DIR : where the project's bulky data lives (data volume)\n# - REPO_ROOT : where the code repository lives (this notebook is inside it)\nDATA_DIR = Path(\"/mnt/data/projects/cupido\")\nREPO_ROOT = Path(\"/home/gg/ownCloud/Work/Projects/coding/cupido/tracking\")\n\n# Pull every other path constant from scripts/config.py so this notebook\n# stays in sync with the rest of the codebase. (Reason: avoids drift when\n# paths change — config.py is the single source of truth.)\nsys.path.insert(0, str(REPO_ROOT / \"scripts\"))\nfrom config import DATA_RAW, DATA_METADATA, DATA_PROCESSED, FIGURES\n\n# Plotting style\nplt.style.use('seaborn-v0_8')\nsns.set_palette(\"husl\")\n\nprint(f\"Data directory: {DATA_DIR}\")\nprint(f\"Repo root: {REPO_ROOT}\")\nprint(f\"Pandas version: {pd.__version__}\")\nprint(f\"NumPy version: {np.__version__}\")\n" "source": "import sys\nfrom pathlib import Path\n\nimport pandas as pd\nimport numpy as np\nimport matplotlib.pyplot as plt\nimport seaborn as sns\nfrom scipy.spatial.distance import euclidean\nfrom scipy import stats\n\n# Two locations to know about:\n# - DATA_DIR : where the project's bulky data lives (mounted into the container)\n# - REPO_ROOT : where the code repository is checked out (your home directory)\n# Path.home() expands to the current user's home, so this works for any\n# user running the container (no hard-coded usernames).\nDATA_DIR = Path(\"/mnt/data/projects/cupido\")\nREPO_ROOT = Path.home() / \"cupido\"\n\n# Pull every other path constant from scripts/config.py so this notebook\n# stays in sync with the rest of the codebase. (Reason: avoids drift when\n# paths change — config.py is the single source of truth.)\nsys.path.insert(0, str(REPO_ROOT / \"scripts\"))\nfrom config import DATA_RAW, DATA_METADATA, DATA_PROCESSED, FIGURES\n\n# Plotting style\nplt.style.use('seaborn-v0_8')\nsns.set_palette(\"husl\")\n\nprint(f\"Data directory: {DATA_DIR}\")\nprint(f\"Repo root: {REPO_ROOT}\")\nprint(f\"Pandas version: {pd.__version__}\")\nprint(f\"NumPy version: {np.__version__}\")\n"
}, },
{ {
"cell_type": "markdown", "cell_type": "markdown",

4
notebooks/getting_started/00_welcome.ipynb
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@ -149,14 +149,14 @@
{ {
"cell_type": "markdown", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": "## Where everything lives\n\nTake a moment to memorize these locations — you'll come back to them often.\n\n| what | where |\n|---|---|\n| Tracking DBs (SQLite, one per video) | `/mnt/data/projects/cupido/tracked/` |\n| Target JSONs (the user-clicked reference points) | `/mnt/data/projects/cupido/targets/` |\n| The metadata table (xlsx + TSV) | `/mnt/data/projects/cupido/all_video_info_merged.tsv` |\n| Source video files | `/mnt/ethoscope_data/videos/` |\n| Project code (this repo) | `/home/gg/ownCloud/Work/Projects/coding/cupido/tracking/` |\n| Your notebooks | `notebooks/getting_started/` (this folder) |\n\nNotice the pattern: **everything bulky or regenerable lives under\n`/mnt/data/projects/cupido/`**. The repository itself only stores code,\ndocumentation, and small metadata files. We'll refer to that data\ndirectory as `DATA_DIR` from here on.\n\nLet's verify a couple of these from inside Python:\n" "source": "## Where everything lives\n\nTake a moment to memorize these locations — you'll come back to them often.\n\n| what | where |\n|---|---|\n| Tracking DBs (SQLite, one per video) | `/mnt/data/projects/cupido/tracked/` |\n| Target JSONs (the user-clicked reference points) | `/mnt/data/projects/cupido/targets/` |\n| The metadata table (xlsx + TSV) | `/mnt/data/projects/cupido/all_video_info_merged.tsv` |\n| Source video files | `/mnt/ethoscope_data/videos/` |\n| Project code (this repo) | `~/cupido/` (your home directory inside the container) |\n| Your notebooks | `~/cupido/notebooks/getting_started/` (this folder) |\n\nNotice the pattern: **everything bulky or regenerable lives under\n`/mnt/data/projects/cupido/`**. The repository itself, with all the\ncode and notebooks, is checked out into your home directory inside the\nJupyterLab container — that's `~/cupido`, where `~` is shorthand for\nyour home directory (`/home/<your-username>`).\n\nWe'll refer to those two roots as `DATA_DIR` and `REPO_ROOT` from here on.\n\nLet's verify a couple of these from inside Python:\n"
}, },
{ {
"cell_type": "code", "cell_type": "code",
"metadata": {}, "metadata": {},
"execution_count": null, "execution_count": null,
"outputs": [], "outputs": [],
"source": "from pathlib import Path\n\n# Single root for all the bulky / regenerable project data.\nDATA_DIR = Path(\"/mnt/data/projects/cupido\")\n\ntracked_dir = DATA_DIR / \"tracked\"\ntargets_dir = DATA_DIR / \"targets\"\nmetadata_tsv = DATA_DIR / \"all_video_info_merged.tsv\"\n\nprint(f\"Tracking DBs available: {len(list(tracked_dir.glob('*_tracking.db')))}\")\nprint(f\"Target JSONs available: {len(list(targets_dir.glob('*.json')))}\")\nprint(f\"Metadata TSV exists: {metadata_tsv.exists()}\")\n" "source": "from pathlib import Path\n\n# The two roots we keep coming back to.\nDATA_DIR = Path(\"/mnt/data/projects/cupido\") # bulky data, mounted into the container\nREPO_ROOT = Path.home() / \"cupido\" # the code repo in your home dir\n\ntracked_dir = DATA_DIR / \"tracked\"\ntargets_dir = DATA_DIR / \"targets\"\nmetadata_tsv = DATA_DIR / \"all_video_info_merged.tsv\"\n\nprint(f\"Repo root: {REPO_ROOT} (exists={REPO_ROOT.exists()})\")\nprint(f\"Tracking DBs available: {len(list(tracked_dir.glob('*_tracking.db')))}\")\nprint(f\"Target JSONs available: {len(list(targets_dir.glob('*.json')))}\")\nprint(f\"Metadata TSV exists: {metadata_tsv.exists()}\")\n"
}, },
{ {
"cell_type": "markdown", "cell_type": "markdown",

2
notebooks/getting_started/03_compare_trained_vs_naive.ipynb
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@ -48,7 +48,7 @@
"metadata": {}, "metadata": {},
"execution_count": null, "execution_count": null,
"outputs": [], "outputs": [],
"source": "import sys\nfrom pathlib import Path\n\nimport numpy as np\nimport pandas as pd\nimport matplotlib.pyplot as plt\nfrom scipy import stats\n\n# Two locations to know about:\n# - DATA_DIR : where the project's data files live (read-only data volume)\n# - REPO_ROOT : where the code repository lives (this notebook is inside it)\n# We build both as Path objects, then derive everything else from them.\nDATA_DIR = Path(\"/mnt/data/projects/cupido\")\nREPO_ROOT = Path(\"/home/gg/ownCloud/Work/Projects/coding/cupido/tracking\")\n\n# Tell Python where to find the project's helper modules (in scripts/).\nsys.path.insert(0, str(REPO_ROOT / \"scripts\"))\n\nfrom load_roi_data import load_roi_data\n" "source": "import sys\nfrom pathlib import Path\n\nimport numpy as np\nimport pandas as pd\nimport matplotlib.pyplot as plt\nfrom scipy import stats\n\n# Two locations to know about:\n# - DATA_DIR : where the project's data files live (mounted into the container)\n# - REPO_ROOT : where the code repository is checked out (your home directory)\n# Path.home() expands to the current user's home directory, so this\n# works for any user running the container — no hard-coded usernames.\nDATA_DIR = Path(\"/mnt/data/projects/cupido\")\nREPO_ROOT = Path.home() / \"cupido\"\n\n# Tell Python where to find the project's helper modules (in scripts/).\nsys.path.insert(0, str(REPO_ROOT / \"scripts\"))\n\nfrom load_roi_data import load_roi_data\n"
}, },
{ {
"cell_type": "markdown", "cell_type": "markdown",

6
scripts/auto_detect_targets.py
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@ -24,10 +24,10 @@ import cv2
import numpy as np import numpy as np
import pandas as pd import pandas as pd
# ethoscope source tree from config import ETHOSCOPE_SRC, INVENTORY_CSV, TARGETS_DIR
sys.path.insert(0, "/home/gg/Code/ethoscope_project/ethoscope/src/ethoscope")
from config import INVENTORY_CSV, TARGETS_DIR # noqa: E402 # ethoscope source tree
sys.path.insert(0, str(ETHOSCOPE_SRC))
from ethoscope.roi_builders.target_roi_builder import TargetGridROIBuilder # noqa: E402 from ethoscope.roi_builders.target_roi_builder import TargetGridROIBuilder # noqa: E402

17
scripts/config.py
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@ -1,5 +1,6 @@
"""Shared path constants for the Cupido tracking project.""" """Shared path constants for the Cupido tracking project."""
import os
from pathlib import Path from pathlib import Path
# Where this code repository lives (the directory containing scripts/, notebooks/, ...). # Where this code repository lives (the directory containing scripts/, notebooks/, ...).
@ -13,9 +14,9 @@ LOGS_DIR = PROJECT_ROOT / "data" / "logs"
# Where the source videos live (read-only NFS mount). # Where the source videos live (read-only NFS mount).
VIDEOS_ROOT = Path("/mnt/ethoscope_data/videos") VIDEOS_ROOT = Path("/mnt/ethoscope_data/videos")
# Where the project's bulky data lives — outside the ownCloud-synced repo so # Where the project's bulky data lives — outside the cloud-synced repo so
# it doesn't churn the cloud sync. This single root holds everything that's # it doesn't churn the sync. This single root holds everything that's big
# big or regenerable: tracking DBs, target-point JSONs, and the metadata # or regenerable: tracking DBs, target-point JSONs, and the metadata
# spreadsheet (xlsx + TSV). # spreadsheet (xlsx + TSV).
DATA_VOLUME = Path("/mnt/data/projects/cupido") DATA_VOLUME = Path("/mnt/data/projects/cupido")
TARGETS_DIR = DATA_VOLUME / "targets" TARGETS_DIR = DATA_VOLUME / "targets"
@ -25,3 +26,13 @@ VIDEO_INFO_TSV = DATA_VOLUME / "all_video_info_merged.tsv"
# A small CSV listing every video file we know about (built locally). # A small CSV listing every video file we know about (built locally).
INVENTORY_CSV = DATA_METADATA / "video_inventory.csv" INVENTORY_CSV = DATA_METADATA / "video_inventory.csv"
# Where the ethoscope source tree is checked out (used by track_videos.py
# and auto_detect_targets.py — host-side scripts that import ethoscope
# from a local clone rather than from pip). Default assumes the standard
# layout `~/Code/ethoscope_project/ethoscope/src/ethoscope`; override with
# the ETHOSCOPE_SRC environment variable if your clone lives elsewhere.
ETHOSCOPE_SRC = Path(os.environ.get(
"ETHOSCOPE_SRC",
str(Path.home() / "Code" / "ethoscope_project" / "ethoscope" / "src" / "ethoscope"),
))

4
scripts/track_videos.py
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@ -27,11 +27,11 @@ from pathlib import Path
import numpy as np import numpy as np
from config import ETHOSCOPE_SRC, TARGETS_DIR, TRACKING_OUTPUT_DIR
# Import ethoscope from the local source tree (no pip install). # Import ethoscope from the local source tree (no pip install).
ETHOSCOPE_SRC = Path("/home/gg/Code/ethoscope_project/ethoscope/src/ethoscope")
sys.path.insert(0, str(ETHOSCOPE_SRC)) sys.path.insert(0, str(ETHOSCOPE_SRC))
from config import TARGETS_DIR, TRACKING_OUTPUT_DIR # noqa: E402
from tracking_geometry import HD_FG_DATA, compute_roi_polygons # noqa: E402 from tracking_geometry import HD_FG_DATA, compute_roi_polygons # noqa: E402