descriptron-vision 2.0.1__tar.gz

descriptron_vision-2.0.1/.gitignore

@@ -0,0 +1,56 @@
+# This tree holds a 116 GB conda installation, a 10 GB tarball, 12 GB of demo
+# imagery and years of run outputs. Exclude everything, then re-include the code.
+*
+
+!.gitignore
+!README.md
+!LICENSE
+!CITATION.cff
+!docs/
+!docs/**
+!docker/
+!docker/**
+!environments/
+!environments/**
+!packages/
+!packages/**
+
+# the Descriptron programs themselves
+!segment-anything-2/
+segment-anything-2/*
+!segment-anything-2/gui/
+segment-anything-2/gui/*
+!segment-anything-2/gui/*.py
+!segment-anything-2/gui/*.sh
+!segment-anything-2/gui/measure/
+segment-anything-2/gui/measure/*
+!segment-anything-2/gui/measure/*.py
+!segment-anything-2/gui/measure/*.sh
+!segment-anything-2/gui/measure/biorag_prompts/
+!segment-anything-2/gui/measure/biorag_prompts/**
+!segment-anything-2/gui/measure/tests/
+!segment-anything-2/gui/measure/tests/*.py
+!segment-anything-2/gui/torchvision_det/
+!segment-anything-2/gui/torchvision_det/**
+!segment-anything-2/gui/detectron2/
+segment-anything-2/gui/detectron2/*
+!segment-anything-2/gui/detectron2/*.py
+!segment-anything-2/gui/icons/
+!segment-anything-2/gui/icons/**
+!segment-anything-2/gui/marmot.jpg
+
+# never, whatever the rules above say
+**/__pycache__/
+**/*.pyc
+**/*.bak*
+**/.ipynb_checkpoints/
+**/*.pth
+**/*.pt
+**/*.ckpt
+**/*.onnx
+**/*.log
+**/dist/
+**/build/
+**/*.egg-info/
+packages/*/src/*/tools/
+packages/*/src/*/data/

descriptron_vision-2.0.1/LICENSE

@@ -0,0 +1,201 @@
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descriptron_vision-2.0.1/NOTICE

@@ -0,0 +1,52 @@
+Descriptron
+Copyright 2024-2026 Alex R. Van Dam (ORCID 0000-0002-1966-0338)
+
+This product includes software developed by Alex R. Van Dam
+https://github.com/alexrvandam/Descriptron
+
+Licensed under the Apache License, Version 2.0 (see LICENSE). Under Section
+4(d) of that licence, this NOTICE file must be included with any
+redistribution of this software or of any work derived from it.
+
+REQUIRED CITATION
+-----------------
+Anyone who uses Descriptron, or any software derived from it (including
+descriptron-core, descriptron-vision, descriptron-gui and descriptron-mcp), in
+work that is published, presented or distributed must cite:
+
+  1. The software (Descriptron v2):
+     Van Dam, A. R. Descriptron (version used). GitHub repository.
+     https://github.com/alexrvandam/Descriptron
+
+  2. The first Descriptron paper:
+     Van Dam, A. R. & Štarhová Serbina, L. (2026). Descriptron: Artificial
+     intelligence for automating taxonomic species descriptions with a
+     user-friendly software package. Systematic Entomology, 51(1), e70005.
+     https://doi.org/10.1111/syen.70005
+
+  3. Once it is published, the Descriptron v2 paper as well. Its reference
+     will be added here and in CITATION.cff on publication.
+
+BibTeX:
+
+@misc{vandam_descriptron_software,
+  author       = {Van Dam, Alex R.},
+  title        = {Descriptron},
+  howpublished = {GitHub repository},
+  url          = {https://github.com/alexrvandam/Descriptron}
+}
+
+@article{vandam2026descriptron,
+  author  = {Van Dam, Alex R. and Štarhová Serbina, Liliya},
+  title   = {Descriptron: Artificial intelligence for automating taxonomic species
+             descriptions with a user-friendly software package},
+  journal = {Systematic Entomology},
+  volume  = {51},
+  number  = {1},
+  pages   = {e70005},
+  year    = {2026},
+  doi     = {10.1111/syen.70005}
+}
+
+The same information is in CITATION.cff, which GitHub shows as
+"Cite this repository".

descriptron_vision-2.0.1/PKG-INFO

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+Metadata-Version: 2.5
+Name: descriptron-vision
+Version: 2.0.1
+Summary: Mask and landmark prediction for Descriptron: torchvision detectors, SAM2-PAL propagation, DINOv3 landmark transfer
+Project-URL: Homepage, https://github.com/alexrvandam/Descriptron
+Author: Alex R. Van Dam
+License: Apache-2.0
+License-File: LICENSE
+License-File: NOTICE
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Image Recognition
+Requires-Python: >=3.9
+Requires-Dist: descriptron-core==2.0.1
+Requires-Dist: einops>=0.7
+Requires-Dist: timm>=0.9
+Requires-Dist: torch>=2.3
+Requires-Dist: torchvision>=0.18
+Requires-Dist: tqdm>=4.65
+Requires-Dist: transformers>=4.38
+Provides-Extra: dev
+Requires-Dist: build>=1; extra == 'dev'
+Requires-Dist: pytest>=7; extra == 'dev'
+Requires-Dist: twine>=5; extra == 'dev'
+Provides-Extra: ocr
+Requires-Dist: easyocr>=1.7; extra == 'ocr'
+Description-Content-Type: text/markdown
+
+# descriptron-vision
+
+Mask and landmark prediction for [Descriptron](https://github.com/alexrvandam/Descriptron):
+torchvision detectors, SAM2-PAL propagation and DINOv3 landmark transfer.
+
+```bash
+pip install descriptron-vision
+descriptron-train --task masks --coco-json annotations.json --img-dir images/ \
+                  --output-dir out/ --total-iters 20000
+descriptron-predict --checkpoint out/model_final_*.pth --coco-json annotations.json \
+                    --img-dir images/ --annotations_out predictions.json
+```
+
+**No compiler required.** torch and torchvision are ordinary wheels on Linux,
+macOS and Windows. For CUDA, install torch from PyTorch's own index first:
+
+```bash
+pip install torch torchvision --index-url https://download.pytorch.org/whl/cu121
+pip install descriptron-vision
+```
+
+On a Mac the detectors can use the Apple GPU through PyTorch's MPS device, which
+is why this backend exists: Detectron2 has no macOS wheels and no Apple Silicon
+support.
+
+## Two optional dependencies that cannot be declared
+
+PyPI rejects a git dependency in package metadata, so neither **SAM2** nor
+**Detectron2** is listed. Both are imported lazily, and the error names the
+command to install them. The Docker image carries both ready to run.
+
+## Choosing a backbone
+
+`--arch v1` (default) is `maskrcnn_resnet50_fpn`; `--arch v2` is
+`maskrcnn_resnet50_fpn_v2`. v2 scores higher on COCO, but on a few hundred
+training images v1 won on 3 of 3 folds of a grouped species hold-out — its
+lighter two-FC box head converges further in the same budget. Measured on the
+data, not assumed from the model zoo.

descriptron_vision-2.0.1/README.md

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+# descriptron-vision
+
+Mask and landmark prediction for [Descriptron](https://github.com/alexrvandam/Descriptron):
+torchvision detectors, SAM2-PAL propagation and DINOv3 landmark transfer.
+
+```bash
+pip install descriptron-vision
+descriptron-train --task masks --coco-json annotations.json --img-dir images/ \
+                  --output-dir out/ --total-iters 20000
+descriptron-predict --checkpoint out/model_final_*.pth --coco-json annotations.json \
+                    --img-dir images/ --annotations_out predictions.json
+```
+
+**No compiler required.** torch and torchvision are ordinary wheels on Linux,
+macOS and Windows. For CUDA, install torch from PyTorch's own index first:
+
+```bash
+pip install torch torchvision --index-url https://download.pytorch.org/whl/cu121
+pip install descriptron-vision
+```
+
+On a Mac the detectors can use the Apple GPU through PyTorch's MPS device, which
+is why this backend exists: Detectron2 has no macOS wheels and no Apple Silicon
+support.
+
+## Two optional dependencies that cannot be declared
+
+PyPI rejects a git dependency in package metadata, so neither **SAM2** nor
+**Detectron2** is listed. Both are imported lazily, and the error names the
+command to install them. The Docker image carries both ready to run.
+
+## Choosing a backbone
+
+`--arch v1` (default) is `maskrcnn_resnet50_fpn`; `--arch v2` is
+`maskrcnn_resnet50_fpn_v2`. v2 scores higher on COCO, but on a few hundred
+training images v1 won on 3 of 3 folds of a grouped species hold-out — its
+lighter two-FC box head converges further in the same budget. Measured on the
+data, not assumed from the model zoo.

descriptron_vision-2.0.1/pyproject.toml

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+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "descriptron-vision"
+version = "2.0.1"
+description = "Mask and landmark prediction for Descriptron: torchvision detectors, SAM2-PAL propagation, DINOv3 landmark transfer"
+readme = "README.md"
+requires-python = ">=3.9"
+license = { text = "Apache-2.0" }
+authors = [{ name = "Alex R. Van Dam" }]
+classifiers = [
+  "Programming Language :: Python :: 3",
+  "Topic :: Scientific/Engineering :: Image Recognition",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: Apache Software License",
+  "Operating System :: OS Independent",
+]
+
+# torch and torchvision are ordinary wheels on Linux, macOS and Windows, so this
+# installs without a compiler. On a Mac the torchvision detectors can use the
+# Apple GPU through PyTorch's MPS device; Detectron2 cannot, which is why the
+# torchvision backend exists.
+#
+# For CUDA, install torch from PyTorch's own index FIRST, then this package:
+#   pip install torch torchvision --index-url https://download.pytorch.org/whl/cu121
+dependencies = [
+  "descriptron-core==2.0.1",
+  # Capped deliberately. Unbounded, pip installs torch 2.14 with ~3 GB of CUDA 13
+  # wheels — not the torch 2.4.0+cu121 this system was validated on, and a version
+  # in which the AMP calls below are already deprecated. Raise the cap only after
+  # testing, not before.
+  "torch>=2.3",           # torch.amp.GradScaler("cuda") in tv_train_v1 needs 2.3
+  "torchvision>=0.18",
+  "transformers>=4.38",   # Florence-2 scale-bar reading
+  "timm>=0.9",
+  "einops>=0.7",
+  "tqdm>=4.65",
+]
+
+[project.optional-dependencies]
+# SAM2 is not on PyPI and PyPI rejects a git dependency in package metadata, so
+# it cannot be declared here. It is imported lazily and the error message gives
+# the install command:
+#   pip install git+https://github.com/facebookresearch/segment-anything-2
+# Detectron2 is the same story, and additionally needs a compiler; see the
+# Docker image if you would rather not build it.
+ocr = ["easyocr>=1.7"]
+dev = ["pytest>=7", "build>=1", "twine>=5"]
+
+[project.scripts]
+descriptron-train      = "descriptron_vision.cli:train"
+descriptron-predict    = "descriptron_vision.cli:predict"
+descriptron-sweep      = "descriptron_vision.cli:sweep"
+descriptron-sam2pal    = "descriptron_vision.cli:sam2_pal"
+descriptron-dinoland   = "descriptron_vision.cli:dinoland"
+descriptron-measure    = "descriptron_vision.cli:measure"
+
+[project.urls]
+Homepage = "https://github.com/alexrvandam/Descriptron"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/descriptron_vision"]

descriptron_vision-2.0.1/src/descriptron_vision/cli.py

@@ -0,0 +1,66 @@
+"""
+descriptron_vision.cli — detectors, propagation and landmark transfer
+=====================================================================
+
+Same dispatch as `descriptron_core.cli`. The two dependencies that are not on
+PyPI — SAM2 and Detectron2 — are not declared anywhere: PyPI rejects a git
+dependency in package metadata. They are imported lazily by the programs that
+need them, and `require()` below turns the resulting ImportError into the exact
+command to run.
+"""
+from __future__ import annotations
+
+import sys
+
+from descriptron_core.cli import run as _run_core   # noqa: F401  (shared behaviour)
+from descriptron_core.cli import data_path          # noqa: F401
+
+import os
+import runpy
+from importlib.resources import files
+from pathlib import Path
+
+INSTALL_HINTS = {
+    "sam2": ("SAM2 is not on PyPI, so it cannot be a declared dependency.\n"
+             "  pip install git+https://github.com/facebookresearch/segment-anything-2"),
+    "detectron2": ("Detectron2 is not on PyPI and must be compiled:\n"
+                   "  pip install git+https://github.com/facebookresearch/detectron2\n"
+                   "It needs a C++/CUDA toolchain and has no macOS wheels. If you would\n"
+                   "rather not build it, the Docker image carries it ready to run, and the\n"
+                   "torchvision backend needs none of this."),
+}
+
+
+def require(module: str):
+    """Import an optional heavyweight dependency, or explain how to get it."""
+    try:
+        return __import__(module)
+    except ImportError as exc:
+        hint = INSTALL_HINTS.get(module, f"  pip install {module}")
+        raise SystemExit(f"{module} is required for this step but is not installed.\n"
+                         f"{hint}\n\n(original error: {exc})") from exc
+
+
+def tools_dir() -> Path:
+    return Path(str(files("descriptron_vision") / "tools"))
+
+
+def _run(script: str, argv: list[str], subdir: str | None = None) -> None:
+    base = tools_dir() / subdir if subdir else tools_dir()
+    path = base / script
+    if not path.exists():
+        raise SystemExit(f"{path} is missing — was sync_sources.py run before building?")
+    sys.path.insert(0, str(path.parent))
+    sys.path.insert(0, str(tools_dir()))
+    os.environ.setdefault("DESCRIPTRON_DATA", str(data_path()))
+    sys.argv = [str(path), *argv]
+    runpy.run_path(str(path), run_name="__main__")
+
+
+def train():      _run("tv_train_v1.py", sys.argv[1:], "torchvision_det")
+def predict():    _run("tv_predict_v1.py", sys.argv[1:], "torchvision_det")
+def sweep():      _run("tv_sweep_v1.py", sys.argv[1:], "torchvision_det")
+def sam2_pal():   _run("sam2_pal_batch_v21.py", sys.argv[1:])
+def dinoland():   _run("dinov3_landmark_transfer_v51.py", sys.argv[1:])
+def measure():
+    _run("measurement_script_to_try_after_kpts_prediction_measure_kpts_V35.py", sys.argv[1:])