trace-tad 0.2.0__tar.gz

trace_tad-0.2.0/LICENSE

@@ -0,0 +1,176 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to the Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by the Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding any notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS

trace_tad-0.2.0/MANIFEST.in

@@ -0,0 +1,21 @@
+# Config files (Python-based configs, included as package data)
+recursive-include configs *.py
+
+# Entry-point scripts
+recursive-include tools *.py
+
+# Bundled frontend assets (built by `trace build-frontend`)
+recursive-include trace_tad/static *
+
+# Documentation
+include README.md
+include LICENSE
+
+# Exclude dev/test files
+exclude .gitignore
+prune trace-annotator
+prune exps
+prune data
+prune pretrained
+prune figures
+prune literature_review

trace_tad-0.2.0/PKG-INFO

@@ -0,0 +1,142 @@
+Metadata-Version: 2.4
+Name: trace-tad
+Version: 0.2.0
+Summary: TRACE: Temporal action detection for animal behavior analysis
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/KunmingS/TRACE
+Project-URL: Documentation, https://kunmings.github.io/TRACE/
+Project-URL: Repository, https://github.com/KunmingS/TRACE
+Project-URL: Issues, https://github.com/KunmingS/TRACE/issues
+Keywords: temporal-action-detection,animal-behavior,video-analysis,deep-learning,pytorch
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Image Recognition
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: torch>=2.0.1
+Requires-Dist: torchvision>=0.15.2
+Requires-Dist: decord>=0.6.0
+Requires-Dist: einops>=0.6.0
+Requires-Dist: scipy>=1.9.0
+Requires-Dist: pandas>=1.5.0
+Requires-Dist: tqdm>=4.64.0
+Requires-Dist: numpy>=1.23.5
+Requires-Dist: opencv-python-headless>=4.6.0
+Requires-Dist: fastapi
+Requires-Dist: uvicorn
+Requires-Dist: python-multipart
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Dynamic: license-file
+
+# TRACE — Temporal Recognition of Animal Behaviors Captured from Video
+
+TRACE is a temporal action detection system for animal behavior analysis in untrimmed video.
+
+![TRACE Annotator](site/assets/screenshot.png)
+
+## Documentation
+
+Project docs are set up for GitHub Pages at
+[kunmings.github.io/TRACE](https://kunmings.github.io/TRACE/). The public site
+source lives in [site/](site/), separate from local engineering notes in
+[docs/](docs/).
+
+## Install
+
+```bash
+python -m pip install trace-tad
+```
+
+For a local checkout:
+
+```bash
+pip install -e .
+```
+
+Training, evaluation, and prediction require a CUDA-capable PyTorch
+environment. The annotation app can still be used for labeling workflows without
+running model jobs locally.
+
+## Usage
+
+```bash
+# Prepare local model weights used by the packaged configs
+trace prepare --weights all
+
+# Check whether PyPI has a newer TRACE release
+trace update
+
+# Start the bundled annotation app
+trace app
+
+# Train from selected video/annotation pairs
+trace train --model large --work-dir /my/dataset --pairs video01.mp4=video01_final.csv video02.mp4=video02.csv
+
+# Evaluate the training artifact, or evaluate on held-out video/annotation pairs
+trace eval --model-dir /my/dataset/model_YYYYMMDD_HHMMSS
+trace eval --model-dir /my/dataset/model_YYYYMMDD_HHMMSS --work-dir /my/testset --pairs video03.mp4=video03.csv
+
+# Predict on new videos and write annotation drafts
+trace predict --model-dir /my/dataset/model_YYYYMMDD_HHMMSS --input /path/to/video.mp4 --annotated-video --threshold 0.25
+
+# Run a configured end-to-end workflow
+trace pipeline configs/small.py --export csv
+```
+
+You can stay in the UI for annotation and still keep training or inference
+reproducible from the command line. The app lets you choose video/annotation
+pairs, configure model runs, and generate the matching CLI command, so a lab
+operator can annotate in the browser while a server or batch job runs the
+generated `trace train`, `trace eval`, `trace predict`, or `trace pipeline`
+command.
+
+`--pairs` is explicit: each item is `VIDEO_PATH=CSV_PATH`. A source video can
+have multiple annotation CSVs beside it, such as `video01_draft.csv`,
+`video01_final.csv`, or a model-generated `video01_predictions.csv`; each
+training or evaluation pair chooses the annotation file to use for that video.
+Relative paths are resolved against `--work-dir`, so
+`video01.mp4=video01_final.csv` means both files are inside the work directory.
+Training creates a self-contained `model_YYYYMMDD_HHMMSS/` folder under
+`--work-dir`.
+
+TRACE annotation CSVs are time-based:
+
+```csv
+labelId,timestamp,endTimestamp
+grooming,12.430,18.970
+rearing,42.100,45.650
+```
+
+Prediction creates a `predict_YYYYMMDD_HHMMSS/` folder beside the selected input
+video or input video directory, unless `--output` is provided. The CSV output
+uses the annotation format, so a reviewer can treat model predictions as draft
+annotation files. Use `--annotated-video` to render MP4 overlays with the same
+confidence threshold as the JSON/CSV outputs.
+
+## Development
+
+```bash
+# Start backend and Vite dev servers
+trace dev serve
+
+# Build the frontend and bundle it into the Python package
+trace dev build-frontend
+```
+
+The committed public website in [site/](site/) is intentionally small and
+publishable; deeper engineering notes stay under [docs/](docs/).
+
+## License
+
+Apache 2.0. See [LICENSE](LICENSE).

trace_tad-0.2.0/README.md

@@ -0,0 +1,101 @@
+# TRACE — Temporal Recognition of Animal Behaviors Captured from Video
+
+TRACE is a temporal action detection system for animal behavior analysis in untrimmed video.
+
+![TRACE Annotator](site/assets/screenshot.png)
+
+## Documentation
+
+Project docs are set up for GitHub Pages at
+[kunmings.github.io/TRACE](https://kunmings.github.io/TRACE/). The public site
+source lives in [site/](site/), separate from local engineering notes in
+[docs/](docs/).
+
+## Install
+
+```bash
+python -m pip install trace-tad
+```
+
+For a local checkout:
+
+```bash
+pip install -e .
+```
+
+Training, evaluation, and prediction require a CUDA-capable PyTorch
+environment. The annotation app can still be used for labeling workflows without
+running model jobs locally.
+
+## Usage
+
+```bash
+# Prepare local model weights used by the packaged configs
+trace prepare --weights all
+
+# Check whether PyPI has a newer TRACE release
+trace update
+
+# Start the bundled annotation app
+trace app
+
+# Train from selected video/annotation pairs
+trace train --model large --work-dir /my/dataset --pairs video01.mp4=video01_final.csv video02.mp4=video02.csv
+
+# Evaluate the training artifact, or evaluate on held-out video/annotation pairs
+trace eval --model-dir /my/dataset/model_YYYYMMDD_HHMMSS
+trace eval --model-dir /my/dataset/model_YYYYMMDD_HHMMSS --work-dir /my/testset --pairs video03.mp4=video03.csv
+
+# Predict on new videos and write annotation drafts
+trace predict --model-dir /my/dataset/model_YYYYMMDD_HHMMSS --input /path/to/video.mp4 --annotated-video --threshold 0.25
+
+# Run a configured end-to-end workflow
+trace pipeline configs/small.py --export csv
+```
+
+You can stay in the UI for annotation and still keep training or inference
+reproducible from the command line. The app lets you choose video/annotation
+pairs, configure model runs, and generate the matching CLI command, so a lab
+operator can annotate in the browser while a server or batch job runs the
+generated `trace train`, `trace eval`, `trace predict`, or `trace pipeline`
+command.
+
+`--pairs` is explicit: each item is `VIDEO_PATH=CSV_PATH`. A source video can
+have multiple annotation CSVs beside it, such as `video01_draft.csv`,
+`video01_final.csv`, or a model-generated `video01_predictions.csv`; each
+training or evaluation pair chooses the annotation file to use for that video.
+Relative paths are resolved against `--work-dir`, so
+`video01.mp4=video01_final.csv` means both files are inside the work directory.
+Training creates a self-contained `model_YYYYMMDD_HHMMSS/` folder under
+`--work-dir`.
+
+TRACE annotation CSVs are time-based:
+
+```csv
+labelId,timestamp,endTimestamp
+grooming,12.430,18.970
+rearing,42.100,45.650
+```
+
+Prediction creates a `predict_YYYYMMDD_HHMMSS/` folder beside the selected input
+video or input video directory, unless `--output` is provided. The CSV output
+uses the annotation format, so a reviewer can treat model predictions as draft
+annotation files. Use `--annotated-video` to render MP4 overlays with the same
+confidence threshold as the JSON/CSV outputs.
+
+## Development
+
+```bash
+# Start backend and Vite dev servers
+trace dev serve
+
+# Build the frontend and bundle it into the Python package
+trace dev build-frontend
+```
+
+The committed public website in [site/](site/) is intentionally small and
+publishable; deeper engineering notes stay under [docs/](docs/).
+
+## License
+
+Apache 2.0. See [LICENSE](LICENSE).

trace_tad-0.2.0/configs/_dataset.py

@@ -0,0 +1,98 @@
+annotation_path = "dataset.json"
+class_map = "classmap.txt"
+data_path = "."
+block_list = None
+
+window_size = 256
+
+dataset = dict(
+    train=dict(
+        type="ThumosPaddingDataset",
+        ann_file=annotation_path,
+        subset_name="training",
+        block_list=block_list,
+        class_map=class_map,
+        data_path=data_path,
+        filter_gt=False,
+        feature_stride=1,
+        sample_stride=1,
+        pipeline=[
+            dict(type="PrepareVideoInfo", format="mp4"),
+            dict(type="VideoInit", num_threads=4),
+            dict(
+                type="LoadFrames",
+                num_clips=1,
+                method="random_trunc",
+                trunc_len=window_size,
+                trunc_thresh=0.5,
+                crop_ratio=[0.9, 1.0],
+            ),
+            dict(type="VideoDecode"),
+            dict(type="VideoResize", scale=(-1, 256)),
+            dict(type="VideoRandomResizedCrop"),
+            dict(type="VideoResize", scale=(224, 224)),
+            dict(type="VideoFlip", flip_ratio=0.5),
+            dict(type="VideoFormatShape", input_format="NCTHW"),
+            dict(type="ConvertToTensor", keys=["imgs", "gt_segments", "gt_labels"]),
+            dict(type="Collect", inputs="imgs", keys=["masks", "gt_segments", "gt_labels"]),
+        ],
+    ),
+    val=dict(
+        type="ThumosSlidingDataset",
+        ann_file=annotation_path,
+        subset_name="validation",
+        block_list=block_list,
+        class_map=class_map,
+        data_path=data_path,
+        filter_gt=False,
+        feature_stride=1,
+        sample_stride=1,
+        window_size=window_size,
+        window_overlap_ratio=0.25,
+        pipeline=[
+            dict(type="PrepareVideoInfo", format="mp4"),
+            dict(type="VideoInit", num_threads=4),
+            dict(type="LoadFrames", num_clips=1, method="sliding_window"),
+            dict(type="VideoDecode"),
+            dict(type="VideoResize", scale=(-1, 224)),
+            dict(type="VideoCenterCrop", crop_size=224),
+            dict(type="VideoFormatShape", input_format="NCTHW"),
+            dict(type="ConvertToTensor", keys=["imgs", "gt_segments", "gt_labels"]),
+            dict(type="Collect", inputs="imgs", keys=["masks", "gt_segments", "gt_labels"]),
+        ],
+    ),
+    test=dict(
+        type="ThumosSlidingDataset",
+        ann_file=annotation_path,
+        subset_name="validation",
+        block_list=block_list,
+        class_map=class_map,
+        data_path=data_path,
+        filter_gt=False,
+        test_mode=True,
+        feature_stride=1,
+        sample_stride=1,
+        window_size=window_size,
+        window_overlap_ratio=0.5,
+        pipeline=[
+            dict(type="PrepareVideoInfo", format="mp4"),
+            dict(type="VideoInit", num_threads=4),
+            dict(type="LoadFrames", num_clips=1, method="sliding_window"),
+            dict(type="VideoDecode"),
+            dict(type="VideoResize", scale=(-1, 224)),
+            dict(type="VideoCenterCrop", crop_size=224),
+            dict(type="VideoFormatShape", input_format="NCTHW"),
+            dict(type="ConvertToTensor", keys=["imgs"]),
+            dict(type="Collect", inputs="imgs", keys=["masks"]),
+        ],
+    ),
+)
+
+evaluation = dict(
+    type="Precision",
+    subset="validation",
+    tiou_thresholds=[0.3, 0.4, 0.5, 0.6, 0.7],
+    ground_truth_filename=annotation_path,
+    gt_fps=30.0,
+    eval_fps=30.0,
+)

trace_tad-0.2.0/configs/_model.py

@@ -0,0 +1,52 @@
+model = dict(
+    type="TriDet",
+    projection=dict(
+        type="TriDetProj",
+        in_channels=2048,
+        out_channels=512,
+        sgp_mlp_dim=768,
+        arch=(2, 2, 5),  # layers in embed / stem / branch
+        downsample_type="max",
+        sgp_win_size=[1, 1, 1, 1, 1, 1],
+        k=5,
+        init_conv_vars=0,
+        conv_cfg=dict(kernel_size=3),
+        norm_cfg=dict(type="LN"),
+        path_pdrop=0.1,
+        use_abs_pe=True,
+        max_seq_len=768,
+        input_noise=0.0,
+    ),
+    neck=dict(
+        type="FPNIdentity",
+        in_channels=512,
+        out_channels=512,
+        num_levels=6,
+    ),
+    rpn_head=dict(
+        type="TriDetHead",
+        num_classes=3,
+        in_channels=512,
+        feat_channels=512,
+        num_convs=2,
+        cls_prior_prob=0.01,
+        prior_generator=dict(
+            type="PointGenerator",
+            strides=[1, 2, 4, 8, 16, 32],
+            regression_range=[(0, 4), (4, 8), (8, 16), (16, 32), (32, 64), (64, 10000)],
+        ),
+        loss_normalizer=100,
+        loss_normalizer_momentum=0.9,
+        center_sample="radius",
+        center_sample_radius=1.5,
+        label_smoothing=0.0,
+        boundary_kernel_size=3,
+        iou_weight_power=0.2,
+        num_bins=16,
+        loss=dict(
+            cls_loss=dict(type="ClassBalancedFocalLoss", beta=0.999),
+            reg_loss=dict(type="DIOULoss"),
+            iou_rate=dict(type="GIOULoss"),
+        ),
+    ),
+)