From 5e29947319b0d3002569ec3999f3a4e5a1ffa8fe Mon Sep 17 00:00:00 2001 From: masquare Date: Tue, 9 Dec 2025 11:25:49 +0100 Subject: [PATCH 1/5] Refactor repo structure and move package management to uv --- .gitignore | 7 +- .gitmodules | 6 - __init__.py => .python-version | 6 +- README.md | 62 +- data/{.gitignore => .gitkeep} | 0 demo/huggingface/.gitignore | 1 - notebooks/{.gitignore => .gitkeep} | 0 pyproject.toml | 75 + requirements.txt | 21 - .../create_doctor_eval_dataset.py | 0 .../get_memory_use.py | 0 hf_test.py => scripts/hf_test.py | 0 .../plot_memory_simulation.py | 0 .../plot_memory_simulation_per_length.py | 0 .../plot_memory_usage.py | 0 .../run_all_memory.sh | 0 .../run_all_memory_missing.sh | 0 src/model/llm/OpenTSLMFlamingo.py | 6 +- .../TimeSeriesFlamingoWithTrainableEncoder.py | 2 +- src/open_flamingo | 1 - test/.gitignore | 1 - uv.lock | 3910 +++++++++++++++++ 22 files changed, 4039 insertions(+), 59 deletions(-) delete mode 100644 .gitmodules rename __init__.py => .python-version (69%) rename data/{.gitignore => .gitkeep} (100%) delete mode 100644 demo/huggingface/.gitignore rename notebooks/{.gitignore => .gitkeep} (100%) create mode 100644 pyproject.toml delete mode 100644 requirements.txt rename create_doctor_eval_dataset.py => scripts/create_doctor_eval_dataset.py (100%) rename get_memory_use.py => scripts/get_memory_use.py (100%) rename hf_test.py => scripts/hf_test.py (100%) rename plot_memory_simulation.py => scripts/plot_memory_simulation.py (100%) rename plot_memory_simulation_per_length.py => scripts/plot_memory_simulation_per_length.py (100%) rename plot_memory_usage.py => scripts/plot_memory_usage.py (100%) rename run_all_memory.sh => scripts/run_all_memory.sh (100%) rename run_all_memory_missing.sh => scripts/run_all_memory_missing.sh (100%) delete mode 160000 src/open_flamingo delete mode 100644 test/.gitignore create mode 100644 uv.lock diff --git a/.gitignore b/.gitignore index b397a0b8..307f5d74 100644 --- a/.gitignore +++ b/.gitignore @@ -1,12 +1,13 @@ -venv +.venv +.vscode __pycache__ .DS_STORE -**/.DS_STORE raw_data +**/data/* +!**/data/.gitkeep *.ts *.zip -./__pycache__ upload_to_huggingface.py diff --git a/.gitmodules b/.gitmodules deleted file mode 100644 index d32896af..00000000 --- a/.gitmodules +++ /dev/null @@ -1,6 +0,0 @@ -[submodule "open_flamingo"] - path = open_flamingo - url = https://github.com/mlfoundations/open_flamingo.git -[submodule "src/open_flamingo"] - path = src/open_flamingo - url = https://github.com/mlfoundations/open_flamingo.git diff --git a/__init__.py b/.python-version similarity index 69% rename from __init__.py rename to .python-version index 7f7c8a33..d66339f8 100644 --- a/__init__.py +++ b/.python-version @@ -1,7 +1,7 @@ # -# This source file is part of the OpenTSLM open-source project -# # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md) # # SPDX-License-Identifier: MIT -# \ No newline at end of file +# + +3.12 diff --git a/README.md b/README.md index ebabd3b8..b534dfbd 100644 --- a/README.md +++ b/README.md @@ -34,13 +34,19 @@ OpenTSLM models can reason over multiple time series of any length at once, gene 1. **Clone the Repository** ```bash - git clone https://github.com/StanfordBDHG/OpenTSLM.git --recurse-submodules + git clone https://github.com/StanfordBDHG/OpenTSLM.git ``` 2. **Install Dependencies** ```bash - pip install -r requirements.txt + # install uv if not exists + which uv > /dev/null || curl -LsSf https://astral.sh/uv/install.sh | sh + + # sync dependencies + uv sync ``` + + OpenTSLM uses [uv](https://docs.astral.sh/uv/) for package management.This will install all dependencies with Python 3.12 as specified in `.python-version`. Follow the [official installation guide](https://docs.astral.sh/uv/getting-started/installation/) for other installation methods. ## LLM Setup @@ -144,11 +150,11 @@ Each script: ```bash # Run any of the demo scripts -python demo/huggingface/01_test_hf_tsqa.py -python demo/huggingface/02_test_hf_m4.py -python demo/huggingface/03_test_hf_har_cot.py -python demo/huggingface/04_test_hf_sleep_cot.py -python demo/huggingface/05_test_hf_ecg_qa_cot.py +uv run demo/huggingface/01_test_hf_tsqa.py +uv run demo/huggingface/02_test_hf_m4.py +uv run demo/huggingface/03_test_hf_har_cot.py +uv run demo/huggingface/04_test_hf_sleep_cot.py +uv run demo/huggingface/05_test_hf_ecg_qa_cot.py ``` **Customizing the model:** @@ -192,30 +198,30 @@ OpenTSLM uses curriculum learning with progressive training stages: ```bash # Run full curriculum with OpenTSLMFlamingo -python curriculum_learning.py --model OpenTSLMSP +uv run curriculum_learning.py --model OpenTSLMSP # Run full curriculum with OpenTSLMSP -python curriculum_learning.py --model OpenTSLMFlamingo +uv run curriculum_learning.py --model OpenTSLMFlamingo # Run specific stages -python curriculum_learning.py --model OpenTSLMFlamingo --stages stage1_mcq -python curriculum_learning.py --model OpenTSLMFlamingo --stages stage2_captioning -python curriculum_learning.py --model OpenTSLMFlamingo --stages stage3_cot -python curriculum_learning.py --model OpenTSLMFlamingo --stages stage4_sleep_cot -python curriculum_learning.py --model OpenTSLMFlamingo --stages stage5_ecg_cot +uv run curriculum_learning.py --model OpenTSLMFlamingo --stages stage1_mcq +uv run curriculum_learning.py --model OpenTSLMFlamingo --stages stage2_captioning +uv run curriculum_learning.py --model OpenTSLMFlamingo --stages stage3_cot +uv run curriculum_learning.py --model OpenTSLMFlamingo --stages stage4_sleep_cot +uv run curriculum_learning.py --model OpenTSLMFlamingo --stages stage5_ecg_cot # Run multiple stages -python curriculum_learning.py --model OpenTSLMFlamingo --stages stage1_mcq stage2_captioning stage3_cot +uv run curriculum_learning.py --model OpenTSLMFlamingo --stages stage1_mcq stage2_captioning stage3_cot # Specify device -python curriculum_learning.py --model OpenTSLMFlamingo --device cuda +uv run curriculum_learning.py --model OpenTSLMFlamingo --device cuda # Use different models -python curriculum_learning.py --model OpenTSLMFlamingo --llm_id meta-llama/Llama-3.2-1B -python curriculum_learning.py --model OpenTSLMFlamingo --llm_id google/gemma-3-270m +uv run curriculum_learning.py --model OpenTSLMFlamingo --llm_id meta-llama/Llama-3.2-1B +uv run curriculum_learning.py --model OpenTSLMFlamingo --llm_id google/gemma-3-270m # Run only evaluation -python curriculum_learning.py --model OpenTSLMFlamingo --eval_only +uv run curriculum_learning.py --model OpenTSLMFlamingo --eval_only ``` ### Command Line Arguments @@ -229,6 +235,24 @@ python curriculum_learning.py --model OpenTSLMFlamingo --eval_only - `--gradient_checkpointing`: Enable gradient checkpointing for memory efficiency - `--verbose`: Enable verbose logging +### Helper Scripts + +Helper scripts for analysis, testing, and batch processing are available in the `scripts/` directory: + +**Shell Scripts:** +- **`run_all_memory.sh`** - Run comprehensive memory usage analysis across all stages +- **`run_all_memory_missing.sh`** - Run memory analysis for missing stages only + +**Python Scripts:** +- **`create_doctor_eval_dataset.py`** - Create evaluation dataset for doctor assessments +- **`get_memory_use.py`** - Analyze and report memory usage across stages +- **`plot_memory_usage.py`** - Visualize memory usage patterns +- **`plot_memory_simulation.py`** - Simulate and plot memory requirements +- **`plot_memory_simulation_per_length.py`** - Analyze memory usage by sequence length +- **`hf_test.py`** - Test HuggingFace model loading and inference + +These scripts can be customized by editing the parameters directly or by passing command-line arguments. + ### Repository Naming Convention - Repository IDs ending with `-sp` will load and return `OpenTSLMSP` models diff --git a/data/.gitignore b/data/.gitkeep similarity index 100% rename from data/.gitignore rename to data/.gitkeep diff --git a/demo/huggingface/.gitignore b/demo/huggingface/.gitignore deleted file mode 100644 index 6320cd24..00000000 --- a/demo/huggingface/.gitignore +++ /dev/null @@ -1 +0,0 @@ -data \ No newline at end of file diff --git a/notebooks/.gitignore b/notebooks/.gitkeep similarity index 100% rename from notebooks/.gitignore rename to notebooks/.gitkeep diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..ebdaab54 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,75 @@ +# +# SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md) +# +# SPDX-License-Identifier: MIT +# + +[project] +name = "opentslm" +version = "0.1.0" +description = "OpenTSLM: Open Time Series Language Model - Curriculum Learning for Multimodal Time Series Understanding with Large Language Models" +readme = "README.md" +requires-python = ">=3.12" +license = {text = "MIT"} +authors = [ + {name = "Stanford Biodesign Digital Health Group"} +] +keywords = [ + "time-series", + "large-language-models", + "curriculum-learning", + "multimodal", + "healthcare" +] +classifiers = [ + "Development Status :: 3 - Alpha", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.12", + "Topic :: Scientific/Engineering :: Artificial Intelligence", + "Topic :: Scientific/Engineering :: Medical Science Apps.", +] + +dependencies = [ + "numpy>=1.21", + "pandas>=1.3", + "torch>=2.0", + "tqdm>=4.62", + "matplotlib>=3.3", + "scikit-learn>=1.0", + "transformers>=4.25", + "huggingface-hub>=0.16", + "datasets>=2.0", + "peft>=0.4", + "requests>=2.28", + "einops>=0.6", + "wfdb>=4.0", + "open-flamingo>=0.0.2", +] + +[tool.uv] +default-groups = ["dev"] + +[dependency-groups] +dev = [ + "ruff>=0.14.0", +] + +eval = [ + "openai>=1.0", +] + +notebook = [ + "jupyter>=1.0", + "ipython>=8.0", +] + +[project.urls] +Repository = "https://github.com/StanfordBDHG/EmbedHealth" +"Bug Tracker" = "https://github.com/StanfordBDHG/EmbedHealth/issues" + +[tool.ruff] +line-length = 120 +target-version = "py312" diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 52540d0d..00000000 --- a/requirements.txt +++ /dev/null @@ -1,21 +0,0 @@ -numpy -pandas -torch -joblib -argparse -tqdm -matplotlib -scikit-learn -torchinfo -transformers -chronos-forecasting -huggingface-hub -datasets -peft -requests -open-clip-torch -einops -einops-exts -pyvim -openai -wfdb \ No newline at end of file diff --git a/create_doctor_eval_dataset.py b/scripts/create_doctor_eval_dataset.py similarity index 100% rename from create_doctor_eval_dataset.py rename to scripts/create_doctor_eval_dataset.py diff --git a/get_memory_use.py b/scripts/get_memory_use.py similarity index 100% rename from get_memory_use.py rename to scripts/get_memory_use.py diff --git a/hf_test.py b/scripts/hf_test.py similarity index 100% rename from hf_test.py rename to scripts/hf_test.py diff --git a/plot_memory_simulation.py b/scripts/plot_memory_simulation.py similarity index 100% rename from plot_memory_simulation.py rename to scripts/plot_memory_simulation.py diff --git a/plot_memory_simulation_per_length.py b/scripts/plot_memory_simulation_per_length.py similarity index 100% rename from plot_memory_simulation_per_length.py rename to scripts/plot_memory_simulation_per_length.py diff --git a/plot_memory_usage.py b/scripts/plot_memory_usage.py similarity index 100% rename from plot_memory_usage.py rename to scripts/plot_memory_usage.py diff --git a/run_all_memory.sh b/scripts/run_all_memory.sh similarity index 100% rename from run_all_memory.sh rename to scripts/run_all_memory.sh diff --git a/run_all_memory_missing.sh b/scripts/run_all_memory_missing.sh similarity index 100% rename from run_all_memory_missing.sh rename to scripts/run_all_memory_missing.sh diff --git a/src/model/llm/OpenTSLMFlamingo.py b/src/model/llm/OpenTSLMFlamingo.py index 58517c77..62a11772 100644 --- a/src/model/llm/OpenTSLMFlamingo.py +++ b/src/model/llm/OpenTSLMFlamingo.py @@ -11,8 +11,8 @@ from model.llm.TimeSeriesFlamingoWithTrainableEncoder import ( TimeSeriesFlamingoWithTrainableEncoder, ) -from open_flamingo.open_flamingo.src.flamingo_lm import FlamingoLMMixin -from open_flamingo.open_flamingo.src.utils import extend_instance +from open_flamingo.src.flamingo_lm import FlamingoLMMixin +from open_flamingo.src.utils import extend_instance import torch import torch._dynamo from typing import List, Dict, Tuple @@ -26,7 +26,7 @@ ) # Monkey-patch FlamingoLayer to add attention_type property for compatibility with newer transformers -from open_flamingo.open_flamingo.src.flamingo_lm import FlamingoLayer +from open_flamingo.src.flamingo_lm import FlamingoLayer def _attention_type_property(self): diff --git a/src/model/llm/TimeSeriesFlamingoWithTrainableEncoder.py b/src/model/llm/TimeSeriesFlamingoWithTrainableEncoder.py index 9bebf84a..322157d4 100644 --- a/src/model/llm/TimeSeriesFlamingoWithTrainableEncoder.py +++ b/src/model/llm/TimeSeriesFlamingoWithTrainableEncoder.py @@ -8,7 +8,7 @@ import torch from torch import nn -from open_flamingo.open_flamingo.src.flamingo import Flamingo +from open_flamingo.src.flamingo import Flamingo from einops import rearrange diff --git a/src/open_flamingo b/src/open_flamingo deleted file mode 160000 index 914076ee..00000000 --- a/src/open_flamingo +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 914076ee07d0235943f1556e9aaf2fb974337f0e diff --git a/test/.gitignore b/test/.gitignore deleted file mode 100644 index 6320cd24..00000000 --- a/test/.gitignore +++ /dev/null @@ -1 +0,0 @@ -data \ 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+0100 Subject: [PATCH 2/5] refactor imports to opentslm package, add pypi publish pipeline --- .github/workflows/publish.yml | 31 ++++ .gitignore | 2 + README.md | 150 +++++++++--------- curriculum_learning.py | 27 ++-- demo/huggingface/01_test_hf_tsqa.py | 14 +- demo/huggingface/02_test_hf_m4.py | 14 +- demo/huggingface/03_test_hf_har_cot.py | 14 +- demo/huggingface/04_test_hf_sleep_cot.py | 14 +- demo/huggingface/05_test_hf_ecg_qa_cot.py | 14 +- evaluation/baseline/common_evaluator.py | 13 +- evaluation/baseline/common_evaluator_plot.py | 12 +- evaluation/baseline/evaluate_all.py | 6 +- evaluation/baseline/evaluate_ecg_qa.py | 2 +- evaluation/baseline/evaluate_ecg_qa_plot.py | 2 +- evaluation/baseline/evaluate_har.py | 2 +- evaluation/baseline/evaluate_har_plot.py | 4 +- evaluation/baseline/evaluate_pamap.py | 2 +- evaluation/baseline/evaluate_sleep_cot.py | 2 +- evaluation/baseline/evaluate_sleep_plot.py | 2 +- evaluation/baseline/evaluate_tsqa.py | 2 +- evaluation/baseline/evaluate_tsqa_plot.py | 2 +- .../baseline/gruver_llmtime_tokenizer.py | 1 - .../baseline/parse_predictions_baseline.py | 7 - .../parse_predictions_sleep_baseline.py | 11 -- .../parse_predictions_tsqa_baseline.py | 6 - .../create_doctor_eval_dataset.py | 11 +- evaluation/memory/get_memory_use.py | 29 ++-- .../opentslm/baseline_parse_predictions.py | 6 +- .../ecg_qa_cot/parse_ecg_qa_cot_data.py | 5 +- .../opentslm/get_pamap_cot_predictions.py | 19 +-- evaluation/opentslm/parse_predictions.py | 6 +- .../sleep/baseline_parse_sleep_cot_data.py | 7 +- .../opentslm/sleep/get_sleep_predictions.py | 20 +-- .../opentslm/sleep/parse_sleep_cot_data.py | 5 +- pyproject.toml | 63 +++++--- requirements.txt | 15 ++ scripts/create_doctor_eval_dataset.py | 10 +- scripts/get_memory_use.py | 25 +-- scripts/hf_test.py | 3 +- src/opentslm/__init__.py | 11 ++ src/{ => opentslm}/data.py | 2 +- src/{ => opentslm}/logger.py | 0 src/{ => opentslm}/model/__init__.py | 0 .../model/encoder/CNNTokenizer.py | 4 +- .../model/encoder/TimeSeriesEncoderBase.py | 2 +- .../model/encoder/TransformerCNNEncoder.py | 4 +- .../model/encoder/TransformerMLPEncoder.py | 4 +- src/{ => opentslm}/model/encoder/__init__.py | 0 src/{ => opentslm}/model/llm/OpenTSLM.py | 2 +- .../model/llm/OpenTSLMFlamingo.py | 14 +- src/{ => opentslm}/model/llm/OpenTSLMSP.py | 6 +- .../TimeSeriesFlamingoWithTrainableEncoder.py | 2 +- src/{ => opentslm}/model/llm/TimeSeriesLLM.py | 11 +- src/{ => opentslm}/model/llm/__init__.py | 0 .../model/projector/LinearProjector.py | 0 .../model/projector/MLPProjector.py | 0 .../model/projector/__init__.py | 0 src/{ => opentslm}/model_config.py | 0 src/opentslm/prompt/__init__.py | 21 +++ src/{ => opentslm}/prompt/full_prompt.py | 4 +- src/{ => opentslm}/prompt/prompt.py | 0 .../prompt/prompt_with_answer.py | 4 +- src/{ => opentslm}/prompt/text_prompt.py | 0 .../prompt/text_time_series_prompt.py | 0 .../time_series_datasets/QADataset.py | 7 +- .../time_series_datasets/TSQADataset.py | 6 +- .../time_series_datasets/__init__.py | 0 .../time_series_datasets/constants.py | 0 .../ecg_qa/ECGQACoTQADataset.py | 18 +-- .../ecg_qa/ECGQADataset.py | 10 +- .../time_series_datasets/ecg_qa/README.md | 2 +- .../time_series_datasets/ecg_qa/__init__.py | 2 +- .../ecg_qa/dataset_distribution.png | Bin .../ecg_qa/ecg_example_real.png | Bin .../ecg_qa/ecgqa_cot_loader.py | 20 +-- .../ecg_qa/ecgqa_loader.py | 4 +- .../ecg_qa/example_prompt.md | 0 .../ecg_qa/plot_example.py | 6 +- .../har_cot/HARAccQADataset.py | 8 +- .../har_cot/HARCoTQADataset.py | 10 +- .../time_series_datasets/har_cot/__init__.py | 0 .../har_cot/har_cot_loader.py | 6 +- .../time_series_datasets/m4/M4QADataset.py | 6 +- .../time_series_datasets/m4/__init__.py | 0 .../time_series_datasets/m4/m4_loader.py | 2 +- .../monash/MonashDataset.py | 2 +- .../monash/MonashSPO2QADataset.py | 8 +- .../time_series_datasets/monash/__init__.py | 0 .../monash/monash_utils.py | 0 .../pamap2/BalancedBatchSampler.py | 0 .../pamap2/PAMAP2AccQADataset.py | 10 +- .../pamap2/PAMAP2CoTQADataset.py | 12 +- .../pamap2/PAMAP2Dataset.py | 2 +- .../time_series_datasets/pamap2/__init__.py | 0 .../pamap2/pamap2_cot_loader.py | 4 +- .../pamap2/pamap2_loader.py | 2 +- .../simulation/SimulationQADataset.py | 4 +- .../sleep/SleepEDFCoTQADataset.py | 8 +- .../sleep/SleepEDFQADataset.py | 11 +- .../time_series_datasets/sleep/__init__.py | 0 .../sleep/sleepedf_cot_loader.py | 2 +- .../time_series_datasets/ucr/__init__.py | 0 .../time_series_datasets/ucr/ucr_loader.py | 0 .../time_series_datasets/util.py | 2 +- src/prompt/__init__.py | 13 -- src/time_series_datasets/tsqa.py | 27 ---- test/ecg_qa_cot_test.py | 18 +-- test/ecg_qa_test.py | 9 +- test/eval_EmbedHealthFlamingo.py | 12 +- test/har_cot_test.py | 13 +- test/m4_loader_test.py | 7 +- test/pamap_cot_loader_test.py | 17 +- test/sleepedf_cot_loader_test.py | 6 +- test/smoke_test.py | 11 ++ test/test_curriculum_trainer.py | 2 - test/test_inference.py | 18 +-- test/test_medgemma_support.py | 7 +- test/test_train_EmbedHealthFlamingo.py | 14 +- test/test_train_EmbedHealthSP.py | 14 +- uv.lock | 37 ++++- 120 files changed, 486 insertions(+), 584 deletions(-) create mode 100644 .github/workflows/publish.yml create mode 100644 requirements.txt create mode 100644 src/opentslm/__init__.py rename src/{ => opentslm}/data.py (99%) rename src/{ => opentslm}/logger.py (100%) rename src/{ => opentslm}/model/__init__.py (100%) rename src/{ => opentslm}/model/encoder/CNNTokenizer.py (94%) rename src/{ => opentslm}/model/encoder/TimeSeriesEncoderBase.py (92%) rename src/{ => opentslm}/model/encoder/TransformerCNNEncoder.py (95%) rename src/{ => opentslm}/model/encoder/TransformerMLPEncoder.py (95%) rename src/{ => opentslm}/model/encoder/__init__.py (100%) rename src/{ => opentslm}/model/llm/OpenTSLM.py (99%) rename src/{ => opentslm}/model/llm/OpenTSLMFlamingo.py (97%) rename src/{ => opentslm}/model/llm/OpenTSLMSP.py (99%) rename src/{ => opentslm}/model/llm/TimeSeriesFlamingoWithTrainableEncoder.py (98%) rename src/{ => opentslm}/model/llm/TimeSeriesLLM.py (74%) rename src/{ => opentslm}/model/llm/__init__.py (100%) rename src/{ => opentslm}/model/projector/LinearProjector.py (100%) rename src/{ => opentslm}/model/projector/MLPProjector.py (100%) rename src/{ => opentslm}/model/projector/__init__.py (100%) rename src/{ => opentslm}/model_config.py (100%) create mode 100644 src/opentslm/prompt/__init__.py rename src/{ => opentslm}/prompt/full_prompt.py (91%) rename src/{ => opentslm}/prompt/prompt.py (100%) rename src/{ => opentslm}/prompt/prompt_with_answer.py (92%) rename src/{ => opentslm}/prompt/text_prompt.py (100%) rename src/{ => opentslm}/prompt/text_time_series_prompt.py (100%) rename src/{ => opentslm}/time_series_datasets/QADataset.py (96%) rename src/{ => opentslm}/time_series_datasets/TSQADataset.py (94%) rename src/{ => opentslm}/time_series_datasets/__init__.py (100%) rename src/{ => opentslm}/time_series_datasets/constants.py (100%) rename src/{ => opentslm}/time_series_datasets/ecg_qa/ECGQACoTQADataset.py (97%) rename src/{ => opentslm}/time_series_datasets/ecg_qa/ECGQADataset.py (97%) rename src/{ => opentslm}/time_series_datasets/ecg_qa/README.md (99%) rename src/{ => opentslm}/time_series_datasets/ecg_qa/__init__.py (95%) rename src/{ => opentslm}/time_series_datasets/ecg_qa/dataset_distribution.png (100%) rename src/{ => opentslm}/time_series_datasets/ecg_qa/ecg_example_real.png (100%) rename src/{ => opentslm}/time_series_datasets/ecg_qa/ecgqa_cot_loader.py (95%) rename src/{ => opentslm}/time_series_datasets/ecg_qa/ecgqa_loader.py (98%) rename src/{ => opentslm}/time_series_datasets/ecg_qa/example_prompt.md (100%) rename src/{ => opentslm}/time_series_datasets/ecg_qa/plot_example.py (97%) rename src/{ => opentslm}/time_series_datasets/har_cot/HARAccQADataset.py (93%) rename src/{ => opentslm}/time_series_datasets/har_cot/HARCoTQADataset.py (95%) rename src/{ => opentslm}/time_series_datasets/har_cot/__init__.py (100%) rename src/{ => opentslm}/time_series_datasets/har_cot/har_cot_loader.py (97%) rename src/{ => opentslm}/time_series_datasets/m4/M4QADataset.py (95%) rename src/{ => opentslm}/time_series_datasets/m4/__init__.py (100%) rename src/{ => opentslm}/time_series_datasets/m4/m4_loader.py (99%) rename src/{ => opentslm}/time_series_datasets/monash/MonashDataset.py (97%) rename src/{ => opentslm}/time_series_datasets/monash/MonashSPO2QADataset.py (90%) rename src/{ => opentslm}/time_series_datasets/monash/__init__.py (100%) rename src/{ => opentslm}/time_series_datasets/monash/monash_utils.py (100%) rename src/{ => opentslm}/time_series_datasets/pamap2/BalancedBatchSampler.py (100%) rename src/{ => opentslm}/time_series_datasets/pamap2/PAMAP2AccQADataset.py (91%) rename src/{ => opentslm}/time_series_datasets/pamap2/PAMAP2CoTQADataset.py (94%) rename src/{ => opentslm}/time_series_datasets/pamap2/PAMAP2Dataset.py (98%) rename src/{ => opentslm}/time_series_datasets/pamap2/__init__.py (100%) rename src/{ => opentslm}/time_series_datasets/pamap2/pamap2_cot_loader.py (98%) rename src/{ => opentslm}/time_series_datasets/pamap2/pamap2_loader.py (97%) rename src/{ => opentslm}/time_series_datasets/simulation/SimulationQADataset.py (97%) rename src/{ => opentslm}/time_series_datasets/sleep/SleepEDFCoTQADataset.py (91%) rename src/{ => opentslm}/time_series_datasets/sleep/SleepEDFQADataset.py (93%) rename src/{ => opentslm}/time_series_datasets/sleep/__init__.py (100%) rename src/{ => opentslm}/time_series_datasets/sleep/sleepedf_cot_loader.py (98%) rename src/{ => opentslm}/time_series_datasets/ucr/__init__.py (100%) rename src/{ => opentslm}/time_series_datasets/ucr/ucr_loader.py (100%) rename src/{ => opentslm}/time_series_datasets/util.py (97%) delete mode 100644 src/prompt/__init__.py delete mode 100644 src/time_series_datasets/tsqa.py create mode 100644 test/smoke_test.py diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 00000000..bcdb730c --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,31 @@ +name: "Publish to PyPI" + +on: + workflow_dispatch: + # push: + # tags: + # # Publish on any tag starting with a `v`, e.g., v0.1.0 + # - v* + +jobs: + run: + runs-on: ubuntu-latest + environment: + name: pypi + permissions: + id-token: write + contents: read + steps: + - name: Checkout + uses: actions/checkout@v5 + - name: Install uv + uses: astral-sh/setup-uv@v7 + - name: Build + run: uv build + # Check that basic features work and we didn't miss to include crucial files + - name: Smoke test (wheel) + run: uv run --isolated --no-project --with dist/*.whl tests/smoke_test.py + - name: Smoke test (source distribution) + run: uv run --isolated --no-project --with dist/*.tar.gz tests/smoke_test.py + - name: Publish + run: uv publish \ No newline at end of file diff --git a/.gitignore b/.gitignore index 307f5d74..03f067e4 100644 --- a/.gitignore +++ b/.gitignore @@ -11,3 +11,5 @@ raw_data *.ts *.zip upload_to_huggingface.py + +dist/ diff --git a/README.md b/README.md index b534dfbd..219da13f 100644 --- a/README.md +++ b/README.md @@ -1,12 +1,12 @@ # OpenTSLM: Time-Series Language Models for Reasoning over Multivariate Medical Text- and Time-Series Data +[![PyPI - Version](https://img.shields.io/pypi/v/opentslm)](https://pypi.org/project/opentslm) [![DOI](https://img.shields.io/badge/DOI-10.13140/RG.2.2.14827.60963-blue.svg)](https://doi.org/10.13140/RG.2.2.14827.60963) [![Static Analysis](https://github.com/StanfordBDHG/OpenTSLM/actions/workflows/static-analysis.yml/badge.svg)](https://github.com/StanfordBDHG/OpenTSLM/actions/workflows/static-analysis.yml) @@ -14,7 +14,7 @@ SPDX-License-Identifier: MIT Large Language Models (LLMs) have emerged as powerful tools for interpreting multimodal data (e.g., images, audio, text), often surpassing specialized models. In medicine, they hold particular promise for synthesizing large volumes of clinical information into actionable insights and patient-facing digital health applications. Yet, a major limitation remains their inability to handle time series data. To overcome this gap, we present OpenTSLM, a family of Time Series Language Models (TSLMs) created by integrating time series as a native modality to pretrained Large Language Models, enabling natural-language prompting and reasoning over multiple time series of any length [...] **[🔗 Read the full paper](https://doi.org/10.13140/RG.2.2.14827.60963)**

- Schematic Overview + Schematic Overview

@@ -23,30 +23,17 @@ Large Language Models (LLMs) have emerged as powerful tools for interpreting mul OpenTSLM models can reason over multiple time series of any length at once, generating findings, captions, and rationales in natural language. We tested these models across a wide range of tasks spanning Human Activity Recognition (HAR) from 3-axis acceleration data, sleep staging from EEG readings, 12-lead ECG question answering, and time series captioning. Some examples are shown below, more are available in the paper.

- ECG Rationale - HAR Rationale - M4 Caption + ECG Rationale + HAR Rationale + M4 Caption

## Installation -1. **Clone the Repository** - - ```bash - git clone https://github.com/StanfordBDHG/OpenTSLM.git - ``` - -2. **Install Dependencies** - ```bash - # install uv if not exists - which uv > /dev/null || curl -LsSf https://astral.sh/uv/install.sh | sh - - # sync dependencies - uv sync - ``` - - OpenTSLM uses [uv](https://docs.astral.sh/uv/) for package management.This will install all dependencies with Python 3.12 as specified in `.python-version`. Follow the [official installation guide](https://docs.astral.sh/uv/getting-started/installation/) for other installation methods. +```bash +pip install opentslm +``` ## LLM Setup @@ -54,19 +41,19 @@ OpenTSLM models can reason over multiple time series of any length at once, gene OpenTSLM is designed to work with Llama and Gemma models, with Llama 3.2 1B as the default. These models are stored in Hugging Face repositories which may require access permissions. Follow these steps to gain access and download: 1. **Request Access (for Llama models)** - Visit the Llama model repository (e.g., https://huggingface.co/meta-llama/Llama-3.2-1B) or Gemma models repository (https://huggingface.co/google/gemma-3-270m) and request access from Meta. + Visit the Llama model repository (e.g., https://huggingface.co/meta-llama/Llama-3.2-1B) or Gemma models repository (https://huggingface.co/google/gemma-3-270m) and request access from Meta. 2. **Authenticate with Hugging Face** - Log in to your Hugging Face account and configure the CLI: + Log in to your Hugging Face account and configure the CLI: - ```bash - huggingface-cli login - ``` + ```bash + huggingface-cli login + ``` 3. **Create an API Token** - - Go to your Hugging Face settings: https://huggingface.co/settings/tokens - - Generate a new token with `read` scope. - - Copy the token for CLI login. + - Go to your Hugging Face settings: https://huggingface.co/settings/tokens + - Generate a new token with `read` scope. + - Copy the token for CLI login. ### Supported Models @@ -93,15 +80,11 @@ A factory class called `OpenTSLM` for easily loading pre-trained models from Hug There are [demo scripts](demo/huggingface/) available which use the following minimal code. If you want to create your own applications, create a new file in **this repo folder** and use the following code as start: ```python -import sys -import os -sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "src"))) - -from model.llm.OpenTSLM import OpenTSLM -from time_series_datasets.TSQADataset import TSQADataset -from time_series_datasets.util import extend_time_series_to_match_patch_size_and_aggregate +from opentslm import OpenTSLM +from opentslm.time_series_datasets.TSQADataset import TSQADataset +from opentslm.time_series_datasets.util import extend_time_series_to_match_patch_size_and_aggregate from torch.utils.data import DataLoader -from model_config import PATCH_SIZE +from opentslm.model_config import PATCH_SIZE REPO_ID = "OpenTSLM/llama-3.2-1b-tsqa-sp" @@ -110,22 +93,41 @@ model = OpenTSLM.load_pretrained(REPO_ID, device="cuda" if torch.cuda.is_availab test_dataset = TSQADataset("test", EOS_TOKEN=model.get_eos_token()) test_loader = DataLoader( - test_dataset, - shuffle=False, - batch_size=1, - collate_fn=lambda batch: extend_time_series_to_match_patch_size_and_aggregate( - batch, patch_size=PATCH_SIZE - ), + test_dataset, + shuffle=False, + batch_size=1, + collate_fn=lambda batch: extend_time_series_to_match_patch_size_and_aggregate( + batch, patch_size=PATCH_SIZE + ), ) for i, batch in enumerate(test_loader): - predictions = model.generate(batch, max_new_tokens=200) - for sample, pred in zip(batch, predictions): - print("Question:", sample.get("pre_prompt", "N/A")) - print("Answer:", sample.get("answer", "N/A")) - print("Output:", pred) - if i >= 4: - break + predictions = model.generate(batch, max_new_tokens=200) + for sample, pred in zip(batch, predictions): + print("Question:", sample.get("pre_prompt", "N/A")) + print("Answer:", sample.get("answer", "N/A")) + print("Output:", pred) + if i >= 4: + break +``` + +## Building and finetuning your own models + +To run the demos and use finetuning scripts **clone the repository** and set up all dependencies. We recommend using [uv](https://docs.astral.sh/uv/) to set up the environment, but you can also use pip: + +```bash +git clone https://github.com/StanfordBDHG/OpenTSLM.git + + +# uv environment management (recommended). Installs uv if it does not exist and creates the virtual environment +command uv > /dev/null || curl -LsSf https://astral.sh/uv/install.sh | sh +uv sync --all-groups +source .venv/bin/activate + + +# or alternatively install via pip: +pip install -r requirements.txt + ``` ### HuggingFace Demo Scripts @@ -150,11 +152,11 @@ Each script: ```bash # Run any of the demo scripts -uv run demo/huggingface/01_test_hf_tsqa.py -uv run demo/huggingface/02_test_hf_m4.py -uv run demo/huggingface/03_test_hf_har_cot.py -uv run demo/huggingface/04_test_hf_sleep_cot.py -uv run demo/huggingface/05_test_hf_ecg_qa_cot.py +python demo/huggingface/01_test_hf_tsqa.py +python demo/huggingface/02_test_hf_m4.py +python demo/huggingface/03_test_hf_har_cot.py +python demo/huggingface/04_test_hf_sleep_cot.py +python demo/huggingface/05_test_hf_ecg_qa_cot.py ``` **Customizing the model:** @@ -172,9 +174,9 @@ REPO_ID = "OpenTSLM/llama-3.2-1b-tsqa-flamingo" # Flamingo model All pretrained models are available under the `OpenTSLM` organization on HuggingFace Hub. Model names follow the pattern: - `OpenTSLM/{base_model}-{dataset}-{model_type}` - - `base_model`: `llama-3.2-1b`, `llama-3.2-3b`, `gemma-3-1b-pt`, `gemma-3-270m` - - `dataset`: `tsqa`, `m4`, `har`, `sleep`, `ecg` - - `model_type`: `sp` (Soft Prompt) or `flamingo` (Flamingo) + - `base_model`: `llama-3.2-1b`, `llama-3.2-3b`, `gemma-3-1b-pt`, `gemma-3-270m` + - `dataset`: `tsqa`, `m4`, `har`, `sleep`, `ecg` + - `model_type`: `sp` (Soft Prompt) or `flamingo` (Flamingo) Example: `OpenTSLM/llama-3.2-1b-ecg-flamingo` @@ -198,30 +200,30 @@ OpenTSLM uses curriculum learning with progressive training stages: ```bash # Run full curriculum with OpenTSLMFlamingo -uv run curriculum_learning.py --model OpenTSLMSP +python curriculum_learning.py --model OpenTSLMSP # Run full curriculum with OpenTSLMSP -uv run curriculum_learning.py --model OpenTSLMFlamingo +python curriculum_learning.py --model OpenTSLMFlamingo # Run specific stages -uv run curriculum_learning.py --model OpenTSLMFlamingo --stages stage1_mcq -uv run curriculum_learning.py --model OpenTSLMFlamingo --stages stage2_captioning -uv run curriculum_learning.py --model OpenTSLMFlamingo --stages stage3_cot -uv run curriculum_learning.py --model OpenTSLMFlamingo --stages stage4_sleep_cot -uv run curriculum_learning.py --model OpenTSLMFlamingo --stages stage5_ecg_cot +python curriculum_learning.py --model OpenTSLMFlamingo --stages stage1_mcq +python curriculum_learning.py --model OpenTSLMFlamingo --stages stage2_captioning +python curriculum_learning.py --model OpenTSLMFlamingo --stages stage3_cot +python curriculum_learning.py --model OpenTSLMFlamingo --stages stage4_sleep_cot +python curriculum_learning.py --model OpenTSLMFlamingo --stages stage5_ecg_cot # Run multiple stages -uv run curriculum_learning.py --model OpenTSLMFlamingo --stages stage1_mcq stage2_captioning stage3_cot +python curriculum_learning.py --model OpenTSLMFlamingo --stages stage1_mcq stage2_captioning stage3_cot # Specify device -uv run curriculum_learning.py --model OpenTSLMFlamingo --device cuda +python curriculum_learning.py --model OpenTSLMFlamingo --device cuda # Use different models -uv run curriculum_learning.py --model OpenTSLMFlamingo --llm_id meta-llama/Llama-3.2-1B -uv run curriculum_learning.py --model OpenTSLMFlamingo --llm_id google/gemma-3-270m +python curriculum_learning.py --model OpenTSLMFlamingo --llm_id meta-llama/Llama-3.2-1B +python curriculum_learning.py --model OpenTSLMFlamingo --llm_id google/gemma-3-270m # Run only evaluation -uv run curriculum_learning.py --model OpenTSLMFlamingo --eval_only +python curriculum_learning.py --model OpenTSLMFlamingo --eval_only ``` ### Command Line Arguments @@ -360,8 +362,8 @@ For researchers and project partners interested in collaboration opportunities, This project is licensed under the MIT License.
- Stanford Biodesign               - ETH Centre for Digital Health Interventions - ETH Agentic Systems Lab + Stanford Biodesign               + ETH Centre for Digital Health Interventions + ETH Agentic Systems Lab
diff --git a/curriculum_learning.py b/curriculum_learning.py index 1269414e..1315e1f2 100644 --- a/curriculum_learning.py +++ b/curriculum_learning.py @@ -6,21 +6,18 @@ # SPDX-License-Identifier: MIT # -import sys import os -sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "src"))) - import json import os as _os import argparse from typing import List, Optional, Dict, Any, Callable -from time_series_datasets.TSQADataset import TSQADataset -from time_series_datasets.m4.M4QADataset import M4QADataset -from time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset -from time_series_datasets.har_cot.HARCoTQADataset import HARCoTQADataset -from time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset -from time_series_datasets.util import ( +from opentslm.time_series_datasets.TSQADataset import TSQADataset +from opentslm.time_series_datasets.m4.M4QADataset import M4QADataset +from opentslm.time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset +from opentslm.time_series_datasets.har_cot.HARCoTQADataset import HARCoTQADataset +from opentslm.time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset +from opentslm.time_series_datasets.util import ( extend_time_series_to_match_patch_size_and_aggregate, ) import torch @@ -42,14 +39,14 @@ from tqdm.auto import tqdm from transformers import get_linear_schedule_with_warmup -from model.encoder.TransformerCNNEncoder import TransformerCNNEncoder -from model.llm.OpenTSLMFlamingo import OpenTSLMFlamingo -from model.llm.OpenTSLMSP import OpenTSLMSP -from model.projector.MLPProjector import MLPProjector +from opentslm.model.encoder.TransformerCNNEncoder import TransformerCNNEncoder +from opentslm.model.llm.OpenTSLMFlamingo import OpenTSLMFlamingo +from opentslm.model.llm.OpenTSLMSP import OpenTSLMSP +from opentslm.model.projector.MLPProjector import MLPProjector import datetime -from logger import get_logger, set_global_verbose +from opentslm.logger import get_logger, set_global_verbose -from model_config import ( +from opentslm.model_config import ( BATCH_SIZE, EARLY_STOP_PAT, GRAD_CLIP_NORM, diff --git a/demo/huggingface/01_test_hf_tsqa.py b/demo/huggingface/01_test_hf_tsqa.py index 23fcfeb8..fb1ebecc 100755 --- a/demo/huggingface/01_test_hf_tsqa.py +++ b/demo/huggingface/01_test_hf_tsqa.py @@ -15,17 +15,11 @@ 4. Prints model outputs """ -import sys -import os - -# Add src to path -sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../../src"))) - -from model.llm.OpenTSLM import OpenTSLM -from time_series_datasets.TSQADataset import TSQADataset -from time_series_datasets.util import extend_time_series_to_match_patch_size_and_aggregate +from opentslm.model.llm.OpenTSLM import OpenTSLM +from opentslm.time_series_datasets.TSQADataset import TSQADataset +from opentslm.time_series_datasets.util import extend_time_series_to_match_patch_size_and_aggregate from torch.utils.data import DataLoader -from model_config import PATCH_SIZE +from opentslm.model_config import PATCH_SIZE import torch # Model repository ID - change this to test different models REPO_ID = "OpenTSLM/llama-3.2-1b-tsqa-sp" diff --git a/demo/huggingface/02_test_hf_m4.py b/demo/huggingface/02_test_hf_m4.py index bf9a3f88..5c4331f5 100755 --- a/demo/huggingface/02_test_hf_m4.py +++ b/demo/huggingface/02_test_hf_m4.py @@ -15,17 +15,11 @@ 4. Prints model outputs """ -import sys -import os - -# Add src to path -sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../../src"))) - -from model.llm.OpenTSLM import OpenTSLM -from time_series_datasets.m4.M4QADataset import M4QADataset -from time_series_datasets.util import extend_time_series_to_match_patch_size_and_aggregate +from opentslm.model.llm.OpenTSLM import OpenTSLM +from opentslm.time_series_datasets.m4.M4QADataset import M4QADataset +from opentslm.time_series_datasets.util import extend_time_series_to_match_patch_size_and_aggregate from torch.utils.data import DataLoader -from model_config import PATCH_SIZE +from opentslm.model_config import PATCH_SIZE import torch # Model repository ID - change this to test different models diff --git a/demo/huggingface/03_test_hf_har_cot.py b/demo/huggingface/03_test_hf_har_cot.py index d6d1ace4..d1f62734 100755 --- a/demo/huggingface/03_test_hf_har_cot.py +++ b/demo/huggingface/03_test_hf_har_cot.py @@ -15,17 +15,11 @@ 4. Prints model outputs """ -import sys -import os - -# Add src to path -sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../../src"))) - -from model.llm.OpenTSLM import OpenTSLM -from time_series_datasets.har_cot.HARCoTQADataset import HARCoTQADataset -from time_series_datasets.util import extend_time_series_to_match_patch_size_and_aggregate +from opentslm.model.llm.OpenTSLM import OpenTSLM +from opentslm.time_series_datasets.har_cot.HARCoTQADataset import HARCoTQADataset +from opentslm.time_series_datasets.util import extend_time_series_to_match_patch_size_and_aggregate from torch.utils.data import DataLoader -from model_config import PATCH_SIZE +from opentslm.model_config import PATCH_SIZE import torch # Model repository ID - change this to test different models diff --git a/demo/huggingface/04_test_hf_sleep_cot.py b/demo/huggingface/04_test_hf_sleep_cot.py index 2c5fa18b..b3316b1a 100755 --- a/demo/huggingface/04_test_hf_sleep_cot.py +++ b/demo/huggingface/04_test_hf_sleep_cot.py @@ -15,17 +15,11 @@ 4. Prints model outputs """ -import sys -import os - -# Add src to path -sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../../src"))) - -from model.llm.OpenTSLM import OpenTSLM -from time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset -from time_series_datasets.util import extend_time_series_to_match_patch_size_and_aggregate +from opentslm.model.llm.OpenTSLM import OpenTSLM +from opentslm.time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset +from opentslm.time_series_datasets.util import extend_time_series_to_match_patch_size_and_aggregate from torch.utils.data import DataLoader -from model_config import PATCH_SIZE +from opentslm.model_config import PATCH_SIZE import torch # Model repository ID - change this to test different models diff --git a/demo/huggingface/05_test_hf_ecg_qa_cot.py b/demo/huggingface/05_test_hf_ecg_qa_cot.py index 153f6a9b..d20096f5 100755 --- a/demo/huggingface/05_test_hf_ecg_qa_cot.py +++ b/demo/huggingface/05_test_hf_ecg_qa_cot.py @@ -15,17 +15,11 @@ 4. Prints model outputs """ -import sys -import os - -# Add src to path -sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../../src"))) - -from model.llm.OpenTSLM import OpenTSLM -from time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset -from time_series_datasets.util import extend_time_series_to_match_patch_size_and_aggregate +from opentslm.model.llm.OpenTSLM import OpenTSLM +from opentslm.time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset +from opentslm.time_series_datasets.util import extend_time_series_to_match_patch_size_and_aggregate from torch.utils.data import DataLoader -from model_config import PATCH_SIZE +from opentslm.model_config import PATCH_SIZE import torch # Model repository ID - change this to test different models diff --git a/evaluation/baseline/common_evaluator.py b/evaluation/baseline/common_evaluator.py index 9edbec4c..fabace7a 100644 --- a/evaluation/baseline/common_evaluator.py +++ b/evaluation/baseline/common_evaluator.py @@ -23,13 +23,9 @@ import matplotlib.pyplot as plt from time import sleep -# Add src to path -sys.path.insert( - 0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "src")) -) +from opentslm.logger import get_logger -# Import OpenAIPipeline -from openai_pipeline import OpenAIPipeline +from .openai_pipeline import OpenAIPipeline class CommonEvaluator: @@ -103,7 +99,7 @@ def load_dataset( print(f"Loading dataset: {dataset_class.__name__}") # Import the gruver formatters - from gruver_llmtime_tokenizer import gpt_formatter, llama_formatter + from .gruver_llmtime_tokenizer import gpt_formatter, llama_formatter # Choose formatter based on model type model_name = getattr(self, "current_model_name", None) @@ -530,9 +526,6 @@ def _get_existing_results_count(self, model_name: str, dataset_name: str) -> int ) if os.path.exists(jsonl_file): - count = 0 - with open(jsonl_file, "r") as f: - for line in f: if line.strip(): count += 1 return count diff --git a/evaluation/baseline/common_evaluator_plot.py b/evaluation/baseline/common_evaluator_plot.py index 886267cb..042b6e8d 100644 --- a/evaluation/baseline/common_evaluator_plot.py +++ b/evaluation/baseline/common_evaluator_plot.py @@ -8,7 +8,6 @@ import os import io -import sys import base64 from typing import Type, Callable, Dict, List, Any, Optional @@ -22,9 +21,7 @@ import pandas as pd # Add src to path -sys.path.insert( - 0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "src")) -) +from opentslm.logger import get_logger # Import OpenAIPipeline from openai_pipeline import OpenAIPipeline @@ -32,12 +29,7 @@ class CommonEvaluatorPlot(CommonEvaluator): - """ - A common evaluation framework for testing LLMs on time series datasets with plot generation. - """ - - def load_model(self, model_name: str, **pipeline_kwargs) -> pipeline: - """ +from opentslm.logger import get_logger Load a model using transformers pipeline or OpenAI API. """ self.current_model_name = ( diff --git a/evaluation/baseline/evaluate_all.py b/evaluation/baseline/evaluate_all.py index 74a8fb2e..abe249f3 100644 --- a/evaluation/baseline/evaluate_all.py +++ b/evaluation/baseline/evaluate_all.py @@ -8,9 +8,9 @@ from typing import Dict, Any, Callable from common_evaluator import CommonEvaluator -from time_series_datasets.TSQADataset import TSQADataset -from time_series_datasets.pamap2.PAMAP2AccQADataset import PAMAP2AccQADataset -from time_series_datasets.pamap2.PAMAP2CoTQADataset import PAMAP2CoTQADataset +from opentslm.time_series_datasets.TSQADataset import TSQADataset +from opentslm.time_series_datasets.pamap2.PAMAP2AccQADataset import PAMAP2AccQADataset +from opentslm.time_series_datasets.pamap2.PAMAP2CoTQADataset import PAMAP2CoTQADataset # Import evaluation functions from evaluate_tsqa import evaluate_tsqa diff --git a/evaluation/baseline/evaluate_ecg_qa.py b/evaluation/baseline/evaluate_ecg_qa.py index 5c657d96..e706e825 100644 --- a/evaluation/baseline/evaluate_ecg_qa.py +++ b/evaluation/baseline/evaluate_ecg_qa.py @@ -12,7 +12,7 @@ from common_evaluator import CommonEvaluator -from time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset +from opentslm.time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset def extract_answer(text: str) -> str: diff --git a/evaluation/baseline/evaluate_ecg_qa_plot.py b/evaluation/baseline/evaluate_ecg_qa_plot.py index 3975e016..92ad43ab 100644 --- a/evaluation/baseline/evaluate_ecg_qa_plot.py +++ b/evaluation/baseline/evaluate_ecg_qa_plot.py @@ -17,7 +17,7 @@ import matplotlib.pyplot as plt from common_evaluator_plot import CommonEvaluatorPlot -from time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset +from opentslm.time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset def extract_answer(text: str) -> str: diff --git a/evaluation/baseline/evaluate_har.py b/evaluation/baseline/evaluate_har.py index c349a097..75628bf2 100644 --- a/evaluation/baseline/evaluate_har.py +++ b/evaluation/baseline/evaluate_har.py @@ -10,7 +10,7 @@ import sys from typing import Dict, Any -from time_series_datasets.har_cot.HARCoTQADataset import HARCoTQADataset +from opentslm.time_series_datasets.har_cot.HARCoTQADataset import HARCoTQADataset def extract_label_from_prediction(prediction: str) -> str: diff --git a/evaluation/baseline/evaluate_har_plot.py b/evaluation/baseline/evaluate_har_plot.py index 05cecd13..487e3b96 100644 --- a/evaluation/baseline/evaluate_har_plot.py +++ b/evaluation/baseline/evaluate_har_plot.py @@ -16,8 +16,8 @@ import matplotlib.pyplot as plt from common_evaluator_plot import CommonEvaluatorPlot -from time_series_datasets.pamap2.PAMAP2AccQADataset import PAMAP2AccQADataset -from time_series_datasets.har_cot.HARAccQADataset import HARAccQADataset +from opentslm.time_series_datasets.pamap2.PAMAP2AccQADataset import PAMAP2AccQADataset +from opentslm.time_series_datasets.har_cot.HARAccQADataset import HARAccQADataset def extract_label_from_prediction(prediction: str) -> str: """ diff --git a/evaluation/baseline/evaluate_pamap.py b/evaluation/baseline/evaluate_pamap.py index 32b81500..6b3b25c8 100644 --- a/evaluation/baseline/evaluate_pamap.py +++ b/evaluation/baseline/evaluate_pamap.py @@ -11,7 +11,7 @@ from typing import Dict, Any from common_evaluator import CommonEvaluator -from time_series_datasets.pamap2.PAMAP2AccQADataset import PAMAP2AccQADataset +from opentslm.time_series_datasets.pamap2.PAMAP2AccQADataset import PAMAP2AccQADataset def extract_label_from_prediction(prediction: str) -> str: diff --git a/evaluation/baseline/evaluate_sleep_cot.py b/evaluation/baseline/evaluate_sleep_cot.py index ba078c46..af967b09 100644 --- a/evaluation/baseline/evaluate_sleep_cot.py +++ b/evaluation/baseline/evaluate_sleep_cot.py @@ -11,7 +11,7 @@ from typing import Dict, Any from common_evaluator import CommonEvaluator -from time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset +from opentslm.time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset def extract_sleep_stage_from_prediction(prediction: str) -> str: diff --git a/evaluation/baseline/evaluate_sleep_plot.py b/evaluation/baseline/evaluate_sleep_plot.py index ca71f0c8..f1517c57 100644 --- a/evaluation/baseline/evaluate_sleep_plot.py +++ b/evaluation/baseline/evaluate_sleep_plot.py @@ -16,7 +16,7 @@ import numpy as np from common_evaluator_plot import CommonEvaluatorPlot -from time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset +from opentslm.time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset def extract_label_from_text(text: str) -> str: diff --git a/evaluation/baseline/evaluate_tsqa.py b/evaluation/baseline/evaluate_tsqa.py index e08738fd..446bd4a2 100644 --- a/evaluation/baseline/evaluate_tsqa.py +++ b/evaluation/baseline/evaluate_tsqa.py @@ -11,7 +11,7 @@ from typing import Dict, Any from common_evaluator import CommonEvaluator -from time_series_datasets.TSQADataset import TSQADataset +from opentslm.time_series_datasets.TSQADataset import TSQADataset def evaluate_tsqa(ground_truth: str, prediction: str) -> Dict[str, Any]: diff --git a/evaluation/baseline/evaluate_tsqa_plot.py b/evaluation/baseline/evaluate_tsqa_plot.py index 3e8d03c2..392f298f 100644 --- a/evaluation/baseline/evaluate_tsqa_plot.py +++ b/evaluation/baseline/evaluate_tsqa_plot.py @@ -15,7 +15,7 @@ import matplotlib.pyplot as plt from common_evaluator_plot import CommonEvaluatorPlot -from time_series_datasets.TSQADataset import TSQADataset +from opentslm.time_series_datasets.TSQADataset import TSQADataset def evaluate_tsqa(ground_truth: str, prediction: str) -> Dict[str, Any]: diff --git a/evaluation/baseline/gruver_llmtime_tokenizer.py b/evaluation/baseline/gruver_llmtime_tokenizer.py index df2a14db..f048fc85 100644 --- a/evaluation/baseline/gruver_llmtime_tokenizer.py +++ b/evaluation/baseline/gruver_llmtime_tokenizer.py @@ -6,7 +6,6 @@ # SPDX-License-Identifier: MIT # -import sys import numpy as np from functools import partial from dataclasses import dataclass diff --git a/evaluation/baseline/parse_predictions_baseline.py b/evaluation/baseline/parse_predictions_baseline.py index 65e2711f..3ec00f20 100644 --- a/evaluation/baseline/parse_predictions_baseline.py +++ b/evaluation/baseline/parse_predictions_baseline.py @@ -16,13 +16,6 @@ from pathlib import Path from typing import Dict, List -import sys - -# Ensure repository root is on sys.path so 'evaluation' package is importable -REPO_ROOT = Path(__file__).resolve().parents[2] -if str(REPO_ROOT) not in sys.path: - sys.path.insert(0, str(REPO_ROOT)) - from evaluation.opentslm.parse_predictions import ( calculate_f1_score, calculate_f1_stats, diff --git a/evaluation/baseline/parse_predictions_sleep_baseline.py b/evaluation/baseline/parse_predictions_sleep_baseline.py index 6352c8fe..ae0e84d1 100644 --- a/evaluation/baseline/parse_predictions_sleep_baseline.py +++ b/evaluation/baseline/parse_predictions_sleep_baseline.py @@ -43,17 +43,6 @@ import json from pathlib import Path from typing import Dict, List -import sys - -# Ensure repository root is on sys.path so 'evaluation' package is importable -REPO_ROOT = Path(__file__).resolve().parents[2] -if str(REPO_ROOT) not in sys.path: - sys.path.insert(0, str(REPO_ROOT)) - -# Also ensure 'src' is on sys.path if needed in the future -SRC_ROOT = REPO_ROOT / "src" -if str(SRC_ROOT) not in sys.path: - sys.path.insert(0, str(SRC_ROOT)) # --- Inline minimal utilities (avoid importing modules that require extra packages) --- import re diff --git a/evaluation/baseline/parse_predictions_tsqa_baseline.py b/evaluation/baseline/parse_predictions_tsqa_baseline.py index 579527b8..3a1719a9 100644 --- a/evaluation/baseline/parse_predictions_tsqa_baseline.py +++ b/evaluation/baseline/parse_predictions_tsqa_baseline.py @@ -44,12 +44,6 @@ import re from pathlib import Path from typing import Dict, List -import sys - -# Ensure repository root is on sys.path so 'evaluation' package is importable -REPO_ROOT = Path(__file__).resolve().parents[2] -if str(REPO_ROOT) not in sys.path: - sys.path.insert(0, str(REPO_ROOT)) from evaluation.opentslm.parse_predictions import ( calculate_f1_score, diff --git a/evaluation/clinician_eval/create_doctor_eval_dataset.py b/evaluation/clinician_eval/create_doctor_eval_dataset.py index 8ebb3d91..f319c680 100644 --- a/evaluation/clinician_eval/create_doctor_eval_dataset.py +++ b/evaluation/clinician_eval/create_doctor_eval_dataset.py @@ -15,22 +15,17 @@ import json import os -import sys import re import pandas as pd import numpy as np import matplotlib.pyplot as plt import wfdb -from pathlib import Path -from typing import Dict, List, Set, Tuple +from typing import Dict, List, Tuple from collections import defaultdict from tqdm import tqdm -import shutil -# Add the src directory to the path -sys.path.append(os.path.join(os.path.dirname(__file__), "src")) -from time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset -from time_series_datasets.ecg_qa.plot_example import draw_ecg, get_ptbxl_ecg_path +from opentslm.time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset +from opentslm.time_series_datasets.ecg_qa.plot_example import get_ptbxl_ecg_path # Configuration MODEL_PREDICTIONS_FILE = "/Users/planger/Development/EmbedHealth/evaluation/opentslm/ecg_qa_cot/llama3b_flamingo_predictions.jsonl" diff --git a/evaluation/memory/get_memory_use.py b/evaluation/memory/get_memory_use.py index cb722a35..dc316a12 100644 --- a/evaluation/memory/get_memory_use.py +++ b/evaluation/memory/get_memory_use.py @@ -9,8 +9,6 @@ import argparse import csv import os -import sys -import time from datetime import datetime from typing import Dict, List, Tuple @@ -22,31 +20,22 @@ import pynvml # type: ignore -_NVML_AVAILABLE = True - - -# Ensure src is on path -REPO_DIR = os.path.dirname(os.path.abspath(__file__)) -if REPO_DIR not in sys.path: - sys.path.append(REPO_DIR) -SRC_DIR = os.path.join(REPO_DIR, "src") -if SRC_DIR not in sys.path: - sys.path.append(SRC_DIR) # Models -from model.llm.OpenTSLMFlamingo import OpenTSLMFlamingo -from model.llm.OpenTSLMSP import OpenTSLMSP +from opentslm.model.llm.OpenTSLMFlamingo import OpenTSLMFlamingo +from opentslm.model.llm.OpenTSLMSP import OpenTSLMSP # Datasets -from time_series_datasets.TSQADataset import TSQADataset -from time_series_datasets.har_cot.HARCoTQADataset import HARCoTQADataset -from time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset -from time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset -from time_series_datasets.simulation.SimulationQADataset import SimulationQADataset -from time_series_datasets.util import ( +from opentslm.time_series_datasets.TSQADataset import TSQADataset +from opentslm.time_series_datasets.har_cot.HARCoTQADataset import HARCoTQADataset +from opentslm.time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset +from opentslm.time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset +from opentslm.time_series_datasets.simulation.SimulationQADataset import SimulationQADataset +from opentslm.time_series_datasets.util import ( extend_time_series_to_match_patch_size_and_aggregate, ) +_NVML_AVAILABLE = True def get_device(device_arg: str | None) -> str: if device_arg: diff --git a/evaluation/opentslm/baseline_parse_predictions.py b/evaluation/opentslm/baseline_parse_predictions.py index 140004df..a7c63f5a 100644 --- a/evaluation/opentslm/baseline_parse_predictions.py +++ b/evaluation/opentslm/baseline_parse_predictions.py @@ -17,12 +17,8 @@ from collections import Counter from tqdm import tqdm -# Add the src directory to the path to import from the dataset class -project_root = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")) -sys.path.append(os.path.join(project_root, "src")) - # Import the dataset class to get labels -from time_series_datasets.har_cot.HARCoTQADataset import HARCoTQADataset +from opentslm.time_series_datasets.har_cot.HARCoTQADataset import HARCoTQADataset # Get the supported labels from the dataset class SUPPORTED_LABELS = HARCoTQADataset.get_labels() diff --git a/evaluation/opentslm/ecg_qa_cot/parse_ecg_qa_cot_data.py b/evaluation/opentslm/ecg_qa_cot/parse_ecg_qa_cot_data.py index c72223db..fc41ebb4 100644 --- a/evaluation/opentslm/ecg_qa_cot/parse_ecg_qa_cot_data.py +++ b/evaluation/opentslm/ecg_qa_cot/parse_ecg_qa_cot_data.py @@ -17,9 +17,8 @@ from collections import Counter, defaultdict from tqdm import tqdm -# Add the src directory to the path to import from the dataset class -sys.path.append(os.path.join(os.path.dirname(__file__), "..", "..", "..", "src")) -from time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset +# Import dataset via package namespace +from opentslm.time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset def calculate_f1_score(prediction, ground_truth, possible_answers): diff --git a/evaluation/opentslm/get_pamap_cot_predictions.py b/evaluation/opentslm/get_pamap_cot_predictions.py index cdc1c4dc..9edea055 100644 --- a/evaluation/opentslm/get_pamap_cot_predictions.py +++ b/evaluation/opentslm/get_pamap_cot_predictions.py @@ -23,26 +23,19 @@ - CSV file with time series data, ground truth labels, and rationale """ -import sys -import os import torch import pandas as pd -import numpy as np import random from typing import List, Dict, Any import json -# Add src to path -sys.path.insert( - 0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "src")) -) -from model.llm.OpenTSLMFlamingo import OpenTSLMFlamingo -from time_series_datasets.pamap2.PAMAP2CoTQADataset import PAMAP2CoTQADataset -from prompt.full_prompt import FullPrompt -from prompt.text_prompt import TextPrompt -from prompt.text_time_series_prompt import TextTimeSeriesPrompt -from time_series_datasets.util import ( +from opentslm.model.llm.OpenTSLMFlamingo import OpenTSLMFlamingo +from opentslm.time_series_datasets.pamap2.PAMAP2CoTQADataset import PAMAP2CoTQADataset +from opentslm.prompt.full_prompt import FullPrompt +from opentslm.prompt.text_prompt import TextPrompt +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.time_series_datasets.util import ( extend_time_series_to_match_patch_size_and_aggregate, ) diff --git a/evaluation/opentslm/parse_predictions.py b/evaluation/opentslm/parse_predictions.py index 8f1c67af..9d018beb 100644 --- a/evaluation/opentslm/parse_predictions.py +++ b/evaluation/opentslm/parse_predictions.py @@ -16,12 +16,8 @@ from pathlib import Path from collections import Counter -# Add the src directory to the path to import from the dataset class -project_root = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")) -sys.path.append(os.path.join(project_root, "src")) - # Import the dataset class to get labels -from time_series_datasets.har_cot.HARCoTQADataset import HARCoTQADataset +from opentslm.time_series_datasets.har_cot.HARCoTQADataset import HARCoTQADataset # Get the supported labels from the dataset class SUPPORTED_LABELS = HARCoTQADataset.get_labels() diff --git a/evaluation/opentslm/sleep/baseline_parse_sleep_cot_data.py b/evaluation/opentslm/sleep/baseline_parse_sleep_cot_data.py index 816a9e06..7fc0385b 100644 --- a/evaluation/opentslm/sleep/baseline_parse_sleep_cot_data.py +++ b/evaluation/opentslm/sleep/baseline_parse_sleep_cot_data.py @@ -11,15 +11,10 @@ import json import re -import sys -import os from pathlib import Path -from collections import Counter from tqdm import tqdm -# Add the src directory to the path to import from the dataset class -sys.path.append(os.path.join(os.path.dirname(__file__), "..", "..", "..", "src")) -from time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset +from opentslm.time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset # We'll determine supported labels dynamically from the actual ground truth data # Start with the dataset class labels as a fallback diff --git a/evaluation/opentslm/sleep/get_sleep_predictions.py b/evaluation/opentslm/sleep/get_sleep_predictions.py index ff826ecb..ec14e1d6 100644 --- a/evaluation/opentslm/sleep/get_sleep_predictions.py +++ b/evaluation/opentslm/sleep/get_sleep_predictions.py @@ -23,26 +23,18 @@ - CSV file with time series data, ground truth labels, and rationale """ -import sys -import os import torch import pandas as pd -import numpy as np import random from typing import List, Dict, Any import json -# Add src to path -sys.path.insert( - 0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "..", "src")) -) - -from model.llm.OpenTSLMSP import OpenTSLMSP -from time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset -from prompt.full_prompt import FullPrompt -from prompt.text_prompt import TextPrompt -from prompt.text_time_series_prompt import TextTimeSeriesPrompt -from time_series_datasets.util import ( +from opentslm.model.llm.OpenTSLMSP import OpenTSLMSP +from opentslm.time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset +from opentslm.prompt.full_prompt import FullPrompt +from opentslm.prompt.text_prompt import TextPrompt +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.time_series_datasets.util import ( extend_time_series_to_match_patch_size_and_aggregate, ) diff --git a/evaluation/opentslm/sleep/parse_sleep_cot_data.py b/evaluation/opentslm/sleep/parse_sleep_cot_data.py index 1fb20868..e02c78f7 100644 --- a/evaluation/opentslm/sleep/parse_sleep_cot_data.py +++ b/evaluation/opentslm/sleep/parse_sleep_cot_data.py @@ -17,9 +17,8 @@ from collections import Counter from tqdm import tqdm -# Add the src directory to the path to import from the dataset class -sys.path.append(os.path.join(os.path.dirname(__file__), "..", "..", "..", "src")) -from time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset +# Import dataset via package namespace +from opentslm.time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset # We'll determine supported labels dynamically from the actual ground truth data # Start with the dataset class labels as a fallback diff --git a/pyproject.toml b/pyproject.toml index ebdaab54..ebc6e9b7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,13 +6,32 @@ [project] name = "opentslm" -version = "0.1.0" +version = "0.1.0.dev0" description = "OpenTSLM: Open Time Series Language Model - Curriculum Learning for Multimodal Time Series Understanding with Large Language Models" readme = "README.md" requires-python = ">=3.12" -license = {text = "MIT"} +license = "MIT" authors = [ - {name = "Stanford Biodesign Digital Health Group"} + {name = "Patrick Langer"}, + {name = "Thomas Kaar"}, + {name = "Max Rosenblattl"}, + {name = "Maxwell A. Xu"}, + {name = "Winnie Chow"}, + {name = "Martin Maritsch"}, + {name = "Robert Jakob"}, + {name = "Aradhana Verma"}, + {name = "Brian Han"}, + {name = "Daniel Seung Kim"}, + {name = "Henry Chubb"}, + {name = "Scott Ceresnak"}, + {name = "Aydin Zahedivash"}, + {name = "Alexander Tarlochan Singh Sandhu"}, + {name = "Fatima Rodriguez"}, + {name = "Daniel McDuff"}, + {name = "Elgar Fleisch"}, + {name = "Oliver Aalami"}, + {name = "Filipe Barata"}, + {name = "Paul Schmiedmayer"} ] keywords = [ "time-series", @@ -21,16 +40,6 @@ keywords = [ "multimodal", "healthcare" ] -classifiers = [ - "Development Status :: 3 - Alpha", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: MIT License", - "Operating System :: OS Independent", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.12", - "Topic :: Scientific/Engineering :: Artificial Intelligence", - "Topic :: Scientific/Engineering :: Medical Science Apps.", -] dependencies = [ "numpy>=1.21", @@ -49,8 +58,10 @@ dependencies = [ "open-flamingo>=0.0.2", ] -[tool.uv] -default-groups = ["dev"] +[project.urls] +Homepage = "https://opentslm.com" +Repository = "https://github.com/StanfordBDHG/OpenTSLM" +"Bug Tracker" = "https://github.com/StanfordBDHG/OpenTSLM/issues" [dependency-groups] dev = [ @@ -64,11 +75,27 @@ eval = [ notebook = [ "jupyter>=1.0", "ipython>=8.0", + "seaborn>=0.13.2", +] + +[build-system] +requires = ["uv_build>=0.9.0,<0.10.0"] +build-backend = "uv_build" + +[tool.uv] +required-version = ">=0.9" + +[[tool.uv.index]] +name = "testpypi" +url = "https://test.pypi.org/simple/" +publish-url = "https://test.pypi.org/legacy/" +explicit = true + +[tool.uv.workspace] +members = [ + "test-install", ] -[project.urls] -Repository = "https://github.com/StanfordBDHG/EmbedHealth" -"Bug Tracker" = "https://github.com/StanfordBDHG/EmbedHealth/issues" [tool.ruff] line-length = 120 diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 00000000..d09a23e2 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,15 @@ +numpy>=2.3.5 +pandas>=2.3.3 +torch>=2.9.1 +tqdm>=4.67.1 +matplotlib>=3.10.7 +scikit-learn>=1.7.2 +transformers>=4.57.3 +huggingface-hub>=0.36.0 +datasets>=4.4.1 +peft>=0.18.0 +requests>=2.32.5 +einops>=0.8.1 +wfdb>=4.3.0 +open-flamingo>=0.0.2 +-e . \ No newline at end of file diff --git a/scripts/create_doctor_eval_dataset.py b/scripts/create_doctor_eval_dataset.py index 7c7216c0..f8ace986 100644 --- a/scripts/create_doctor_eval_dataset.py +++ b/scripts/create_doctor_eval_dataset.py @@ -13,22 +13,18 @@ import json import os -import sys import re import pandas as pd import numpy as np import matplotlib.pyplot as plt import wfdb -from pathlib import Path -from typing import Dict, List, Set, Tuple +from typing import Dict, List, Tuple from collections import defaultdict from tqdm import tqdm -import shutil # Add the src directory to the path -sys.path.append(os.path.join(os.path.dirname(__file__), 'src')) -from time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset -from time_series_datasets.ecg_qa.plot_example import draw_ecg, get_ptbxl_ecg_path +from opentslm.time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset +from opentslm.time_series_datasets.ecg_qa.plot_example import get_ptbxl_ecg_path # Configuration MODEL_PREDICTIONS_FILE = "/Users/planger/Development/EmbedHealth/evaluation/embedhealth/ecg_qa_cot/llama3b_flamingo_predictions.jsonl" diff --git a/scripts/get_memory_use.py b/scripts/get_memory_use.py index f39f4e1d..573eb8d5 100644 --- a/scripts/get_memory_use.py +++ b/scripts/get_memory_use.py @@ -9,7 +9,6 @@ import argparse import csv import os -import sys import time from datetime import datetime from typing import Dict, List, Tuple @@ -24,25 +23,17 @@ _NVML_AVAILABLE = True -# Ensure src is on path -REPO_DIR = os.path.dirname(os.path.abspath(__file__)) -if REPO_DIR not in sys.path: - sys.path.append(REPO_DIR) -SRC_DIR = os.path.join(REPO_DIR, "src") -if SRC_DIR not in sys.path: - sys.path.append(SRC_DIR) - # Models -from model.llm.OpenTSLMFlamingo import OpenTSLMFlamingo -from model.llm.OpenTSLMSP import OpenTSLMSP +from opentslm.model.llm.OpenTSLMFlamingo import OpenTSLMFlamingo +from opentslm.model.llm.OpenTSLMSP import OpenTSLMSP # Datasets -from time_series_datasets.TSQADataset import TSQADataset -from time_series_datasets.har_cot.HARCoTQADataset import HARCoTQADataset -from time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset -from time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset -from time_series_datasets.simulation.SimulationQADataset import SimulationQADataset -from time_series_datasets.util import ( +from opentslm.time_series_datasets.TSQADataset import TSQADataset +from opentslm.time_series_datasets.har_cot.HARCoTQADataset import HARCoTQADataset +from opentslm.time_series_datasets.sleep.SleepEDFCoTQADataset import SleepEDFCoTQADataset +from opentslm.time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset +from opentslm.time_series_datasets.simulation.SimulationQADataset import SimulationQADataset +from opentslm.time_series_datasets.util import ( extend_time_series_to_match_patch_size_and_aggregate, ) diff --git a/scripts/hf_test.py b/scripts/hf_test.py index dba29e57..d0bea2b4 100644 --- a/scripts/hf_test.py +++ b/scripts/hf_test.py @@ -5,7 +5,8 @@ # # SPDX-License-Identifier: MIT # -from src import OpenTSLM, TextPrompt, TextTimeSeriesPrompt, FullPrompt +from opentslm import OpenTSLM +from opentslm.prompt import TextPrompt, TextTimeSeriesPrompt, FullPrompt # Load model model = OpenTSLM.load_pretrained("OpenTSLM/gemma-3-270m-pt-har-flamingo") diff --git a/src/opentslm/__init__.py b/src/opentslm/__init__.py new file mode 100644 index 00000000..538f194b --- /dev/null +++ b/src/opentslm/__init__.py @@ -0,0 +1,11 @@ +# +# This source file is part of the OpenTSLM open-source project +# +# SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md) +# +# SPDX-License-Identifier: MIT +# + +from opentslm.model.llm.OpenTSLM import OpenTSLM + +__all__ = ["OpenTSLM"] \ No newline at end of file diff --git a/src/data.py b/src/opentslm/data.py similarity index 99% rename from src/data.py rename to src/opentslm/data.py index f6e2195c..eb79d675 100644 --- a/src/data.py +++ b/src/opentslm/data.py @@ -12,7 +12,7 @@ import torch from datasets import load_dataset from torch.utils.data import DataLoader -from src.model_config import * +from opentslm.model_config import * # --------------------------- # Constants diff --git a/src/logger.py b/src/opentslm/logger.py similarity index 100% rename from src/logger.py rename to src/opentslm/logger.py diff --git a/src/model/__init__.py b/src/opentslm/model/__init__.py similarity index 100% rename from src/model/__init__.py rename to src/opentslm/model/__init__.py diff --git a/src/model/encoder/CNNTokenizer.py b/src/opentslm/model/encoder/CNNTokenizer.py similarity index 94% rename from src/model/encoder/CNNTokenizer.py rename to src/opentslm/model/encoder/CNNTokenizer.py index bee3780b..e3409947 100644 --- a/src/model/encoder/CNNTokenizer.py +++ b/src/opentslm/model/encoder/CNNTokenizer.py @@ -10,8 +10,8 @@ import torch.nn as nn -from model_config import TRANSFORMER_INPUT_DIM, ENCODER_OUTPUT_DIM, PATCH_SIZE -from model.encoder.TimeSeriesEncoderBase import TimeSeriesEncoderBase +from opentslm.model_config import TRANSFORMER_INPUT_DIM, ENCODER_OUTPUT_DIM, PATCH_SIZE +from opentslm.model.encoder.TimeSeriesEncoderBase import TimeSeriesEncoderBase class CNNTokenizer(TimeSeriesEncoderBase): diff --git a/src/model/encoder/TimeSeriesEncoderBase.py b/src/opentslm/model/encoder/TimeSeriesEncoderBase.py similarity index 92% rename from src/model/encoder/TimeSeriesEncoderBase.py rename to src/opentslm/model/encoder/TimeSeriesEncoderBase.py index fde57d62..2ddd8e59 100644 --- a/src/model/encoder/TimeSeriesEncoderBase.py +++ b/src/opentslm/model/encoder/TimeSeriesEncoderBase.py @@ -10,7 +10,7 @@ import torch import torch.nn as nn -from model_config import ENCODER_OUTPUT_DIM +from opentslm.model_config import ENCODER_OUTPUT_DIM class TimeSeriesEncoderBase(nn.Module): diff --git a/src/model/encoder/TransformerCNNEncoder.py b/src/opentslm/model/encoder/TransformerCNNEncoder.py similarity index 95% rename from src/model/encoder/TransformerCNNEncoder.py rename to src/opentslm/model/encoder/TransformerCNNEncoder.py index 5c96844d..e32985e0 100644 --- a/src/model/encoder/TransformerCNNEncoder.py +++ b/src/opentslm/model/encoder/TransformerCNNEncoder.py @@ -10,8 +10,8 @@ import torch.nn as nn -from model_config import TRANSFORMER_INPUT_DIM, ENCODER_OUTPUT_DIM, PATCH_SIZE -from model.encoder.TimeSeriesEncoderBase import TimeSeriesEncoderBase +from opentslm.model_config import TRANSFORMER_INPUT_DIM, ENCODER_OUTPUT_DIM, PATCH_SIZE +from opentslm.model.encoder.TimeSeriesEncoderBase import TimeSeriesEncoderBase class TransformerCNNEncoder(TimeSeriesEncoderBase): diff --git a/src/model/encoder/TransformerMLPEncoder.py b/src/opentslm/model/encoder/TransformerMLPEncoder.py similarity index 95% rename from src/model/encoder/TransformerMLPEncoder.py rename to src/opentslm/model/encoder/TransformerMLPEncoder.py index 6aa59e5d..6f9b27bc 100644 --- a/src/model/encoder/TransformerMLPEncoder.py +++ b/src/opentslm/model/encoder/TransformerMLPEncoder.py @@ -10,8 +10,8 @@ import torch.nn as nn -from src.model_config import TRANSFORMER_INPUT_DIM, ENCODER_OUTPUT_DIM, PATCH_SIZE -from model.encoder.TimeSeriesEncoderBase import TimeSeriesEncoderBase +from opentslm.model_config import TRANSFORMER_INPUT_DIM, ENCODER_OUTPUT_DIM, PATCH_SIZE +from opentslm.model.encoder.TimeSeriesEncoderBase import TimeSeriesEncoderBase class TransformerMLPEncoder(TimeSeriesEncoderBase): diff --git a/src/model/encoder/__init__.py b/src/opentslm/model/encoder/__init__.py similarity index 100% rename from src/model/encoder/__init__.py rename to src/opentslm/model/encoder/__init__.py diff --git a/src/model/llm/OpenTSLM.py b/src/opentslm/model/llm/OpenTSLM.py similarity index 99% rename from src/model/llm/OpenTSLM.py rename to src/opentslm/model/llm/OpenTSLM.py index d705e9bd..aa30ad9f 100644 --- a/src/model/llm/OpenTSLM.py +++ b/src/opentslm/model/llm/OpenTSLM.py @@ -41,7 +41,7 @@ class OpenTSLM: Example: >>> model = OpenTSLM.load_pretrained("OpenTSLM/gemma-3-270m-pt-sleep-flamingo") >>> - >>> from prompt.full_prompt import FullPrompt + >>> from opentslm.prompt.full_prompt import FullPrompt >>> prompt = FullPrompt(...) >>> response = model.eval_prompt(prompt) """ diff --git a/src/model/llm/OpenTSLMFlamingo.py b/src/opentslm/model/llm/OpenTSLMFlamingo.py similarity index 97% rename from src/model/llm/OpenTSLMFlamingo.py rename to src/opentslm/model/llm/OpenTSLMFlamingo.py index 62a11772..2fc2243b 100644 --- a/src/model/llm/OpenTSLMFlamingo.py +++ b/src/opentslm/model/llm/OpenTSLMFlamingo.py @@ -7,8 +7,8 @@ # from types import SimpleNamespace -from model.encoder.CNNTokenizer import CNNTokenizer -from model.llm.TimeSeriesFlamingoWithTrainableEncoder import ( +from opentslm.model.encoder.CNNTokenizer import CNNTokenizer +from opentslm.model.llm.TimeSeriesFlamingoWithTrainableEncoder import ( TimeSeriesFlamingoWithTrainableEncoder, ) from open_flamingo.src.flamingo_lm import FlamingoLMMixin @@ -18,10 +18,10 @@ from typing import List, Dict, Tuple from transformers import AutoTokenizer, AutoModelForCausalLM -from model_config import ENCODER_OUTPUT_DIM -from model.llm.TimeSeriesLLM import TimeSeriesLLM -from prompt.full_prompt import FullPrompt -from time_series_datasets.util import ( +from opentslm.model_config import ENCODER_OUTPUT_DIM +from opentslm.model.llm.TimeSeriesLLM import TimeSeriesLLM +from opentslm.prompt.full_prompt import FullPrompt +from opentslm.time_series_datasets.util import ( extend_time_series_to_match_patch_size_and_aggregate, ) @@ -35,7 +35,7 @@ def _attention_type_property(self): # Add the attention_type property to FlamingoLayer -FlamingoLayer.attention_type = property(_attention_type_property) +FlamingoLayer.attention_type = property(_attention_type_property) # type: ignore class OpenTSLMFlamingo(TimeSeriesLLM): diff --git a/src/model/llm/OpenTSLMSP.py b/src/opentslm/model/llm/OpenTSLMSP.py similarity index 99% rename from src/model/llm/OpenTSLMSP.py rename to src/opentslm/model/llm/OpenTSLMSP.py index d5944339..1f8ca54e 100644 --- a/src/model/llm/OpenTSLMSP.py +++ b/src/opentslm/model/llm/OpenTSLMSP.py @@ -20,12 +20,12 @@ PEFT_AVAILABLE = False print("Warning: peft not available. LoRA fine-tuning will be disabled.") -from model_config import ENCODER_OUTPUT_DIM +from opentslm.model_config import ENCODER_OUTPUT_DIM from .TimeSeriesLLM import TimeSeriesLLM from ..encoder.TransformerCNNEncoder import TransformerCNNEncoder from ..projector.MLPProjector import MLPProjector -from prompt.full_prompt import FullPrompt -from time_series_datasets.util import ( +from opentslm.prompt.full_prompt import FullPrompt +from opentslm.time_series_datasets.util import ( extend_time_series_to_match_patch_size_and_aggregate, ) diff --git a/src/model/llm/TimeSeriesFlamingoWithTrainableEncoder.py b/src/opentslm/model/llm/TimeSeriesFlamingoWithTrainableEncoder.py similarity index 98% rename from src/model/llm/TimeSeriesFlamingoWithTrainableEncoder.py rename to src/opentslm/model/llm/TimeSeriesFlamingoWithTrainableEncoder.py index 322157d4..267639ec 100644 --- a/src/model/llm/TimeSeriesFlamingoWithTrainableEncoder.py +++ b/src/opentslm/model/llm/TimeSeriesFlamingoWithTrainableEncoder.py @@ -8,7 +8,7 @@ import torch from torch import nn -from open_flamingo.src.flamingo import Flamingo +from open_flamingo import Flamingo from einops import rearrange diff --git a/src/model/llm/TimeSeriesLLM.py b/src/opentslm/model/llm/TimeSeriesLLM.py similarity index 74% rename from src/model/llm/TimeSeriesLLM.py rename to src/opentslm/model/llm/TimeSeriesLLM.py index 987f52ff..04029bde 100644 --- a/src/model/llm/TimeSeriesLLM.py +++ b/src/opentslm/model/llm/TimeSeriesLLM.py @@ -1,3 +1,4 @@ +from typing import List, Dict, Any # # This source file is part of the OpenTSLM open-source project # @@ -8,12 +9,8 @@ import torch import torch.nn as nn -from typing import List, Dict, Tuple -from transformers import AutoTokenizer, AutoModelForCausalLM -from torch.nn.utils.rnn import pad_sequence -from model_config import ENCODER_OUTPUT_DIM -from prompt.full_prompt import FullPrompt +from opentslm.prompt.full_prompt import FullPrompt class TimeSeriesLLM(nn.Module): def __init__( @@ -25,12 +22,12 @@ def __init__( def generate( - self, batch: List[Dict[str, any]], max_new_tokens: int = 50, **generate_kwargs + self, batch: List[Dict[str, Any]], max_new_tokens: int = 50, **generate_kwargs ) -> List[str]: raise NotImplementedError("Generate method should be implemented by the subclass") - def compute_loss(self, batch: List[Dict[str, any]]) -> torch.Tensor: + def compute_loss(self, batch: List[Dict[str, Any]]) -> torch.Tensor: """ batch: same format as generate() answers: List[str] of length B diff --git a/src/model/llm/__init__.py b/src/opentslm/model/llm/__init__.py similarity index 100% rename from src/model/llm/__init__.py rename to src/opentslm/model/llm/__init__.py diff --git a/src/model/projector/LinearProjector.py b/src/opentslm/model/projector/LinearProjector.py similarity index 100% rename from src/model/projector/LinearProjector.py rename to src/opentslm/model/projector/LinearProjector.py diff --git a/src/model/projector/MLPProjector.py b/src/opentslm/model/projector/MLPProjector.py similarity index 100% rename from src/model/projector/MLPProjector.py rename to src/opentslm/model/projector/MLPProjector.py diff --git a/src/model/projector/__init__.py b/src/opentslm/model/projector/__init__.py similarity index 100% rename from src/model/projector/__init__.py rename to src/opentslm/model/projector/__init__.py diff --git a/src/model_config.py b/src/opentslm/model_config.py similarity index 100% rename from src/model_config.py rename to src/opentslm/model_config.py diff --git a/src/opentslm/prompt/__init__.py b/src/opentslm/prompt/__init__.py new file mode 100644 index 00000000..88dcbb86 --- /dev/null +++ b/src/opentslm/prompt/__init__.py @@ -0,0 +1,21 @@ +# +# This source file is part of the OpenTSLM open-source project +# +# SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md) +# +# SPDX-License-Identifier: MIT +# + +from .prompt import Prompt +from .full_prompt import FullPrompt +from .text_prompt import TextPrompt +from .text_time_series_prompt import TextTimeSeriesPrompt +from .prompt_with_answer import PromptWithAnswer + +__all__ = [ + "Prompt", + "FullPrompt", + "TextPrompt", + "TextTimeSeriesPrompt", + "PromptWithAnswer", +] diff --git a/src/prompt/full_prompt.py b/src/opentslm/prompt/full_prompt.py similarity index 91% rename from src/prompt/full_prompt.py rename to src/opentslm/prompt/full_prompt.py index 6d18239a..c8ebccdf 100644 --- a/src/prompt/full_prompt.py +++ b/src/opentslm/prompt/full_prompt.py @@ -7,8 +7,8 @@ # from typing import List -from prompt.text_prompt import TextPrompt -from prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.prompt.text_prompt import TextPrompt +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt class FullPrompt: diff --git a/src/prompt/prompt.py b/src/opentslm/prompt/prompt.py similarity index 100% rename from src/prompt/prompt.py rename to src/opentslm/prompt/prompt.py diff --git a/src/prompt/prompt_with_answer.py b/src/opentslm/prompt/prompt_with_answer.py similarity index 92% rename from src/prompt/prompt_with_answer.py rename to src/opentslm/prompt/prompt_with_answer.py index 21e2477d..a57ec123 100644 --- a/src/prompt/prompt_with_answer.py +++ b/src/opentslm/prompt/prompt_with_answer.py @@ -7,8 +7,8 @@ # from typing import List -from prompt.text_prompt import TextPrompt -from prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.prompt.text_prompt import TextPrompt +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt class PromptWithAnswer: diff --git a/src/prompt/text_prompt.py b/src/opentslm/prompt/text_prompt.py similarity index 100% rename from src/prompt/text_prompt.py rename to src/opentslm/prompt/text_prompt.py diff --git a/src/prompt/text_time_series_prompt.py b/src/opentslm/prompt/text_time_series_prompt.py similarity index 100% rename from src/prompt/text_time_series_prompt.py rename to src/opentslm/prompt/text_time_series_prompt.py diff --git a/src/time_series_datasets/QADataset.py b/src/opentslm/time_series_datasets/QADataset.py similarity index 96% rename from src/time_series_datasets/QADataset.py rename to src/opentslm/time_series_datasets/QADataset.py index e8b492f6..7b502695 100644 --- a/src/time_series_datasets/QADataset.py +++ b/src/opentslm/time_series_datasets/QADataset.py @@ -11,10 +11,9 @@ from typing import Callable, List, Literal, Tuple import numpy as np -import sys -from prompt.prompt_with_answer import PromptWithAnswer -from prompt.text_prompt import TextPrompt -from prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.prompt.prompt_with_answer import PromptWithAnswer +from opentslm.prompt.text_prompt import TextPrompt +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt from torch.utils.data import Dataset diff --git a/src/time_series_datasets/TSQADataset.py b/src/opentslm/time_series_datasets/TSQADataset.py similarity index 94% rename from src/time_series_datasets/TSQADataset.py rename to src/opentslm/time_series_datasets/TSQADataset.py index dd826a0d..9f8f5bd9 100644 --- a/src/time_series_datasets/TSQADataset.py +++ b/src/opentslm/time_series_datasets/TSQADataset.py @@ -11,9 +11,9 @@ from datasets import Dataset, load_dataset -from prompt.text_time_series_prompt import TextTimeSeriesPrompt -from time_series_datasets.QADataset import QADataset -from time_series_datasets.util import ( +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.time_series_datasets.QADataset import QADataset +from opentslm.time_series_datasets.util import ( extend_time_series_to_match_patch_size_and_aggregate, ) from torch.utils.data import DataLoader diff --git a/src/time_series_datasets/__init__.py b/src/opentslm/time_series_datasets/__init__.py similarity index 100% rename from src/time_series_datasets/__init__.py rename to src/opentslm/time_series_datasets/__init__.py diff --git a/src/time_series_datasets/constants.py b/src/opentslm/time_series_datasets/constants.py similarity index 100% rename from src/time_series_datasets/constants.py rename to src/opentslm/time_series_datasets/constants.py diff --git a/src/time_series_datasets/ecg_qa/ECGQACoTQADataset.py b/src/opentslm/time_series_datasets/ecg_qa/ECGQACoTQADataset.py similarity index 97% rename from src/time_series_datasets/ecg_qa/ECGQACoTQADataset.py rename to src/opentslm/time_series_datasets/ecg_qa/ECGQACoTQADataset.py index 03ad80b3..aa56b1c8 100644 --- a/src/time_series_datasets/ecg_qa/ECGQACoTQADataset.py +++ b/src/opentslm/time_series_datasets/ecg_qa/ECGQACoTQADataset.py @@ -8,12 +8,10 @@ from datasets import Dataset from typing import List, Tuple, Literal -import sys import os -sys.path.append(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))) -from prompt.text_time_series_prompt import TextTimeSeriesPrompt -from time_series_datasets.QADataset import QADataset -from time_series_datasets.ecg_qa.ecgqa_cot_loader import load_ecg_qa_cot_splits +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.time_series_datasets.QADataset import QADataset +from opentslm.time_series_datasets.ecg_qa.ecgqa_cot_loader import load_ecg_qa_cot_splits import numpy as np class ECGQACoTQADataset(QADataset): @@ -173,7 +171,7 @@ def _load_template_answers_cache(cls): try: import pandas as pd import ast - from time_series_datasets.ecg_qa.ecgqa_loader import ECG_QA_DIR + from opentslm.time_series_datasets.ecg_qa.ecgqa_loader import ECG_QA_DIR # Load template answers directly template_answers_path = os.path.join(ECG_QA_DIR, "ecgqa", "ptbxl", "answers_for_each_template.csv") @@ -211,7 +209,7 @@ def get_labels() -> List[str]: try: import pandas as pd import ast - from time_series_datasets.ecg_qa.ecgqa_loader import ECG_QA_DIR + from opentslm.time_series_datasets.ecg_qa.ecgqa_loader import ECG_QA_DIR template_answers_path = os.path.join(ECG_QA_DIR, "ecgqa", "ptbxl", "answers_for_each_template.csv") df = pd.read_csv(template_answers_path) @@ -301,7 +299,7 @@ def preload_ecg_data(cls, dataset_splits: List[Dataset]): # Fallback: construct path from ecg_id ecg_id = sample.get("ecg_id") if ecg_id and isinstance(ecg_id, list) and len(ecg_id) > 0: - from time_series_datasets.ecg_qa.ecgqa_loader import get_ptbxl_ecg_path + from opentslm.time_series_datasets.ecg_qa.ecgqa_loader import get_ptbxl_ecg_path ecg_path = get_ptbxl_ecg_path(ecg_id[0]) + ".dat" ecg_paths.add(ecg_path) @@ -338,7 +336,7 @@ def preload_processed_ecg_data(cls, dataset_splits: List[Dataset]): # Fallback: construct path from ecg_id ecg_id = sample.get("ecg_id") if ecg_id and isinstance(ecg_id, list) and len(ecg_id) > 0: - from time_series_datasets.ecg_qa.ecgqa_loader import get_ptbxl_ecg_path + from opentslm.time_series_datasets.ecg_qa.ecgqa_loader import get_ptbxl_ecg_path ecg_path = get_ptbxl_ecg_path(ecg_id[0]) + ".dat" ecg_signal, _, _ = cls._load_ecg_data(ecg_path) n_leads = ecg_signal.shape[1] if len(ecg_signal.shape) > 1 else 1 @@ -441,7 +439,7 @@ def _get_text_time_series_prompt_list(self, row) -> List[TextTimeSeriesPrompt]: if not isinstance(ecg_id, list) or len(ecg_id) == 0: raise ValueError(f"Sample 'ecg_id' must be a non-empty list: {ecg_id}") - from time_series_datasets.ecg_qa.ecgqa_loader import get_ptbxl_ecg_path + from opentslm.time_series_datasets.ecg_qa.ecgqa_loader import get_ptbxl_ecg_path ecg_path = get_ptbxl_ecg_path(ecg_id[0]) + ".dat" ecg_paths = [ecg_path] diff --git a/src/time_series_datasets/ecg_qa/ECGQADataset.py b/src/opentslm/time_series_datasets/ecg_qa/ECGQADataset.py similarity index 97% rename from src/time_series_datasets/ecg_qa/ECGQADataset.py rename to src/opentslm/time_series_datasets/ecg_qa/ECGQADataset.py index dacaffaf..89aa7ddc 100644 --- a/src/time_series_datasets/ecg_qa/ECGQADataset.py +++ b/src/opentslm/time_series_datasets/ecg_qa/ECGQADataset.py @@ -20,9 +20,9 @@ "Please install it with: pip install wfdb" ) -from prompt.text_time_series_prompt import TextTimeSeriesPrompt -from time_series_datasets.QADataset import QADataset -from time_series_datasets.ecg_qa.ecgqa_loader import ( +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.time_series_datasets.QADataset import QADataset +from opentslm.time_series_datasets.ecg_qa.ecgqa_loader import ( load_ecg_qa_ptbxl_splits, load_ecg_qa_answers, ) @@ -199,7 +199,7 @@ def get_possible_answers_for_template(self, template_id: int) -> List[str]: try: import pandas as pd import ast - from time_series_datasets.ecg_qa.ecgqa_loader import ECG_QA_DIR + from opentslm.time_series_datasets.ecg_qa.ecgqa_loader import ECG_QA_DIR # Load template answers directly template_answers_path = os.path.join( @@ -233,7 +233,7 @@ def _get_text_time_series_prompt_list(self, row) -> List[TextTimeSeriesPrompt]: # Fallback: single ECG path ecg_id = row["ecg_id"][0] if row["ecg_id"] else None if ecg_id: - from time_series_datasets.ecg_qa.ecgqa_loader import get_ptbxl_ecg_path + from opentslm.time_series_datasets.ecg_qa.ecgqa_loader import get_ptbxl_ecg_path ecg_path = get_ptbxl_ecg_path(ecg_id) + ".dat" ecg_paths = [ecg_path] diff --git a/src/time_series_datasets/ecg_qa/README.md b/src/opentslm/time_series_datasets/ecg_qa/README.md similarity index 99% rename from src/time_series_datasets/ecg_qa/README.md rename to src/opentslm/time_series_datasets/ecg_qa/README.md index 50a97ebf..b6e09d69 100644 --- a/src/time_series_datasets/ecg_qa/README.md +++ b/src/opentslm/time_series_datasets/ecg_qa/README.md @@ -99,7 +99,7 @@ yes ## Quick Start ```python -from time_series_datasets.ecg_qa.ECGQADataset import ECGQADataset +from opentslm.time_series_datasets.ecg_qa.ECGQADataset import ECGQADataset # Load ECG-QA splits (auto-downloads ~6GB of data on first run) train_dataset = ECGQADataset(split="train", EOS_TOKEN="") diff --git a/src/time_series_datasets/ecg_qa/__init__.py b/src/opentslm/time_series_datasets/ecg_qa/__init__.py similarity index 95% rename from src/time_series_datasets/ecg_qa/__init__.py rename to src/opentslm/time_series_datasets/ecg_qa/__init__.py index 5c02d220..ae9a8be6 100644 --- a/src/time_series_datasets/ecg_qa/__init__.py +++ b/src/opentslm/time_series_datasets/ecg_qa/__init__.py @@ -17,7 +17,7 @@ https://github.com/Jwoo5/ecg-qa Usage: - from time_series_datasets.ecg_qa.ECGQADataset import ECGQADataset + from opentslm.time_series_datasets.ecg_qa.ECGQADataset import ECGQADataset # Create dataset instance dataset = ECGQADataset(split="train", EOS_TOKEN="") diff --git a/src/time_series_datasets/ecg_qa/dataset_distribution.png b/src/opentslm/time_series_datasets/ecg_qa/dataset_distribution.png similarity index 100% rename from src/time_series_datasets/ecg_qa/dataset_distribution.png rename to src/opentslm/time_series_datasets/ecg_qa/dataset_distribution.png diff --git a/src/time_series_datasets/ecg_qa/ecg_example_real.png b/src/opentslm/time_series_datasets/ecg_qa/ecg_example_real.png similarity index 100% rename from src/time_series_datasets/ecg_qa/ecg_example_real.png rename to src/opentslm/time_series_datasets/ecg_qa/ecg_example_real.png diff --git a/src/time_series_datasets/ecg_qa/ecgqa_cot_loader.py b/src/opentslm/time_series_datasets/ecg_qa/ecgqa_cot_loader.py similarity index 95% rename from src/time_series_datasets/ecg_qa/ecgqa_cot_loader.py rename to src/opentslm/time_series_datasets/ecg_qa/ecgqa_cot_loader.py index 868c125b..6a818e1e 100644 --- a/src/time_series_datasets/ecg_qa/ecgqa_cot_loader.py +++ b/src/opentslm/time_series_datasets/ecg_qa/ecgqa_cot_loader.py @@ -6,24 +6,16 @@ # SPDX-License-Identifier: MIT # -import os import subprocess -import json import requests import shutil -import pandas as pd -from pathlib import Path from typing import Tuple, Dict, List from datasets import Dataset -import sys import os import zipfile -import tempfile -sys.path.append(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))) -from time_series_datasets.constants import RAW_DATA as RAW_DATA_PATH -from time_series_datasets.ecg_qa.ecgqa_loader import ( - load_ecg_qa_ptbxl_splits, +from opentslm.time_series_datasets.constants import RAW_DATA as RAW_DATA_PATH +from opentslm.time_series_datasets.ecg_qa.ecgqa_loader import ( download_ecg_qa_if_not_exists, download_ptbxl_if_not_exists ) @@ -152,7 +144,7 @@ def load_ecg_qa_cot_splits() -> Tuple[Dataset, Dataset, Dataset]: download_ecg_qa_cot_if_not_exists() import pandas as pd - from time_series_datasets.ecg_qa.ecgqa_loader import get_ptbxl_ecg_path + from opentslm.time_series_datasets.ecg_qa.ecgqa_loader import get_ptbxl_ecg_path def parse_ecg_id(ecg_id_raw: str) -> int: if ecg_id_raw is None: @@ -177,7 +169,7 @@ def load_split_from_csv(split_name: str) -> List[Dict]: raise FileNotFoundError(f"CoT split file not found: {split_file}") print(f"Loading CoT data for {split_name} split from {split_file}...") - print(f"Reading CSV file...") + print("Reading CSV file...") df = pd.read_csv(split_file) print(f"CSV loaded: {len(df)} rows, {len(df.columns)} columns") @@ -279,13 +271,13 @@ def get_label_distribution(dataset: Dataset) -> Dict[str, int]: try: train, val, test = load_ecg_qa_cot_splits() - print(f"Loaded ECG-QA CoT dataset:") + print("Loaded ECG-QA CoT dataset:") print(f" Train: {len(train)} samples") print(f" Validation: {len(val)} samples") print(f" Test: {len(test)} samples") if len(train) > 0: - print(f"\nSample from training set:") + print("\nSample from training set:") sample = train[0] for key, value in sample.items(): if isinstance(value, list) and len(value) > 3: diff --git a/src/time_series_datasets/ecg_qa/ecgqa_loader.py b/src/opentslm/time_series_datasets/ecg_qa/ecgqa_loader.py similarity index 98% rename from src/time_series_datasets/ecg_qa/ecgqa_loader.py rename to src/opentslm/time_series_datasets/ecg_qa/ecgqa_loader.py index 2b82dc73..67d1bb99 100644 --- a/src/time_series_datasets/ecg_qa/ecgqa_loader.py +++ b/src/opentslm/time_series_datasets/ecg_qa/ecgqa_loader.py @@ -16,11 +16,9 @@ from pathlib import Path from typing import Tuple, Dict, List from datasets import Dataset -import sys import os -sys.path.append(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))) ) -from time_series_datasets.constants import RAW_DATA as RAW_DATA_PATH +from opentslm.time_series_datasets.constants import RAW_DATA as RAW_DATA_PATH from tqdm import tqdm diff --git a/src/time_series_datasets/ecg_qa/example_prompt.md b/src/opentslm/time_series_datasets/ecg_qa/example_prompt.md similarity index 100% rename from src/time_series_datasets/ecg_qa/example_prompt.md rename to src/opentslm/time_series_datasets/ecg_qa/example_prompt.md diff --git a/src/time_series_datasets/ecg_qa/plot_example.py b/src/opentslm/time_series_datasets/ecg_qa/plot_example.py similarity index 97% rename from src/time_series_datasets/ecg_qa/plot_example.py rename to src/opentslm/time_series_datasets/ecg_qa/plot_example.py index 0dc4238e..83449635 100644 --- a/src/time_series_datasets/ecg_qa/plot_example.py +++ b/src/opentslm/time_series_datasets/ecg_qa/plot_example.py @@ -13,16 +13,12 @@ """ import os -import sys import json import matplotlib.pyplot as plt import numpy as np import wfdb -# Add the src directory to path for imports -sys.path.append(os.path.join(os.path.dirname(__file__), "..", "..")) - -from time_series_datasets.ecg_qa.ECGQADataset import ECGQADataset +from opentslm.time_series_datasets.ecg_qa.ECGQADataset import ECGQADataset # ECG plotting configuration lead_names = ["I", "II", "III", "aVR", "aVL", "aVF", "V1", "V2", "V3", "V4", "V5", "V6"] diff --git a/src/time_series_datasets/har_cot/HARAccQADataset.py b/src/opentslm/time_series_datasets/har_cot/HARAccQADataset.py similarity index 93% rename from src/time_series_datasets/har_cot/HARAccQADataset.py rename to src/opentslm/time_series_datasets/har_cot/HARAccQADataset.py index 8250b03d..8f942bb5 100644 --- a/src/time_series_datasets/har_cot/HARAccQADataset.py +++ b/src/opentslm/time_series_datasets/har_cot/HARAccQADataset.py @@ -9,13 +9,13 @@ from datasets import Dataset from typing import List, Tuple, Literal -from prompt.text_time_series_prompt import TextTimeSeriesPrompt -from time_series_datasets.QADataset import QADataset -from time_series_datasets.har_cot.har_cot_loader import load_har_cot_splits +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.time_series_datasets.QADataset import QADataset +from opentslm.time_series_datasets.har_cot.har_cot_loader import load_har_cot_splits import torch from torch.utils.data import DataLoader from tqdm.auto import tqdm -from time_series_datasets.util import ( +from opentslm.time_series_datasets.util import ( extend_time_series_to_match_patch_size_and_aggregate, ) diff --git a/src/time_series_datasets/har_cot/HARCoTQADataset.py b/src/opentslm/time_series_datasets/har_cot/HARCoTQADataset.py similarity index 95% rename from src/time_series_datasets/har_cot/HARCoTQADataset.py rename to src/opentslm/time_series_datasets/har_cot/HARCoTQADataset.py index b23c6a4f..37fc3e64 100644 --- a/src/time_series_datasets/har_cot/HARCoTQADataset.py +++ b/src/opentslm/time_series_datasets/har_cot/HARCoTQADataset.py @@ -8,16 +8,14 @@ from datasets import Dataset from typing import List, Tuple, Literal -import sys import os -sys.path.append(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))) -from prompt.text_time_series_prompt import TextTimeSeriesPrompt -from time_series_datasets.QADataset import QADataset -from time_series_datasets.har_cot.har_cot_loader import load_har_cot_splits +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.time_series_datasets.QADataset import QADataset +from opentslm.time_series_datasets.har_cot.har_cot_loader import load_har_cot_splits import torch from torch.utils.data import DataLoader from tqdm.auto import tqdm -from time_series_datasets.util import ( +from opentslm.time_series_datasets.util import ( extend_time_series_to_match_patch_size_and_aggregate, ) import numpy as np diff --git a/src/time_series_datasets/har_cot/__init__.py b/src/opentslm/time_series_datasets/har_cot/__init__.py similarity index 100% rename from src/time_series_datasets/har_cot/__init__.py rename to src/opentslm/time_series_datasets/har_cot/__init__.py diff --git a/src/time_series_datasets/har_cot/har_cot_loader.py b/src/opentslm/time_series_datasets/har_cot/har_cot_loader.py similarity index 97% rename from src/time_series_datasets/har_cot/har_cot_loader.py rename to src/opentslm/time_series_datasets/har_cot/har_cot_loader.py index 89c9ff83..ff50b7f5 100644 --- a/src/time_series_datasets/har_cot/har_cot_loader.py +++ b/src/opentslm/time_series_datasets/har_cot/har_cot_loader.py @@ -13,12 +13,10 @@ import ast import urllib.request import zipfile -import sys -sys.path.append(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))) -from time_series_datasets.constants import RAW_DATA +from opentslm.time_series_datasets.constants import RAW_DATA from tqdm.auto import tqdm import logging -from logger import get_logger +from opentslm.logger import get_logger HAR_COT_DATA_DIR = os.path.join(RAW_DATA, "har_cot") HAR_COT_ZIP = os.path.join(HAR_COT_DATA_DIR, "har_cot.zip") diff --git a/src/time_series_datasets/m4/M4QADataset.py b/src/opentslm/time_series_datasets/m4/M4QADataset.py similarity index 95% rename from src/time_series_datasets/m4/M4QADataset.py rename to src/opentslm/time_series_datasets/m4/M4QADataset.py index 518678cf..f9e3e5d7 100644 --- a/src/time_series_datasets/m4/M4QADataset.py +++ b/src/opentslm/time_series_datasets/m4/M4QADataset.py @@ -19,9 +19,9 @@ import torch from datasets import Dataset -from prompt.text_time_series_prompt import TextTimeSeriesPrompt -from time_series_datasets.QADataset import QADataset -from time_series_datasets.m4.m4_loader import load_all_m4_data, create_combined_dataset +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.time_series_datasets.QADataset import QADataset +from opentslm.time_series_datasets.m4.m4_loader import load_all_m4_data, create_combined_dataset class M4QADataset(QADataset): diff --git a/src/time_series_datasets/m4/__init__.py b/src/opentslm/time_series_datasets/m4/__init__.py similarity index 100% rename from src/time_series_datasets/m4/__init__.py rename to src/opentslm/time_series_datasets/m4/__init__.py diff --git a/src/time_series_datasets/m4/m4_loader.py b/src/opentslm/time_series_datasets/m4/m4_loader.py similarity index 99% rename from src/time_series_datasets/m4/m4_loader.py rename to src/opentslm/time_series_datasets/m4/m4_loader.py index 34c89743..c04bae22 100644 --- a/src/time_series_datasets/m4/m4_loader.py +++ b/src/opentslm/time_series_datasets/m4/m4_loader.py @@ -28,7 +28,7 @@ from typing import Dict, List, Literal, Optional, Tuple from datasets import Dataset from sklearn.model_selection import train_test_split -from time_series_datasets.constants import RAW_DATA +from opentslm.time_series_datasets.constants import RAW_DATA # --------------------------- # Constants diff --git a/src/time_series_datasets/monash/MonashDataset.py b/src/opentslm/time_series_datasets/monash/MonashDataset.py similarity index 97% rename from src/time_series_datasets/monash/MonashDataset.py rename to src/opentslm/time_series_datasets/monash/MonashDataset.py index 30419aab..9e12daf3 100644 --- a/src/time_series_datasets/monash/MonashDataset.py +++ b/src/opentslm/time_series_datasets/monash/MonashDataset.py @@ -14,7 +14,7 @@ from tqdm.auto import tqdm -from time_series_datasets.monash.monash_utils import ( +from opentslm.time_series_datasets.monash.monash_utils import ( download_and_extract_monash_ucr, load_from_tsfile_to_dataframe, ) diff --git a/src/time_series_datasets/monash/MonashSPO2QADataset.py b/src/opentslm/time_series_datasets/monash/MonashSPO2QADataset.py similarity index 90% rename from src/time_series_datasets/monash/MonashSPO2QADataset.py rename to src/opentslm/time_series_datasets/monash/MonashSPO2QADataset.py index 87f2ead1..d0e88c48 100644 --- a/src/time_series_datasets/monash/MonashSPO2QADataset.py +++ b/src/opentslm/time_series_datasets/monash/MonashSPO2QADataset.py @@ -8,10 +8,10 @@ from typing import List, Literal, Optional, Tuple from datasets import Dataset -from prompt.text_time_series_prompt import TextTimeSeriesPrompt -from time_series_datasets.monash.MonashDataset import MonashDataset -from time_series_datasets.QADataset import QADataset -from time_series_datasets.util import ( +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.time_series_datasets.monash.MonashDataset import MonashDataset +from opentslm.time_series_datasets.QADataset import QADataset +from opentslm.time_series_datasets.util import ( extend_time_series_to_match_patch_size_and_aggregate, ) import torch diff --git a/src/time_series_datasets/monash/__init__.py b/src/opentslm/time_series_datasets/monash/__init__.py similarity index 100% rename from src/time_series_datasets/monash/__init__.py rename to src/opentslm/time_series_datasets/monash/__init__.py diff --git a/src/time_series_datasets/monash/monash_utils.py b/src/opentslm/time_series_datasets/monash/monash_utils.py similarity index 100% rename from src/time_series_datasets/monash/monash_utils.py rename to src/opentslm/time_series_datasets/monash/monash_utils.py diff --git a/src/time_series_datasets/pamap2/BalancedBatchSampler.py b/src/opentslm/time_series_datasets/pamap2/BalancedBatchSampler.py similarity index 100% rename from src/time_series_datasets/pamap2/BalancedBatchSampler.py rename to src/opentslm/time_series_datasets/pamap2/BalancedBatchSampler.py diff --git a/src/time_series_datasets/pamap2/PAMAP2AccQADataset.py b/src/opentslm/time_series_datasets/pamap2/PAMAP2AccQADataset.py similarity index 91% rename from src/time_series_datasets/pamap2/PAMAP2AccQADataset.py rename to src/opentslm/time_series_datasets/pamap2/PAMAP2AccQADataset.py index b57bf8ef..5eec8b90 100644 --- a/src/time_series_datasets/pamap2/PAMAP2AccQADataset.py +++ b/src/opentslm/time_series_datasets/pamap2/PAMAP2AccQADataset.py @@ -10,11 +10,11 @@ from typing import List, Tuple import numpy as np -from prompt.text_time_series_prompt import TextTimeSeriesPrompt -from time_series_datasets.QADataset import QADataset -from time_series_datasets.pamap2.PAMAP2Dataset import PAMAP2Dataset, ACTIVITIY_ID_DICT -from time_series_datasets.pamap2.pamap2_loader import PAMAP2_DIR -from time_series_datasets.util import ( +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.time_series_datasets.QADataset import QADataset +from opentslm.time_series_datasets.pamap2.PAMAP2Dataset import PAMAP2Dataset, ACTIVITIY_ID_DICT +from opentslm.time_series_datasets.pamap2.pamap2_loader import PAMAP2_DIR +from opentslm.time_series_datasets.util import ( extend_time_series_to_match_patch_size_and_aggregate, ) import torch diff --git a/src/time_series_datasets/pamap2/PAMAP2CoTQADataset.py b/src/opentslm/time_series_datasets/pamap2/PAMAP2CoTQADataset.py similarity index 94% rename from src/time_series_datasets/pamap2/PAMAP2CoTQADataset.py rename to src/opentslm/time_series_datasets/pamap2/PAMAP2CoTQADataset.py index 4ec30d3d..77ad63a9 100644 --- a/src/time_series_datasets/pamap2/PAMAP2CoTQADataset.py +++ b/src/opentslm/time_series_datasets/pamap2/PAMAP2CoTQADataset.py @@ -8,22 +8,20 @@ from datasets import Dataset from typing import List, Tuple, Literal -import sys import os -sys.path.append(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))) -from prompt.text_time_series_prompt import TextTimeSeriesPrompt -from time_series_datasets.QADataset import QADataset -from time_series_datasets.pamap2.pamap2_cot_loader import load_pamap2_cot_splits +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.time_series_datasets.QADataset import QADataset +from opentslm.time_series_datasets.pamap2.pamap2_cot_loader import load_pamap2_cot_splits import torch from torch.utils.data import DataLoader from tqdm.auto import tqdm -from time_series_datasets.util import ( +from opentslm.time_series_datasets.util import ( extend_time_series_to_match_patch_size_and_aggregate, ) from collections import defaultdict import numpy as np from torch.utils.data import Sampler -from time_series_datasets.pamap2.BalancedBatchSampler import BalancedBatchSampler +from opentslm.time_series_datasets.pamap2.BalancedBatchSampler import BalancedBatchSampler TIME_SERIES_LABELS = [ diff --git a/src/time_series_datasets/pamap2/PAMAP2Dataset.py b/src/opentslm/time_series_datasets/pamap2/PAMAP2Dataset.py similarity index 98% rename from src/time_series_datasets/pamap2/PAMAP2Dataset.py rename to src/opentslm/time_series_datasets/pamap2/PAMAP2Dataset.py index ffe1bbef..9266c89c 100644 --- a/src/time_series_datasets/pamap2/PAMAP2Dataset.py +++ b/src/opentslm/time_series_datasets/pamap2/PAMAP2Dataset.py @@ -8,7 +8,7 @@ from typing import Tuple import pandas as pd -from time_series_datasets.pamap2.pamap2_loader import ensure_pamap2_data +from opentslm.time_series_datasets.pamap2.pamap2_loader import ensure_pamap2_data from torch.utils.data import Dataset ACTIVITIY_ID_DICT = { diff --git a/src/time_series_datasets/pamap2/__init__.py b/src/opentslm/time_series_datasets/pamap2/__init__.py similarity index 100% rename from src/time_series_datasets/pamap2/__init__.py rename to src/opentslm/time_series_datasets/pamap2/__init__.py diff --git a/src/time_series_datasets/pamap2/pamap2_cot_loader.py b/src/opentslm/time_series_datasets/pamap2/pamap2_cot_loader.py similarity index 98% rename from src/time_series_datasets/pamap2/pamap2_cot_loader.py rename to src/opentslm/time_series_datasets/pamap2/pamap2_cot_loader.py index 88a5c23e..965976f4 100644 --- a/src/time_series_datasets/pamap2/pamap2_cot_loader.py +++ b/src/opentslm/time_series_datasets/pamap2/pamap2_cot_loader.py @@ -14,10 +14,10 @@ import urllib.request import zipfile import shutil -from time_series_datasets.constants import RAW_DATA +from opentslm.time_series_datasets.constants import RAW_DATA import math import logging -from logger import get_logger +from opentslm.logger import get_logger PAMAP_DATA_DIR = os.path.join(RAW_DATA, "pamap") diff --git a/src/time_series_datasets/pamap2/pamap2_loader.py b/src/opentslm/time_series_datasets/pamap2/pamap2_loader.py similarity index 97% rename from src/time_series_datasets/pamap2/pamap2_loader.py rename to src/opentslm/time_series_datasets/pamap2/pamap2_loader.py index 0b3bb65c..7eba04ae 100644 --- a/src/time_series_datasets/pamap2/pamap2_loader.py +++ b/src/opentslm/time_series_datasets/pamap2/pamap2_loader.py @@ -10,7 +10,7 @@ import zipfile import requests -from time_series_datasets.constants import RAW_DATA as RAW_DATA_PATH +from opentslm.time_series_datasets.constants import RAW_DATA as RAW_DATA_PATH # --------------------------- diff --git a/src/time_series_datasets/simulation/SimulationQADataset.py b/src/opentslm/time_series_datasets/simulation/SimulationQADataset.py similarity index 97% rename from src/time_series_datasets/simulation/SimulationQADataset.py rename to src/opentslm/time_series_datasets/simulation/SimulationQADataset.py index ceedc226..419747f3 100644 --- a/src/time_series_datasets/simulation/SimulationQADataset.py +++ b/src/opentslm/time_series_datasets/simulation/SimulationQADataset.py @@ -11,8 +11,8 @@ from typing import List, Tuple from datasets import Dataset -from prompt.text_time_series_prompt import TextTimeSeriesPrompt -from time_series_datasets.QADataset import QADataset +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.time_series_datasets.QADataset import QADataset DATASET_SIZE = 200 diff --git a/src/time_series_datasets/sleep/SleepEDFCoTQADataset.py b/src/opentslm/time_series_datasets/sleep/SleepEDFCoTQADataset.py similarity index 91% rename from src/time_series_datasets/sleep/SleepEDFCoTQADataset.py rename to src/opentslm/time_series_datasets/sleep/SleepEDFCoTQADataset.py index a9b2241f..24491349 100644 --- a/src/time_series_datasets/sleep/SleepEDFCoTQADataset.py +++ b/src/opentslm/time_series_datasets/sleep/SleepEDFCoTQADataset.py @@ -8,12 +8,10 @@ from datasets import Dataset from typing import List, Tuple, Literal -import sys import os -sys.path.append(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))) ) -from prompt.text_time_series_prompt import TextTimeSeriesPrompt -from time_series_datasets.QADataset import QADataset -from time_series_datasets.sleep.sleepedf_cot_loader import load_sleepedf_cot_splits +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.time_series_datasets.QADataset import QADataset +from opentslm.time_series_datasets.sleep.sleepedf_cot_loader import load_sleepedf_cot_splits import numpy as np class SleepEDFCoTQADataset(QADataset): diff --git a/src/time_series_datasets/sleep/SleepEDFQADataset.py b/src/opentslm/time_series_datasets/sleep/SleepEDFQADataset.py similarity index 93% rename from src/time_series_datasets/sleep/SleepEDFQADataset.py rename to src/opentslm/time_series_datasets/sleep/SleepEDFQADataset.py index 24c7ead3..d355bf14 100644 --- a/src/time_series_datasets/sleep/SleepEDFQADataset.py +++ b/src/opentslm/time_series_datasets/sleep/SleepEDFQADataset.py @@ -8,15 +8,10 @@ from datasets import Dataset from typing import List, Tuple, Literal -import sys import os - -sys.path.append( - os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))) -) -from prompt.text_time_series_prompt import TextTimeSeriesPrompt -from time_series_datasets.QADataset import QADataset -from time_series_datasets.sleep.sleepedf_cot_loader import load_sleepedf_cot_splits +from opentslm.prompt.text_time_series_prompt import TextTimeSeriesPrompt +from opentslm.time_series_datasets.QADataset import QADataset +from opentslm.time_series_datasets.sleep.sleepedf_cot_loader import load_sleepedf_cot_splits import numpy as np diff --git a/src/time_series_datasets/sleep/__init__.py b/src/opentslm/time_series_datasets/sleep/__init__.py similarity index 100% rename from src/time_series_datasets/sleep/__init__.py rename to src/opentslm/time_series_datasets/sleep/__init__.py diff --git a/src/time_series_datasets/sleep/sleepedf_cot_loader.py b/src/opentslm/time_series_datasets/sleep/sleepedf_cot_loader.py similarity index 98% rename from src/time_series_datasets/sleep/sleepedf_cot_loader.py rename to src/opentslm/time_series_datasets/sleep/sleepedf_cot_loader.py index 19d7ad34..79cd876c 100644 --- a/src/time_series_datasets/sleep/sleepedf_cot_loader.py +++ b/src/opentslm/time_series_datasets/sleep/sleepedf_cot_loader.py @@ -12,7 +12,7 @@ from typing import Tuple, Dict import ast import urllib.request -from time_series_datasets.constants import RAW_DATA +from opentslm.time_series_datasets.constants import RAW_DATA from tqdm.auto import tqdm from sklearn.model_selection import train_test_split diff --git a/src/time_series_datasets/ucr/__init__.py b/src/opentslm/time_series_datasets/ucr/__init__.py similarity index 100% rename from src/time_series_datasets/ucr/__init__.py rename to src/opentslm/time_series_datasets/ucr/__init__.py diff --git a/src/time_series_datasets/ucr/ucr_loader.py b/src/opentslm/time_series_datasets/ucr/ucr_loader.py similarity index 100% rename from src/time_series_datasets/ucr/ucr_loader.py rename to src/opentslm/time_series_datasets/ucr/ucr_loader.py diff --git a/src/time_series_datasets/util.py b/src/opentslm/time_series_datasets/util.py similarity index 97% rename from src/time_series_datasets/util.py rename to src/opentslm/time_series_datasets/util.py index 36492458..4cb38987 100644 --- a/src/time_series_datasets/util.py +++ b/src/opentslm/time_series_datasets/util.py @@ -8,7 +8,7 @@ import math from typing import List -from model_config import PATCH_SIZE +from opentslm.model_config import PATCH_SIZE import torch.nn.functional as F diff --git a/src/prompt/__init__.py b/src/prompt/__init__.py deleted file mode 100644 index a0e99417..00000000 --- a/src/prompt/__init__.py +++ /dev/null @@ -1,13 +0,0 @@ -# -# This source file is part of the OpenTSLM open-source project -# -# SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md) -# -# SPDX-License-Identifier: MIT -# - -# from .prompt import Prompt -# from .full_prompt import FullPrompt -# from .text_prompt import TextPrompt -# from .text_time_series_prompt import TextTimeSeriesPrompt -# from .prompt_with_answer import PromptWithAnswer diff --git a/src/time_series_datasets/tsqa.py b/src/time_series_datasets/tsqa.py deleted file mode 100644 index 58b2b2ac..00000000 --- a/src/time_series_datasets/tsqa.py +++ /dev/null @@ -1,27 +0,0 @@ -# -# This source file is part of the OpenTSLM open-source project -# -# SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md) -# -# SPDX-License-Identifier: MIT -# - -from typing import Literal, Optional - -from time_series_datasets.util import load_qa_dataset -from datasets import load_dataset -from src.model_config import * - - -def get_tsqa_dataset( - split: Literal["train", "validation", "test"] = "train", - *, - EOS_TOKEN, - max_samples: Optional[int] = None, -): - return load_qa_dataset( - load_dataset("ChengsenWang/TSQA", split="train"), - split=split, - max_samples=max_samples, - EOS_TOKEN=EOS_TOKEN, - ) diff --git a/test/ecg_qa_cot_test.py b/test/ecg_qa_cot_test.py index a213551b..6c795ad7 100644 --- a/test/ecg_qa_cot_test.py +++ b/test/ecg_qa_cot_test.py @@ -12,16 +12,12 @@ """ import unittest -import sys -import os -sys.path.append(os.path.join(os.path.dirname(__file__), '..', "src")) - -# Import and set up global logger with verbose mode -from logger import get_logger, set_global_verbose +from opentslm.time_series_datasets.ecg_qa.ECGQACoTQADataset import ECGQACoTQADataset +from opentslm.logger import get_logger, set_global_verbose def pretty_print_label_distribution(dataset, name): """Pretty print label distribution for a dataset.""" - from time_series_datasets.ecg_qa.ecgqa_cot_loader import get_label_distribution + from opentslm.time_series_datasets.ecg_qa.ecgqa_cot_loader import get_label_distribution label_dist = get_label_distribution(dataset) total = len(dataset) print(f"\n{name} dataset:") @@ -39,7 +35,7 @@ def setUp(self): set_global_verbose(True) self.logger = get_logger() - from time_series_datasets.ecg_qa.ecgqa_cot_loader import load_ecg_qa_cot_splits + from opentslm.time_series_datasets.ecg_qa.ecgqa_cot_loader import load_ecg_qa_cot_splits self.load_ecg_qa_cot_splits = load_ecg_qa_cot_splits self.logger.loading("Loading ECG-QA CoT dataset splits...") @@ -61,7 +57,7 @@ def test_label_distribution(self): pretty_print_label_distribution(self.val, "Validation") pretty_print_label_distribution(self.test, "Test") - from time_series_datasets.ecg_qa.ecgqa_cot_loader import get_label_distribution + from opentslm.time_series_datasets.ecg_qa.ecgqa_cot_loader import get_label_distribution train_dist = get_label_distribution(self.train) val_dist = get_label_distribution(self.val) test_dist = get_label_distribution(self.test) @@ -193,7 +189,7 @@ def setUp(self): set_global_verbose(True) self.logger = get_logger() - from time_series_datasets.ecg_qa import ECGQACoTQADataset + from opentslm.time_series_datasets.ecg_qa import ECGQACoTQADataset self.ECGQACoTQADataset = ECGQACoTQADataset self.logger.loading("Initializing ECGQACoTQADataset...") @@ -388,7 +384,7 @@ def test_error_handling_missing_fields(self): self.logger.info("Testing error handling for missing fields...") # Create a sample with missing fields to test error handling - from time_series_datasets.ecg_qa import ECGQACoTQADataset + from opentslm.time_series_datasets.ecg_qa import ECGQACoTQADataset # This should work normally try: diff --git a/test/ecg_qa_test.py b/test/ecg_qa_test.py index 105f9cde..f5054b8b 100644 --- a/test/ecg_qa_test.py +++ b/test/ecg_qa_test.py @@ -19,17 +19,14 @@ Usage: python test_ecgqa.py """ - -import sys import sys -import os -sys.path.append(os.path.join(os.path.dirname(__file__), '..', "src")) + def test_ecgqa_loader(): """Test the ECG-QA loader functions.""" print("Testing ECG-QA loader...") try: - from time_series_datasets.ecg_qa.ecgqa_loader import ( + from opentslm.time_series_datasets.ecg_qa.ecgqa_loader import ( does_ecg_qa_exist, does_ptbxl_exist, download_ecg_qa_if_not_exists, @@ -58,7 +55,7 @@ def test_ecgqa_dataset(): print("\nTesting ECGQADataset...") try: - from time_series_datasets.ecg_qa.ECGQADataset import ECGQADataset + from opentslm.time_series_datasets.ecg_qa.ECGQADataset import ECGQADataset # Try to create dataset instances with limited samples for faster testing print("Creating dataset instances (limited to 5 samples each for testing)...") diff --git a/test/eval_EmbedHealthFlamingo.py b/test/eval_EmbedHealthFlamingo.py index dce2c1bc..49a8dd4b 100644 --- a/test/eval_EmbedHealthFlamingo.py +++ b/test/eval_EmbedHealthFlamingo.py @@ -8,18 +8,18 @@ import json from typing import List -from time_series_datasets.TSQADataset import TSQADataset -from time_series_datasets.monash.MonashSPO2QADataset import MonashSPO2QADataset -from time_series_datasets.util import ( +from opentslm.time_series_datasets.TSQADataset import TSQADataset +from opentslm.time_series_datasets.monash.MonashSPO2QADataset import MonashSPO2QADataset +from opentslm.time_series_datasets.util import ( extend_time_series_to_match_patch_size_and_aggregate, ) import torch from torch.utils.data import ConcatDataset, DataLoader, Dataset from tqdm.auto import tqdm -from model.encoder.TransformerCNNEncoder import TransformerCNNEncoder -from model.llm.OpenTSLMFlamingo import OpenTSLMFlamingo -from src.model_config import ( +from opentslm.model.encoder.TransformerCNNEncoder import TransformerCNNEncoder +from opentslm.model.llm.OpenTSLMFlamingo import OpenTSLMFlamingo +from opentslm.model_config import ( PATCH_SIZE, RESULTS_FILE, ) diff --git a/test/har_cot_test.py b/test/har_cot_test.py index 44226eeb..48ea9ded 100644 --- a/test/har_cot_test.py +++ b/test/har_cot_test.py @@ -12,16 +12,13 @@ """ import unittest -import sys -import os -sys.path.append(os.path.join(os.path.dirname(__file__), '..', "src")) # Import and set up global logger with verbose mode -from logger import get_logger, set_global_verbose +from opentslm.logger import get_logger, set_global_verbose def pretty_print_label_distribution(dataset, name): """Pretty print label distribution for a dataset.""" - from time_series_datasets.har_cot.har_cot_loader import get_label_distribution + from opentslm.time_series_datasets.har_cot.har_cot_loader import get_label_distribution label_dist = get_label_distribution(dataset) total = len(dataset) print(f"\n{name} dataset:") @@ -39,7 +36,7 @@ def setUp(self): set_global_verbose(True) self.logger = get_logger() - from time_series_datasets.har_cot.har_cot_loader import load_har_cot_splits + from opentslm.time_series_datasets.har_cot.har_cot_loader import load_har_cot_splits self.load_har_cot_splits = load_har_cot_splits self.logger.loading("Loading HAR CoT dataset splits...") @@ -61,7 +58,7 @@ def test_label_distribution(self): pretty_print_label_distribution(self.val, "Validation") pretty_print_label_distribution(self.test, "Test") - from time_series_datasets.har_cot.har_cot_loader import get_label_distribution + from opentslm.time_series_datasets.har_cot.har_cot_loader import get_label_distribution train_dist = get_label_distribution(self.train) val_dist = get_label_distribution(self.val) test_dist = get_label_distribution(self.test) @@ -151,7 +148,7 @@ def setUp(self): set_global_verbose(True) self.logger = get_logger() - from time_series_datasets.har_cot.HARCoTQADataset import HARCoTQADataset + from opentslm.time_series_datasets.har_cot.HARCoTQADataset import HARCoTQADataset self.HARCoTQADataset = HARCoTQADataset self.logger.loading("Initializing HARCoTQADataset...") diff --git a/test/m4_loader_test.py b/test/m4_loader_test.py index e80d8082..e735edd7 100644 --- a/test/m4_loader_test.py +++ b/test/m4_loader_test.py @@ -12,17 +12,14 @@ """ import unittest -import sys -import os -sys.path.append(os.path.join(os.path.dirname(__file__), '..', "src")) +from opentslm.time_series_datasets.m4.M4QADataset import M4QADataset as _M4QADataset class TestM4QADataset(unittest.TestCase): """ Unit tests for the M4QADataset class and loader. """ def setUp(self): - from time_series_datasets.m4.M4QADataset import M4QADataset - self.M4QADataset = M4QADataset + self.M4QADataset = _M4QADataset self.train_dataset = self.M4QADataset("train", "") self.val_dataset = self.M4QADataset("validation", "") self.test_dataset = self.M4QADataset("test", "") diff --git a/test/pamap_cot_loader_test.py b/test/pamap_cot_loader_test.py index 99f3cd8b..30091ae2 100644 --- a/test/pamap_cot_loader_test.py +++ b/test/pamap_cot_loader_test.py @@ -12,13 +12,12 @@ """ import unittest -import sys -import os -sys.path.append(os.path.join(os.path.dirname(__file__), '..', "src")) +from opentslm.logger import get_logger, set_global_verbose +from opentslm.time_series_datasets.pamap2.BalancedBatchSampler import BalancedBatchSampler # Import and set up global logger with verbose mode -from logger import get_logger, set_global_verbose -from time_series_datasets.pamap2.BalancedBatchSampler import BalancedBatchSampler +from opentslm.logger import get_logger, set_global_verbose +from opentslm.time_series_datasets.pamap2.BalancedBatchSampler import BalancedBatchSampler class TestPAMAP2CoTLoader(unittest.TestCase): """ Unit tests for the PAMAP2 CoT loader functions. @@ -28,7 +27,7 @@ def setUp(self): set_global_verbose(True) self.logger = get_logger() - from time_series_datasets.pamap2.pamap2_cot_loader import load_pamap2_cot_splits + from opentslm.time_series_datasets.pamap2.pamap2_cot_loader import load_pamap2_cot_splits self.load_pamap2_cot_splits = load_pamap2_cot_splits self.logger.loading("Loading PAMAP2 CoT dataset splits...") @@ -91,7 +90,7 @@ def setUp(self): set_global_verbose(True) self.logger = get_logger() - from time_series_datasets.pamap2.PAMAP2CoTQADataset import PAMAP2CoTQADataset + from opentslm.time_series_datasets.pamap2.PAMAP2CoTQADataset import PAMAP2CoTQADataset self.PAMAP2CoTQADataset = PAMAP2CoTQADataset self.logger.loading("Initializing PAMAP2CoTQADataset...") @@ -197,8 +196,8 @@ def test_balanced_batches_pamap2cot(self): Test that BalancedBatchSampler produces balanced batches on the real PAMAP2CoTQADataset training split. Prints batch labels and class counts for each batch. """ - from time_series_datasets.pamap2.PAMAP2CoTQADataset import PAMAP2CoTQADataset - from time_series_datasets.pamap2.BalancedBatchSampler import BalancedBatchSampler + from opentslm.time_series_datasets.pamap2.PAMAP2CoTQADataset import PAMAP2CoTQADataset + from opentslm.time_series_datasets.pamap2.BalancedBatchSampler import BalancedBatchSampler # Helper to extract label from answer string def extract_label_from_answer(answer: str) -> str: # Assumes answer ends with 'Answer: