chugr 0.2.0.dev0__tar.gz

chugr-0.2.0.dev0/LICENSE

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chugr-0.2.0.dev0/PKG-INFO

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+Metadata-Version: 2.4
+Name: chugr
+Version: 0.2.0.dev0
+Summary: Data pipelines for document and image-text training: webdataset and Hugging Face datasets, PDF decoding, NaFlex batching
+Keywords: webdataset,datasets,data-loading,documents,pdf,pytorch
+Author-Email: Ross Wightman <rwightman@gmail.com>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Project-URL: homepage, https://github.com/rwightman/chugr
+Project-URL: repository, https://github.com/rwightman/chugr
+Requires-Python: >=3.10
+Requires-Dist: webdataset
+Requires-Dist: braceexpand
+Requires-Dist: datasets
+Requires-Dist: timm
+Requires-Dist: torch
+Requires-Dist: torchvision
+Requires-Dist: numpy
+Requires-Dist: pillow
+Requires-Dist: pyyaml
+Requires-Dist: pypdfium2
+Provides-Extra: alb
+Requires-Dist: albumentations; extra == "alb"
+Requires-Dist: opencv-python-headless; extra == "alb"
+Provides-Extra: text
+Requires-Dist: transformers; extra == "text"
+Requires-Dist: fonttools; extra == "text"
+Description-Content-Type: text/markdown
+
+# Chugging Data (`chugr`)
+
+Data pipelines for training multi-modal models on documents and image + text pairs, built on
+[`webdataset`](https://github.com/webdataset/webdataset) and Hugging Face [`datasets`](https://github.com/huggingface/datasets).
+
+* `webdataset` tar shards for scalable (streamed, sharded) pretraining, Hugging Face `datasets` (map-style or streaming)
+  for exploration, validation and fine-tuning, behind one config driven `create_loader()`
+* On the fly PDF decoding and rendering, so large collections of native `.pdf` files can be streamed w/o pre-rendering
+  pages to `.png` / `.tiff`. The PDF decoder works at the webdataset level and can be plugged into other pipelines
+* Document image transforms (incl. an `albumentations` port of the `nougat` augmentations) and NaFlex (native aspect,
+  variable resolution) patch sequence transforms
+* NaFlex batching: per batch sequence lengths sized to a token budget, w/ a rank-identical schedule. This padded,
+  per sample scheme is the focus for variable aspect / size images, not NaViT style multi-image sequence packing
+* Task pipelines for document reading (OCR targets), document VQA and image-text, w/ tokenization and prompt handling
+* Interval based training: fixed sample counts per interval, the same number of batches on every rank, shard lists that
+  repeat (reshuffled per pass) or are resampled, distributed eval w/o padded or repeated samples
+
+`chugr` is the continuation of the original `chug` library (huggingface/chug), renamed and revived. It provides the
+data pipelines for [`pixr`](https://github.com/rwightman/pixr).
+
+## Installation
+
+```bash
+pip install --pre chugr
+# optional extras: albumentations based transforms (doc_nougat), HF tokenizers by name + synthetic text font checks
+pip install --pre "chugr[alb,text]"
+```
+
+PDF rendering uses [pypdfium2](https://github.com/pypdfium2-team/pypdfium2) by default.
+[fitz / PyMuPDF](https://github.com/pymupdf/PyMuPDF) can be used instead if your use case is okay with its AGPL-3.0
+license, it must be installed separately and enabled w/ `CHUGR_USE_AGPL_PYMUPDF=1`.
+
+## Status
+
+Alpha. Major features work and have been used for document reading pretraining and DocVQA fine-tuning, expect breaking
+changes. `pip install --pre chugr` installs the current dev version.
+
+### Changes since `chug`
+* `simple_parsing` dependency replaced by a minimal `Serializable` mixin and nested dataclass CLI parser (`chugr.common.parse_args`)
+* NaFlex (native aspect, variable resolution) document transforms (`doc_naflex`) producing patch sequences + coords, padded by `chugr.common.collate`
+* Fixes for `doc_basic` / `doc_better` train transforms, albumentations 2.x support for `doc_nougat`
+* HF datasets loader: shuffled & sharded `IntervalSampler` for training (w/ intervals shorter than an epoch), split slicing (`train[:1000]`)
+* `python -m chugr.app.test` to benchmark loaders and dump (reassembled) samples
+* NaFlex batching (`chugr.naflex`, adapted from OpenCLIP's streaming NaFlex loader): a rank-identical schedule of
+  `(seq_len, batch_size)` per batch drawn from `naflex_seq_lens` / `naflex_seq_len_probs` and sized to a token budget
+  (`naflex_max_tokens`, w/ optional per row `naflex_text_tokens` cost), samples are resized to each batch's patch
+  budget. `length_bucketing` pool sorts samples by target text length. `mean_batch_size` is exposed on the loader for
+  loss scaling.
+* Webdataset shard lists repeat (reshuffled per pass) instead of requiring `resampled`, so fixed sample count
+  intervals and NaFlex batching work w/o sampling shards w/ replacement
+* NaFlex batching for HF datasets. Map-style (`format hfds`, `NaFlexMapDataset` adapted from OpenCLIP's
+  `NaFlexMapDatasetWrapper`): the same schedule over rank sharded shuffled indices that continue through the dataset
+  across intervals, failed samples are replaced. Streaming (`hfids`): `NaFlexBatcher` over the repeating stream.
+* Streaming HF datasets yield a fixed number of train batches per worker (the stream wraps around), so every rank
+  sees the same number of batches per interval, as the webdataset loader. `num_workers` is limited to the number of
+  data shards (files) per rank. The dataset epoch (shard / shuffle seed) is set from the main process only.
+* Ranks are split w/ the explicit `DistributedCfg` rank / world size (no reliance on `RANK` / `WORLD_SIZE` env vars
+  in dataloader workers), per rank seeds are spaced by a large stride (`chugr.common.rank_seed`) so runs w/ nearby
+  seeds don't share streams.
+* Eval splits are exact: map-style HF datasets are split across ranks w/o padding or repeated samples (uneven per rank
+  counts), uncapped streaming eval reads every sample once.
+* Webdataset eval: `num_samples` below the dataset size caps the eval set to exactly the first `num_samples` samples
+  for any number of ranks / workers (every worker reads that head of the stream, keep it small). W/o a cap all
+  samples are used, split by shard if there are at least `ranks * workers` shards, otherwise by sample.
+* Text preprocessing w/ a `prompt_end_token`: an over-long prompt (question) is shortened so the prompt end token
+  and target (answer) still fit in `max_length`.
+
+## Roadmap
+
+### Nearish
+* Cleanup and refinement, codebase will change
+* Documentation & unit-tests
+* Support reading of info .json/.yaml files for automatic shard info resolution for webdatasets (like timm)
+
+### Mediumish
+* Option to output bbox annotations for lines (or word + word output) for tasks that leverage layout
+* Unified preprocessor functions for combined image + text tokenization (img+text token interleaving, etc.)
+
+### Longish 
+* Increase range of task pipelines for other tasks, modelling needs
+* Support additional modalities & targets (video, audio, detection/dense pixel targets, image/video/audio targets)
+* Explore alternatives to .tar shards (array_record, arrow, etc)
+
+## Design
+
+### Submodule Hierarchy
+
+The library has been designed so that functions, classes at different levels can be used independently.
+
+If one wants to build a loader & pipeline with JSON/YAML serializable configs, use the top-level `chugr.create_loader()` in `chugr/loader.py`. Depending on dataset sources, one can easily switch this between webdataset, HF datasets (in the future, other sources).
+
+Bypassing the highest level, one can also call `build_pipeline_*` methods in `task_pipeline` and then call `create_loader_wds` with a full array of args for `wds` only use cases.
+
+If one doesn't want to use `chugr` loaders and pipelines at all, `image`, `text`, and `wds` (especially decoder) functionality may be useful in other projects.
+
+#### Library modules (highest to lowest level)
+
+The dependencies of modules within the library are intended to follow the hierarchy below. e.g. doc depends on wds, but wds should never depend on doc.
+
+```
+app
+|
+loader (chugr/loader.py)
+|
+task_pipeline
+|
+doc
+|
+wds, hfds, image, text
+|
+common
+```
+
+### Submodules
+
+#### `common`
+
+Configs, structures (dataclasses) for general use across the library
+
+#### `wds`
+
+Webdataset (`wds` for short) specific code. Extensions and alterations of webdataset functionality to fit covered use case and improve robustness.
+
+All data pipelines in `chugr` currently leverage `wds` pipelines, even when not using `wds` datasets. 
+
+Document oriented decoding (pdf decoder) is present in `chugr/wds/decode.py`, it can be used with any webdataset pipeline as a decoder. e.g. `wds.decode(chugr.wds.DecodeDoc('pill'), 'pill')`
+
+#### `hfds`
+
+Hugging Face `datasets` support. A minimal wrapper that allows `datasets` to be used with chugr processing pipelines. 
+
+The processing pipelines remain webdataset based when using `datasets`, they are invoked by a custom collate class.
+
+#### `image`
+
+Image processing, `torchvision` and `albumentations` based transform building code. A mix of generic image (imagenet, simclr) transforms and document specific transforms, including an implementation of `albumentations` based `nougat` transforms.
+
+#### `text`
+
+Text processing, tokenization code.
+
+#### `doc`
+
+Document processing code. Currently focused on processors that apply image/pdf decoders and process document OCR or VQA annotations.
+
+#### `task_pipeline`
+
+Task specific pipelines, where dataset formats meet modelling needs. 
+
+Inputs to task pipelines are sample dictionaries based on the dataset form, they are decoded and then processed into outputs that match model input requirements.
+
+Task specific pipelines that handle the data <--> model input interface are inserted into an encompassing data pipeline which handles shard lists, shuffle, wrapping, distributed worker, splitting, batching, etc.
+
+#### `naflex`
+
+NaFlex (variable sequence length) batching helpers: `NaFlexBatchScheduler` (rank-identical seq len / batch size
+schedule from a token budget), `NaFlexBatcher` (per seq len processors + batching of a sample stream),
+`NaFlexMapDataset` (the same over a map-style dataset), `LengthBucketer`.
+
+#### `chugr.loader`
+
+This lone top-level file includes the main factory methods for creating loaders w/ associated pipelines from config dataclasses.
+
+#### `app`
+
+Most applications using `chugr` will exist outside of the lib in training libraries, etc. Some builtin utility / exploration apps will be included here.
+
+## Datasets
+
+Datasets that work well with this library can be found on the Hugging Face Hub under the `pixparse` organization (https://huggingface.co/pixparse).
+
+We'll add links to other noteworthy datasets that can be used as we become aware of them.
+
+
+## Usage / Examples
+
+### Document Reading, Training w/ IDL
+```python
+import chugr
+img_cfg = chugr.ImageInputCfg(size=(1024, 768), transform_type='doc_better')
+img_fn = chugr.create_image_preprocessor(input_cfg=img_cfg, is_training=True)
+txt_fn = chugr.create_text_preprocessor(
+    'naver-clova-ix/donut-base',
+    prompt_end_token='<s_idl>',
+    task_start_token='<s_idl>',  # NOTE needs to be added to tokenizer
+)
+
+task_cfg = chugr.DataTaskDocReadCfg(
+    image_process_fn=img_fn,
+    text_process_fn=txt_fn,
+    page_sampling='random',
+    error_handler='dump_and_reraise',
+)
+data_cfg = chugr.DataCfg(
+    source='pipe:curl -s -f -L https://huggingface.co/datasets/pixparse/idl-wds/resolve/main/idl-train-0{0000..2999}.tar',
+    batch_size=8,
+    num_samples=3144726,
+    format='wds',
+)
+lb = chugr.create_loader(
+    data_cfg,
+    task_cfg,
+    is_training=True,
+)
+ii = iter(lb)
+sample = next(ii)
+```
+
+### Document Reading, Exploring IDL
+```python
+import chugr
+task_cfg = chugr.DataTaskDocReadCfg(page_sampling='all')
+data_cfg = chugr.DataCfg(
+    source='pixparse/idl-wds',
+    split='train',
+    batch_size=None,
+    format='hfids',
+    num_workers=0,    
+)
+lb = chugr.create_loader(
+    data_cfg,
+    task_cfg,
+)
+ii = iter(lb)
+sample = next(ii)
+```
+
+### Document Reading, Training with PDFA
+
+```python
+import chugr
+img_cfg = chugr.ImageInputCfg(size=(1024, 768), transform_type='doc_nougat')
+img_fn = chugr.create_image_preprocessor(input_cfg=img_cfg, is_training=True)
+txt_fn = chugr.create_text_preprocessor(
+    'naver-clova-ix/donut-base',
+    prompt_end_token='<s_pdfa>',
+    task_start_token='<s_pdfa>',  # NOTE needs to be added to tokenizer
+)
+
+task_cfg = chugr.DataTaskDocReadCfg(
+    image_process_fn=img_fn,
+    text_process_fn=txt_fn,
+    page_sampling='random',
+)
+data_cfg = chugr.DataCfg(
+    source='pipe:curl -s -f -L https://huggingface.co/datasets/pixparse/pdfa-english-train/resolve/main/pdfa-eng-train-{000000..005000}.tar',
+    batch_size=8,
+    num_samples=1000000,  # FIXME replace with actual
+    format='wds',   
+)
+lb = chugr.create_loader(
+    data_cfg,
+    task_cfg,
+    is_training=True,
+)
+ii = iter(lb)
+sample = next(ii)
+```
+
+### Document Reading, Exploring PDFA
+
+```python
+import chugr
+
+task_cfg = chugr.DataTaskDocReadCfg(
+    page_sampling='all',
+)
+data_cfg = chugr.DataCfg(
+    source='pixparse/pdfa-eng-wds',
+    split='train',
+    batch_size=None,
+    format='hfids',
+    num_workers=0,
+)
+lb = chugr.create_loader(
+    data_cfg,
+    task_cfg,
+)
+ii = iter(lb)
+sample = next(ii)
+```
+
+
+### NaFlex (variable resolution) document input
+
+```python
+import chugr
+from PIL import Image
+
+# pages keep their aspect ratio, resized to fit a patch budget (max_seq_len patches of patch_size x patch_size)
+img_cfg = chugr.ImageInputCfg(transform_type='doc_naflex', patch_size=16, max_seq_len=1024)
+img_fn = chugr.create_image_preprocessor(input_cfg=img_cfg, is_training=True)
+out = img_fn(Image.new('L', (850, 1100), 255))
+# {'patches': [N, 256], 'patch_coord': [N, 2] (y, x), 'patch_valid': [N] bool}, N <= max_seq_len
+```
+
+For batches w/ a sequence length (patch budget) drawn per batch and the batch size set by a token budget, set
+`naflex_seq_lens`, `naflex_seq_len_probs` and `naflex_max_tokens` in `DataCfg` (webdataset, map-style or streaming
+HF datasets).
+
+### Image + Text
+
+#### Training
+
+```python
+import chugr
+import transformers
+from functools import partial
+img_cfg = chugr.ImageInputCfg(size=(512, 512), transform_type='image_timm')
+img_fn = chugr.create_image_preprocessor(input_cfg=img_cfg, is_training=True)
+tokenizer = transformers.AutoTokenizer.from_pretrained('laion/CLIP-ViT-H-14-laion2B-s32B-b79K')
+txt_fn = partial(chugr.tokenize, max_length=1000, tokenizer=tokenizer)
+task_cfg = chugr.DataTaskImageTextCfg(
+    image_process_fn=img_fn,
+    text_process_fn=txt_fn,
+)
+data_cfg = chugr.DataCfg(
+    source='pipe:curl -s -f -L https://huggingface.co/datasets/pixparse/cc12m-wds/resolve/main/cc12m-train-{0000..2175}.tar',
+    batch_size=8,
+    num_samples=10968539,
+    format='wds',   
+)
+lb = chugr.create_loader(
+    data_cfg,
+    task_cfg,
+    is_training=True,
+)
+ii = iter(lb)
+sample = next(ii)
+```
+
+### Document VQA
+
+#### Training, Fine-tuning
+```python
+import chugr
+img_cfg = chugr.ImageInputCfg(size=(1024, 768), transform_type='doc_basic')
+img_fn = chugr.create_image_preprocessor(img_cfg, is_training=True)
+txt_fn = chugr.create_text_preprocessor(
+    'naver-clova-ix/donut-base-finetuned-docvqa',
+    prompt_end_token='<s_answer>',
+    task_start_token='<s_docvqa>',
+)
+
+task_cfg = chugr.DataTaskDocVqaCfg(
+    image_process_fn=img_fn,
+    text_process_fn=txt_fn,
+)
+data_cfg = chugr.DataCfg(
+    source='pipe:curl -s -f -L https://huggingface.co/datasets/pixparse/docvqa-wds/resolve/main/docvqa-train-{000..383}.tar',
+    batch_size=8,
+    format='wds',
+    num_samples=39463,
+)
+lb = chugr.create_loader(
+    data_cfg,
+    task_cfg,
+    is_training=True,
+)
+ii = iter(lb)
+sample = next(ii)
+```
+
+#### Exploration
+
+```python
+import chugr
+task_cfg = chugr.DataTaskDocVqaCfg(
+    question_prefix='Question: ',
+    question_suffix='',
+    answer_prefix='Answer: ',
+    answer_suffix=''
+)
+data_cfg = chugr.DataCfg(
+    source='pixparse/docvqa-single-page-questions',
+    split='validation',
+    batch_size=None,
+    format='hfids',
+    num_workers=0,
+)
+lb = chugr.create_loader(
+    data_cfg,
+    task_cfg
+)
+ii = iter(lb)
+sample = next(ii)
+```
+
+## Acknowledgement
+
+`chugr` evolved from the `webdataset` datapipeline used successfully in the [OpenCLIP](https://github.com/mlfoundations/open_clip) project. Thanks to all the contributors in that project. Future work will likely involve closing the loop and leveraging `chugr` in OpenCLIP for increased capability.
+
+The image/document augmentations in `chugr` rely on a number of external influences. Our document oriented `doc_better` torchvision augmentations are influenced by `nougat`, and the `doc_nougat` is a direct adaptation of the [`albumentations`](https://albumentations.ai/) + `cv2` document pipeline in [`nougat`](https://github.com/facebookresearch/nougat). Several image augmentations leverage existing work in the `timm` library.
+
+Also, big thanks to the maintainers of [`webdataset`](https://github.com/webdataset/webdataset) and Hugging Face [`datasets`](https://github.com/huggingface/datasets).
+
+## License
+
+Apache 2.0, see [LICENSE](LICENSE). The optional PyMuPDF backend is AGPL-3.0 licensed (see above).