update model.py and add coco files

coco_dataset_script.py

@@ -0,0 +1,142 @@
+import csv
+import json
+import os
+
+import datasets
+import pandas as pd
+import numpy as np
+
+
+# TODO: Add BibTeX citation
+# Find for instance the citation on arxiv or on the dataset repo/website
+_CITATION = """\
+@InProceedings{huggingface:dataset,
+title = {A great new dataset},
+author={huggingface, Inc.
+},
+year={2020}
+}
+"""
+
+# TODO: Add description of the dataset here
+# You can copy an official description
+_DESCRIPTION = """\
+This new dataset is designed to solve this great NLP task and is crafted with a lot of care.
+"""
+
+# TODO: Add a link to an official homepage for the dataset here
+_HOMEPAGE = ""
+
+# TODO: Add the licence for the dataset here if you can find it
+_LICENSE = ""
+
+# TODO: Add link to the official dataset URLs here
+# The HuggingFace dataset library don't host the datasets but only point to the original files
+# This can be an arbitrary nested dict/list of URLs (see below in `_split_generators` method)
+_URLs = {
+}
+
+
+# TODO: Name of the dataset usually match the script name with CamelCase instead of snake_case
+class COCODataset(datasets.GeneratorBasedBuilder):
+    """TODO: Short description of my dataset."""
+
+    VERSION = datasets.Version("1.1.0")
+
+    DEFAULT_CONFIG_NAME = "en"
+
+    def _info(self):
+        # TODO: This method specifies the datasets.DatasetInfo object which contains informations and typings for the dataset
+
+        features = datasets.Features(
+            {
+                "id": datasets.Value("int64"),
+                "en": datasets.Value("string"),
+                "fr": datasets.Value("string"),
+                "image_id": datasets.Value("int64"),
+                "image_file": datasets.Value("string")
+                # These are the features of your dataset like images, labels ...
+            }
+        )
+
+        return datasets.DatasetInfo(
+            # This is the description that will appear on the datasets page.
+            description=_DESCRIPTION,
+            # This defines the different columns of the dataset and their types
+            features=features,  # Here we define them above because they are different between the two configurations
+            # If there's a common (input, target) tuple from the features,
+            # specify them here. They'll be used if as_supervised=True in
+            # builder.as_dataset.
+            supervised_keys=None,
+            # Homepage of the dataset for documentation
+            homepage=_HOMEPAGE,
+            # License for the dataset if available
+            license=_LICENSE,
+            # Citation for the dataset
+            citation=_CITATION,
+        )
+
+    def _split_generators(self, dl_manager):
+        """Returns SplitGenerators."""
+        # TODO: This method is tasked with downloading/extracting the data and defining the splits depending on the configuration
+        # If several configurations are possible (listed in BUILDER_CONFIGS), the configuration selected by the user is in self.config.name
+
+        data_dir = self.config.data_dir
+
+        return [
+            datasets.SplitGenerator(
+                name=datasets.Split.TRAIN,
+                # These kwargs will be passed to _generate_examples
+                gen_kwargs={
+                    "data_dir": data_dir,
+                    "split": "train",
+                },
+            ),
+            datasets.SplitGenerator(
+                name=datasets.Split.TEST,
+                # These kwargs will be passed to _generate_examples
+                gen_kwargs={
+                    "data_dir": data_dir,
+                    "split": "test"
+                },
+            ),
+            datasets.SplitGenerator(
+                name=datasets.Split.VALIDATION,
+                # These kwargs will be passed to _generate_examples
+                gen_kwargs={
+                    "data_dir": data_dir,
+                    "split": "val",
+                },
+            ),
+        ]
+
+    def _generate_examples(
+        self, data_dir, split  # method parameters are unpacked from `gen_kwargs` as given in `_split_generators`
+    ):
+        """ Yields examples as (key, example) tuples. """
+        # This method handles input defined in _split_generators to yield (key, example) tuples from the dataset.
+        # The `key` is here for legacy reason (tfds) and is not important in itself.
+
+        # /home/33611/caption/
+        # train2014
+
+        if split == 'dev':
+            split == 'val'
+
+        with open(os.path.join(data_dir, f'{split}.json')) as fp:
+            examples = json.load(fp)
+
+        for id_, ex in enumerate(examples):
+
+            image_id = ex["image_id"]
+            fn = f'COCO_{split}2014_{str(image_id).zfill(12)}.jpg'
+
+            image_file = os.path.join(data_dir, f'{split}2014', fn)
+
+            yield id_, {
+                "id": ex["id"],
+                "en": ex["caption"],
+                "fr": ex["fr"],
+                "image_id": ex["image_id"],
+                "image_file": image_file
+            }

model.py

@@ -3,6 +3,9 @@ import sys, os
 current_path = os.path.dirname(os.path.abspath(__file__))
 sys.path.append(current_path)
 
+# jax
+import jax
+
 # Main model -  ViTGPT2LM
 from vit_gpt2.modeling_flax_vit_gpt2_lm import FlaxViTGPT2LMForConditionalGeneration
 
@@ -24,21 +27,27 @@ feature_extractor = ViTFeatureExtractor.from_pretrained(vit_model_name)
 gpt2_model_name = 'asi/gpt-fr-cased-small'
 tokenizer = GPT2Tokenizer.from_pretrained(gpt2_model_name)
 
-max_length = 16
-num_beams = 4
+max_length = 64
+num_beams = 16
 gen_kwargs = {"max_length": max_length, "num_beams": num_beams}
 
 
-def predict(image):
+@jax.jit
+def predict_fn(pixel_values):
+
+    return flax_vit_gpt2_lm.generate(pixel_values, **gen_kwargs)
+
+def predict(image, pxs=None):
 
-    image = Image.open(requests.get(url, stream=True).raw)
     # batch dim is added automatically
     encoder_inputs = feature_extractor(images=image, return_tensors="jax")
     pixel_values = encoder_inputs.pixel_values
 
+    if pxs is not None:
+        pixel_values = pxs
+
     # generation
-    batch = {'pixel_values': pixel_values}
-    generation = flax_vit_gpt2_lm.generate(batch['pixel_values'], **gen_kwargs)
+    generation = predict_fn(pixel_values)
 
     token_ids = np.array(generation.sequences)[0]
     caption = tokenizer.decode(token_ids)
@@ -48,10 +57,33 @@ def predict(image):
 
 if __name__ == '__main__':
 
+    from datetime import datetime
+
+    idx = 11
+    url = f'./wit_data_dir/train/images/{idx}.jpg'
+    image = Image.open(url)
+
+    encoder_inputs = feature_extractor(images=image, return_tensors="np")
+    pv1 = encoder_inputs.pixel_values
+    pv2 = np.load(f'./wit_data_dir/train/numpy/{idx}.npy')
+    print(np.sum(np.abs(pv1 - pv2)))
+
+    s = datetime.now()
+    caption, token_ids = predict(image, pxs=pv2)
+    e = datetime.now()
+    e = (e - s).total_seconds()
+    print(e)
+
+    print(f'token_ids: {token_ids}')
+    print(f'caption: {caption}')
 
-    url = 'http://images.cocodataset.org/val2017/000000039769.jpg'
-    image = Image.open(requests.get(url, stream=True).raw)
-    caption, token_ids = predict(image)
+    for _ in range(1):
+        s = datetime.now()
+        caption, token_ids = predict(image, pxs=None)
+        e = datetime.now()
+        e = (e - s).total_seconds()
+        print(e)
+        print('-' * 20)
 
     print(f'token_ids: {token_ids}')
     print(f'caption: {caption}')

run_summarization_coco.py

@@ -0,0 +1,826 @@
+#!/usr/bin/env python
+# coding=utf-8
+# Copyright 2021 The HuggingFace Team All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+Fine-tuning the library models for summarization.
+"""
+# You can also adapt this script on your own sequence to sequence task. Pointers for this are left as comments.
+
+import sys, os
+
+current_path = os.path.dirname(os.path.abspath(__file__))
+sys.path.append(current_path)
+
+import logging
+import os
+import sys
+import time
+from dataclasses import dataclass, field
+from functools import partial
+from pathlib import Path
+from typing import Callable, Optional
+
+import datasets
+import nltk  # Here to have a nice missing dependency error message early on
+import numpy as np
+from datasets import Dataset, load_dataset, load_metric
+from tqdm import tqdm
+
+import jax
+import jax.numpy as jnp
+import optax
+import transformers
+from filelock import FileLock
+from flax import jax_utils, traverse_util
+from flax.jax_utils import unreplicate
+from flax.training import train_state
+from flax.training.common_utils import get_metrics, onehot, shard, shard_prng_key
+from transformers import (
+    CONFIG_MAPPING,
+    FLAX_MODEL_FOR_SEQ_TO_SEQ_CAUSAL_LM_MAPPING,
+    AutoConfig,
+    AutoTokenizer,
+    FlaxAutoModelForSeq2SeqLM,
+    HfArgumentParser,
+    TrainingArguments,
+    is_tensorboard_available,
+)
+from transformers.file_utils import is_offline_mode
+
+from transformers import ViTFeatureExtractor, GPT2Tokenizer, GPT2Config
+from vit_gpt2.modeling_flax_vit_gpt2_lm import FlaxViTGPT2LMForConditionalGeneration
+
+logger = logging.getLogger(__name__)
+
+try:
+    nltk.data.find("tokenizers/punkt")
+except (LookupError, OSError):
+    if is_offline_mode():
+        raise LookupError(
+            "Offline mode: run this script without TRANSFORMERS_OFFLINE first to download nltk data files"
+        )
+    with FileLock(".lock") as lock:
+        nltk.download("punkt", quiet=True)
+
+
+MODEL_CONFIG_CLASSES = list(FLAX_MODEL_FOR_SEQ_TO_SEQ_CAUSAL_LM_MAPPING.keys())
+MODEL_TYPES = tuple(conf.model_type for conf in MODEL_CONFIG_CLASSES)
+
+
+@dataclass
+class ModelArguments:
+    """
+    Arguments pertaining to which model/config/tokenizer we are going to fine-tune, or train from scratch.
+    """
+
+    model_name_or_path: Optional[str] = field(
+        default=None,
+        metadata={
+            "help": "The model checkpoint for weights initialization."
+            "Don't set if you want to train a model from scratch."
+        },
+    )
+    model_type: Optional[str] = field(
+        default=None,
+        metadata={"help": "If training from scratch, pass a model type from the list: " + ", ".join(MODEL_TYPES)},
+    )
+    config_name: Optional[str] = field(
+        default=None, metadata={"help": "Pretrained config name or path if not the same as model_name"}
+    )
+    tokenizer_name: Optional[str] = field(
+        default=None, metadata={"help": "Pretrained tokenizer name or path if not the same as model_name"}
+    )
+    cache_dir: Optional[str] = field(
+        default=None, metadata={"help": "Where do you want to store the pretrained models downloaded from s3"}
+    )
+    use_fast_tokenizer: bool = field(
+        default=True,
+        metadata={"help": "Whether to use one of the fast tokenizer (backed by the tokenizers library) or not."},
+    )
+    dtype: Optional[str] = field(
+        default="float32",
+        metadata={
+            "help": "Floating-point format in which the model weights should be initialized and trained. Choose one of `[float32, float16, bfloat16]`."
+        },
+    )
+
+
+@dataclass
+class DataTrainingArguments:
+    """
+    Arguments pertaining to what data we are going to input our model for training and eval.
+    """
+
+    dataset_name: Optional[str] = field(
+        default=None, metadata={"help": "The name of the dataset to use (via the datasets library)."}
+    )
+    dataset_config_name: Optional[str] = field(
+        default=None, metadata={"help": "The configuration name of the dataset to use (via the datasets library)."}
+    )
+    text_column: Optional[str] = field(
+        default=None,
+        metadata={"help": "The name of the column in the datasets containing the full texts (for summarization)."},
+    )
+    summary_column: Optional[str] = field(
+        default=None,
+        metadata={"help": "The name of the column in the datasets containing the summaries (for summarization)."},
+    )
+    train_file: Optional[str] = field(default=None, metadata={"help": "The input training data file (a text file)."})
+    validation_file: Optional[str] = field(
+        default=None,
+        metadata={"help": "An optional input evaluation data file to evaluate the perplexity on (a text file)."},
+    )
+    max_source_length: Optional[int] = field(
+        default=1024,
+        metadata={
+            "help": "The maximum total input sequence length after tokenization. Sequences longer "
+            "than this will be truncated, sequences shorter will be padded."
+        },
+    )
+    max_target_length: Optional[int] = field(
+        default=128,
+        metadata={
+            "help": "The maximum total sequence length for target text after tokenization. Sequences longer "
+            "than this will be truncated, sequences shorter will be padded."
+        },
+    )
+    val_max_target_length: Optional[int] = field(
+        default=None,
+        metadata={
+            "help": "The maximum total sequence length for validation target text after tokenization. Sequences longer "
+            "than this will be truncated, sequences shorter will be padded. Will default to `max_target_length`."
+            "This argument is also used to override the `max_length` param of `model.generate`, which is used "
+            "during evaluation."
+        },
+    )
+    max_train_samples: Optional[int] = field(
+        default=None,
+        metadata={
+            "help": "For debugging purposes or quicker training, truncate the number of training examples to this "
+            "value if set."
+        },
+    )
+    max_eval_samples: Optional[int] = field(
+        default=None,
+        metadata={
+            "help": "For debugging purposes or quicker training, truncate the number of evaluation examples to this "
+            "value if set."
+        },
+    )
+    max_predict_samples: Optional[int] = field(
+        default=None,
+        metadata={
+            "help": "For debugging purposes or quicker training, truncate the number of prediction examples to this "
+            "value if set."
+        },
+    )
+    preprocessing_num_workers: Optional[int] = field(
+        default=None,
+        metadata={"help": "The number of processes to use for the preprocessing."},
+    )
+    source_prefix: Optional[str] = field(
+        default=None, metadata={"help": "A prefix to add before every source text (useful for T5 models)."}
+    )
+    predict_with_generate: bool = field(
+        default=False, metadata={"help": "Whether to use generate to calculate generative metrics (ROUGE, BLEU)."}
+    )
+    num_beams: Optional[int] = field(
+        default=None,
+        metadata={
+            "help": "Number of beams to use for evaluation. This argument will be passed to `model.generate`, "
+            "which is used during evaluation."
+        },
+    )
+    overwrite_cache: bool = field(
+        default=False, metadata={"help": "Overwrite the cached training and evaluation sets"}
+    )
+
+    def __post_init__(self):
+        if self.dataset_name is None and self.train_file is None and self.validation_file is None:
+            raise ValueError("Need either a dataset name or a training/validation file.")
+        else:
+            if self.train_file is not None:
+                extension = self.train_file.split(".")[-1]
+                assert extension in ["csv", "json"], "`train_file` should be a csv or a json file."
+            if self.validation_file is not None:
+                extension = self.validation_file.split(".")[-1]
+                assert extension in ["csv", "json"], "`validation_file` should be a csv or a json file."
+        if self.val_max_target_length is None:
+            self.val_max_target_length = self.max_target_length
+
+
+summarization_name_mapping = {
+    "amazon_reviews_multi": ("review_body", "review_title"),
+    "big_patent": ("description", "abstract"),
+    "cnn_dailymail": ("article", "highlights"),
+    "orange_sum": ("text", "summary"),
+    "pn_summary": ("article", "summary"),
+    "psc": ("extract_text", "summary_text"),
+    "samsum": ("dialogue", "summary"),
+    "thaisum": ("body", "summary"),
+    "xglue": ("news_body", "news_title"),
+    "xsum": ("document", "summary"),
+    "wiki_summary": ("article", "highlights"),
+}
+
+
+class TrainState(train_state.TrainState):
+    dropout_rng: jnp.ndarray
+
+    def replicate(self):
+        return jax_utils.replicate(self).replace(dropout_rng=shard_prng_key(self.dropout_rng))
+
+
+def data_loader(rng: jax.random.PRNGKey, dataset: Dataset, batch_size: int, shuffle: bool = False):
+    """
+    Returns batches of size `batch_size` from truncated `dataset`, sharded over all local devices.
+    Shuffle batches if `shuffle` is `True`.
+    """
+    steps_per_epoch = len(dataset) // batch_size
+
+    if shuffle:
+        batch_idx = jax.random.permutation(rng, len(dataset))
+    else:
+        batch_idx = jnp.arange(len(dataset))
+
+    batch_idx = batch_idx[: steps_per_epoch * batch_size]  # Skip incomplete batch.
+    batch_idx = batch_idx.reshape((steps_per_epoch, batch_size))
+
+    for idx in batch_idx:
+        batch = dataset[idx]
+        batch = {k: jnp.array(v) for k, v in batch.items()}
+
+        batch = shard(batch)
+
+        yield batch
+
+
+def write_metric(summary_writer, train_metrics, eval_metrics, train_time, step):
+    summary_writer.scalar("train_time", train_time, step)
+
+    train_metrics = get_metrics(train_metrics)
+    for key, vals in train_metrics.items():
+        tag = f"train_{key}"
+        for i, val in enumerate(vals):
+            summary_writer.scalar(tag, val, step - len(vals) + i + 1)
+
+    for metric_name, value in eval_metrics.items():
+        summary_writer.scalar(f"eval_{metric_name}", value, step)
+
+
+def create_learning_rate_fn(
+    train_ds_size: int, train_batch_size: int, num_train_epochs: int, num_warmup_steps: int, learning_rate: float
+) -> Callable[[int], jnp.array]:
+    """Returns a linear warmup, linear_decay learning rate function."""
+    steps_per_epoch = train_ds_size // train_batch_size
+    num_train_steps = steps_per_epoch * num_train_epochs
+    warmup_fn = optax.linear_schedule(init_value=0.0, end_value=learning_rate, transition_steps=num_warmup_steps)
+    decay_fn = optax.linear_schedule(
+        init_value=learning_rate, end_value=0, transition_steps=num_train_steps - num_warmup_steps
+    )
+    schedule_fn = optax.join_schedules(schedules=[warmup_fn, decay_fn], boundaries=[num_warmup_steps])
+    return schedule_fn
+
+
+def main():
+    # See all possible arguments in src/transformers/training_args.py
+    # or by passing the --help flag to this script.
+    # We now keep distinct sets of args, for a cleaner separation of concerns.
+
+    parser = HfArgumentParser((ModelArguments, DataTrainingArguments, TrainingArguments))
+    if len(sys.argv) == 2 and sys.argv[1].endswith(".json"):
+        # If we pass only one argument to the script and it's the path to a json file,
+        # let's parse it to get our arguments.
+        model_args, data_args, training_args = parser.parse_json_file(json_file=os.path.abspath(sys.argv[1]))
+    else:
+        model_args, data_args, training_args = parser.parse_args_into_dataclasses()
+
+    if (
+        os.path.exists(training_args.output_dir)
+        and os.listdir(training_args.output_dir)
+        and training_args.do_train
+        and not training_args.overwrite_output_dir
+    ):
+        raise ValueError(
+            f"Output directory ({training_args.output_dir}) already exists and is not empty."
+            "Use --overwrite_output_dir to overcome."
+        )
+
+    # Make one log on every process with the configuration for debugging.
+    logging.basicConfig(
+        format="%(asctime)s - %(levelname)s - %(name)s - %(message)s",
+        datefmt="%m/%d/%Y %H:%M:%S",
+        level=logging.INFO,
+    )
+    # Setup logging, we only want one process per machine to log things on the screen.
+    logger.setLevel(logging.INFO if jax.process_index() == 0 else logging.ERROR)
+    if jax.process_index() == 0:
+        datasets.utils.logging.set_verbosity_warning()
+        transformers.utils.logging.set_verbosity_info()
+    else:
+        datasets.utils.logging.set_verbosity_error()
+        transformers.utils.logging.set_verbosity_error()
+
+    # Set the verbosity to info of the Transformers logger (on main process only):
+    logger.info(f"Training/evaluation parameters {training_args}")
+
+    # Get the datasets: you can either provide your own CSV/JSON training and evaluation files (see below)
+    # or just provide the name of one of the public datasets available on the hub at https://huggingface.co/datasets/
+    # (the dataset will be downloaded automatically from the datasets Hub).
+    #
+    # For CSV/JSON files this script will use the first column for the full texts and the second column for the
+    # summaries (unless you specify column names for this with the `text_column` and `summary_column` arguments).
+    #
+    if data_args.dataset_name is not None:
+        # Downloading and loading a dataset from the hub.
+        dataset = load_dataset(
+            data_args.dataset_name, data_args.dataset_config_name, cache_dir=model_args.cache_dir, keep_in_memory=False, data_dir='/home/33611/caption/'
+        )
+    else:
+        data_files = {}
+        if data_args.train_file is not None:
+            data_files["train"] = data_args.train_file
+            extension = data_args.train_file.split(".")[-1]
+        if data_args.validation_file is not None:
+            data_files["validation"] = data_args.validation_file
+            extension = data_args.validation_file.split(".")[-1]
+        if data_args.test_file is not None:
+            data_files["test"] = data_args.test_file
+            extension = data_args.test_file.split(".")[-1]
+        dataset = load_dataset(extension, data_files=data_files, cache_dir=model_args.cache_dir)
+
+    vit_name_path = 'google/vit-base-patch16-224-in21k'
+    gpt2_name_path = 'asi/gpt-fr-cased-small'
+    
+    gpt2_config = GPT2Config.from_pretrained(gpt2_name_path)
+    gpt2_config.add_cross_attention = True
+    
+    
+    vit_gpt2_name_path = ''
+
+    feature_extractor = ViTFeatureExtractor.from_pretrained(vit_name_path)
+
+    tokenizer = GPT2Tokenizer.from_pretrained(gpt2_name_path)
+
+    if not vit_gpt2_name_path:
+        assert vit_name_path
+        assert gpt2_name_path
+        vit_gpt2_model = FlaxViTGPT2LMForConditionalGeneration.from_vit_gpt2_pretrained(
+            vit_name_path, gpt2_name_path
+        )
+    else:
+        vit_gpt2_model = FlaxViTGPT2LMForConditionalGeneration.from_pretrained(
+            vit_gpt2_name_path
+        )
+
+    model = vit_gpt2_model
+    model.config.is_encoder_decoder = True
+    model.config.decoder_start_token_id = gpt2_config.bos_token_id
+    model.config.bos_token_id = gpt2_config.bos_token_id
+    model.config.eos_token_id = gpt2_config.eos_token_id
+    model.config.pad_token_id = gpt2_config.pad_token_id
+
+    # Preprocessing the datasets.
+    # We need to tokenize inputs and targets.
+    if training_args.do_train:
+        column_names = dataset["train"].column_names
+    elif training_args.do_eval:
+        column_names = dataset["validation"].column_names
+    elif training_args.do_predict:
+        column_names = dataset["test"].column_names
+    else:
+        logger.info("There is nothing to do. Please pass `do_train`, `do_eval` and/or `do_predict`.")
+        return
+
+    image_file_column = 'image_file'
+    caption_column = 'fr'
+
+    # Temporarily set max_target_length for training.
+    max_target_length = data_args.max_target_length
+
+    # In Flax, for seq2seq models we need to pass `decoder_input_ids`
+    # as the Flax models don't accept `labels`, we need to prepare the decoder_input_ids here
+    # for that dynamically import the `shift_tokens_right` function from the model file
+    model_module = __import__(vit_gpt2_model.__module__, fromlist=["shift_tokens_right"])
+    shift_tokens_right_fn = getattr(model_module, "shift_tokens_right")
+
+    # Setting padding="max_length" as we need fixed length inputs for jitted functions
+    def preprocess_function(examples):
+    
+        _pixel_values = []
+        for y in examples[image_file_column]:
+            with Image.open(y) as image:
+                encoder_inputs = feature_extractor(images=image, return_tensors="np")
+                x = encoder_inputs.pixel_values
+                _pixel_values.append(x)
+        pixel_values = np.concatenate(_pixel_values)
+
+        targets = examples[caption_column]
+
+        # Add eos_token!!
+        targets = [x.lower() + ' ' + tokenizer.eos_token for x in targets]
+
+        model_inputs = {}
+        model_inputs['pixel_values'] = pixel_values
+
+        # Setup the tokenizer for targets
+        with tokenizer.as_target_tokenizer():
+            labels = tokenizer(
+                targets, max_length=max_target_length, padding="max_length", truncation=True, return_tensors="np"
+            )
+
+        model_inputs["labels"] = labels["input_ids"]
+
+        #print(labels["input_ids"])
+        #print(gpt2_config.pad_token_id)
+        #rint(gpt2_config.bos_token_id)
+
+        decoder_input_ids = shift_tokens_right_fn(
+            jnp.array(labels["input_ids"]), gpt2_config.pad_token_id, gpt2_config.bos_token_id
+        )
+        model_inputs["input_ids"] = np.asarray(decoder_input_ids)
+
+        # We need decoder_attention_mask so we can ignore pad tokens from loss
+        model_inputs["attention_mask"] = labels["attention_mask"]
+
+        return model_inputs
+
+    if training_args.do_train:
+        if "train" not in dataset:
+            raise ValueError("--do_train requires a train dataset")
+        train_dataset = dataset["train"]
+        if data_args.max_train_samples is not None:
+            train_dataset = train_dataset.select(range(data_args.max_train_samples))
+            
+        train_dataset = train_dataset.map(
+            preprocess_function,
+            batched=True,
+            num_proc=data_args.preprocessing_num_workers,
+            remove_columns=column_names,
+            load_from_cache_file=not data_args.overwrite_cache,
+            desc="Running tokenizer on train dataset",
+        )
+
+    if training_args.do_eval:
+        max_target_length = data_args.val_max_target_length
+        if "validation" not in dataset:
+            raise ValueError("--do_eval requires a validation dataset")
+        eval_dataset = dataset["validation"]
+        if data_args.max_eval_samples is not None:
+            eval_dataset = eval_dataset.select(range(data_args.max_eval_samples))
+        eval_dataset = eval_dataset.map(
+            preprocess_function,
+            batched=True,
+            num_proc=data_args.preprocessing_num_workers,
+            remove_columns=column_names,
+            load_from_cache_file=not data_args.overwrite_cache,
+            desc="Running tokenizer on validation dataset",
+        )
+
+    if training_args.do_predict:
+        max_target_length = data_args.val_max_target_length
+        if "test" not in dataset:
+            raise ValueError("--do_predict requires a test dataset")
+        predict_dataset = dataset["test"]
+        if data_args.max_predict_samples is not None:
+            predict_dataset = predict_dataset.select(range(data_args.max_predict_samples))
+        predict_dataset = predict_dataset.map(
+            preprocess_function,
+            batched=True,
+            num_proc=data_args.preprocessing_num_workers,
+            remove_columns=column_names,
+            load_from_cache_file=not data_args.overwrite_cache,
+            desc="Running tokenizer on prediction dataset",
+        )
+
+    # Metric
+    metric = load_metric("rouge")
+
+    def postprocess_text(preds, labels):
+        preds = [pred.strip() for pred in preds]
+        labels = [label.strip() for label in labels]
+
+        # rougeLSum expects newline after each sentence
+        preds = ["\n".join(nltk.sent_tokenize(pred)) for pred in preds]
+        labels = ["\n".join(nltk.sent_tokenize(label)) for label in labels]
+
+        return preds, labels
+
+    def compute_metrics(preds, labels):
+        decoded_preds = tokenizer.batch_decode(preds, skip_special_tokens=True)
+        decoded_labels = tokenizer.batch_decode(labels, skip_special_tokens=True)
+
+        # Some simple post-processing
+        decoded_preds, decoded_labels = postprocess_text(decoded_preds, decoded_labels)
+
+        result = metric.compute(predictions=decoded_preds, references=decoded_labels, use_stemmer=True)
+        # Extract a few results from ROUGE
+        result = {key: value.mid.fmeasure * 100 for key, value in result.items()}
+
+        prediction_lens = [np.count_nonzero(pred != tokenizer.pad_token_id) for pred in preds]
+        result["gen_len"] = np.mean(prediction_lens)
+        result = {k: round(v, 4) for k, v in result.items()}
+        return result
+
+    # Enable tensorboard only on the master node
+    has_tensorboard = is_tensorboard_available()
+    if has_tensorboard and jax.process_index() == 0:
+        try:
+            from flax.metrics.tensorboard import SummaryWriter
+
+            summary_writer = SummaryWriter(log_dir=Path(training_args.output_dir))
+        except ImportError as ie:
+            has_tensorboard = False
+            logger.warning(
+                f"Unable to display metrics through TensorBoard because some package are not installed: {ie}"
+            )
+    else:
+        logger.warning(
+            "Unable to display metrics through TensorBoard because the package is not installed: "
+            "Please run pip install tensorboard to enable."
+        )
+
+    # Initialize our training
+    rng = jax.random.PRNGKey(training_args.seed)
+    rng, dropout_rng = jax.random.split(rng)
+
+    # Store some constant
+    num_epochs = int(training_args.num_train_epochs)
+    train_batch_size = int(training_args.per_device_train_batch_size) * jax.device_count()
+    eval_batch_size = int(training_args.per_device_eval_batch_size) * jax.device_count()
+    steps_per_epoch = len(train_dataset) // train_batch_size
+    total_train_steps = steps_per_epoch * num_epochs
+
+    # Create learning rate schedule
+    linear_decay_lr_schedule_fn = create_learning_rate_fn(
+        len(train_dataset),
+        train_batch_size,
+        training_args.num_train_epochs,
+        training_args.warmup_steps,
+        training_args.learning_rate,
+    )
+
+    # We use Optax's "masking" functionality to not apply weight decay
+    # to bias and LayerNorm scale parameters. decay_mask_fn returns a
+    # mask boolean with the same structure as the parameters.
+    # The mask is True for parameters that should be decayed.
+    # Note that this mask is specifically adapted for FlaxBart.
+    # For FlaxT5, one should correct the layer norm parameter naming
+    # accordingly - see `run_t5_mlm_flax.py` e.g.
+    def decay_mask_fn(params):
+        flat_params = traverse_util.flatten_dict(params)
+        layer_norm_params = [
+            (name, "scale") for name in ["self_attn_layer_norm", "layernorm_embedding", "final_layer_norm"]
+        ]
+        flat_mask = {path: (path[-1] != "bias" and path[-2:] not in layer_norm_params) for path in flat_params}
+        return traverse_util.unflatten_dict(flat_mask)
+
+    # create adam optimizer
+    adamw = optax.adamw(
+        learning_rate=linear_decay_lr_schedule_fn,
+        b1=training_args.adam_beta1,
+        b2=training_args.adam_beta2,
+        eps=training_args.adam_epsilon,
+        weight_decay=training_args.weight_decay,
+        mask=decay_mask_fn,
+    )
+
+    # Setup train state
+    state = TrainState.create(apply_fn=vit_gpt2_model.__call__, params=vit_gpt2_model.params, tx=adamw, dropout_rng=dropout_rng)
+
+    # label smoothed cross entropy
+    def loss_fn(logits, labels, padding_mask, label_smoothing_factor=0.0):
+        """
+        The label smoothing implementation is adapted from Flax's official example:
+        https://github.com/google/flax/blob/87a211135c6a377c8f29048a1cac3840e38b9da4/examples/wmt/train.py#L104
+        """
+        vocab_size = logits.shape[-1]
+        confidence = 1.0 - label_smoothing_factor
+        low_confidence = (1.0 - confidence) / (vocab_size - 1)
+        normalizing_constant = -(
+            confidence * jnp.log(confidence) + (vocab_size - 1) * low_confidence * jnp.log(low_confidence + 1e-20)
+        )
+        soft_labels = onehot(labels, vocab_size, on_value=confidence, off_value=low_confidence)
+
+        loss = optax.softmax_cross_entropy(logits, soft_labels)
+        loss = loss - normalizing_constant
+
+        # ignore padded tokens from loss
+        loss = loss * padding_mask
+        loss = loss.sum() / padding_mask.sum()
+        return loss
+
+    # Define gradient update step fn
+    def train_step(state, batch, label_smoothing_factor=0.0):
+        dropout_rng, new_dropout_rng = jax.random.split(state.dropout_rng)
+
+        def compute_loss(params):
+            labels = batch.pop("labels")
+            logits = state.apply_fn(**batch, params=params, dropout_rng=dropout_rng, train=True)[0]
+            loss = loss_fn(logits, labels, batch["attention_mask"], label_smoothing_factor)
+            return loss
+
+        grad_fn = jax.value_and_grad(compute_loss)
+        loss, grad = grad_fn(state.params)
+        grad = jax.lax.pmean(grad, "batch")
+
+        new_state = state.apply_gradients(grads=grad, dropout_rng=new_dropout_rng)
+
+        metrics = {"loss": loss, "learning_rate": linear_decay_lr_schedule_fn(state.step)}
+        metrics = jax.lax.pmean(metrics, axis_name="batch")
+
+        return new_state, metrics
+
+    # Define eval fn
+    def eval_step(params, batch, label_smoothing_factor=0.0):
+        labels = batch.pop("labels")
+        logits = model(**batch, params=params, train=False)[0]
+        loss = loss_fn(logits, labels, batch["attention_mask"], label_smoothing_factor)
+
+        # summarize metrics
+        metrics = {"loss": loss}
+        metrics = jax.lax.pmean(metrics, axis_name="batch")
+        return metrics
+
+    # Define generation function
+    max_length = (
+        data_args.val_max_target_length if data_args.val_max_target_length is not None else model.config.max_length
+    )
+    num_beams = data_args.num_beams if data_args.num_beams is not None else model.config.num_beams
+    gen_kwargs = {"max_length": max_length, "num_beams": num_beams}
+
+    def generate_step(params, batch):
+        model.params = params
+        # output_ids = model.generate(batch["pixel_values"], **gen_kwargs)
+
+        #encoder_outputs = model.encode(pixel_values=batch['pixel_values'])
+        #output_ids = model.generate(batch["input_ids"], attention_mask=batch["attention_mask"], encoder_outputs=encoder_outputs, **gen_kwargs)
+
+        # encoder_outputs = model.encode(pixel_values=batch['pixel_values'], params=params, train=False)
+        output_ids = model.generate(batch['pixel_values'], **gen_kwargs)
+
+
+        return output_ids.sequences
+
+    # Create parallel version of the train and eval step
+    p_train_step = jax.pmap(
+        partial(train_step, label_smoothing_factor=training_args.label_smoothing_factor), "batch", donate_argnums=(0,)
+    )
+    p_eval_step = jax.pmap(partial(eval_step, label_smoothing_factor=training_args.label_smoothing_factor), "batch")
+    p_generate_step = jax.pmap(generate_step, "batch")
+
+    # Replicate the train state on each device
+    state = state.replicate()
+
+    logger.info("***** Running training *****")
+    logger.info(f"  Num examples = {len(train_dataset)}")
+    logger.info(f"  Num Epochs = {num_epochs}")
+    logger.info(f"  Instantaneous batch size per device = {training_args.per_device_train_batch_size}")
+    logger.info(f"  Total train batch size (w. parallel & distributed) = {train_batch_size}")
+    logger.info(f"  Total optimization steps = {total_train_steps}")
+
+    train_time = 0
+    epochs = tqdm(range(num_epochs), desc=f"Epoch ... (1/{num_epochs})", position=0)
+    for epoch in epochs:
+        # ======================== Training ================================
+        train_start = time.time()
+
+        # Create sampling rng
+        rng, input_rng = jax.random.split(rng)
+        train_metrics = []
+
+        # Generate an epoch by shuffling sampling indices from the train dataset
+        train_loader = data_loader(input_rng, train_dataset, train_batch_size, shuffle=True)
+        steps_per_epoch = len(train_dataset) // train_batch_size
+        # train
+        for _ in tqdm(range(steps_per_epoch), desc="Training...", position=1, leave=False):
+            batch = next(train_loader)
+            state, train_metric = p_train_step(state, batch)
+            train_metrics.append(train_metric)
+
+        train_time += time.time() - train_start
+
+        train_metric = unreplicate(train_metric)
+
+        desc = f"Epoch... ({epoch + 1}/{num_epochs} | Loss: {train_metric['loss']}, Learning Rate: {train_metric['learning_rate']})"
+        epochs.write(desc)
+        epochs.desc = desc
+        logger.info(desc)
+        with open(os.path.join(training_args.output_dir, f'report.txt'), 'a', encoding='UTF-8') as fp:
+            fp.write(desc + '\n')
+
+
+        # ======================== Evaluating ==============================
+        eval_metrics = []
+        eval_preds = []
+        eval_labels = []
+
+        eval_loader = data_loader(input_rng, eval_dataset, eval_batch_size)
+        eval_steps = len(eval_dataset) // eval_batch_size
+        for _ in tqdm(range(eval_steps), desc="Evaluating...", position=2, leave=False):
+            # Model forward
+            batch = next(eval_loader)
+            labels = batch["labels"]
+
+            metrics = p_eval_step(state.params, batch)
+            eval_metrics.append(metrics)
+
+            # generation
+            if data_args.predict_with_generate:
+                generated_ids = p_generate_step(state.params, batch)
+                eval_preds.extend(jax.device_get(generated_ids.reshape(-1, gen_kwargs["max_length"])))
+                eval_labels.extend(jax.device_get(labels.reshape(-1, labels.shape[-1])))
+
+        # normalize eval metrics
+        eval_metrics = get_metrics(eval_metrics)
+        eval_metrics = jax.tree_map(jnp.mean, eval_metrics)
+
+        # compute ROUGE metrics
+        rouge_desc = ""
+        if data_args.predict_with_generate:
+            rouge_metrics = compute_metrics(eval_preds, eval_labels)
+            eval_metrics.update(rouge_metrics)
+            rouge_desc = " ".join([f"Eval {key}: {value} |" for key, value in rouge_metrics.items()])
+
+        # Print metrics and update progress bar
+        desc = f"Epoch... ({epoch + 1}/{num_epochs} | Eval Loss: {eval_metrics['loss']} | {rouge_desc})"
+        epochs.write(desc)
+        epochs.desc = desc
+        logger.info(desc)
+        with open(os.path.join(training_args.output_dir, f'report.txt'), 'a', encoding='UTF-8') as fp:
+            fp.write(desc + '\n')
+
+
+        # Save metrics
+        if has_tensorboard and jax.process_index() == 0:
+            cur_step = epoch * (len(train_dataset) // train_batch_size)
+            write_metric(summary_writer, train_metrics, eval_metrics, train_time, cur_step)
+
+        # ======================== Prediction loop ==============================
+        if training_args.do_predict:
+            logger.info("*** Predict ***")
+    
+            pred_metrics = []
+            pred_generations = []
+            pred_labels = []
+    
+            pred_loader = data_loader(input_rng, predict_dataset, eval_batch_size)
+            pred_steps = len(predict_dataset) // eval_batch_size
+            for _ in tqdm(range(pred_steps), desc="Predicting...", position=2, leave=False):
+                # Model forward
+                batch = next(pred_loader)
+                labels = batch["labels"]
+    
+                metrics = p_eval_step(state.params, batch)
+                pred_metrics.append(metrics)
+    
+                # generation
+                if data_args.predict_with_generate:
+                    generated_ids = p_generate_step(state.params, batch)
+                    pred_generations.extend(jax.device_get(generated_ids.reshape(-1, gen_kwargs["max_length"])))
+                    pred_labels.extend(jax.device_get(labels.reshape(-1, labels.shape[-1])))
+    
+            # normalize prediction metrics
+            pred_metrics = get_metrics(pred_metrics)
+            pred_metrics = jax.tree_map(jnp.mean, pred_metrics)
+    
+            # compute ROUGE metrics
+            rouge_desc = ""
+            if data_args.predict_with_generate:
+                rouge_metrics = compute_metrics(pred_generations, pred_labels)
+                pred_metrics.update(rouge_metrics)
+                rouge_desc = " ".join([f"Predict {key}: {value} |" for key, value in rouge_metrics.items()])
+    
+            # Print metrics
+            desc = f"Predict Loss: {pred_metrics['loss']} | {rouge_desc})"
+            epochs.write(desc)
+            epochs.desc = desc
+            logger.info(desc)
+            with open(os.path.join(training_args.output_dir, f'report.txt'), 'a', encoding='UTF-8') as fp:
+                fp.write(desc + '\n')
+    
+
+        # save checkpoint after each epoch and push checkpoint to the hub
+        if jax.process_index() == 0:
+            params = jax.device_get(jax.tree_map(lambda x: x[0], state.params))
+            model.save_pretrained(
+                os.path.join(training_args.output_dir, f'ckpt_{epoch+1}'),
+                params=params,
+                push_to_hub=training_args.push_to_hub,
+                commit_message=f"Saving weights and logs of epoch {epoch+1}",
+            )
+
+if __name__ == "__main__":
+    main()

test_coco_dataset_script.py

@@ -0,0 +1,27 @@
+import csv
+import json
+import os
+
+import datasets
+import pandas as pd
+import numpy as np
+
+ds = datasets.load_dataset('./coco_dataset_script.py', data_dir='/home/33611/caption/')
+ds = ds['train']
+
+
+def transform(example):
+
+    example['pixel_values'] = np.load(example['pixels_file'])
+    return example
+
+
+# ds = ds.map(transform)
+
+n = 0
+for x in ds:
+    n += 1
+    assert os.path.isfile(x['image_file'])
+    if n == 10:
+        print(x)
+        break