Inital commit for refactoring to lightning

9 files changed, 461 insertions, 0 deletions

diff --git a/tasks/build_transitions.py b/tasks/build_transitions.py
new file mode 100644
index 0000000..91f8c1a
--- /dev/null
+++ b/tasks/build_transitions.py
@@ -0,0 +1,263 @@
+"""Builds transition graph.
+
+Most code stolen from here:
+
+    https://github.com/facebookresearch/gtn_applications/blob/master/scripts/build_transitions.py
+
+"""
+
+import collections
+import itertools
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+import click
+import gtn
+from loguru import logger
+
+
+START_IDX = -1
+END_IDX = -2
+WORDSEP = "▁"
+
+
+def build_graph(ngrams: List, disable_backoff: bool = False) -> gtn.Graph:
+    """Returns a gtn Graph based on the ngrams."""
+    graph = gtn.Graph(False)
+    ngram = len(ngrams)
+    state_to_node = {}
+
+    def get_node(state: Optional[List]) -> Any:
+        node = state_to_node.get(state, None)
+
+        if node is not None:
+            return node
+
+        start = state == tuple([START_IDX]) if ngram > 1 else True
+        end = state == tuple([END_IDX]) if ngram > 1 else True
+        node = graph.add_node(start, end)
+        state_to_node[state] = node
+
+        if not disable_backoff and not end:
+            # Add back off when adding node.
+            for n in range(1, len(state) + 1):
+                backoff_node = state_to_node.get(state[n:], None)
+
+                # Epsilon transition to the back-off state.
+                if backoff_node is not None:
+                    graph.add_arc(node, backoff_node, gtn.epsilon)
+                    break
+        return node
+
+    for grams in ngrams:
+        for gram in grams:
+            istate, ostate = gram[:-1], gram[len(gram) - ngram + 1 :]
+            inode = get_node(istate)
+
+            if END_IDX not in gram[1:] and gram[1:] not in state_to_node:
+                raise ValueError(
+                    "Ill formed counts: if (x, y_1, ..., y_{n-1}) is above"
+                    "the n-gram threshold, then (y_1, ..., y_{n-1}) must be"
+                    "above the (n-1)-gram threshold"
+                )
+
+            if END_IDX in ostate:
+                # Merge all state having </s> into one as final graph generated
+                # will be similar.
+                ostate = tuple([END_IDX])
+
+            onode = get_node(ostate)
+            # p(gram[-1] | gram[:-1])
+            graph.add_arc(
+                inode, onode, gtn.epsilon if gram[-1] == END_IDX else gram[-1]
+            )
+    return graph
+
+
+def count_ngrams(lines: List, ngram: List, tokens_to_index: Dict) -> List:
+    """Counts the number of ngrams."""
+    counts = [collections.Counter() for _ in range(ngram)]
+    for line in lines:
+        # Prepend implicit start token.
+        token_line = [START_IDX]
+        for t in line:
+            token_line.append(tokens_to_index[t])
+        token_line.append(END_IDX)
+        for n, counter in enumerate(counts):
+            start_offset = n == 0
+            end_offset = ngram == 1
+            for e in range(n + start_offset, len(token_line) - end_offset):
+                counter[tuple(token_line[e - n : e + 1])] += 1
+
+    return counts
+
+
+def prune_ngrams(ngrams: List, prune: List) -> List:
+    """Prunes ngrams."""
+    pruned_ngrams = []
+    for n, grams in enumerate(ngrams):
+        grams = grams.most_common()
+        pruned_grams = [gram for gram, c in grams if c > prune[n]]
+        pruned_ngrams.append(pruned_grams)
+    return pruned_ngrams
+
+
+def add_blank_grams(pruned_ngrams: List, num_tokens: int, blank: str) -> List:
+    """Adds blank token to grams."""
+    all_grams = [gram for grams in pruned_ngrams for gram in grams]
+    maxorder = len(pruned_ngrams)
+    blank_grams = {}
+    if blank == "forced":
+        pruned_ngrams = [pruned_ngrams[0] if i == 0 else [] for i in range(maxorder)]
+    pruned_ngrams[0].append(tuple([num_tokens]))
+    blank_grams[tuple([num_tokens])] = True
+
+    for gram in all_grams:
+        # Iterate over all possibilities by using a vector of 0s, 1s to
+        # denote whether a blank is being used at each position.
+        if blank == "optional":
+            # Given a gram ab.. if order n, we have n + 1 positions
+            # available whether to use blank or not.
+            onehot_vectors = itertools.product([0, 1], repeat=len(gram) + 1)
+        elif blank == "forced":
+            # Must include a blank token in between.
+            onehot_vectors = [[1] * (len(gram) + 1)]
+        else:
+            raise ValueError(
+                "Invalid value specificed for blank. Must be in |optional|forced|none|"
+            )
+
+    for j in onehot_vectors:
+        new_array = []
+        for idx, oz in enumerate(j[:-1]):
+            if oz == 1 and gram[idx] != START_IDX:
+                new_array.append(num_tokens)
+            new_array.append(gram[idx])
+        if j[-1] == 1 and gram[-1] != END_IDX:
+            new_array.append(num_tokens)
+        for n in range(maxorder):
+            for e in range(n, len(new_array)):
+                cur_gram = tuple(new_array[e - n : e + 1])
+                if num_tokens in cur_gram and cur_gram not in blank_grams:
+                    pruned_ngrams[n].append(cur_gram)
+                    blank_grams[cur_gram] = True
+
+    return pruned_ngrams
+
+
+def add_self_loops(pruned_ngrams: List) -> List:
+    """Adds self loops to the ngrams."""
+    maxorder = len(pruned_ngrams)
+
+    # Use dict for fast search.
+    all_grams = set([gram for grams in pruned_ngrams for gram in grams])
+    for o in range(1, maxorder):
+        for gram in pruned_ngrams[o - 1]:
+            # Repeat one of the tokens.
+            for pos in range(len(gram)):
+                if gram[pos] == START_IDX or gram[pos] == END_IDX:
+                    continue
+                new_gram = gram[:pos] + (gram[pos],) + gram[pos:]
+
+                if new_gram not in all_grams:
+                    pruned_ngrams[o].append(new_gram)
+                    all_grams.add(new_gram)
+    return pruned_ngrams
+
+
+def parse_lines(lines: List, lexicon: Path) -> List:
+    """Parses lines with a lexicon."""
+    with open(lexicon, "r") as f:
+        lex = (line.strip().split() for line in f)
+        lex = {line[0]: line[1:] for line in lex}
+        print(len(lex))
+    return [[t for w in line.split(WORDSEP) for t in lex[w]] for line in lines]
+
+
+@click.command()
+@click.option("--data_dir", type=str, default=None, help="Path to dataset root.")
+@click.option(
+    "--tokens", type=str, help="Path to token list (in order used with training)."
+)
+@click.option("--lexicon", type=str, default=None, help="Path to lexicon")
+@click.option(
+    "--prune",
+    nargs=2,
+    type=int,
+    help="Threshold values for prune unigrams, bigrams, etc.",
+)
+@click.option(
+    "--blank",
+    default=click.Choice(["none", "optional", "forced"]),
+    help="Specifies the usage of blank token"
+    "'none' - do not use blank token "
+    "'optional' - allow an optional blank inbetween tokens"
+    "'forced' - force a blank inbetween tokens (also referred to as garbage token)",
+)
+@click.option("--self_loops", is_flag=True, help="Add self loops for tokens")
+@click.option("--disable_backoff", is_flag=True, help="Disable backoff transitions")
+@click.option("--save_path", default=None, help="Path to save transition graph.")
+def cli(
+    data_dir: str,
+    tokens: str,
+    lexicon: str,
+    prune: List[int],
+    blank: str,
+    self_loops: bool,
+    disable_backoff: bool,
+    save_path: str,
+) -> None:
+    """CLI for creating the transitions."""
+    logger.info(f"Building {len(prune)}-gram transition models.")
+
+    if data_dir is None:
+        data_dir = (
+            Path(__file__).resolve().parents[2] / "data" / "processed" / "iam_lines"
+        )
+        logger.debug(f"Using data dir: {data_dir}")
+        if not data_dir.exists():
+            raise RuntimeError(f"Could not locate iamdb directory at {data_dir}")
+    else:
+        data_dir = Path(data_dir)
+
+    # Build table of counts and the back-off if below threshold.
+    with open(data_dir / "train.txt", "r") as f:
+        lines = [line.strip() for line in f]
+
+    with open(data_dir / tokens, "r") as f:
+        tokens = [line.strip() for line in f]
+
+    if lexicon is not None:
+        lexicon = data_dir / lexicon
+        lines = parse_lines(lines, lexicon)
+
+    tokens_to_idx = {t: e for e, t in enumerate(tokens)}
+
+    ngram = len(prune)
+
+    logger.info("Counting data...")
+    ngrams = count_ngrams(lines, ngram, tokens_to_idx)
+
+    pruned_ngrams = prune_ngrams(ngrams, prune)
+
+    for n in range(ngram):
+        logger.info(f"Kept {len(pruned_ngrams[n])} of {len(ngrams[n])} {n + 1}-grams")
+
+    if blank == "none":
+        pruned_ngrams = add_blank_grams(pruned_ngrams, len(tokens_to_idx), blank)
+
+    if self_loops:
+        pruned_ngrams = add_self_loops(pruned_ngrams)
+
+    logger.info("Building graph from pruned ngrams...")
+    graph = build_graph(pruned_ngrams, disable_backoff)
+    logger.info(f"Graph has {graph.num_arcs()} arcs and {graph.num_nodes()} nodes.")
+
+    save_path = str(data_dir / save_path)
+
+    logger.info(f"Saving graph to {save_path}")
+    gtn.save(save_path, graph)
+
+
+if __name__ == "__main__":
+    cli()
diff --git a/tasks/create_emnist_lines_datasets.sh b/tasks/create_emnist_lines_datasets.sh
new file mode 100755
index 0000000..6416277
--- /dev/null
+++ b/tasks/create_emnist_lines_datasets.sh
@@ -0,0 +1,4 @@
+#!/usr/bin/fish
+command="python text_recognizer/datasets/emnist_lines_dataset.py --max_length 34 --min_overlap 0.0 --max_overlap 0.33 --num_train 100000 --num_test 10000"
+echo $command
+eval $command
diff --git a/tasks/create_iam_paragraphs.sh b/tasks/create_iam_paragraphs.sh
new file mode 100755
index 0000000..fa2bfb0
--- /dev/null
+++ b/tasks/create_iam_paragraphs.sh
@@ -0,0 +1,2 @@
+#!/usr/bin/fish
+poetry run create-iam-paragraphs
diff --git a/tasks/download_emnist.sh b/tasks/download_emnist.sh
new file mode 100755
index 0000000..18c8e29
--- /dev/null
+++ b/tasks/download_emnist.sh
@@ -0,0 +1,3 @@
+#!/usr/bin/fish
+poetry run download-emnist
+poetry run create-emnist-support-files
diff --git a/tasks/download_iam.sh b/tasks/download_iam.sh
new file mode 100755
index 0000000..e3cf76b
--- /dev/null
+++ b/tasks/download_iam.sh
@@ -0,0 +1,2 @@
+#!/usr/bin/fish
+poetry run download-iam
diff --git a/tasks/make_wordpieces.py b/tasks/make_wordpieces.py
new file mode 100644
index 0000000..2ac0e2c
--- /dev/null
+++ b/tasks/make_wordpieces.py
@@ -0,0 +1,114 @@
+"""Creates word pieces from a text file.
+
+Most code stolen from:
+
+    https://github.com/facebookresearch/gtn_applications/blob/master/scripts/make_wordpieces.py
+
+"""
+import io
+from pathlib import Path
+from typing import List, Optional, Union
+
+import click
+from loguru import logger
+import sentencepiece as spm
+
+from text_recognizer.datasets.iam_preprocessor import load_metadata
+
+
+def iamdb_pieces(
+    data_dir: Path, text_file: str, num_pieces: int, output_prefix: str
+) -> None:
+    """Creates word pieces from the iamdb train text."""
+    # Load training text.
+    with open(data_dir / text_file, "r") as f:
+        text = [line.strip() for line in f]
+
+    sp = train_spm_model(
+        iter(text),
+        num_pieces + 1,  # To account for <unk>
+        user_symbols=["/"],  # added so token is in the output set
+    )
+
+    vocab = sorted(set(w for t in text for w in t.split("▁") if w))
+    if "move" not in vocab:
+        raise RuntimeError("`MOVE` not in vocab")
+
+    save_pieces(sp, num_pieces, data_dir, output_prefix, vocab)
+
+
+def train_spm_model(
+    sentences: iter, vocab_size: int, user_symbols: Union[str, List[str]] = ""
+) -> spm.SentencePieceProcessor:
+    """Trains the sentence piece model."""
+    model = io.BytesIO()
+    spm.SentencePieceTrainer.train(
+        sentence_iterator=sentences,
+        model_writer=model,
+        vocab_size=vocab_size,
+        bos_id=-1,
+        eos_id=-1,
+        character_coverage=1.0,
+        user_defined_symbols=user_symbols,
+    )
+    sp = spm.SentencePieceProcessor(model_proto=model.getvalue())
+    return sp
+
+
+def save_pieces(
+    sp: spm.SentencePieceProcessor,
+    num_pieces: int,
+    data_dir: Path,
+    output_prefix: str,
+    vocab: set,
+) -> None:
+    """Saves word pieces to disk."""
+    logger.info(f"Generating word piece list of size {num_pieces}.")
+    pieces = [sp.id_to_piece(i) for i in range(1, num_pieces + 1)]
+    logger.info(f"Encoding vocabulary of size {len(vocab)}.")
+    encoded_vocab = [sp.encode_as_pieces(v) for v in vocab]
+
+    # Save pieces to file.
+    with open(data_dir / f"{output_prefix}_tokens_{num_pieces}.txt", "w") as f:
+        f.write("\n".join(pieces))
+
+    # Save lexicon to a file.
+    with open(data_dir / f"{output_prefix}_lex_{num_pieces}.txt", "w") as f:
+        for v, p in zip(vocab, encoded_vocab):
+            f.write(f"{v} {' '.join(p)}\n")
+
+
+@click.command()
+@click.option("--data_dir", type=str, default=None, help="Path to processed iam dir.")
+@click.option(
+    "--text_file", type=str, default=None, help="Name of sentence piece training text."
+)
+@click.option(
+    "--output_prefix",
+    type=str,
+    default="word_pieces",
+    help="Prefix name to store tokens and lexicon.",
+)
+@click.option("--num_pieces", type=int, default=1000, help="Number of word pieces.")
+def cli(
+    data_dir: Optional[str],
+    text_file: Optional[str],
+    output_prefix: Optional[str],
+    num_pieces: Optional[int],
+) -> None:
+    """CLI for training the sentence piece model."""
+    if data_dir is None:
+        data_dir = (
+            Path(__file__).resolve().parents[2] / "data" / "processed" / "iam_lines"
+        )
+        logger.debug(f"Using data dir: {data_dir}")
+        if not data_dir.exists():
+            raise RuntimeError(f"Could not locate iamdb directory at {data_dir}")
+    else:
+        data_dir = Path(data_dir)
+
+    iamdb_pieces(data_dir, text_file, num_pieces, output_prefix)
+
+
+if __name__ == "__main__":
+    cli()
diff --git a/tasks/prepare_experiments.sh b/tasks/prepare_experiments.sh
new file mode 100755
index 0000000..95a538f
--- /dev/null
+++ b/tasks/prepare_experiments.sh
@@ -0,0 +1,3 @@
+#!/usr/bin/fish
+experiments_filename=${1:-training/experiments/sample_experiment.yml}
+poetry run prepare-experiments --experiments_filename $experiments_filename
diff --git a/tasks/test_functionality.sh b/tasks/test_functionality.sh
new file mode 100755
index 0000000..5ccf0cd
--- /dev/null
+++ b/tasks/test_functionality.sh
@@ -0,0 +1,2 @@
+#!/usr/bin/fish
+pytest -s -q text_recognizer
diff --git a/tasks/train.sh b/tasks/train.sh
new file mode 100755
index 0000000..60cbd23
--- /dev/null
+++ b/tasks/train.sh
@@ -0,0 +1,68 @@
+#!/bin/bash
+
+
+# Add checkpoint and resume experiment
+usage() {
+    cat << EOF
+    usage: ./tasks/train_crnn_line_ctc_model.sh
+    -f | --experiment_config                    Name of the experiment config.
+    -c | --checkpoint           (Optional)      The experiment name to continue from.
+    -p | --pretrained_weights   (Optional)      Path to pretrained weights.
+    -n | --notrain              (Optional)      Evaluates a trained model.
+    -t | --test                 (Optional)      If set, evaluates the model on test set.
+    -v | --verbose              (Optional)      Sets the verbosity.
+    -h | --help                                 Shows this message.
+EOF
+exit 1
+}
+
+experiment_config=""
+checkpoint=""
+pretrained_weights=""
+notrain=""
+test=""
+verbose=""
+train_command=""
+
+while getopts 'f:c:p:nthv' flag; do
+  case "${flag}" in
+    f) experiment_config="${OPTARG}" ;;
+    c) checkpoint="${OPTARG}" ;;
+    p) pretrained_weights="${OPTARG}" ;;
+    n) notrain="--notrain" ;;
+    t) test="--test" ;;
+    v) verbose="${verbose}v" ;;
+    h) usage ;;
+    *) error "Unexpected option ${flag}" ;;
+  esac
+done
+
+
+if [ -z ${experiment_config} ];
+then
+    echo "experiment_config not specified!"
+    usage
+    exit 1
+fi
+
+experiments_filename="training/experiments/${experiment_config}"
+train_command=$(bash tasks/prepare_experiments.sh $experiments_filename)
+
+if [ ${checkpoint} ];
+then
+    train_command="${train_command} --checkpoint $checkpoint"
+fi
+
+if [ ${pretrained_weights} ];
+then
+    train_command="${train_command} --pretrained_weights $pretrained_weights"
+fi
+
+if [ ${verbose} ];
+then
+    train_command="${train_command} -$verbose"
+fi
+
+train_command="${train_command} $test $notrain"
+echo $train_command
+eval $train_command