spaCy/spacy/training/converters/conll_ner_to_docs.py

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Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
from wasabi import Printer
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 17:34:12 +00:00
from .. import tags_to_entities
from ...training import iob_to_biluo
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 17:34:12 +00:00
from ...tokens import Doc, Span
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from ...errors import Errors
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from ...util import load_model, get_lang_class
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2020-09-22 09:50:19 +00:00
def conll_ner_to_docs(
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input_data, n_sents=10, seg_sents=False, model=None, no_print=False, **kwargs
):
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"""
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
Convert files in the CoNLL-2003 NER format and similar
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 17:34:12 +00:00
whitespace-separated columns into Doc objects.
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
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The first column is the tokens, the final column is the IOB tags. If an
additional second column is present, the second column is the tags.
Sentences are separated with whitespace and documents can be separated
using the line "-DOCSTART- -X- O O".
Sample format:
-DOCSTART- -X- O O
I O
like O
London B-GPE
and O
New B-GPE
York I-GPE
City I-GPE
. O
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"""
msg = Printer(no_print=no_print)
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
doc_delimiter = "-DOCSTART- -X- O O"
# check for existing delimiters, which should be preserved
if "\n\n" in input_data and seg_sents:
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msg.warn(
"Sentence boundaries found, automatic sentence segmentation with "
"`-s` disabled."
)
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
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seg_sents = False
if doc_delimiter in input_data and n_sents:
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msg.warn(
"Document delimiters found, automatic document segmentation with "
"`-n` disabled."
)
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
n_sents = 0
# do document segmentation with existing sentences
2019-08-31 11:39:06 +00:00
if "\n\n" in input_data and doc_delimiter not in input_data and n_sents:
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
n_sents_info(msg, n_sents)
input_data = segment_docs(input_data, n_sents, doc_delimiter)
# do sentence segmentation with existing documents
2019-08-31 11:39:06 +00:00
if "\n\n" not in input_data and doc_delimiter in input_data and seg_sents:
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
input_data = segment_sents_and_docs(input_data, 0, "", model=model, msg=msg)
# do both sentence segmentation and document segmentation according
# to options
2019-08-31 11:39:06 +00:00
if "\n\n" not in input_data and doc_delimiter not in input_data:
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
# sentence segmentation required for document segmentation
if n_sents > 0 and not seg_sents:
2019-08-31 11:39:06 +00:00
msg.warn(
f"No sentence boundaries found to use with option `-n {n_sents}`. "
f"Use `-s` to automatically segment sentences or `-n 0` "
f"to disable."
2019-08-31 11:39:06 +00:00
)
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
else:
n_sents_info(msg, n_sents)
2019-08-31 11:39:06 +00:00
input_data = segment_sents_and_docs(
input_data, n_sents, doc_delimiter, model=model, msg=msg
)
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
# provide warnings for problematic data
2019-08-31 11:39:06 +00:00
if "\n\n" not in input_data:
msg.warn(
"No sentence boundaries found. Use `-s` to automatically segment "
"sentences."
)
if doc_delimiter not in input_data:
msg.warn(
"No document delimiters found. Use `-n` to automatically group "
"sentences into documents."
)
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 17:34:12 +00:00
if model:
nlp = load_model(model)
else:
2020-10-04 09:10:26 +00:00
nlp = get_lang_class("xx")()
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 17:34:12 +00:00
for conll_doc in input_data.strip().split(doc_delimiter):
conll_doc = conll_doc.strip()
if not conll_doc:
2017-10-10 03:03:26 +00:00
continue
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 17:34:12 +00:00
words = []
sent_starts = []
pos_tags = []
biluo_tags = []
for conll_sent in conll_doc.split("\n\n"):
conll_sent = conll_sent.strip()
if not conll_sent:
2017-10-10 03:03:26 +00:00
continue
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 17:34:12 +00:00
lines = [line.strip() for line in conll_sent.split("\n") if line.strip()]
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
cols = list(zip(*[line.split() for line in lines]))
if len(cols) < 2:
2020-10-05 11:43:32 +00:00
raise ValueError(Errors.E903)
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 17:34:12 +00:00
length = len(cols[0])
words.extend(cols[0])
sent_starts.extend([True] + [False] * (length - 1))
biluo_tags.extend(iob_to_biluo(cols[-1]))
pos_tags.extend(cols[1] if len(cols) > 2 else ["-"] * length)
doc = Doc(nlp.vocab, words=words)
for i, token in enumerate(doc):
token.tag_ = pos_tags[i]
token.is_sent_start = sent_starts[i]
entities = tags_to_entities(biluo_tags)
doc.ents = [Span(doc, start=s, end=e + 1, label=L) for L, s, e in entities]
yield doc
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
def segment_sents_and_docs(doc, n_sents, doc_delimiter, model=None, msg=None):
sentencizer = None
if model:
nlp = load_model(model)
if "parser" in nlp.pipe_names:
msg.info(f"Segmenting sentences with parser from model '{model}'.")
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
sentencizer = nlp.get_pipe("parser")
if not sentencizer:
2019-08-31 11:39:06 +00:00
msg.info(
"Segmenting sentences with sentencizer. (Use `-b model` for "
"improved parser-based sentence segmentation.)"
)
2020-10-04 09:10:26 +00:00
nlp = get_lang_class("xx")()
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
sentencizer = nlp.create_pipe("sentencizer")
lines = doc.strip().split("\n")
words = [line.strip().split()[0] for line in lines]
nlpdoc = Doc(nlp.vocab, words=words)
sentencizer(nlpdoc)
lines_with_segs = []
sent_count = 0
for i, token in enumerate(nlpdoc):
if token.is_sent_start:
if n_sents and sent_count % n_sents == 0:
lines_with_segs.append(doc_delimiter)
lines_with_segs.append("")
sent_count += 1
lines_with_segs.append(lines[i])
return "\n".join(lines_with_segs)
def segment_docs(input_data, n_sents, doc_delimiter):
sent_delimiter = "\n\n"
sents = input_data.split(sent_delimiter)
2019-08-31 11:39:06 +00:00
docs = [sents[i : i + n_sents] for i in range(0, len(sents), n_sents)]
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
input_data = ""
for doc in docs:
input_data += sent_delimiter + doc_delimiter
input_data += sent_delimiter.join(doc)
return input_data
def n_sents_info(msg, n_sents):
msg.info(f"Grouping every {n_sents} sentences into a document.")
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
if n_sents == 1:
2019-08-31 11:39:06 +00:00
msg.warn(
"To generate better training data, you may want to group "
"sentences into documents with `-n 10`."
)