| Name | SisC JSON |
| Version |
0.0.3
JSON |
| download |
| home_page | None |
| Summary | SisC is a tool to automatically separate annotations from the underlying text. SisC uses a fingerprint, that is, a masked version of the text to merge stand-off annotations with another version of the original text, for example, extracted from a PDF file. The fingerprint cannot be used on its own to recreate (meaningful parts of) the original text and can therefore be shared. |
| upload_time | 2024-12-05 15:04:26 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.11 |
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| keywords |
sharing
annotation
openaccess
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
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|
# Readme
SisC is a tool to automatically separate annotations from the underlying text. SisC uses a fingerprint, that is,
a masked version of the text to merge stand-off annotations with another version of the original text, for example,
extracted from a PDF file. The fingerprint cannot be used on its own to recreate (meaningful parts of) the original
text and can therefore be shared.
## Example
~~~
<TEI>
<text>
<body>
<p>Some text with <q>an annotated quote</q>.</p>
</body>
</text>
</TEI>
~~~
The given simple TEI XML file would result in the following file with fingerprint with uniform masking:
~~~
<TEI>
<text>
<body sisc_start="0" sisc_end="36"><p sisc_start="1" sisc_end="35"><q sisc_start="16" sisc_end="34" /></p></body>
</text>
<standoff>
S___ _ex_ ___h __ __no_____ q____.
</standoff>
</TEI>
~~~
## Installation
~~~
pip install sisc
~~~
## PDF Processing
For PDF processing, SisC uses [pdf2image](https://github.com/Belval/pdf2image) and [Tesseract](https://github.com/tesseract-ocr/tesseract).
For pdf2image, depending on the operating system, [Poppler](https://poppler.freedesktop.org) needs to be installed and
available in `PATH`, see [pdf2image documentation](https://github.com/Belval/pdf2image/blob/master/README.md).
Tesseract needs to be manually installed and also available in `PATH`. By default, PDF processing uses German,
`--tess-lang` can be used to set [another language](https://tesseract-ocr.github.io/tessdoc/Data-Files-in-different-versions.html).
Make sure that required languages are installed.
As an alternative to using `PATH`, the command line interface offers arguments to specify the paths, `--tess-path`
and `--poppler-path`.
## Usage
SisC provides a command line interface for easy usage.
Sisc currently best supports TEI XML as the input format. [Other formats](#supported-formats) are partially supported
and [more formats can easily be added](#adding-new-formats).
### Creating a Fingerprint
For XML files, two types of [masking](#masking) are available, `uniform` and `context`. A fingerprint with uniform
masking is created with:
~~~
sisc fingerprint uniform input_path output_path
~~~
If `input_path` is a folder, all files in that folder which are of the type specified with `--file-type` will be processed.
By default, `--file-type` is set to xml.
For TEI XML files, SisC supports moving footnotes to the end of the page if the TEI XML file contains annotations for
footnotes and page breaks. This can be useful when the footnotes are moved to their anchor position during annotation.
To turn on moving of footnotes, set `--move-notes`.
<details>
<summary>All command line options for uniform fingerprinting</summary>
~~~
usage: sisc fingerprint uniform [-h] [--file-type {txt,xml}]
[--move-notes | --no-move-notes]
[--add-quotation-marks | --no-add-quotation-marks]
[-s SYMBOL] [-k KEEP_COUNT] [-d DISTANCE]
input-path output-path
Command to use uniform masking for the fingerprint.
positional arguments:
input-path Path to txt or xml file to create fingerprint from.
Can be a folder in which case all files will be
processed.
output-path Output folder path.
options:
-h, --help show this help message and exit
--file-type {txt,xml}
The input file type to process. Only used when
input_path is a folder (default: xml).
--move-notes, --no-move-notes
This will move footnotes and endnotes to the end of
their page/the whole text. Only works withXML file
which are annotated with footnotes/endnotes and
pagebreaks. (default: False)
--add-quotation-marks, --no-add-quotation-marks
Add quotation marks in the fingerprint. Useful when
quotations marks are not present in the annotated XML
file. (default: False)
-s SYMBOL, --symbol SYMBOL
The character to use for masking (default: _).
-k KEEP_COUNT, --keep-count KEEP_COUNT
Number of characters which not to mask.
-d DISTANCE, --distance DISTANCE
The number of characters to mask between not masked
characters (default: 10)
~~~
</details>
#### Masking
We currently support two types of masking: `Uniform` masking and `context` masking. Uniform masking keeps a certain
number of characters, for example two, then masks a certain number of characters, for example five, then keeps two
characters and so on. The result can be seen in the [example above](#example).
The number of characters to keep can be set with the `--keep-count` argument and the number of characters to mask with
`--distance`.
Context masking keeps the text around a specified tag unmasked and masked the rest of the text. The previous
[example](#example) with context masking would result in the following fingerprint:
~~~
____ text with __ _________ _____.
~~~
To specify the tag, use `--tag`. `--context-size` specify the context size on either side.
By default, the text of the tag itself is masked, to can be changed with `--keep-text`.
### Aligning Texts
To align PDF files with TEI XML fingerprints, run:
~~~
sisc align content_path fingerprint_path output_path
~~~
If `content_path` is a folder, all PDF and Txt files in that path will be processed. If `content_path` points to a file,
then `fingerprint_path` also needs to be a file. Otherwise, `fingerprint_path` needs to be a folder. In that case,
by default, SisC will look for XML files in `fingerprint_path`.
For annotations in external files, for example, json, `--annotation-type` can be set to `json` and `--annotation-path`
to the path with the annotation files.
<details>
<summary>All command line options for aligning texts</summary>
~~~
usage: sisc align [-h] [--annotation-path ANNOTATION_PATH]
[--annotation-type {txt,json}] [-f FIRST_PAGE]
[-l LAST_PAGE] [-k KEYS_TO_UPDATE [KEYS_TO_UPDATE ...]]
[--max-num-processes MAX_NUM_PROCESSES]
[--max-text-length MAX_TEXT_LENGTH] [--tess-lang TESS_LANG]
[--tess-path TESS_PATH] [--poppler-path POPPLER_PATH]
content-path fingerprint-path output-path
Command to align fingerprint and PDF or text.
positional arguments:
content-path Path to the file (or folder) with the content for
alignment (txt or pdf).
fingerprint-path Path to the file (or folder) with the fingerprint
file(s) (txt or xml).
output-path Output folder path.
options:
-h, --help show this help message and exit
--annotation-path ANNOTATION_PATH
Can be used to specify the path to the annotations.
Only needed when the annotations are not part of the
files specified in fingerprint_path.
--annotation-type {txt,json}
The type of the annotations to process. Only used when
content_path isa folder. (default: xml).
-f FIRST_PAGE, --first-page FIRST_PAGE
Can be used to specify the first page to process. Only
used for PDF files and when processing a single PDF
file (default: 1).
-l LAST_PAGE, --last-page LAST_PAGE
Can be used to specify the last page to process. Only
used for PDF files and when processing a single PDF
file (default: -1).
-k KEYS_TO_UPDATE [KEYS_TO_UPDATE ...], --keys KEYS_TO_UPDATE [KEYS_TO_UPDATE ...]
Only used for json standoff annotations. Used to
specify json keys which represent a position and need
to be updated.
--max-num-processes MAX_NUM_PROCESSES
Maximum number of processes to use for parallel
processing (default: 1).
--max-text-length MAX_TEXT_LENGTH
The maximum length (in characters) of a text to align
(default: 200000).
--tess-lang TESS_LANG
Language to use for PDF processing (default: deu).
--tess-path TESS_PATH
Path to Tesseract.
--poppler-path POPPLER_PATH
Path to Poppler.
~~~
</details>
## Supported Formats
TEI XML is the best supported format. Other formats, which have limited support, are txt and json.
To align a PDF file with a fingerprint stored in a Txt file and annotations in a json file, the following command can
be used:
~~~
sisc align path_to_file.pdf path_to_fingerprint.txt output_path --annotation-path path_to_file.json --annotation-type json --keys start end
~~~
For an annotation file, that looks something like the following example, this would update the start and end positions.
~~~
[
{
"text": "quote",
"start": 5,
"end": 10
},
{
"text": "quote 2",
"start": 25,
"end": 32
}
]
~~~
More fine-grained matching of keys is also possible, for example `key.start` will only match for `start` that appears
as a child of `key`.
## Custom Masking
To use custom masking, SisC needs to be run from code, for example:
~~~
from sisc.obfuscate.BaseObfuscater import BaseObfuscater
from sisc.fingerprint.TeiXmlFingerprinter import TeiXmlFingerprinter
class CustomObfuscater(BaseObfuscater):
# overriding abstract method
def obfuscate(self, text: str, positions: List[Tuple[int,int]]) -> str:
...
obfuscater = CustomObfuscater()
fingerprinter = TeiXmlFingerprinter(obfuscater)
result = fingerprinter.fingerprint(...)
~~~
## Adding New Formats
To add support for a new file format, a custom fingerprinter and aligner can be implemented. For example:
~~~
from typing import Any, List
from sisc.fingerprint.BaseFingerprinter import BaseFingerprinter
from sisc.obfuscate.BaseObfuscater import BaseObfuscater
from sisc.alignment.BaseFileAligner import BaseFileAligner
class CustomFingerprinter(BaseFingerprinter[str, Any]):
def __init__(self, obfuscater: BaseObfuscater):
self.obfuscater = obfuscater
# overriding abstract method
def fingerprint(self, text: str, annotations: Any) -> str:
return self.obfuscater.obfuscate(text, [])
class CustomAligner(BaseFileAligner[str]):
# overriding abstract method
def align(self, input_content: str, aligned_text: str, aligned_fingerprint: str, text_gap_positions: List[int],
fingerprint_gap_positions: List[int]) -> str:
...
~~~
<!--
## Citation
Coming soon!
--->
Raw data
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"author_email": "Frederik Arnold <frederik.arnold@hu-berlin.de>",
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"description": "# Readme\n\nSisC is a tool to automatically separate annotations from the underlying text. SisC uses a fingerprint, that is,\na masked version of the text to merge stand-off annotations with another version of the original text, for example,\nextracted from a PDF file. The fingerprint cannot be used on its own to recreate (meaningful parts of) the original\ntext and can therefore be shared.\n\n## Example\n\n~~~\n<TEI>\n <text>\n <body>\n <p>Some text with <q>an annotated quote</q>.</p>\n </body>\n </text>\n</TEI>\n~~~\n\nThe given simple TEI XML file would result in the following file with fingerprint with uniform masking:\n\n~~~\n<TEI>\n <text>\n <body sisc_start=\"0\" sisc_end=\"36\"><p sisc_start=\"1\" sisc_end=\"35\"><q sisc_start=\"16\" sisc_end=\"34\" /></p></body>\n </text>\n <standoff>\n S___ _ex_ ___h __ __no_____ q____.\n </standoff>\n</TEI>\n~~~\n\n## Installation\n\n~~~\npip install sisc\n~~~\n\n## PDF Processing\n\nFor PDF processing, SisC uses [pdf2image](https://github.com/Belval/pdf2image) and [Tesseract](https://github.com/tesseract-ocr/tesseract).\nFor pdf2image, depending on the operating system, [Poppler](https://poppler.freedesktop.org) needs to be installed and\navailable in `PATH`, see [pdf2image documentation](https://github.com/Belval/pdf2image/blob/master/README.md).\nTesseract needs to be manually installed and also available in `PATH`. By default, PDF processing uses German,\n`--tess-lang` can be used to set [another language](https://tesseract-ocr.github.io/tessdoc/Data-Files-in-different-versions.html).\nMake sure that required languages are installed.\n\nAs an alternative to using `PATH`, the command line interface offers arguments to specify the paths, `--tess-path`\nand `--poppler-path`.\n\n## Usage\n\nSisC provides a command line interface for easy usage.\n\nSisc currently best supports TEI XML as the input format. [Other formats](#supported-formats) are partially supported\nand [more formats can easily be added](#adding-new-formats).\n\n### Creating a Fingerprint\n\nFor XML files, two types of [masking](#masking) are available, `uniform` and `context`. A fingerprint with uniform\nmasking is created with:\n\n~~~\nsisc fingerprint uniform input_path output_path\n~~~\n\nIf `input_path` is a folder, all files in that folder which are of the type specified with `--file-type` will be processed.\nBy default, `--file-type` is set to xml.\n\nFor TEI XML files, SisC supports moving footnotes to the end of the page if the TEI XML file contains annotations for\nfootnotes and page breaks. This can be useful when the footnotes are moved to their anchor position during annotation.\nTo turn on moving of footnotes, set `--move-notes`.\n\n<details>\n<summary>All command line options for uniform fingerprinting</summary>\n\n~~~\nusage: sisc fingerprint uniform [-h] [--file-type {txt,xml}]\n [--move-notes | --no-move-notes]\n [--add-quotation-marks | --no-add-quotation-marks]\n [-s SYMBOL] [-k KEEP_COUNT] [-d DISTANCE]\n input-path output-path\n\nCommand to use uniform masking for the fingerprint.\n\npositional arguments:\n input-path Path to txt or xml file to create fingerprint from.\n Can be a folder in which case all files will be\n processed.\n output-path Output folder path.\n\noptions:\n -h, --help show this help message and exit\n --file-type {txt,xml}\n The input file type to process. Only used when\n input_path is a folder (default: xml).\n --move-notes, --no-move-notes\n This will move footnotes and endnotes to the end of\n their page/the whole text. Only works withXML file\n which are annotated with footnotes/endnotes and\n pagebreaks. (default: False)\n --add-quotation-marks, --no-add-quotation-marks\n Add quotation marks in the fingerprint. Useful when\n quotations marks are not present in the annotated XML\n file. (default: False)\n -s SYMBOL, --symbol SYMBOL\n The character to use for masking (default: _).\n -k KEEP_COUNT, --keep-count KEEP_COUNT\n Number of characters which not to mask.\n -d DISTANCE, --distance DISTANCE\n The number of characters to mask between not masked\n characters (default: 10)\n~~~\n\n</details>\n\n\n\n#### Masking\n\nWe currently support two types of masking: `Uniform` masking and `context` masking. Uniform masking keeps a certain\nnumber of characters, for example two, then masks a certain number of characters, for example five, then keeps two\ncharacters and so on. The result can be seen in the [example above](#example).\n\nThe number of characters to keep can be set with the `--keep-count` argument and the number of characters to mask with\n`--distance`.\n\nContext masking keeps the text around a specified tag unmasked and masked the rest of the text. The previous\n[example](#example) with context masking would result in the following fingerprint:\n\n~~~\n____ text with __ _________ _____.\n~~~\n\nTo specify the tag, use `--tag`. `--context-size` specify the context size on either side.\nBy default, the text of the tag itself is masked, to can be changed with `--keep-text`.\n\n### Aligning Texts\n\nTo align PDF files with TEI XML fingerprints, run:\n\n~~~\nsisc align content_path fingerprint_path output_path\n~~~\n\nIf `content_path` is a folder, all PDF and Txt files in that path will be processed. If `content_path` points to a file,\nthen `fingerprint_path` also needs to be a file. Otherwise, `fingerprint_path` needs to be a folder. In that case,\nby default, SisC will look for XML files in `fingerprint_path`.\n\nFor annotations in external files, for example, json, `--annotation-type` can be set to `json` and `--annotation-path`\nto the path with the annotation files.\n\n<details>\n<summary>All command line options for aligning texts</summary>\n\n~~~\nusage: sisc align [-h] [--annotation-path ANNOTATION_PATH]\n [--annotation-type {txt,json}] [-f FIRST_PAGE]\n [-l LAST_PAGE] [-k KEYS_TO_UPDATE [KEYS_TO_UPDATE ...]]\n [--max-num-processes MAX_NUM_PROCESSES]\n [--max-text-length MAX_TEXT_LENGTH] [--tess-lang TESS_LANG]\n [--tess-path TESS_PATH] [--poppler-path POPPLER_PATH]\n content-path fingerprint-path output-path\n\nCommand to align fingerprint and PDF or text.\n\npositional arguments:\n content-path Path to the file (or folder) with the content for\n alignment (txt or pdf).\n fingerprint-path Path to the file (or folder) with the fingerprint\n file(s) (txt or xml).\n output-path Output folder path.\n\noptions:\n -h, --help show this help message and exit\n --annotation-path ANNOTATION_PATH\n Can be used to specify the path to the annotations.\n Only needed when the annotations are not part of the\n files specified in fingerprint_path.\n --annotation-type {txt,json}\n The type of the annotations to process. Only used when\n content_path isa folder. (default: xml).\n -f FIRST_PAGE, --first-page FIRST_PAGE\n Can be used to specify the first page to process. Only\n used for PDF files and when processing a single PDF\n file (default: 1).\n -l LAST_PAGE, --last-page LAST_PAGE\n Can be used to specify the last page to process. Only\n used for PDF files and when processing a single PDF\n file (default: -1).\n -k KEYS_TO_UPDATE [KEYS_TO_UPDATE ...], --keys KEYS_TO_UPDATE [KEYS_TO_UPDATE ...]\n Only used for json standoff annotations. Used to\n specify json keys which represent a position and need\n to be updated.\n --max-num-processes MAX_NUM_PROCESSES\n Maximum number of processes to use for parallel\n processing (default: 1).\n --max-text-length MAX_TEXT_LENGTH\n The maximum length (in characters) of a text to align\n (default: 200000).\n --tess-lang TESS_LANG\n Language to use for PDF processing (default: deu).\n --tess-path TESS_PATH\n Path to Tesseract.\n --poppler-path POPPLER_PATH\n Path to Poppler.\n~~~\n\n</details>\n\n## Supported Formats\n\nTEI XML is the best supported format. Other formats, which have limited support, are txt and json.\n\nTo align a PDF file with a fingerprint stored in a Txt file and annotations in a json file, the following command can\nbe used:\n\n~~~\nsisc align path_to_file.pdf path_to_fingerprint.txt output_path --annotation-path path_to_file.json --annotation-type json --keys start end\n~~~\n\nFor an annotation file, that looks something like the following example, this would update the start and end positions.\n\n~~~\n[\n {\n \"text\": \"quote\",\n \"start\": 5,\n \"end\": 10\n },\n {\n \"text\": \"quote 2\",\n \"start\": 25,\n \"end\": 32\n }\n]\n~~~\n\nMore fine-grained matching of keys is also possible, for example `key.start` will only match for `start` that appears\nas a child of `key`.\n\n## Custom Masking\n\nTo use custom masking, SisC needs to be run from code, for example:\n\n~~~\nfrom sisc.obfuscate.BaseObfuscater import BaseObfuscater\nfrom sisc.fingerprint.TeiXmlFingerprinter import TeiXmlFingerprinter\n\nclass CustomObfuscater(BaseObfuscater):\n \n # overriding abstract method\n def obfuscate(self, text: str, positions: List[Tuple[int,int]]) -> str:\n ...\n\nobfuscater = CustomObfuscater()\nfingerprinter = TeiXmlFingerprinter(obfuscater)\nresult = fingerprinter.fingerprint(...) \n~~~\n\n## Adding New Formats\n\nTo add support for a new file format, a custom fingerprinter and aligner can be implemented. For example:\n\n~~~\nfrom typing import Any, List\nfrom sisc.fingerprint.BaseFingerprinter import BaseFingerprinter\nfrom sisc.obfuscate.BaseObfuscater import BaseObfuscater\nfrom sisc.alignment.BaseFileAligner import BaseFileAligner\n\nclass CustomFingerprinter(BaseFingerprinter[str, Any]):\n\n def __init__(self, obfuscater: BaseObfuscater):\n self.obfuscater = obfuscater\n\n # overriding abstract method\n def fingerprint(self, text: str, annotations: Any) -> str:\n return self.obfuscater.obfuscate(text, [])\n\nclass CustomAligner(BaseFileAligner[str]):\n\n # overriding abstract method\n def align(self, input_content: str, aligned_text: str, aligned_fingerprint: str, text_gap_positions: List[int],\n fingerprint_gap_positions: List[int]) -> str:\n ...\n\n~~~\n\n<!-- \n\n## Citation\n\nComing soon!\n\n--->\n",
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