Path to notebook: https://www.github.com/microsoft/presidio/blob/main/docs/samples/python/example_pdf_annotation.ipynb¶

Annotating PII in a PDF¶

This sample takes a PDF as an input, extracts the text, identifies PII using Presidio and annotates the PII using highlight annotations.

Prerequisites¶

Before getting started, make sure the following packages are installed. For detailed documentation, see the installation docs.

Install from PyPI:

In [ ]:

!pip install presidio_analyzer
!pip install presidio_anonymizer
!python -m spacy download en_core_web_lg
!pip install pdfminer.six
!pip install pikepdf

!pip install presidio_analyzer !pip install presidio_anonymizer !python -m spacy download en_core_web_lg !pip install pdfminer.six !pip install pikepdf

In [4]:

# For Presidio
from presidio_analyzer import AnalyzerEngine, PatternRecognizer
from presidio_anonymizer import AnonymizerEngine
from presidio_anonymizer.entities import OperatorConfig

# For console output
from pprint import pprint

# For extracting text
from pdfminer.high_level import extract_text, extract_pages
from pdfminer.layout import LTTextContainer, LTChar, LTTextLine

# For updating the PDF
from pikepdf import Pdf, AttachedFileSpec, Name, Dictionary, Array

# For Presidio from presidio_analyzer import AnalyzerEngine, PatternRecognizer from presidio_anonymizer import AnonymizerEngine from presidio_anonymizer.entities import OperatorConfig # For console output from pprint import pprint # For extracting text from pdfminer.high_level import extract_text, extract_pages from pdfminer.layout import LTTextContainer, LTChar, LTTextLine # For updating the PDF from pikepdf import Pdf, AttachedFileSpec, Name, Dictionary, Array

Analyze the text in the PDF¶

To extract the text from the PDF, we use the pdf miner library. We extract the text from the PDF at the text container level. This is roughly equivalent to a paragraph.

We then use Presidio Analyzer to identify the PII and it's location in the text.

The Presidio analyzer is using pre-defined entity recognizers, and offers the option to create custom recognizers.

In [5]:

analyzer = AnalyzerEngine()

analyzed_character_sets = []

for page_layout in extract_pages("./sample_data/sample.pdf"):
    for text_container in page_layout:
        if isinstance(text_container, LTTextContainer):

            # The element is a LTTextContainer, containing a paragraph of text.
            text_to_anonymize = text_container.get_text()

            # Analyze the text using the analyzer engine
            analyzer_results = analyzer.analyze(text=text_to_anonymize, language='en')
 
            if text_to_anonymize.isspace() == False:
                print(text_to_anonymize)
                print(analyzer_results)

            characters = list([])

            # Grab the characters from the PDF
            for text_line in filter(lambda t: isinstance(t, LTTextLine), text_container):
                    for character in filter(lambda t: isinstance(t, LTChar), text_line):
                            characters.append(character)


            # Slice out the characters that match the analyzer results.
            for result in analyzer_results:
                start = result.start
                end = result.end
                analyzed_character_sets.append({"characters": characters[start:end], "result": result})

analyzer = AnalyzerEngine() analyzed_character_sets = [] for page_layout in extract_pages("./sample_data/sample.pdf"): for text_container in page_layout: if isinstance(text_container, LTTextContainer): # The element is a LTTextContainer, containing a paragraph of text. text_to_anonymize = text_container.get_text() # Analyze the text using the analyzer engine analyzer_results = analyzer.analyze(text=text_to_anonymize, language='en') if text_to_anonymize.isspace() == False: print(text_to_anonymize) print(analyzer_results) characters = list([]) # Grab the characters from the PDF for text_line in filter(lambda t: isinstance(t, LTTextLine), text_container): for character in filter(lambda t: isinstance(t, LTChar), text_line): characters.append(character) # Slice out the characters that match the analyzer results. for result in analyzer_results: start = result.start end = result.end analyzed_character_sets.append({"characters": characters[start:end], "result": result})

This is a test PDF, created by Microsoft Word. 

[]
Hi my name is Charles Darwin and my email is cdarwin@hmsbeagle.org 

[type: EMAIL_ADDRESS, start: 45, end: 66, score: 1.0, type: PERSON, start: 14, end: 28, score: 0.85, type: URL, start: 53, end: 66, score: 0.5]
You can contact me on 01234 567890. 

[type: PHONE_NUMBER, start: 22, end: 34, score: 0.4, type: US_DRIVER_LICENSE, start: 28, end: 34, score: 0.01]

Create phrase bounding boxes¶

The next task is to take the character data, and inflate it into full phrase bounding boxes.

For example, for an email address, we'll turn the bounding boxes for each character in the email address into one single bounding box.

In [6]:

# Combine the bounding boxes into a single bounding box.
def combine_rect(rectA, rectB):
    a, b = rectA, rectB
    startX = min( a[0], b[0] )
    startY = min( a[1], b[1] )
    endX = max( a[2], b[2] )
    endY = max( a[3], b[3] )
    return (startX, startY, endX, endY)

analyzed_bounding_boxes = []

# For each character set, combine the bounding boxes into a single bounding box.
for analyzed_character_set in analyzed_character_sets:
    completeBoundingBox = analyzed_character_set["characters"][0].bbox
    
    for character in analyzed_character_set["characters"]:
        completeBoundingBox = combine_rect(completeBoundingBox, character.bbox)
    
    analyzed_bounding_boxes.append({"boundingBox": completeBoundingBox, "result": analyzed_character_set["result"]})

# Combine the bounding boxes into a single bounding box. def combine_rect(rectA, rectB): a, b = rectA, rectB startX = min( a[0], b[0] ) startY = min( a[1], b[1] ) endX = max( a[2], b[2] ) endY = max( a[3], b[3] ) return (startX, startY, endX, endY) analyzed_bounding_boxes = [] # For each character set, combine the bounding boxes into a single bounding box. for analyzed_character_set in analyzed_character_sets: completeBoundingBox = analyzed_character_set["characters"][0].bbox for character in analyzed_character_set["characters"]: completeBoundingBox = combine_rect(completeBoundingBox, character.bbox) analyzed_bounding_boxes.append({"boundingBox": completeBoundingBox, "result": analyzed_character_set["result"]})

Add highlight annotations¶

We finally iterate through all the analyzed bounding boxes and create highlight annotations for all of them.

In [7]:

pdf = Pdf.open("./sample_data/sample.pdf")

annotations = []

# Create a highlight annotation for each bounding box.
for analyzed_bounding_box in analyzed_bounding_boxes:

    boundingBox = analyzed_bounding_box["boundingBox"]

    # Create the annotation. 
    # We could also create a redaction annotation if the ongoing workflows supports them.
    highlight = Dictionary(
        Type=Name.Annot,
        Subtype=Name.Highlight,
        QuadPoints=[boundingBox[0], boundingBox[3],
                    boundingBox[2], boundingBox[3],
                    boundingBox[0], boundingBox[1],
                    boundingBox[2], boundingBox[1]],
        Rect=[boundingBox[0], boundingBox[1], boundingBox[2], boundingBox[3]],
        C=[1, 0, 0],
        CA=0.5,
        T=analyzed_bounding_box["result"].entity_type,
    )
    
    annotations.append(highlight)

# Add the annotations to the PDF.
pdf.pages[0].Annots = pdf.make_indirect(annotations)

# And save.
pdf.save("./sample_data/sample_annotated.pdf")

pdf = Pdf.open("./sample_data/sample.pdf") annotations = [] # Create a highlight annotation for each bounding box. for analyzed_bounding_box in analyzed_bounding_boxes: boundingBox = analyzed_bounding_box["boundingBox"] # Create the annotation. # We could also create a redaction annotation if the ongoing workflows supports them. highlight = Dictionary( Type=Name.Annot, Subtype=Name.Highlight, QuadPoints=[boundingBox[0], boundingBox[3], boundingBox[2], boundingBox[3], boundingBox[0], boundingBox[1], boundingBox[2], boundingBox[1]], Rect=[boundingBox[0], boundingBox[1], boundingBox[2], boundingBox[3]], C=[1, 0, 0], CA=0.5, T=analyzed_bounding_box["result"].entity_type, ) annotations.append(highlight) # Add the annotations to the PDF. pdf.pages[0].Annots = pdf.make_indirect(annotations) # And save. pdf.save("./sample_data/sample_annotated.pdf")

Result¶

The output from the samples above creates a new PDF. This contains the original content, with text highlight annotations where the PII has been found.

Each text annotation contains the name of the entity found.

Note¶

Before relying on this methodology to detect or markup PII from a PDF, please be aware of the following:

Text extraction¶

We purposely use a different library specifically for extracting text from the PDF. This is because text extraction is hard to get right, and it's worth using a library specifically developed with the purpose in mind.

For more details, see:

https://pdfminersix.readthedocs.io/en/latest/topic/converting_pdf_to_text.html

That said, even with a purpose built library, there may be occasions where PII is present and visible in a PDF, but it is not detected by the sample code.

This includes, but is not limited to:

• Text that cannot be reliable extracted to be analyzed. (e.g. incorrect spacing, wrong reading order)
• Text present in previous iterations of the PDF which is hidden from text extraction. (See incremental editing)
• Text present in images. (requires OCRing)
• Text present in annotations.

In [ ]: