import time import re import json import io import os from PIL import Image, ImageChops, ImageDraw from typing import List import pandas as pd from presidio_image_redactor.entities import ImageRecognizerResult from pdfminer.high_level import extract_pages from pdfminer.layout import LTTextContainer, LTChar, LTTextLine #, LTAnno from pikepdf import Pdf, Dictionary, Name import gradio as gr from gradio import Progress from collections import defaultdict # For efficient grouping from tools.custom_image_analyser_engine import CustomImageAnalyzerEngine, OCRResult from tools.file_conversion import process_file from tools.load_spacy_model_custom_recognisers import nlp_analyser, score_threshold from tools.helper_functions import get_file_path_end, output_folder from tools.file_conversion import process_file, is_pdf, convert_text_pdf_to_img_pdf from tools.data_anonymise import generate_decision_process_output from tools.aws_textract import analyse_page_with_textract, convert_pike_pdf_page_to_bytes, json_to_ocrresult def choose_and_run_redactor(file_paths:List[str], image_paths:List[str], language:str, chosen_redact_entities:List[str], in_redact_method:str, in_allow_list:List[List[str]]=None, latest_file_completed:int=0, out_message:list=[], out_file_paths:list=[], log_files_output_paths:list=[], first_loop_state:bool=False, page_min:int=0, page_max:int=999, estimated_time_taken_state:float=0.0, progress=gr.Progress(track_tqdm=True)): tic = time.perf_counter() # If this is the first time around, set variables to 0/blank if first_loop_state==True: latest_file_completed = 0 #out_message = [] out_file_paths = [] # If out message is string or out_file_paths are blank, change to a list so it can be appended to if isinstance(out_message, str): out_message = [out_message] if not out_file_paths: out_file_paths = [] latest_file_completed = int(latest_file_completed) # If we have already redacted the last file, return the input out_message and file list to the relevant components if latest_file_completed >= len(file_paths): print("Last file reached") # Set to a very high number so as not to mess with subsequent file processing by the user latest_file_completed = 99 final_out_message = '\n'.join(out_message) #final_out_message = final_out_message + "\n\nGo to to the Redaction settings tab to see redaction logs. Please give feedback on the results below to help improve this app." def sum_numbers_before_seconds(string): """Extracts numbers that precede the word 'seconds' from a string and adds them up. Args: string: The input string. Returns: The sum of all numbers before 'seconds' in the string. """ # Extract numbers before 'seconds' using regular expression numbers = re.findall(r'(\d+\.\d+)?\s*seconds', string) # Extract the numbers from the matches numbers = [float(num.split()[0]) for num in numbers] # Sum up the extracted numbers sum_of_numbers = round(sum(numbers),1) return sum_of_numbers estimate_total_processing_time = sum_numbers_before_seconds(final_out_message) print("Estimated total processing time:", str(estimate_total_processing_time)) return final_out_message, out_file_paths, out_file_paths, latest_file_completed, log_files_output_paths, log_files_output_paths, estimate_total_processing_time file_paths_loop = [file_paths[int(latest_file_completed)]] if in_allow_list: in_allow_list_flat = [item for sublist in in_allow_list for item in sublist] for file in progress.tqdm(file_paths_loop, desc="Redacting files", unit = "files"): file_path = file.name if file_path: file_path_without_ext = get_file_path_end(file_path) is_a_pdf = is_pdf(file_path) == True if is_a_pdf == False: # If user has not submitted a pdf, assume it's an image print("File is not a pdf, assuming that image analysis needs to be used.") in_redact_method = "Image analysis" else: out_message = "No file selected" print(out_message) return out_message, out_file_paths, out_file_paths, latest_file_completed, log_files_output_paths, log_files_output_paths, estimated_time_taken_state if in_redact_method == "Image analysis" or in_redact_method == "AWS Textract": # Analyse and redact image-based pdf or image # if is_pdf_or_image(file_path) == False: # return "Please upload a PDF file or image file (JPG, PNG) for image analysis.", None print("Redacting file" + file_path_without_ext + "as an image-based file") pdf_images, output_logs, logging_file_paths = redact_image_pdf(file_path, image_paths, language, chosen_redact_entities, in_allow_list_flat, is_a_pdf, page_min, page_max, in_redact_method) out_image_file_path = output_folder + file_path_without_ext + "_redacted_as_img.pdf" pdf_images[0].save(out_image_file_path, "PDF" ,resolution=100.0, save_all=True, append_images=pdf_images[1:]) out_file_paths.append(out_image_file_path) if logging_file_paths: log_files_output_paths.extend(logging_file_paths) out_message.append("File '" + file_path_without_ext + "' successfully redacted") output_logs_str = str(output_logs) logs_output_file_name = out_image_file_path + "_decision_process_output.txt" with open(logs_output_file_name, "w") as f: f.write(output_logs_str) log_files_output_paths.append(logs_output_file_name) # Increase latest file completed count unless we are at the last file if latest_file_completed != len(file_paths): print("Completed file number:", str(latest_file_completed)) latest_file_completed += 1 elif in_redact_method == "Text analysis": if is_pdf(file_path) == False: return "Please upload a PDF file for text analysis. If you have an image, select 'Image analysis'.", None, None # Analyse text-based pdf print('Redacting file as text-based PDF') pdf_text, output_logs = redact_text_pdf(file_path, language, chosen_redact_entities, in_allow_list_flat, page_min, page_max, "Text analysis") out_text_file_path = output_folder + file_path_without_ext + "_text_redacted.pdf" pdf_text.save(out_text_file_path) # Convert message convert_message="Converting PDF to image-based PDF to embed redactions." #progress(0.8, desc=convert_message) print(convert_message) # Convert document to image-based document to 'embed' redactions img_output_summary, img_output_file_path = convert_text_pdf_to_img_pdf(file_path, [out_text_file_path]) out_file_paths.extend(img_output_file_path) output_logs_str = str(output_logs) logs_output_file_name = img_output_file_path[0] + "_decision_process_output.txt" with open(logs_output_file_name, "w") as f: f.write(output_logs_str) log_files_output_paths.append(logs_output_file_name) # Add confirmation for converting to image if you want # out_message.append(img_output_summary) #out_file_paths.append(out_text_file_path) out_message_new = "File '" + file_path_without_ext + "' successfully redacted" out_message.append(out_message_new) if latest_file_completed != len(file_paths): print("Completed file number:", str(latest_file_completed), "more files to do") latest_file_completed += 1 else: out_message = "No redaction method selected" print(out_message) return out_message, out_file_paths, out_file_paths, latest_file_completed, log_files_output_paths, log_files_output_paths, estimated_time_taken_state toc = time.perf_counter() out_time = f"in {toc - tic:0.1f} seconds." print(out_time) out_message_out = '\n'.join(out_message) out_message_out = out_message_out + " " + out_time return out_message_out, out_file_paths, out_file_paths, latest_file_completed, log_files_output_paths, log_files_output_paths, estimated_time_taken_state def merge_img_bboxes(bboxes, handwriting_or_signature_boxes = [], horizontal_threshold=150, vertical_threshold=25): merged_bboxes = [] grouped_bboxes = defaultdict(list) if handwriting_or_signature_boxes: print("Handwriting or signature boxes exist at merge:", handwriting_or_signature_boxes) bboxes.extend(handwriting_or_signature_boxes) # 1. Group by approximate vertical proximity for box in bboxes: grouped_bboxes[round(box.top / vertical_threshold)].append(box) # 2. Merge within each group for _, group in grouped_bboxes.items(): group.sort(key=lambda box: box.left) merged_box = group[0] for next_box in group[1:]: if next_box.left - (merged_box.left + merged_box.width) <= horizontal_threshold: #print("Merging a box") # Calculate new dimensions for the merged box print("Merged box:", merged_box) new_left = min(merged_box.left, next_box.left) new_top = min(merged_box.top, next_box.top) new_width = max(merged_box.left + merged_box.width, next_box.left + next_box.width) - new_left new_height = max(merged_box.top + merged_box.height, next_box.top + next_box.height) - new_top merged_box = ImageRecognizerResult( merged_box.entity_type, merged_box.start, merged_box.end, merged_box.score, new_left, new_top, new_width, new_height ) else: merged_bboxes.append(merged_box) merged_box = next_box merged_bboxes.append(merged_box) return merged_bboxes def redact_image_pdf(file_path:str, image_paths:List[str], language:str, chosen_redact_entities:List[str], allow_list:List[str]=None, is_a_pdf:bool=True, page_min:int=0, page_max:int=999, analysis_type:str="Image analysis", progress=Progress(track_tqdm=True)): ''' Take an path for an image of a document, then run this image through the Presidio ImageAnalyzer and PIL to get a redacted page back. Adapted from Presidio ImageRedactorEngine. ''' # json_file_path is for AWS Textract outputs logging_file_paths = [] file_name = get_file_path_end(file_path) fill = (0, 0, 0) # Fill colour decision_process_output_str = "" images = [] image_analyser = CustomImageAnalyzerEngine(nlp_analyser) if not image_paths: out_message = "PDF does not exist as images. Converting pages to image" print(out_message) image_paths = process_file(file_path) if not isinstance(image_paths, list): print("Converting image_paths to list") image_paths = [image_paths] #print("Image paths:", image_paths) number_of_pages = len(image_paths[0]) print("Number of pages:", str(number_of_pages)) out_message = "Redacting pages" print(out_message) #progress(0.1, desc=out_message) # Check that page_min and page_max are within expected ranges if page_max > number_of_pages or page_max == 0: page_max = number_of_pages if page_min <= 0: page_min = 0 else: page_min = page_min - 1 print("Page range:", str(page_min + 1), "to", str(page_max)) #for i in progress.tqdm(range(0,number_of_pages), total=number_of_pages, unit="pages", desc="Redacting pages"): for n in range(0, number_of_pages): handwriting_or_signature_boxes = [] try: image = image_paths[0][n]#.copy() print("Skipping page", str(n)) #print("image:", image) except Exception as e: print("Could not redact page:", str(n), "due to:") print(e) continue if n >= page_min and n < page_max: i = n reported_page_number = str(i + 1) print("Redacting page", reported_page_number) # Assuming image_paths[i] is your PIL image object try: image = image_paths[0][i]#.copy() #print("image:", image) except Exception as e: print("Could not redact page:", reported_page_number, "due to:") print(e) continue # %% # image_analyser = ImageAnalyzerEngine(nlp_analyser) # engine = ImageRedactorEngine(image_analyser) if language == 'en': ocr_lang = 'eng' else: ocr_lang = language # bboxes = image_analyser.analyze(image, # ocr_kwargs={"lang": ocr_lang}, # **{ # "allow_list": allow_list, # "language": language, # "entities": chosen_redact_entities, # "score_threshold": score_threshold, # "return_decision_process":True, # }) # Step 1: Perform OCR. Either with Tesseract, or with AWS Textract if analysis_type == "Image analysis": ocr_results = image_analyser.perform_ocr(image) # Process all OCR text with bounding boxes #print("OCR results:", ocr_results) ocr_results_str = str(ocr_results) ocr_results_file_path = output_folder + "ocr_results_" + file_name + "_page_" + reported_page_number + ".txt" with open(ocr_results_file_path, "w") as f: f.write(ocr_results_str) logging_file_paths.append(ocr_results_file_path) # Import results from json and convert if analysis_type == "AWS Textract": # Ensure image is a PIL Image object # if isinstance(image, str): # image = Image.open(image) # elif not isinstance(image, Image.Image): # print(f"Unexpected image type on page {i}: {type(image)}") # continue # Convert the image to bytes using an in-memory buffer image_buffer = io.BytesIO() image.save(image_buffer, format='PNG') # Save as PNG, or adjust format if needed pdf_page_as_bytes = image_buffer.getvalue() json_file_path = output_folder + file_name + "_page_" + reported_page_number + "_textract.json" if not os.path.exists(json_file_path): text_blocks = analyse_page_with_textract(pdf_page_as_bytes, json_file_path) # Analyse page with Textract logging_file_paths.append(json_file_path) else: # Open the file and load the JSON data print("Found existing Textract json results file for this page.") with open(json_file_path, 'r') as json_file: text_blocks = json.load(json_file) text_blocks = text_blocks['Blocks'] # Need image size to convert textract OCR outputs to the correct sizes #print("Image size:", image.size) page_width, page_height = image.size ocr_results, handwriting_or_signature_boxes = json_to_ocrresult(text_blocks, page_width, page_height) #print("OCR results:", ocr_results) ocr_results_str = str(ocr_results) textract_ocr_results_file_path = output_folder + "ocr_results_" + file_name + "_page_" + reported_page_number + "_textract.txt" with open(textract_ocr_results_file_path, "w") as f: f.write(ocr_results_str) logging_file_paths.append(textract_ocr_results_file_path) # Step 2: Analyze text and identify PII bboxes = image_analyser.analyze_text( ocr_results, language=language, entities=chosen_redact_entities, allow_list=allow_list, score_threshold=score_threshold, ) # Process the bboxes (PII entities) if bboxes: for bbox in bboxes: print(f"Entity: {bbox.entity_type}, Text: {bbox.text}, Bbox: ({bbox.left}, {bbox.top}, {bbox.width}, {bbox.height})") decision_process_output_str = str(bboxes) print("Decision process:", decision_process_output_str) # Merge close bounding boxes merged_bboxes = merge_img_bboxes(bboxes, handwriting_or_signature_boxes) #print("For page:", str(i), "Merged bounding boxes:", merged_bboxes) #from PIL import Image #image_object = Image.open(image) # 3. Draw the merged boxes draw = ImageDraw.Draw(image) for box in merged_bboxes: x0 = box.left y0 = box.top x1 = x0 + box.width y1 = y0 + box.height draw.rectangle([x0, y0, x1, y1], fill=fill) images.append(image) return images, decision_process_output_str, logging_file_paths def analyze_text_container(text_container, language, chosen_redact_entities, score_threshold, allow_list): if isinstance(text_container, LTTextContainer): text_to_analyze = text_container.get_text() analyzer_results = nlp_analyser.analyze(text=text_to_analyze, language=language, entities=chosen_redact_entities, score_threshold=score_threshold, return_decision_process=True, allow_list=allow_list) characters = [char for line in text_container if isinstance(line, LTTextLine) for char in line] return analyzer_results, characters return [], [] # Inside the loop where you process analyzer_results, merge bounding boxes that are right next to each other: # def merge_bounding_boxes(analyzer_results, characters, combine_pixel_dist, vertical_padding=2): # ''' # Merge identified bounding boxes containing PII that are very close to one another # ''' # analyzed_bounding_boxes = [] # if len(analyzer_results) > 0 and len(characters) > 0: # merged_bounding_boxes = [] # current_box = None # current_y = None # for i, result in enumerate(analyzer_results): # print("Considering result", str(i)) # for char in characters[result.start : result.end]: # if isinstance(char, LTChar): # char_box = list(char.bbox) # # Add vertical padding to the top of the box # char_box[3] += vertical_padding # if current_y is None or current_box is None: # current_box = char_box # current_y = char_box[1] # else: # vertical_diff_bboxes = abs(char_box[1] - current_y) # horizontal_diff_bboxes = abs(char_box[0] - current_box[2]) # if ( # vertical_diff_bboxes <= 5 # and horizontal_diff_bboxes <= combine_pixel_dist # ): # current_box[2] = char_box[2] # Extend the current box horizontally # current_box[3] = max(current_box[3], char_box[3]) # Ensure the top is the highest # else: # merged_bounding_boxes.append( # {"boundingBox": current_box, "result": result}) # # Reset current_box and current_y after appending # current_box = char_box # current_y = char_box[1] # # After finishing with the current result, add the last box for this result # if current_box: # merged_bounding_boxes.append({"boundingBox": current_box, "result": result}) # current_box = None # current_y = None # Reset for the next result # if not merged_bounding_boxes: # analyzed_bounding_boxes.extend( # {"boundingBox": char.bbox, "result": result} # for result in analyzer_results # for char in characters[result.start:result.end] # if isinstance(char, LTChar) # ) # else: # analyzed_bounding_boxes.extend(merged_bounding_boxes) # print("analysed_bounding_boxes:\n\n", analyzed_bounding_boxes) # return analyzed_bounding_boxes def merge_bounding_boxes(analyzer_results, characters, combine_pixel_dist, vertical_padding=2, signature_bounding_boxes=None): ''' Merge identified bounding boxes containing PII or signatures that are very close to one another. ''' analyzed_bounding_boxes = [] merged_bounding_boxes = [] current_box = None current_y = None # Handle PII and text bounding boxes first if len(analyzer_results) > 0 and len(characters) > 0: for i, result in enumerate(analyzer_results): #print("Considering result", str(i)) #print("Result:", result) #print("Characters:", characters) for char in characters[result.start: result.end]: if isinstance(char, LTChar): char_box = list(char.bbox) # Add vertical padding to the top of the box char_box[3] += vertical_padding if current_y is None or current_box is None: current_box = char_box current_y = char_box[1] else: vertical_diff_bboxes = abs(char_box[1] - current_y) horizontal_diff_bboxes = abs(char_box[0] - current_box[2]) if ( vertical_diff_bboxes <= 5 and horizontal_diff_bboxes <= combine_pixel_dist ): current_box[2] = char_box[2] # Extend the current box horizontally current_box[3] = max(current_box[3], char_box[3]) # Ensure the top is the highest else: merged_bounding_boxes.append( {"boundingBox": current_box, "result": result}) # Reset current_box and current_y after appending current_box = char_box current_y = char_box[1] # After finishing with the current result, add the last box for this result if current_box: merged_bounding_boxes.append({"boundingBox": current_box, "result": result}) current_box = None current_y = None # Reset for the next result # Handle signature bounding boxes (without specific characters) if signature_bounding_boxes is not None: for sig_box in signature_bounding_boxes: sig_box = list(sig_box) # Ensure it's a list to modify the values if current_y is None or current_box is None: current_box = sig_box current_y = sig_box[1] else: vertical_diff_bboxes = abs(sig_box[1] - current_y) horizontal_diff_bboxes = abs(sig_box[0] - current_box[2]) if ( vertical_diff_bboxes <= 5 and horizontal_diff_bboxes <= combine_pixel_dist ): current_box[2] = sig_box[2] # Extend the current box horizontally current_box[3] = max(current_box[3], sig_box[3]) # Ensure the top is the highest else: merged_bounding_boxes.append({"boundingBox": current_box, "type": "signature"}) # Reset current_box and current_y after appending current_box = sig_box current_y = sig_box[1] # Add the last bounding box for the signature if current_box: merged_bounding_boxes.append({"boundingBox": current_box, "type": "signature"}) current_box = None current_y = None # If no bounding boxes were merged, add individual character bounding boxes if not merged_bounding_boxes: analyzed_bounding_boxes.extend( {"boundingBox": char.bbox, "result": result} for result in analyzer_results for char in characters[result.start:result.end] if isinstance(char, LTChar) ) else: analyzed_bounding_boxes.extend(merged_bounding_boxes) #print("analysed_bounding_boxes:\n\n", analyzed_bounding_boxes) return analyzed_bounding_boxes def create_text_redaction_process_results(analyzer_results, analyzed_bounding_boxes, page_num): decision_process_table = pd.DataFrame() if len(analyzer_results) > 0: # Create summary df of annotations to be made analyzed_bounding_boxes_df_new = pd.DataFrame(analyzed_bounding_boxes) analyzed_bounding_boxes_df_text = analyzed_bounding_boxes_df_new['result'].astype(str).str.split(",",expand=True).replace(".*: ", "", regex=True) analyzed_bounding_boxes_df_text.columns = ["type", "start", "end", "score"] analyzed_bounding_boxes_df_new = pd.concat([analyzed_bounding_boxes_df_new, analyzed_bounding_boxes_df_text], axis = 1) analyzed_bounding_boxes_df_new['page'] = page_num + 1 decision_process_table = pd.concat([decision_process_table, analyzed_bounding_boxes_df_new], axis = 0).drop('result', axis=1) print('\n\ndecision_process_table:\n\n', decision_process_table) return decision_process_table def create_annotations_for_bounding_boxes(analyzed_bounding_boxes): annotations_on_page = [] for analyzed_bounding_box in analyzed_bounding_boxes: bounding_box = analyzed_bounding_box["boundingBox"] annotation = Dictionary( Type=Name.Annot, Subtype=Name.Square, #Name.Highlight, QuadPoints=[bounding_box[0], bounding_box[3], bounding_box[2], bounding_box[3], bounding_box[0], bounding_box[1], bounding_box[2], bounding_box[1]], Rect=[bounding_box[0], bounding_box[1], bounding_box[2], bounding_box[3]], C=[0, 0, 0], IC=[0, 0, 0], CA=1, # Transparency T=analyzed_bounding_box["result"].entity_type, BS=Dictionary( W=0, # Border width: 1 point S=Name.S # Border style: solid ) ) annotations_on_page.append(annotation) return annotations_on_page def redact_text_pdf(filename:str, language:str, chosen_redact_entities:List[str], allow_list:List[str]=None, page_min:int=0, page_max:int=999, analysis_type:str = "Text analysis", progress=Progress(track_tqdm=True)): ''' Redact chosen entities from a pdf that is made up of multiple pages that are not images. ''' annotations_all_pages = [] decision_process_table_all_pages = [] combine_pixel_dist = 100 # Horizontal distance between PII bounding boxes under/equal they are combined into one pdf = Pdf.open(filename) page_num = 0 number_of_pages = len(pdf.pages) # Check that page_min and page_max are within expected ranges if page_max > number_of_pages or page_max == 0: page_max = number_of_pages #else: # page_max = page_max - 1 if page_min <= 0: page_min = 0 else: page_min = page_min - 1 print("Page range is",str(page_min), "to", str(page_max)) for page_no in range(page_min, page_max): page = pdf.pages[page_no] print("Page number is:", page_no) # The /MediaBox in a PDF specifies the size of the page [left, bottom, right, top] media_box = page.MediaBox page_width = media_box[2] - media_box[0] page_height = media_box[3] - media_box[1] annotations_on_page = [] decision_process_table_on_page = [] for page_layout in extract_pages(filename, page_numbers = [page_no], maxpages=1): page_analyzer_results = [] page_analyzed_bounding_boxes = [] text_container_analyzer_results = [] text_container_analyzed_bounding_boxes = [] characters = [] if analysis_type == "Text analysis": for i, text_container in enumerate(page_layout): text_container_analyzer_results, characters = analyze_text_container(text_container, language, chosen_redact_entities, score_threshold, allow_list) # Merge bounding boxes if very close together text_container_analyzed_bounding_boxes = merge_bounding_boxes(text_container_analyzer_results, characters, combine_pixel_dist, vertical_padding = 2) page_analyzed_bounding_boxes.extend(text_container_analyzed_bounding_boxes) page_analyzer_results.extend(text_container_analyzer_results) # Merge bounding boxes if very close together text_container_analyzed_bounding_boxes = merge_bounding_boxes(text_container_analyzer_results, characters, combine_pixel_dist, vertical_padding = 2) page_analyzed_bounding_boxes.extend(text_container_analyzed_bounding_boxes) page_analyzer_results.extend(text_container_analyzer_results) decision_process_table_on_page = create_text_redaction_process_results(page_analyzer_results, page_analyzed_bounding_boxes, page_num) annotations_on_page = create_annotations_for_bounding_boxes(page_analyzed_bounding_boxes) #print('\n\nannotations_on_page:', annotations_on_page) # Make page annotations page.Annots = pdf.make_indirect(annotations_on_page) annotations_all_pages.extend([annotations_on_page]) decision_process_table_all_pages.extend([decision_process_table_on_page]) print("For page number:", page_no, "there are", len(annotations_all_pages[page_num]), "annotations") #page_num += 1 return pdf, decision_process_table_all_pages