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Update app.py
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app.py
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#################################################################################################
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import subprocess
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import sys
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import spaces
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import torch
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import gradio as gr
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from PIL import Image
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import numpy as np
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import cv2
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import pypdfium2 as pdfium
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from transformers import (
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LightOnOCRForConditionalGeneration,
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LightOnOCRProcessor,
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)
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from transformers import AutoTokenizer, AutoModelForTokenClassification, pipeline
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import re
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device = "cuda" if torch.cuda.is_available() else "cpu"
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if device == "cuda":
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attn_implementation = "sdpa"
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dtype = torch.bfloat16
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else:
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attn_implementation = "eager"
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dtype = torch.float32
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ocr_model = LightOnOCRForConditionalGeneration.from_pretrained(
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"lightonai/LightOnOCR-1B-1025",
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attn_implementation=attn_implementation,
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torch_dtype=dtype,
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trust_remote_code=True,
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).to(device).eval()
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processor = LightOnOCRProcessor.from_pretrained(
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"lightonai/LightOnOCR-1B-1025",
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trust_remote_code=True,
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)
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ner_tokenizer = AutoTokenizer.from_pretrained("samrawal/bert-base-uncased_clinical-ner")
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ner_model = AutoModelForTokenClassification.from_pretrained("samrawal/bert-base-uncased_clinical-ner")
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ner_pipeline = pipeline(
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"ner",
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model=ner_model,
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tokenizer=ner_tokenizer,
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aggregation_strategy="simple",
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)
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def render_pdf_page(page, max_resolution=1540, scale=2.77):
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width, height = page.get_size()
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pixel_width = width * scale
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pixel_height = height * scale
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resize_factor = min(1, max_resolution / pixel_width, max_resolution / pixel_height)
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target_scale = scale * resize_factor
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return page.render(scale=target_scale, rev_byteorder=True).to_pil()
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def process_pdf(pdf_path, page_num=1):
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pdf = pdfium.PdfDocument(pdf_path)
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total_pages = len(pdf)
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page_idx = min(max(int(page_num) - 1, 0), total_pages - 1)
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page = pdf[page_idx]
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img = render_pdf_page(page)
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pdf.close()
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return img, total_pages, page_idx + 1
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def clean_output_text(text):
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markers_to_remove = ["system", "user", "assistant"]
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lines = text.split('\n')
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cleaned_lines = []
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for line in lines:
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stripped = line.strip()
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if stripped.lower() not in markers_to_remove:
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cleaned_lines.append(line)
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cleaned = '\n'.join(cleaned_lines).strip()
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if "assistant" in text.lower():
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parts = text.split("assistant", 1)
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if len(parts) > 1:
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cleaned = parts[1].strip()
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return cleaned
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def preprocess_image_for_ocr(image):
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image_rgb = image.convert("RGB")
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img_np = np.array(image_rgb)
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gray = cv2.cvtColor(img_np, cv2.COLOR_RGB2GRAY)
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adaptive_threshold = cv2.adaptiveThreshold(
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gray,
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255,
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cv2.ADAPTIVE_THRESH_GAUSSIAN_C,
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cv2.THRESH_BINARY,
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85,
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11,
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)
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preprocessed_pil = Image.fromarray(adaptive_threshold)
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return preprocessed_pil
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def extract_medication_lines(text):
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"""
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Extracts medication/drug lines from text using regex.
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Matches lines beginning with tab, tablet, cap, capsule, syrup, syp, oral, inj, injection, ointment, drops, patch, sol, solution, etc.
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Handles case-insensitivity and abbreviations like T., C., tab., cap. etc.
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"""
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# "|" means OR. (?:...) is a non-capturing group.
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pattern = r"""^\s* # Leading spaces allowed
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(
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T\.?|TAB\.?|TABLET # T., T, TAB, TAB., TABLET
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|C\.?|CAP\.?|CAPSULE # C., C, CAP, CAP., CAPSULE
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|SYRUP|SYP
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|ORAL
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|INJ\.?|INJECTION # INJ., INJ, INJECTION
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|OINTMENT|DROPS|PATCH|SOL\.?|SOLUTION
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)
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\s+[A-Z0-9 \-\(\)/,.]+ # Name/dose/other info (at least one space/letter after the pattern)
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"""
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# Compile with re.IGNORECASE and re.VERBOSE for readability
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med_regex = re.compile(pattern, re.IGNORECASE | re.VERBOSE)
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meds = []
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for line in text.split('\n'):
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line = line.strip()
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if med_regex.match(line):
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meds.append(line)
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return '\n'.join(meds)
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def extract_meds(text, use_ner):
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"""
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Switches between Clinical NER or regex extraction.
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Returns medications string.
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"""
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if use_ner:
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entities = ner_pipeline(text)
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meds = []
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for ent in entities:
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if ent["entity_group"] == "treatment":
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word = ent["word"]
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if word.startswith("##") and meds:
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meds[-1] += word[2:]
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else:
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meds.append(word)
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return ", ".join(set(meds)) if meds else "None detected"
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else:
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return extract_medication_lines(text) or "None detected"
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@spaces.GPU
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def extract_text_from_image(image, temperature=0.2):
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"""OCR with adaptive thresholding."""
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processed_img = preprocess_image_for_ocr(image)
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chat = [
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{
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"role": "user",
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"content": [
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{"type": "image", "image": processed_img}
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],
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}
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]
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inputs = processor.apply_chat_template(
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chat,
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add_generation_prompt=True,
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tokenize=True,
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return_dict=True,
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return_tensors="pt",
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)
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# Move inputs to device
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inputs = {
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k: (
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v.to(device=device, dtype=dtype)
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if isinstance(v, torch.Tensor) and v.dtype in [torch.float32, torch.float16, torch.bfloat16]
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else v.to(device)
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if isinstance(v, torch.Tensor)
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else v
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)
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for k, v in inputs.items()
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}
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generation_kwargs = dict(
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**inputs,
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max_new_tokens=2048,
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temperature=temperature if temperature > 0 else 0.0,
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use_cache=True,
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do_sample=temperature > 0,
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)
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with torch.no_grad():
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outputs = ocr_model.generate(**generation_kwargs)
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output_text = processor.decode(outputs[0], skip_special_tokens=True)
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cleaned_text = clean_output_text(output_text)
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yield cleaned_text, output_text, processed_img
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def process_input(file_input, temperature, page_num, extraction_mode):
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if file_input is None:
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yield "Please upload an image or PDF first.", "", "", "", "No file!", 1
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return
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image_to_process = None
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page_info = ""
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slider_value = page_num
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file_path = file_input if isinstance(file_input, str) else file_input.name
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if file_path.lower().endswith(".pdf"):
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try:
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image_to_process, total_pages, actual_page = process_pdf(file_path, int(page_num))
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page_info = f"Processing page {actual_page} of {total_pages}"
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slider_value = actual_page
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except Exception as e:
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msg = f"Error processing PDF: {str(e)}"
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yield msg, "", msg, "", None, slider_value
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return
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else:
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try:
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image_to_process = Image.open(file_path)
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page_info = "Processing image"
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except Exception as e:
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msg = f"Error opening image: {str(e)}"
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yield msg, "", msg, "", None, slider_value
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return
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use_ner = extraction_mode == "Regex" #"Clinical NER"
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try:
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for cleaned_text, raw_md, processed_img in extract_text_from_image(
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image_to_process, temperature
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):
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meds_out = extract_meds(cleaned_text, use_ner)
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yield cleaned_text, meds_out, raw_md, page_info, processed_img, slider_value
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except Exception as e:
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error_msg = f"Error during text extraction: {str(e)}"
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yield error_msg, "", error_msg, page_info, image_to_process, slider_value
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def update_slider(file_input):
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if file_input is None:
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return gr.update(maximum=20, value=1)
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file_path = file_input if isinstance(file_input, str) else file_input.name
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if file_path.lower().endswith('.pdf'):
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try:
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pdf = pdfium.PdfDocument(file_path)
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total_pages = len(pdf)
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pdf.close()
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return gr.update(maximum=total_pages, value=1)
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except:
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return gr.update(maximum=20, value=1)
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else:
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return gr.update(maximum=1, value=1)
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with gr.Blocks(title="💊 Medicine Extraction", theme=gr.themes.Soft()) as demo:
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file_input = gr.File(
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label="🖼️ Upload Image or PDF",
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file_types=[".pdf", ".png", ".jpg", ".jpeg"],
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type="filepath"
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)
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temperature = gr.Slider(
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minimum=0.0,
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maximum=1.0,
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value=0.2,
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step=0.05,
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label="Temperature"
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)
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page_slider = gr.Slider(
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minimum=1, maximum=20, value=1, step=1,
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label="Page Number (PDF only)",
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interactive=True
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)
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extraction_mode = gr.Radio(
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choices=["Clinical NER", "Regex"],
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value="Regex",
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label="Extraction Method",
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info="Clinical NER uses ML, Regex uses rules"
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)
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output_text = gr.Textbox(
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label="📝 Extracted Text",
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lines=4,
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max_lines=10,
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interactive=False,
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show_copy_button=True
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)
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medicines_output = gr.Textbox(
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label="💊 Extracted Medicines/Drugs",
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placeholder="Medicine/drug names will appear here...",
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lines=2,
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max_lines=10,
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interactive=False,
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show_copy_button=True
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)
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raw_output = gr.Textbox(
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label="Raw Model Output",
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lines=2,
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max_lines=5,
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interactive=False
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)
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page_info = gr.Markdown(
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value="" # Info of PDF page
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)
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rendered_image = gr.Image(
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label="Processed Image (Thresholded for OCR)",
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interactive=False
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)
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num_pages = gr.Number(
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value=1, label="Current Page (slider)", visible=False
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)
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submit_btn = gr.Button("Extract Medicines", variant="primary")
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submit_btn.click(
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fn=process_input,
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inputs=[file_input, temperature, page_slider, extraction_mode],
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outputs=[output_text, medicines_output, raw_output, page_info, rendered_image, num_pages]
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)
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file_input.change(
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fn=update_slider,
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inputs=[file_input],
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outputs=[page_slider]
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)
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if __name__ == "__main__":
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demo.launch()
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#################################################### running code only NER #######################
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#!/usr/bin/env python3
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# import subprocess
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# import sys
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@@ -334,6 +16,7 @@ if __name__ == "__main__":
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# LightOnOCRProcessor,
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# )
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# from transformers import AutoTokenizer, AutoModelForTokenClassification, pipeline
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# device = "cuda" if torch.cuda.is_available() else "cpu"
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# if device == "cuda":
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# return cleaned
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# def preprocess_image_for_ocr(image):
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# """Convert PIL.Image to adaptive thresholded image for OCR."""
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# image_rgb = image.convert("RGB")
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# img_np = np.array(image_rgb)
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# gray = cv2.cvtColor(img_np, cv2.COLOR_RGB2GRAY)
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# preprocessed_pil = Image.fromarray(adaptive_threshold)
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# return preprocessed_pil
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# @spaces.GPU
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# def extract_text_from_image(image, temperature=0.2):
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# """OCR
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# processed_img = preprocess_image_for_ocr(image)
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# chat = [
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# {
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# )
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# with torch.no_grad():
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# outputs = ocr_model.generate(**generation_kwargs)
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# output_text = processor.decode(outputs[0], skip_special_tokens=True)
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# cleaned_text = clean_output_text(output_text)
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#
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#
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# if ent["entity_group"] == "treatment":
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# word = ent["word"]
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# if word.startswith("##") and medications:
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# medications[-1] += word[2:]
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# else:
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# medications.append(word)
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# medications_str = ", ".join(set(medications)) if medications else "None detected"
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# yield cleaned_text, medications_str, output_text, processed_img
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# def process_input(file_input, temperature, page_num):
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# if file_input is None:
|
| 471 |
# yield "Please upload an image or PDF first.", "", "", "", "No file!", 1
|
| 472 |
# return
|
|
@@ -494,11 +214,13 @@ if __name__ == "__main__":
|
|
| 494 |
# yield msg, "", msg, "", None, slider_value
|
| 495 |
# return
|
| 496 |
|
|
|
|
| 497 |
# try:
|
| 498 |
-
# for cleaned_text,
|
| 499 |
# image_to_process, temperature
|
| 500 |
# ):
|
| 501 |
-
#
|
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|
| 502 |
# except Exception as e:
|
| 503 |
# error_msg = f"Error during text extraction: {str(e)}"
|
| 504 |
# yield error_msg, "", error_msg, page_info, image_to_process, slider_value
|
|
@@ -536,6 +258,12 @@ if __name__ == "__main__":
|
|
| 536 |
# label="Page Number (PDF only)",
|
| 537 |
# interactive=True
|
| 538 |
# )
|
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| 539 |
# output_text = gr.Textbox(
|
| 540 |
# label="📝 Extracted Text",
|
| 541 |
# lines=4,
|
|
@@ -547,7 +275,7 @@ if __name__ == "__main__":
|
|
| 547 |
# label="💊 Extracted Medicines/Drugs",
|
| 548 |
# placeholder="Medicine/drug names will appear here...",
|
| 549 |
# lines=2,
|
| 550 |
-
# max_lines=
|
| 551 |
# interactive=False,
|
| 552 |
# show_copy_button=True
|
| 553 |
# )
|
|
@@ -558,7 +286,7 @@ if __name__ == "__main__":
|
|
| 558 |
# interactive=False
|
| 559 |
# )
|
| 560 |
# page_info = gr.Markdown(
|
| 561 |
-
# value=""
|
| 562 |
# )
|
| 563 |
# rendered_image = gr.Image(
|
| 564 |
# label="Processed Image (Thresholded for OCR)",
|
|
@@ -571,7 +299,7 @@ if __name__ == "__main__":
|
|
| 571 |
|
| 572 |
# submit_btn.click(
|
| 573 |
# fn=process_input,
|
| 574 |
-
# inputs=[file_input, temperature, page_slider],
|
| 575 |
# outputs=[output_text, medicines_output, raw_output, page_info, rendered_image, num_pages]
|
| 576 |
# )
|
| 577 |
|
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@@ -586,6 +314,278 @@ if __name__ == "__main__":
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| 589 |
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| 590 |
########################################## #############################################################
|
| 591 |
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| 1 |
#################################################################################################
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|
| 3 |
# import subprocess
|
| 4 |
# import sys
|
| 5 |
|
|
|
|
| 16 |
# LightOnOCRProcessor,
|
| 17 |
# )
|
| 18 |
# from transformers import AutoTokenizer, AutoModelForTokenClassification, pipeline
|
| 19 |
+
# import re
|
| 20 |
|
| 21 |
# device = "cuda" if torch.cuda.is_available() else "cpu"
|
| 22 |
# if device == "cuda":
|
|
|
|
| 80 |
# return cleaned
|
| 81 |
|
| 82 |
# def preprocess_image_for_ocr(image):
|
|
|
|
| 83 |
# image_rgb = image.convert("RGB")
|
| 84 |
# img_np = np.array(image_rgb)
|
| 85 |
# gray = cv2.cvtColor(img_np, cv2.COLOR_RGB2GRAY)
|
|
|
|
| 94 |
# preprocessed_pil = Image.fromarray(adaptive_threshold)
|
| 95 |
# return preprocessed_pil
|
| 96 |
|
| 97 |
+
|
| 98 |
+
|
| 99 |
+
# def extract_medication_lines(text):
|
| 100 |
+
# """
|
| 101 |
+
# Extracts medication/drug lines from text using regex.
|
| 102 |
+
# Matches lines beginning with tab, tablet, cap, capsule, syrup, syp, oral, inj, injection, ointment, drops, patch, sol, solution, etc.
|
| 103 |
+
# Handles case-insensitivity and abbreviations like T., C., tab., cap. etc.
|
| 104 |
+
# """
|
| 105 |
+
# # "|" means OR. (?:...) is a non-capturing group.
|
| 106 |
+
# pattern = r"""^\s* # Leading spaces allowed
|
| 107 |
+
# (
|
| 108 |
+
# T\.?|TAB\.?|TABLET # T., T, TAB, TAB., TABLET
|
| 109 |
+
# |C\.?|CAP\.?|CAPSULE # C., C, CAP, CAP., CAPSULE
|
| 110 |
+
# |SYRUP|SYP
|
| 111 |
+
# |ORAL
|
| 112 |
+
# |INJ\.?|INJECTION # INJ., INJ, INJECTION
|
| 113 |
+
# |OINTMENT|DROPS|PATCH|SOL\.?|SOLUTION
|
| 114 |
+
# )
|
| 115 |
+
# \s+[A-Z0-9 \-\(\)/,.]+ # Name/dose/other info (at least one space/letter after the pattern)
|
| 116 |
+
# """
|
| 117 |
+
# # Compile with re.IGNORECASE and re.VERBOSE for readability
|
| 118 |
+
# med_regex = re.compile(pattern, re.IGNORECASE | re.VERBOSE)
|
| 119 |
+
# meds = []
|
| 120 |
+
# for line in text.split('\n'):
|
| 121 |
+
# line = line.strip()
|
| 122 |
+
# if med_regex.match(line):
|
| 123 |
+
# meds.append(line)
|
| 124 |
+
# return '\n'.join(meds)
|
| 125 |
+
|
| 126 |
+
|
| 127 |
+
# def extract_meds(text, use_ner):
|
| 128 |
+
# """
|
| 129 |
+
# Switches between Clinical NER or regex extraction.
|
| 130 |
+
# Returns medications string.
|
| 131 |
+
# """
|
| 132 |
+
# if use_ner:
|
| 133 |
+
# entities = ner_pipeline(text)
|
| 134 |
+
# meds = []
|
| 135 |
+
# for ent in entities:
|
| 136 |
+
# if ent["entity_group"] == "treatment":
|
| 137 |
+
# word = ent["word"]
|
| 138 |
+
# if word.startswith("##") and meds:
|
| 139 |
+
# meds[-1] += word[2:]
|
| 140 |
+
# else:
|
| 141 |
+
# meds.append(word)
|
| 142 |
+
# return ", ".join(set(meds)) if meds else "None detected"
|
| 143 |
+
# else:
|
| 144 |
+
# return extract_medication_lines(text) or "None detected"
|
| 145 |
+
|
| 146 |
# @spaces.GPU
|
| 147 |
# def extract_text_from_image(image, temperature=0.2):
|
| 148 |
+
# """OCR with adaptive thresholding."""
|
| 149 |
# processed_img = preprocess_image_for_ocr(image)
|
| 150 |
# chat = [
|
| 151 |
# {
|
|
|
|
| 182 |
# )
|
| 183 |
# with torch.no_grad():
|
| 184 |
# outputs = ocr_model.generate(**generation_kwargs)
|
|
|
|
| 185 |
# output_text = processor.decode(outputs[0], skip_special_tokens=True)
|
| 186 |
# cleaned_text = clean_output_text(output_text)
|
| 187 |
+
# yield cleaned_text, output_text, processed_img
|
| 188 |
+
|
| 189 |
+
# def process_input(file_input, temperature, page_num, extraction_mode):
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
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|
|
| 190 |
# if file_input is None:
|
| 191 |
# yield "Please upload an image or PDF first.", "", "", "", "No file!", 1
|
| 192 |
# return
|
|
|
|
| 214 |
# yield msg, "", msg, "", None, slider_value
|
| 215 |
# return
|
| 216 |
|
| 217 |
+
# use_ner = extraction_mode == "Regex" #"Clinical NER"
|
| 218 |
# try:
|
| 219 |
+
# for cleaned_text, raw_md, processed_img in extract_text_from_image(
|
| 220 |
# image_to_process, temperature
|
| 221 |
# ):
|
| 222 |
+
# meds_out = extract_meds(cleaned_text, use_ner)
|
| 223 |
+
# yield cleaned_text, meds_out, raw_md, page_info, processed_img, slider_value
|
| 224 |
# except Exception as e:
|
| 225 |
# error_msg = f"Error during text extraction: {str(e)}"
|
| 226 |
# yield error_msg, "", error_msg, page_info, image_to_process, slider_value
|
|
|
|
| 258 |
# label="Page Number (PDF only)",
|
| 259 |
# interactive=True
|
| 260 |
# )
|
| 261 |
+
# extraction_mode = gr.Radio(
|
| 262 |
+
# choices=["Clinical NER", "Regex"],
|
| 263 |
+
# value="Regex",
|
| 264 |
+
# label="Extraction Method",
|
| 265 |
+
# info="Clinical NER uses ML, Regex uses rules"
|
| 266 |
+
# )
|
| 267 |
# output_text = gr.Textbox(
|
| 268 |
# label="📝 Extracted Text",
|
| 269 |
# lines=4,
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|
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|
| 275 |
# label="💊 Extracted Medicines/Drugs",
|
| 276 |
# placeholder="Medicine/drug names will appear here...",
|
| 277 |
# lines=2,
|
| 278 |
+
# max_lines=10,
|
| 279 |
# interactive=False,
|
| 280 |
# show_copy_button=True
|
| 281 |
# )
|
|
|
|
| 286 |
# interactive=False
|
| 287 |
# )
|
| 288 |
# page_info = gr.Markdown(
|
| 289 |
+
# value="" # Info of PDF page
|
| 290 |
# )
|
| 291 |
# rendered_image = gr.Image(
|
| 292 |
# label="Processed Image (Thresholded for OCR)",
|
|
|
|
| 299 |
|
| 300 |
# submit_btn.click(
|
| 301 |
# fn=process_input,
|
| 302 |
+
# inputs=[file_input, temperature, page_slider, extraction_mode],
|
| 303 |
# outputs=[output_text, medicines_output, raw_output, page_info, rendered_image, num_pages]
|
| 304 |
# )
|
| 305 |
|
|
|
|
| 314 |
|
| 315 |
|
| 316 |
|
| 317 |
+
#################################################### running code only NER #######################
|
| 318 |
+
|
| 319 |
+
#!/usr/bin/env python3
|
| 320 |
+
|
| 321 |
+
import subprocess
|
| 322 |
+
import sys
|
| 323 |
+
|
| 324 |
+
import spaces
|
| 325 |
+
import torch
|
| 326 |
+
|
| 327 |
+
import gradio as gr
|
| 328 |
+
from PIL import Image
|
| 329 |
+
import numpy as np
|
| 330 |
+
import cv2
|
| 331 |
+
import pypdfium2 as pdfium
|
| 332 |
+
from transformers import (
|
| 333 |
+
LightOnOCRForConditionalGeneration,
|
| 334 |
+
LightOnOCRProcessor,
|
| 335 |
+
)
|
| 336 |
+
from transformers import AutoTokenizer, AutoModelForTokenClassification, pipeline
|
| 337 |
+
|
| 338 |
+
device = "cuda" if torch.cuda.is_available() else "cpu"
|
| 339 |
+
if device == "cuda":
|
| 340 |
+
attn_implementation = "sdpa"
|
| 341 |
+
dtype = torch.bfloat16
|
| 342 |
+
else:
|
| 343 |
+
attn_implementation = "eager"
|
| 344 |
+
dtype = torch.float32
|
| 345 |
+
|
| 346 |
+
ocr_model = LightOnOCRForConditionalGeneration.from_pretrained(
|
| 347 |
+
"lightonai/LightOnOCR-1B-1025",
|
| 348 |
+
attn_implementation=attn_implementation,
|
| 349 |
+
torch_dtype=dtype,
|
| 350 |
+
trust_remote_code=True,
|
| 351 |
+
).to(device).eval()
|
| 352 |
+
|
| 353 |
+
processor = LightOnOCRProcessor.from_pretrained(
|
| 354 |
+
"lightonai/LightOnOCR-1B-1025",
|
| 355 |
+
trust_remote_code=True,
|
| 356 |
+
)
|
| 357 |
+
|
| 358 |
+
ner_tokenizer = AutoTokenizer.from_pretrained("samrawal/bert-base-uncased_clinical-ner")
|
| 359 |
+
ner_model = AutoModelForTokenClassification.from_pretrained("samrawal/bert-base-uncased_clinical-ner")
|
| 360 |
+
ner_pipeline = pipeline(
|
| 361 |
+
"ner",
|
| 362 |
+
model=ner_model,
|
| 363 |
+
tokenizer=ner_tokenizer,
|
| 364 |
+
aggregation_strategy="simple",
|
| 365 |
+
)
|
| 366 |
+
|
| 367 |
+
def render_pdf_page(page, max_resolution=1540, scale=2.77):
|
| 368 |
+
width, height = page.get_size()
|
| 369 |
+
pixel_width = width * scale
|
| 370 |
+
pixel_height = height * scale
|
| 371 |
+
resize_factor = min(1, max_resolution / pixel_width, max_resolution / pixel_height)
|
| 372 |
+
target_scale = scale * resize_factor
|
| 373 |
+
return page.render(scale=target_scale, rev_byteorder=True).to_pil()
|
| 374 |
+
|
| 375 |
+
def process_pdf(pdf_path, page_num=1):
|
| 376 |
+
pdf = pdfium.PdfDocument(pdf_path)
|
| 377 |
+
total_pages = len(pdf)
|
| 378 |
+
page_idx = min(max(int(page_num) - 1, 0), total_pages - 1)
|
| 379 |
+
page = pdf[page_idx]
|
| 380 |
+
img = render_pdf_page(page)
|
| 381 |
+
pdf.close()
|
| 382 |
+
return img, total_pages, page_idx + 1
|
| 383 |
+
|
| 384 |
+
def clean_output_text(text):
|
| 385 |
+
markers_to_remove = ["system", "user", "assistant"]
|
| 386 |
+
lines = text.split('\n')
|
| 387 |
+
cleaned_lines = []
|
| 388 |
+
for line in lines:
|
| 389 |
+
stripped = line.strip()
|
| 390 |
+
if stripped.lower() not in markers_to_remove:
|
| 391 |
+
cleaned_lines.append(line)
|
| 392 |
+
cleaned = '\n'.join(cleaned_lines).strip()
|
| 393 |
+
if "assistant" in text.lower():
|
| 394 |
+
parts = text.split("assistant", 1)
|
| 395 |
+
if len(parts) > 1:
|
| 396 |
+
cleaned = parts[1].strip()
|
| 397 |
+
return cleaned
|
| 398 |
+
|
| 399 |
+
def preprocess_image_for_ocr(image):
|
| 400 |
+
"""Convert PIL.Image to adaptive thresholded image for OCR."""
|
| 401 |
+
image_rgb = image.convert("RGB")
|
| 402 |
+
img_np = np.array(image_rgb)
|
| 403 |
+
gray = cv2.cvtColor(img_np, cv2.COLOR_RGB2GRAY)
|
| 404 |
+
adaptive_threshold = cv2.adaptiveThreshold(
|
| 405 |
+
gray,
|
| 406 |
+
255,
|
| 407 |
+
cv2.ADAPTIVE_THRESH_GAUSSIAN_C,
|
| 408 |
+
cv2.THRESH_BINARY,
|
| 409 |
+
85,
|
| 410 |
+
11,
|
| 411 |
+
)
|
| 412 |
+
preprocessed_pil = Image.fromarray(adaptive_threshold)
|
| 413 |
+
return preprocessed_pil
|
| 414 |
+
|
| 415 |
+
@spaces.GPU
|
| 416 |
+
def extract_text_from_image(image, temperature=0.2):
|
| 417 |
+
"""OCR + clinical NER, with preprocessing."""
|
| 418 |
+
processed_img = preprocess_image_for_ocr(image)
|
| 419 |
+
chat = [
|
| 420 |
+
{
|
| 421 |
+
"role": "user",
|
| 422 |
+
"content": [
|
| 423 |
+
{"type": "image", "image": processed_img}
|
| 424 |
+
],
|
| 425 |
+
}
|
| 426 |
+
]
|
| 427 |
+
inputs = processor.apply_chat_template(
|
| 428 |
+
chat,
|
| 429 |
+
add_generation_prompt=True,
|
| 430 |
+
tokenize=True,
|
| 431 |
+
return_dict=True,
|
| 432 |
+
return_tensors="pt",
|
| 433 |
+
)
|
| 434 |
+
# Move inputs to device
|
| 435 |
+
inputs = {
|
| 436 |
+
k: (
|
| 437 |
+
v.to(device=device, dtype=dtype)
|
| 438 |
+
if isinstance(v, torch.Tensor) and v.dtype in [torch.float32, torch.float16, torch.bfloat16]
|
| 439 |
+
else v.to(device)
|
| 440 |
+
if isinstance(v, torch.Tensor)
|
| 441 |
+
else v
|
| 442 |
+
)
|
| 443 |
+
for k, v in inputs.items()
|
| 444 |
+
}
|
| 445 |
+
generation_kwargs = dict(
|
| 446 |
+
**inputs,
|
| 447 |
+
max_new_tokens=2048,
|
| 448 |
+
temperature=temperature if temperature > 0 else 0.0,
|
| 449 |
+
use_cache=True,
|
| 450 |
+
do_sample=temperature > 0,
|
| 451 |
+
)
|
| 452 |
+
with torch.no_grad():
|
| 453 |
+
outputs = ocr_model.generate(**generation_kwargs)
|
| 454 |
+
|
| 455 |
+
output_text = processor.decode(outputs[0], skip_special_tokens=True)
|
| 456 |
+
cleaned_text = clean_output_text(output_text)
|
| 457 |
+
entities = ner_pipeline(cleaned_text)
|
| 458 |
+
medications = []
|
| 459 |
+
for ent in entities:
|
| 460 |
+
if ent["entity_group"] == "treatment":
|
| 461 |
+
word = ent["word"]
|
| 462 |
+
if word.startswith("##") and medications:
|
| 463 |
+
medications[-1] += word[2:]
|
| 464 |
+
else:
|
| 465 |
+
medications.append(word)
|
| 466 |
+
medications_str = ", ".join(set(medications)) if medications else "None detected"
|
| 467 |
+
yield cleaned_text, medications_str, output_text, processed_img
|
| 468 |
+
|
| 469 |
+
def process_input(file_input, temperature, page_num):
|
| 470 |
+
if file_input is None:
|
| 471 |
+
yield "Please upload an image or PDF first.", "", "", "", "No file!", 1
|
| 472 |
+
return
|
| 473 |
+
|
| 474 |
+
image_to_process = None
|
| 475 |
+
page_info = ""
|
| 476 |
+
slider_value = page_num
|
| 477 |
+
file_path = file_input if isinstance(file_input, str) else file_input.name
|
| 478 |
+
|
| 479 |
+
if file_path.lower().endswith(".pdf"):
|
| 480 |
+
try:
|
| 481 |
+
image_to_process, total_pages, actual_page = process_pdf(file_path, int(page_num))
|
| 482 |
+
page_info = f"Processing page {actual_page} of {total_pages}"
|
| 483 |
+
slider_value = actual_page
|
| 484 |
+
except Exception as e:
|
| 485 |
+
msg = f"Error processing PDF: {str(e)}"
|
| 486 |
+
yield msg, "", msg, "", None, slider_value
|
| 487 |
+
return
|
| 488 |
+
else:
|
| 489 |
+
try:
|
| 490 |
+
image_to_process = Image.open(file_path)
|
| 491 |
+
page_info = "Processing image"
|
| 492 |
+
except Exception as e:
|
| 493 |
+
msg = f"Error opening image: {str(e)}"
|
| 494 |
+
yield msg, "", msg, "", None, slider_value
|
| 495 |
+
return
|
| 496 |
+
|
| 497 |
+
try:
|
| 498 |
+
for cleaned_text, medications, raw_md, processed_img in extract_text_from_image(
|
| 499 |
+
image_to_process, temperature
|
| 500 |
+
):
|
| 501 |
+
yield cleaned_text, medications, raw_md, page_info, processed_img, slider_value
|
| 502 |
+
except Exception as e:
|
| 503 |
+
error_msg = f"Error during text extraction: {str(e)}"
|
| 504 |
+
yield error_msg, "", error_msg, page_info, image_to_process, slider_value
|
| 505 |
+
|
| 506 |
+
def update_slider(file_input):
|
| 507 |
+
if file_input is None:
|
| 508 |
+
return gr.update(maximum=20, value=1)
|
| 509 |
+
file_path = file_input if isinstance(file_input, str) else file_input.name
|
| 510 |
+
if file_path.lower().endswith('.pdf'):
|
| 511 |
+
try:
|
| 512 |
+
pdf = pdfium.PdfDocument(file_path)
|
| 513 |
+
total_pages = len(pdf)
|
| 514 |
+
pdf.close()
|
| 515 |
+
return gr.update(maximum=total_pages, value=1)
|
| 516 |
+
except:
|
| 517 |
+
return gr.update(maximum=20, value=1)
|
| 518 |
+
else:
|
| 519 |
+
return gr.update(maximum=1, value=1)
|
| 520 |
+
|
| 521 |
+
with gr.Blocks(title="💊 Medicine Extraction", theme=gr.themes.Soft()) as demo:
|
| 522 |
+
file_input = gr.File(
|
| 523 |
+
label="🖼️ Upload Image or PDF",
|
| 524 |
+
file_types=[".pdf", ".png", ".jpg", ".jpeg"],
|
| 525 |
+
type="filepath"
|
| 526 |
+
)
|
| 527 |
+
temperature = gr.Slider(
|
| 528 |
+
minimum=0.0,
|
| 529 |
+
maximum=1.0,
|
| 530 |
+
value=0.2,
|
| 531 |
+
step=0.05,
|
| 532 |
+
label="Temperature"
|
| 533 |
+
)
|
| 534 |
+
page_slider = gr.Slider(
|
| 535 |
+
minimum=1, maximum=20, value=1, step=1,
|
| 536 |
+
label="Page Number (PDF only)",
|
| 537 |
+
interactive=True
|
| 538 |
+
)
|
| 539 |
+
output_text = gr.Textbox(
|
| 540 |
+
label="📝 Extracted Text",
|
| 541 |
+
lines=4,
|
| 542 |
+
max_lines=10,
|
| 543 |
+
interactive=False,
|
| 544 |
+
show_copy_button=True
|
| 545 |
+
)
|
| 546 |
+
medicines_output = gr.Textbox(
|
| 547 |
+
label="💊 Extracted Medicines/Drugs",
|
| 548 |
+
placeholder="Medicine/drug names will appear here...",
|
| 549 |
+
lines=2,
|
| 550 |
+
max_lines=5,
|
| 551 |
+
interactive=False,
|
| 552 |
+
show_copy_button=True
|
| 553 |
+
)
|
| 554 |
+
raw_output = gr.Textbox(
|
| 555 |
+
label="Raw Model Output",
|
| 556 |
+
lines=2,
|
| 557 |
+
max_lines=5,
|
| 558 |
+
interactive=False
|
| 559 |
+
)
|
| 560 |
+
page_info = gr.Markdown(
|
| 561 |
+
value="" # Info of PDF page
|
| 562 |
+
)
|
| 563 |
+
rendered_image = gr.Image(
|
| 564 |
+
label="Processed Image (Thresholded for OCR)",
|
| 565 |
+
interactive=False
|
| 566 |
+
)
|
| 567 |
+
num_pages = gr.Number(
|
| 568 |
+
value=1, label="Current Page (slider)", visible=False
|
| 569 |
+
)
|
| 570 |
+
submit_btn = gr.Button("Extract Medicines", variant="primary")
|
| 571 |
+
|
| 572 |
+
submit_btn.click(
|
| 573 |
+
fn=process_input,
|
| 574 |
+
inputs=[file_input, temperature, page_slider],
|
| 575 |
+
outputs=[output_text, medicines_output, raw_output, page_info, rendered_image, num_pages]
|
| 576 |
+
)
|
| 577 |
+
|
| 578 |
+
file_input.change(
|
| 579 |
+
fn=update_slider,
|
| 580 |
+
inputs=[file_input],
|
| 581 |
+
outputs=[page_slider]
|
| 582 |
+
)
|
| 583 |
+
|
| 584 |
+
if __name__ == "__main__":
|
| 585 |
+
demo.launch()
|
| 586 |
+
|
| 587 |
+
|
| 588 |
+
|
| 589 |
|
| 590 |
########################################## #############################################################
|
| 591 |
|