Update README.md

README.md

@@ -5,3 +5,108 @@ library_name: transformers
 tags:
 - image-to-text
 ---
+
+Requirements:
+```bash
+pip install transformers
+pip install torch
+```
+
+Adapted sample script for SRRG
+```python 
+import torch
+from PIL import Image
+from transformers import BertTokenizer, ViTImageProcessor, VisionEncoderDecoderModel, GenerationConfig
+import requests
+import re
+
+model_name  = "StanfordAIMI/chexpert-plus-srrg_impression"
+model = VisionEncoderDecoderModel.from_pretrained(model_name).eval()
+tokenizer = BertTokenizer.from_pretrained(model_name)
+image_processor = ViTImageProcessor.from_pretrained(model_name)
+generation_args = {
+   "bos_token_id": model.config.bos_token_id,
+   "eos_token_id": model.config.eos_token_id,
+   "pad_token_id": model.config.pad_token_id,
+   "num_return_sequences": 1,
+   "max_length": 128,
+   "use_cache": True,
+   "beam_width": 2,
+}
+
+# Inference
+with torch.no_grad():
+   url = "https://huggingface.co/IAMJB/interpret-cxr-impression-baseline/resolve/main/effusions-bibasal.jpg"
+   image = Image.open(requests.get(url, stream=True).raw)
+   pixel_values = image_processor(image, return_tensors="pt").pixel_values
+   # Generate predictions
+   generated_ids = model.generate(
+       pixel_values,
+       generation_config=GenerationConfig(
+           **{**generation_args, "decoder_start_token_id": tokenizer.cls_token_id})
+   )
+   generated_texts = tokenizer.batch_decode(generated_ids, skip_special_tokens=True)
+
+impression = generated_texts[0]
+print("Output raw impression:\n", impression)
+
+# format impression
+def process_impression_line(line):
+    """
+    Process one report line.
+
+    - First, deduce from the first valid impression header the expected style:
+      e.g. "1." vs. "1 ."
+    - Then, only when a candidate match’s number equals the expected impression number,
+      treat it as an impression header. For the first valid header, leave it unchanged.
+      For subsequent valid headers, insert a newline before it.
+    - Any candidate that does not match the expected number is assumed not to be an impression header.
+    """
+    impression_pattern = re.compile(r'(\d+)(\s*\.)(?!\d)')
+    expected_impression = 1
+    first_valid = True
+    deduced_style = None
+
+    def replacement(match):
+        nonlocal expected_impression, first_valid, deduced_style
+        candidate_num = int(match.group(1))
+        candidate_style = match.group(2)  # may be " ." or "."
+
+        # Only consider a candidate a valid impression header if it equals the expected number.
+        if candidate_num == expected_impression:
+            if first_valid:
+                # This is our first valid impression header.
+                first_valid = False
+                deduced_style = candidate_style  # record style (with or without whitespace)
+                expected_impression += 1
+                return match.group(0)  # leave unchanged (i.e. no preceding newline)
+            else:
+                # For subsequent valid headers, we require the style to be the same as deduced.
+                if candidate_style == deduced_style:
+                    expected_impression += 1
+                    return "\n" + match.group(0)
+                else:
+                    # If the style does not match the deduced style, leave it unchanged.
+                    return match.group(0)
+        else:
+            # This candidate does not match the expected number; likely it's not a header.
+            return match.group(0)
+
+    processed = impression_pattern.sub(replacement, line)
+    return processed
+
+
+impression = impression.strip()
+impression = process_impression_line(impression)
+print("Formatted impression:\n", impression)
+```
+
+Output
+```
+Output raw impression:
+ 1. moderate bilateral pleural effusions with associated bibasilar opacities, which may represent atelectasis or consolidation. 2. mild pulmonary edema.
+
+Formatted impression:
+1. moderate bilateral pleural effusions with associated bibasilar opacities, which may represent atelectasis or consolidation. 
+2. mild pulmonary edema.
+```