File size: 4,770 Bytes
dc94d87 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 |
from pathlib import Path
from skimage import io as io_img
import io
import requests
import torch
from PIL import Image
import numpy as np
from huggingface_hub import snapshot_download
from LLAVA_Biovil.llava.mm_utils import tokenizer_image_token, get_model_name_from_path, KeywordsStoppingCriteria, remap_to_uint8
from LLAVA_Biovil.llava.model.builder import load_pretrained_model
from LLAVA_Biovil.llava.conversation import SeparatorStyle, conv_vicuna_v1
from LLAVA_Biovil.llava.constants import IMAGE_TOKEN_INDEX
from utils import create_chest_xray_transform_for_inference
def load_model_from_huggingface(repo_id, model_filename):
# Download model files
model_path = snapshot_download(repo_id=repo_id, revision="main")
model_path = Path(model_path) / model_filename
tokenizer, model, image_processor, context_len = load_pretrained_model(model_path, model_base='liuhaotian/llava-v1.5-7b',
model_name="llava-v1.5-7b-task-lora_radialog_instruct_llava_biovil_unfrozen_2e-5_5epochs_v5_checkpoint-21000", load_8bit=False, load_4bit=False)
return tokenizer, model, image_processor, context_len
if __name__ == '__main__':
# config = None
# model_path = "/home/guests/chantal_pellegrini/RaDialog_LLaVA/LLAVA/checkpoints/llava-v1.5-7b-task-lora_radialog_instruct_llava_biovil_unfrozen_2e-5_5epochs_v5/checkpoint-21000" #TODO hardcoded in huggingface repo probably
# model_name = get_model_name_from_path(model_path)
tokenizer, model, image_processor, context_len = load_model_from_huggingface(repo_id="Chantal/RaDialog-interactive-radiology-report-generation", model_filename="model")
model.config.tokenizer_padding_side = "left"
findings = "edema, pleural effusion" #TODO should these come from chexpert classifier? Or not needed for this demo/test?
conv = conv_vicuna_v1.copy()
REPORT_GEN_PROMPT = f"<image>. Predicted Findings: {findings}. You are to act as a radiologist and write the finding section of a chest x-ray radiology report for this X-ray image and the given predicted findings. Write in the style of a radiologist, write one fluent text without enumeration, be concise and don't provide explanations or reasons."
print("USER: ", REPORT_GEN_PROMPT)
conv.append_message("USER", REPORT_GEN_PROMPT)
conv.append_message("ASSISTANT", None)
text_input = conv.get_prompt()
# get the image
vis_transforms_biovil = create_chest_xray_transform_for_inference(512, center_crop_size=448)
sample_img_path = "https://openi.nlm.nih.gov/imgs/512/10/10/CXR10_IM-0002-2001.png?keywords=Calcified%20Granuloma" #TODO find good image
response = requests.get(sample_img_path)
image = Image.open(io.BytesIO(response.content))
image = remap_to_uint8(np.array(image))
image = Image.fromarray(image).convert("L")
image_tensor = vis_transforms_biovil(image).unsqueeze(0)
image_tensor = image_tensor.to(model.device, dtype=torch.bfloat16)
input_ids = tokenizer_image_token(text_input, tokenizer, IMAGE_TOKEN_INDEX, return_tensors='pt').unsqueeze(0).to(model.device)
stop_str = conv.sep if conv.sep_style != SeparatorStyle.TWO else conv.sep2
stopping_criteria = KeywordsStoppingCriteria([stop_str], tokenizer, input_ids)
# generate a report
with torch.inference_mode():
output_ids = model.generate(
input_ids,
images=image_tensor,
do_sample=False,
use_cache=True,
max_new_tokens=300,
stopping_criteria=[stopping_criteria],
pad_token_id=tokenizer.pad_token_id
)
pred = tokenizer.decode(output_ids[0, input_ids.shape[1]:]).strip().replace("</s>", "")
print("ASSISTANT: ", pred)
# add prediction to conversation
conv.messages.pop()
conv.append_message("ASSISTANT", pred)
conv.append_message("USER", "Translate this report to easy language for a patient to understand.")
conv.append_message("ASSISTANT", None)
text_input = conv.get_prompt()
print("USER: ", "Translate this report to easy language for a patient to understand.")
# generate easy language report
input_ids = tokenizer_image_token(text_input, tokenizer, IMAGE_TOKEN_INDEX, return_tensors='pt').unsqueeze(0).to(model.device)
with torch.inference_mode():
output_ids = model.generate(
input_ids,
images=image_tensor,
do_sample=False,
use_cache=True,
max_new_tokens=300,
stopping_criteria=[stopping_criteria],
pad_token_id=tokenizer.pad_token_id
)
pred = tokenizer.decode(output_ids[0, input_ids.shape[1]:]).strip().replace("</s>", "")
print("ASSISTANT: ", pred)
|