Spaces:
Sleeping
Sleeping
fix with endpoints 2
Browse files
app.py
CHANGED
|
@@ -17,7 +17,7 @@ device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
|
|
| 17 |
HF_TOKEN = os.getenv("HF_TOKEN")
|
| 18 |
os.environ["HF_HOME"] = "/tmp/huggingface_cache"
|
| 19 |
|
| 20 |
-
#
|
| 21 |
tokenizer = AutoTokenizer.from_pretrained("baliddeki/phronesis-ml", token=HF_TOKEN)
|
| 22 |
video_model = models.video.r3d_18(weights="KINETICS400_V1")
|
| 23 |
video_model.fc = torch.nn.Linear(video_model.fc.in_features, 512)
|
|
@@ -27,29 +27,19 @@ projector = ImageToTextProjector(512, report_generator.config.d_model)
|
|
| 27 |
|
| 28 |
num_classes = 4
|
| 29 |
class_names = ["acute", "normal", "chronic", "lacunar"]
|
| 30 |
-
combined_model = CombinedModel(
|
| 31 |
-
video_model, report_generator, num_classes, projector, tokenizer
|
| 32 |
-
)
|
| 33 |
|
| 34 |
-
model_file = hf_hub_download(
|
| 35 |
-
"baliddeki/phronesis-ml", "pytorch_model.bin", token=HF_TOKEN
|
| 36 |
-
)
|
| 37 |
state_dict = torch.load(model_file, map_location=device)
|
| 38 |
combined_model.load_state_dict(state_dict)
|
| 39 |
combined_model.to(device)
|
| 40 |
combined_model.eval()
|
| 41 |
|
| 42 |
-
|
| 43 |
-
|
| 44 |
-
|
| 45 |
-
|
| 46 |
-
|
| 47 |
-
transforms.Normalize(
|
| 48 |
-
mean=[0.43216, 0.394666, 0.37645], std=[0.22803, 0.22145, 0.216989]
|
| 49 |
-
),
|
| 50 |
-
]
|
| 51 |
-
)
|
| 52 |
-
|
| 53 |
|
| 54 |
def dicom_to_image(file_bytes):
|
| 55 |
dicom_file = pydicom.dcmread(io.BytesIO(file_bytes))
|
|
@@ -58,32 +48,28 @@ def dicom_to_image(file_bytes):
|
|
| 58 |
pixel_array = pixel_array.astype(np.uint8)
|
| 59 |
return Image.fromarray(pixel_array).convert("RGB")
|
| 60 |
|
| 61 |
-
|
| 62 |
def predict(files):
|
| 63 |
if not files:
|
| 64 |
-
return "No
|
| 65 |
|
| 66 |
processed_imgs = []
|
| 67 |
-
for
|
| 68 |
-
filename =
|
| 69 |
if filename.endswith((".dcm", ".ima")):
|
| 70 |
-
file_bytes =
|
| 71 |
-
|
| 72 |
-
processed_imgs.append(dicom_img)
|
| 73 |
else:
|
| 74 |
-
|
| 75 |
-
|
| 76 |
|
| 77 |
n_frames = 16
|
| 78 |
if len(processed_imgs) >= n_frames:
|
| 79 |
images_sampled = [
|
| 80 |
processed_imgs[i]
|
| 81 |
-
for i in np.linspace(0, len(processed_imgs)
|
| 82 |
]
|
| 83 |
else:
|
| 84 |
-
images_sampled = processed_imgs + [processed_imgs[-1]] * (
|
| 85 |
-
n_frames - len(processed_imgs)
|
| 86 |
-
)
|
| 87 |
|
| 88 |
tensor_imgs = [image_transform(i) for i in images_sampled]
|
| 89 |
input_tensor = torch.stack(tensor_imgs).permute(1, 0, 2, 3).unsqueeze(0).to(device)
|
|
@@ -99,19 +85,22 @@ def predict(files):
|
|
| 99 |
|
| 100 |
return class_name, report[0] if report else "No report generated."
|
| 101 |
|
| 102 |
-
|
| 103 |
-
# Gradio Blocks setup (explicitly)
|
| 104 |
with gr.Blocks() as demo:
|
| 105 |
-
gr.Markdown("
|
| 106 |
-
|
| 107 |
-
|
| 108 |
-
|
| 109 |
-
|
| 110 |
-
)
|
| 111 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
| 112 |
class_output = gr.Textbox(label="Predicted Class")
|
| 113 |
report_output = gr.Textbox(label="Generated Report")
|
| 114 |
|
| 115 |
-
|
| 116 |
|
| 117 |
demo.launch()
|
|
|
|
| 17 |
HF_TOKEN = os.getenv("HF_TOKEN")
|
| 18 |
os.environ["HF_HOME"] = "/tmp/huggingface_cache"
|
| 19 |
|
| 20 |
+
# Model loading
|
| 21 |
tokenizer = AutoTokenizer.from_pretrained("baliddeki/phronesis-ml", token=HF_TOKEN)
|
| 22 |
video_model = models.video.r3d_18(weights="KINETICS400_V1")
|
| 23 |
video_model.fc = torch.nn.Linear(video_model.fc.in_features, 512)
|
|
|
|
| 27 |
|
| 28 |
num_classes = 4
|
| 29 |
class_names = ["acute", "normal", "chronic", "lacunar"]
|
| 30 |
+
combined_model = CombinedModel(video_model, report_generator, num_classes, projector, tokenizer)
|
|
|
|
|
|
|
| 31 |
|
| 32 |
+
model_file = hf_hub_download("baliddeki/phronesis-ml", "pytorch_model.bin", token=HF_TOKEN)
|
|
|
|
|
|
|
| 33 |
state_dict = torch.load(model_file, map_location=device)
|
| 34 |
combined_model.load_state_dict(state_dict)
|
| 35 |
combined_model.to(device)
|
| 36 |
combined_model.eval()
|
| 37 |
|
| 38 |
+
image_transform = transforms.Compose([
|
| 39 |
+
transforms.Resize((112, 112)),
|
| 40 |
+
transforms.ToTensor(),
|
| 41 |
+
transforms.Normalize(mean=[0.43216, 0.394666, 0.37645], std=[0.22803, 0.22145, 0.216989]),
|
| 42 |
+
])
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 43 |
|
| 44 |
def dicom_to_image(file_bytes):
|
| 45 |
dicom_file = pydicom.dcmread(io.BytesIO(file_bytes))
|
|
|
|
| 48 |
pixel_array = pixel_array.astype(np.uint8)
|
| 49 |
return Image.fromarray(pixel_array).convert("RGB")
|
| 50 |
|
|
|
|
| 51 |
def predict(files):
|
| 52 |
if not files:
|
| 53 |
+
return "No images uploaded.", ""
|
| 54 |
|
| 55 |
processed_imgs = []
|
| 56 |
+
for file_obj in files:
|
| 57 |
+
filename = file_obj.name.lower()
|
| 58 |
if filename.endswith((".dcm", ".ima")):
|
| 59 |
+
file_bytes = file_obj.read()
|
| 60 |
+
img = dicom_to_image(file_bytes)
|
|
|
|
| 61 |
else:
|
| 62 |
+
img = Image.open(file_obj).convert("RGB")
|
| 63 |
+
processed_imgs.append(img)
|
| 64 |
|
| 65 |
n_frames = 16
|
| 66 |
if len(processed_imgs) >= n_frames:
|
| 67 |
images_sampled = [
|
| 68 |
processed_imgs[i]
|
| 69 |
+
for i in np.linspace(0, len(processed_imgs)-1, n_frames, dtype=int)
|
| 70 |
]
|
| 71 |
else:
|
| 72 |
+
images_sampled = processed_imgs + [processed_imgs[-1]] * (n_frames - len(processed_imgs))
|
|
|
|
|
|
|
| 73 |
|
| 74 |
tensor_imgs = [image_transform(i) for i in images_sampled]
|
| 75 |
input_tensor = torch.stack(tensor_imgs).permute(1, 0, 2, 3).unsqueeze(0).to(device)
|
|
|
|
| 85 |
|
| 86 |
return class_name, report[0] if report else "No report generated."
|
| 87 |
|
| 88 |
+
# Gradio Blocks (100% reliable approach)
|
|
|
|
| 89 |
with gr.Blocks() as demo:
|
| 90 |
+
gr.Markdown("# 🩺 Phronesis Medical Report Generator")
|
| 91 |
+
|
| 92 |
+
upload_button = gr.UploadButton("Upload CT Scan Images", file_types=[".dcm", ".jpg", ".jpeg", ".png"], file_count="multiple")
|
| 93 |
+
files_state = gr.State([])
|
| 94 |
+
|
| 95 |
+
def store_files(new_files):
|
| 96 |
+
return new_files
|
| 97 |
+
|
| 98 |
+
upload_button.upload(store_files, upload_button, files_state)
|
| 99 |
+
|
| 100 |
+
generate_btn = gr.Button("Generate Report")
|
| 101 |
class_output = gr.Textbox(label="Predicted Class")
|
| 102 |
report_output = gr.Textbox(label="Generated Report")
|
| 103 |
|
| 104 |
+
generate_btn.click(predict, files_state, [class_output, report_output])
|
| 105 |
|
| 106 |
demo.launch()
|