Spaces:
Sleeping
Sleeping
fix with endpoints
Browse files
app.py
CHANGED
@@ -14,9 +14,11 @@ import gc
|
|
14 |
|
15 |
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
|
16 |
|
17 |
-
#
|
18 |
HF_TOKEN = os.getenv("HF_TOKEN")
|
|
|
19 |
|
|
|
20 |
tokenizer = AutoTokenizer.from_pretrained("baliddeki/phronesis-ml", token=HF_TOKEN)
|
21 |
video_model = models.video.r3d_18(weights="KINETICS400_V1")
|
22 |
video_model.fc = torch.nn.Linear(video_model.fc.in_features, 512)
|
@@ -26,27 +28,20 @@ projector = ImageToTextProjector(512, report_generator.config.d_model)
|
|
26 |
|
27 |
num_classes = 4
|
28 |
class_names = ["acute", "normal", "chronic", "lacunar"]
|
29 |
-
combined_model = CombinedModel(
|
30 |
-
|
31 |
-
)
|
32 |
-
model_file = hf_hub_download(
|
33 |
-
"baliddeki/phronesis-ml", "pytorch_model.bin", token=HF_TOKEN
|
34 |
-
)
|
35 |
state_dict = torch.load(model_file, map_location=device)
|
36 |
combined_model.load_state_dict(state_dict)
|
|
|
37 |
combined_model.eval()
|
38 |
|
39 |
# Image transforms
|
40 |
-
image_transform = transforms.Compose(
|
41 |
-
|
42 |
-
|
43 |
-
|
44 |
-
|
45 |
-
mean=[0.43216, 0.394666, 0.37645], std=[0.22803, 0.22145, 0.216989]
|
46 |
-
),
|
47 |
-
]
|
48 |
-
)
|
49 |
-
|
50 |
|
51 |
def dicom_to_image(file_bytes):
|
52 |
dicom_file = pydicom.dcmread(io.BytesIO(file_bytes))
|
@@ -55,23 +50,21 @@ def dicom_to_image(file_bytes):
|
|
55 |
pixel_array = pixel_array.astype(np.uint8)
|
56 |
return Image.fromarray(pixel_array).convert("RGB")
|
57 |
|
58 |
-
|
59 |
def predict(images):
|
60 |
if not images:
|
61 |
return "No image uploaded.", ""
|
62 |
|
63 |
-
# Convert images
|
64 |
processed_imgs = []
|
65 |
for img in images:
|
66 |
filename = img.name.lower()
|
67 |
if filename.endswith((".dcm", ".ima")):
|
68 |
-
|
|
|
69 |
processed_imgs.append(dicom_img)
|
70 |
else:
|
71 |
pil_img = Image.open(img).convert("RGB")
|
72 |
processed_imgs.append(pil_img)
|
73 |
|
74 |
-
# Sample or pad
|
75 |
n_frames = 16
|
76 |
if len(processed_imgs) >= n_frames:
|
77 |
images_sampled = [
|
@@ -79,9 +72,7 @@ def predict(images):
|
|
79 |
for i in np.linspace(0, len(processed_imgs) - 1, n_frames, dtype=int)
|
80 |
]
|
81 |
else:
|
82 |
-
images_sampled = processed_imgs + [processed_imgs[-1]] * (
|
83 |
-
n_frames - len(processed_imgs)
|
84 |
-
)
|
85 |
|
86 |
tensor_imgs = [image_transform(i) for i in images_sampled]
|
87 |
input_tensor = torch.stack(tensor_imgs).permute(1, 0, 2, 3).unsqueeze(0).to(device)
|
@@ -97,8 +88,7 @@ def predict(images):
|
|
97 |
|
98 |
return class_name, report[0] if report else "No report generated."
|
99 |
|
100 |
-
|
101 |
-
# Gradio interface
|
102 |
demo = gr.Interface(
|
103 |
fn=predict,
|
104 |
inputs=gr.File(
|
@@ -106,9 +96,13 @@ demo = gr.Interface(
|
|
106 |
file_count="multiple",
|
107 |
label="Upload CT Scan Images",
|
108 |
),
|
109 |
-
outputs=[
|
|
|
|
|
|
|
110 |
title="Phronesis Medical Report Generator",
|
111 |
description="Upload CT scan DICOM or image files. Returns diagnosis classification and generated report.",
|
112 |
)
|
113 |
|
|
|
114 |
demo.launch()
|
|
|
14 |
|
15 |
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
|
16 |
|
17 |
+
# Environment setup
|
18 |
HF_TOKEN = os.getenv("HF_TOKEN")
|
19 |
+
os.environ["HF_HOME"] = "/tmp/huggingface_cache"
|
20 |
|
21 |
+
# Model initialization
|
22 |
tokenizer = AutoTokenizer.from_pretrained("baliddeki/phronesis-ml", token=HF_TOKEN)
|
23 |
video_model = models.video.r3d_18(weights="KINETICS400_V1")
|
24 |
video_model.fc = torch.nn.Linear(video_model.fc.in_features, 512)
|
|
|
28 |
|
29 |
num_classes = 4
|
30 |
class_names = ["acute", "normal", "chronic", "lacunar"]
|
31 |
+
combined_model = CombinedModel(video_model, report_generator, num_classes, projector, tokenizer)
|
32 |
+
|
33 |
+
model_file = hf_hub_download("baliddeki/phronesis-ml", "pytorch_model.bin", token=HF_TOKEN)
|
|
|
|
|
|
|
34 |
state_dict = torch.load(model_file, map_location=device)
|
35 |
combined_model.load_state_dict(state_dict)
|
36 |
+
combined_model.to(device)
|
37 |
combined_model.eval()
|
38 |
|
39 |
# Image transforms
|
40 |
+
image_transform = transforms.Compose([
|
41 |
+
transforms.Resize((112, 112)),
|
42 |
+
transforms.ToTensor(),
|
43 |
+
transforms.Normalize(mean=[0.43216, 0.394666, 0.37645], std=[0.22803, 0.22145, 0.216989]),
|
44 |
+
])
|
|
|
|
|
|
|
|
|
|
|
45 |
|
46 |
def dicom_to_image(file_bytes):
|
47 |
dicom_file = pydicom.dcmread(io.BytesIO(file_bytes))
|
|
|
50 |
pixel_array = pixel_array.astype(np.uint8)
|
51 |
return Image.fromarray(pixel_array).convert("RGB")
|
52 |
|
|
|
53 |
def predict(images):
|
54 |
if not images:
|
55 |
return "No image uploaded.", ""
|
56 |
|
|
|
57 |
processed_imgs = []
|
58 |
for img in images:
|
59 |
filename = img.name.lower()
|
60 |
if filename.endswith((".dcm", ".ima")):
|
61 |
+
file_bytes = img.read()
|
62 |
+
dicom_img = dicom_to_image(file_bytes)
|
63 |
processed_imgs.append(dicom_img)
|
64 |
else:
|
65 |
pil_img = Image.open(img).convert("RGB")
|
66 |
processed_imgs.append(pil_img)
|
67 |
|
|
|
68 |
n_frames = 16
|
69 |
if len(processed_imgs) >= n_frames:
|
70 |
images_sampled = [
|
|
|
72 |
for i in np.linspace(0, len(processed_imgs) - 1, n_frames, dtype=int)
|
73 |
]
|
74 |
else:
|
75 |
+
images_sampled = processed_imgs + [processed_imgs[-1]] * (n_frames - len(processed_imgs))
|
|
|
|
|
76 |
|
77 |
tensor_imgs = [image_transform(i) for i in images_sampled]
|
78 |
input_tensor = torch.stack(tensor_imgs).permute(1, 0, 2, 3).unsqueeze(0).to(device)
|
|
|
88 |
|
89 |
return class_name, report[0] if report else "No report generated."
|
90 |
|
91 |
+
# Define Gradio Interface explicitly
|
|
|
92 |
demo = gr.Interface(
|
93 |
fn=predict,
|
94 |
inputs=gr.File(
|
|
|
96 |
file_count="multiple",
|
97 |
label="Upload CT Scan Images",
|
98 |
),
|
99 |
+
outputs=[
|
100 |
+
gr.Textbox(label="Predicted Class"),
|
101 |
+
gr.Textbox(label="Generated Report")
|
102 |
+
],
|
103 |
title="Phronesis Medical Report Generator",
|
104 |
description="Upload CT scan DICOM or image files. Returns diagnosis classification and generated report.",
|
105 |
)
|
106 |
|
107 |
+
# Launch with explicit api_name for REST API compatibility
|
108 |
demo.launch()
|