Spaces:
Sleeping
Sleeping
Upload folder using huggingface_hub
Browse files- dicom_processor.py +35 -17
- explainability.py +246 -139
dicom_processor.py
CHANGED
|
@@ -15,7 +15,6 @@ REQUIRED_TAGS = [
|
|
| 15 |
'SeriesInstanceUID',
|
| 16 |
'Modality',
|
| 17 |
'PixelSpacing', # Crucial for measurements
|
| 18 |
-
# 'ImageOrientationPatient' # Often missing in simple CR/DX, but critical for CT/MRI
|
| 19 |
]
|
| 20 |
|
| 21 |
# Tags to Anonymize (PHI)
|
|
@@ -41,7 +40,6 @@ def validate_dicom(file_bytes: bytes) -> pydicom.dataset.FileDataset:
|
|
| 41 |
# 2. Check Mandatory Tags
|
| 42 |
missing_tags = [tag for tag in REQUIRED_TAGS if tag not in ds]
|
| 43 |
if missing_tags:
|
| 44 |
-
# Modality specific relaxation could go here, but strict for now
|
| 45 |
raise ValueError(f"Missing critical DICOM tags: {missing_tags}")
|
| 46 |
|
| 47 |
# 3. Check Pixel Data presence
|
|
@@ -85,18 +83,16 @@ def process_dicom_upload(file_bytes: bytes, username: str) -> Tuple[bytes, Dict[
|
|
| 85 |
# 2. Anonymize
|
| 86 |
ds = anonymize_dicom(ds)
|
| 87 |
|
| 88 |
-
# 3. Extract safe metadata
|
| 89 |
metadata = {
|
| 90 |
"modality": ds.get("Modality", "Unknown"),
|
| 91 |
"body_part": ds.get("BodyPartExamined", "Unknown"),
|
| 92 |
"study_uid": str(ds.get("StudyInstanceUID", "")),
|
| 93 |
-
"series_uid": str(ds.get("SeriesInstanceUID", "")),
|
| 94 |
"pixel_spacing": ds.get("PixelSpacing", [1.0, 1.0]),
|
| 95 |
-
"original_filename_hint": "dicom_file.dcm"
|
| 96 |
}
|
| 97 |
|
| 98 |
# 4. Convert back to bytes for storage
|
| 99 |
-
# We save the ANONYMIZED version
|
| 100 |
with io.BytesIO() as buffer:
|
| 101 |
ds.save_as(buffer)
|
| 102 |
safe_bytes = buffer.getvalue()
|
|
@@ -105,27 +101,49 @@ def process_dicom_upload(file_bytes: bytes, username: str) -> Tuple[bytes, Dict[
|
|
| 105 |
|
| 106 |
def convert_dicom_to_image(ds: pydicom.dataset.FileDataset) -> Any:
|
| 107 |
"""
|
| 108 |
-
Convert DICOM to PIL Image / Numpy array
|
| 109 |
-
|
|
|
|
|
|
|
| 110 |
"""
|
| 111 |
import numpy as np
|
| 112 |
from PIL import Image
|
| 113 |
|
| 114 |
try:
|
| 115 |
-
#
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 116 |
pixel_array = ds.pixel_array.astype(float)
|
| 117 |
|
| 118 |
-
# Rescale Slope/Intercept (
|
| 119 |
slope = getattr(ds, 'RescaleSlope', 1)
|
| 120 |
intercept = getattr(ds, 'RescaleIntercept', 0)
|
| 121 |
pixel_array = (pixel_array * slope) + intercept
|
| 122 |
|
| 123 |
-
#
|
| 124 |
-
|
| 125 |
-
# window_center = ds.get("WindowCenter", ... )
|
| 126 |
|
| 127 |
-
|
| 128 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 129 |
pixel_min = np.min(pixel_array)
|
| 130 |
pixel_max = np.max(pixel_array)
|
| 131 |
|
|
@@ -136,11 +154,11 @@ def convert_dicom_to_image(ds: pydicom.dataset.FileDataset) -> Any:
|
|
| 136 |
|
| 137 |
pixel_array = pixel_array.astype(np.uint8)
|
| 138 |
|
| 139 |
-
#
|
| 140 |
if len(pixel_array.shape) == 2:
|
| 141 |
image = Image.fromarray(pixel_array).convert("RGB")
|
| 142 |
else:
|
| 143 |
-
image = Image.fromarray(pixel_array)
|
| 144 |
|
| 145 |
return image
|
| 146 |
|
|
|
|
| 15 |
'SeriesInstanceUID',
|
| 16 |
'Modality',
|
| 17 |
'PixelSpacing', # Crucial for measurements
|
|
|
|
| 18 |
]
|
| 19 |
|
| 20 |
# Tags to Anonymize (PHI)
|
|
|
|
| 40 |
# 2. Check Mandatory Tags
|
| 41 |
missing_tags = [tag for tag in REQUIRED_TAGS if tag not in ds]
|
| 42 |
if missing_tags:
|
|
|
|
| 43 |
raise ValueError(f"Missing critical DICOM tags: {missing_tags}")
|
| 44 |
|
| 45 |
# 3. Check Pixel Data presence
|
|
|
|
| 83 |
# 2. Anonymize
|
| 84 |
ds = anonymize_dicom(ds)
|
| 85 |
|
| 86 |
+
# 3. Extract safe metadata
|
| 87 |
metadata = {
|
| 88 |
"modality": ds.get("Modality", "Unknown"),
|
| 89 |
"body_part": ds.get("BodyPartExamined", "Unknown"),
|
| 90 |
"study_uid": str(ds.get("StudyInstanceUID", "")),
|
|
|
|
| 91 |
"pixel_spacing": ds.get("PixelSpacing", [1.0, 1.0]),
|
| 92 |
+
"original_filename_hint": "dicom_file.dcm"
|
| 93 |
}
|
| 94 |
|
| 95 |
# 4. Convert back to bytes for storage
|
|
|
|
| 96 |
with io.BytesIO() as buffer:
|
| 97 |
ds.save_as(buffer)
|
| 98 |
safe_bytes = buffer.getvalue()
|
|
|
|
| 101 |
|
| 102 |
def convert_dicom_to_image(ds: pydicom.dataset.FileDataset) -> Any:
|
| 103 |
"""
|
| 104 |
+
Convert DICOM to PIL Image / Numpy array with Medical Physics awareness.
|
| 105 |
+
1. Check RAS Orientation (Basic Validation).
|
| 106 |
+
2. Apply Hounsfield Units (CT) or Intensity Normalization (MRI/XRay).
|
| 107 |
+
3. Windowing (Lung/Bone/Soft Tissue).
|
| 108 |
"""
|
| 109 |
import numpy as np
|
| 110 |
from PIL import Image
|
| 111 |
|
| 112 |
try:
|
| 113 |
+
# 1. Image Geometry & Orientation Check (RAS)
|
| 114 |
+
# We enforce that slices are roughly axial/standard for now, or at least valid.
|
| 115 |
+
orientation = ds.get("ImageOrientationPatient")
|
| 116 |
+
if orientation:
|
| 117 |
+
# Check for orthogonality (basic sanity)
|
| 118 |
+
row_cosine = np.array(orientation[:3])
|
| 119 |
+
col_cosine = np.array(orientation[3:])
|
| 120 |
+
if np.abs(np.dot(row_cosine, col_cosine)) > 1e-3:
|
| 121 |
+
logger.warning("DICOM Orientation vectors are not orthogonal. Image might be skewed.")
|
| 122 |
+
|
| 123 |
+
# 2. Extract Raw Pixels
|
| 124 |
pixel_array = ds.pixel_array.astype(float)
|
| 125 |
|
| 126 |
+
# 3. Apply Rescale Slope/Intercept (Physics -> HU)
|
| 127 |
slope = getattr(ds, 'RescaleSlope', 1)
|
| 128 |
intercept = getattr(ds, 'RescaleIntercept', 0)
|
| 129 |
pixel_array = (pixel_array * slope) + intercept
|
| 130 |
|
| 131 |
+
# 4. Modality-Specific Normalization
|
| 132 |
+
modality = ds.get("Modality", "Unknown")
|
|
|
|
| 133 |
|
| 134 |
+
if modality == 'CT':
|
| 135 |
+
# Hounsfield Units: Air -1000, Bone +1000
|
| 136 |
+
# Robust Min-Max scaling for visualization feeding
|
| 137 |
+
# Clip outlier HU (metal artifacts > 3000, air < -1000)
|
| 138 |
+
pixel_array = np.clip(pixel_array, -1000, 3000)
|
| 139 |
+
|
| 140 |
+
elif modality == 'MR':
|
| 141 |
+
# MRI is relative intensity.
|
| 142 |
+
# Simple 1-99 percentile clipping removes spikes.
|
| 143 |
+
p1, p99 = np.percentile(pixel_array, [1, 99])
|
| 144 |
+
pixel_array = np.clip(pixel_array, p1, p99)
|
| 145 |
+
|
| 146 |
+
# 5. Normalization to 0-255 (Display Space)
|
| 147 |
pixel_min = np.min(pixel_array)
|
| 148 |
pixel_max = np.max(pixel_array)
|
| 149 |
|
|
|
|
| 154 |
|
| 155 |
pixel_array = pixel_array.astype(np.uint8)
|
| 156 |
|
| 157 |
+
# 6. Color Space
|
| 158 |
if len(pixel_array.shape) == 2:
|
| 159 |
image = Image.fromarray(pixel_array).convert("RGB")
|
| 160 |
else:
|
| 161 |
+
image = Image.fromarray(pixel_array)
|
| 162 |
|
| 163 |
return image
|
| 164 |
|
explainability.py
CHANGED
|
@@ -5,19 +5,77 @@ import numpy as np
|
|
| 5 |
import cv2
|
| 6 |
from PIL import Image
|
| 7 |
import logging
|
| 8 |
-
from typing import List, Dict, Any, Optional, Tuple
|
| 9 |
from pytorch_grad_cam import GradCAMPlusPlus
|
| 10 |
from pytorch_grad_cam.utils.image import show_cam_on_image
|
|
|
|
| 11 |
|
| 12 |
logger = logging.getLogger(__name__)
|
| 13 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 14 |
# =========================================================================
|
| 15 |
# WRAPPERS AND UTILS
|
| 16 |
# =========================================================================
|
| 17 |
|
| 18 |
class HuggingFaceWeirdCLIPWrapper(nn.Module):
|
| 19 |
-
"""
|
| 20 |
-
|
|
|
|
|
|
|
| 21 |
def __init__(self, model, text_input_ids, attention_mask):
|
| 22 |
super(HuggingFaceWeirdCLIPWrapper, self).__init__()
|
| 23 |
self.model = model
|
|
@@ -30,57 +88,66 @@ class HuggingFaceWeirdCLIPWrapper(nn.Module):
|
|
| 30 |
input_ids=self.text_input_ids,
|
| 31 |
attention_mask=self.attention_mask
|
| 32 |
)
|
|
|
|
|
|
|
|
|
|
| 33 |
return outputs.logits_per_image
|
| 34 |
|
| 35 |
def reshape_transform(tensor, width=32, height=32):
|
| 36 |
"""Reshape Transformer attention/embeddings for Grad-CAM."""
|
| 37 |
-
#
|
| 38 |
-
#
|
| 39 |
-
# Exclude CLS token if present (depends on model config, usually index 0)
|
| 40 |
-
# SigLIP generally doesn't use CLS token for pooling? It uses attention pooling.
|
| 41 |
-
# Assuming tensor includes all visual tokens.
|
| 42 |
-
|
| 43 |
num_tokens = tensor.size(1)
|
| 44 |
side = int(np.sqrt(num_tokens))
|
| 45 |
result = tensor.reshape(tensor.size(0), side, side, tensor.size(2))
|
| 46 |
-
|
| 47 |
-
# Bring channels to first dimension for GradCAM: (B, C, H, W)
|
| 48 |
result = result.transpose(2, 3).transpose(1, 2)
|
| 49 |
return result
|
| 50 |
|
| 51 |
# =========================================================================
|
| 52 |
-
# EXPLAINABILITY ENGINE
|
| 53 |
# =========================================================================
|
| 54 |
|
| 55 |
class ExplainabilityEngine:
|
| 56 |
def __init__(self, model_wrapper):
|
| 57 |
-
"""
|
| 58 |
-
Initialize with the MedSigClipWrapper instance.
|
| 59 |
-
"""
|
| 60 |
self.wrapper = model_wrapper
|
| 61 |
self.model = model_wrapper.model
|
| 62 |
self.processor = model_wrapper.processor
|
|
|
|
| 63 |
|
| 64 |
-
def
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 65 |
"""
|
| 66 |
-
|
| 67 |
-
|
| 68 |
-
Algorithm:
|
| 69 |
-
1. Encode text prompt ("lung parenchyma").
|
| 70 |
-
2. Extract patch embeddings from vision model.
|
| 71 |
-
3. Compute Cosine Similarity (Patch vs Text).
|
| 72 |
-
4. Threshold and Upscale.
|
| 73 |
"""
|
|
|
|
|
|
|
|
|
|
|
|
|
| 74 |
try:
|
| 75 |
-
|
| 76 |
-
|
| 77 |
-
|
| 78 |
-
inputs = self.processor(text=[prompt], images=image, padding="max_length", return_tensors="pt")
|
| 79 |
-
inputs = {k: v.to(device) for k, v in inputs.items()}
|
| 80 |
|
| 81 |
with torch.no_grad():
|
| 82 |
-
#
|
| 83 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 84 |
text_outputs = self.model.text_model(
|
| 85 |
input_ids=inputs["input_ids"],
|
| 86 |
attention_mask=inputs["attention_mask"]
|
|
@@ -88,141 +155,181 @@ class ExplainabilityEngine:
|
|
| 88 |
text_embeds = text_outputs.pooler_output
|
| 89 |
text_embeds = text_embeds / text_embeds.norm(p=2, dim=-1, keepdim=True)
|
| 90 |
|
| 91 |
-
#
|
| 92 |
-
|
| 93 |
-
|
| 94 |
-
|
| 95 |
-
output_hidden_states=True
|
| 96 |
-
)
|
| 97 |
-
last_hidden_state = vision_outputs.last_hidden_state # (1, num_tokens, dim)
|
| 98 |
|
| 99 |
-
#
|
| 100 |
-
|
| 101 |
-
|
| 102 |
-
|
| 103 |
-
# Let's use the raw hidden states.
|
| 104 |
|
| 105 |
-
|
| 106 |
-
|
| 107 |
-
|
| 108 |
-
|
| 109 |
-
|
| 110 |
-
|
| 111 |
-
# If they differ, we can't do direct dot product without projection.
|
| 112 |
-
# For safety/speed in this Proxy, we skip the projection check and assume compatibility
|
| 113 |
-
# OR we fallback to a simpler dummy mask (Center Crop) if dimensions mismatch.
|
| 114 |
|
| 115 |
-
#
|
| 116 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 117 |
|
| 118 |
-
#
|
| 119 |
-
|
| 120 |
-
|
| 121 |
|
| 122 |
-
|
| 123 |
-
|
| 124 |
-
|
| 125 |
-
# Ellipse for lungs/body
|
| 126 |
-
cv2.ellipse(mask, (w//2, h//2), (w//3, h//3), 0, 0, 360, 1.0, -1)
|
| 127 |
-
mask = cv2.GaussianBlur(mask, (101, 101), 0)
|
| 128 |
|
| 129 |
-
return mask
|
| 130 |
|
| 131 |
except Exception as e:
|
| 132 |
-
logger.
|
| 133 |
-
|
|
|
|
| 134 |
|
| 135 |
-
def
|
| 136 |
-
|
| 137 |
-
Full Pipeline: Image -> Grad-CAM++ (G) -> MedSegCLIP (M) -> G*M
|
| 138 |
-
"""
|
| 139 |
-
# 1. Generate Grad-CAM++ (The "Why")
|
| 140 |
-
# Reuse existing logic but cleaned up
|
| 141 |
-
gradcam_map = self._run_gradcam(image, target_text)
|
| 142 |
-
|
| 143 |
-
# 2. Generate Anatomical Mask (The "Where")
|
| 144 |
-
seg_mask = self.generate_anatomical_mask(image, anatomical_context)
|
| 145 |
-
|
| 146 |
-
# 3. Constrain
|
| 147 |
-
# Resize seg_mask to match gradcam_map (both should be HxW float 0..1)
|
| 148 |
-
if gradcam_map is None:
|
| 149 |
-
return {
|
| 150 |
-
"heatmap_array": None,
|
| 151 |
-
"heatmap_raw": None,
|
| 152 |
-
"reliability_score": 0.0,
|
| 153 |
-
"confidence_label": "LOW"
|
| 154 |
-
}
|
| 155 |
-
|
| 156 |
-
# Ensure shapes match
|
| 157 |
-
if seg_mask.shape != gradcam_map.shape:
|
| 158 |
-
seg_mask = cv2.resize(seg_mask, (gradcam_map.shape[1], gradcam_map.shape[0]))
|
| 159 |
-
|
| 160 |
-
constrained_map = gradcam_map * seg_mask
|
| 161 |
|
| 162 |
-
|
| 163 |
-
|
| 164 |
-
|
| 165 |
-
|
| 166 |
-
reliability = 0.0
|
| 167 |
-
if total_energy > 0:
|
| 168 |
-
reliability = retained_energy / total_energy
|
| 169 |
|
| 170 |
-
|
| 171 |
-
|
| 172 |
-
#
|
| 173 |
-
|
| 174 |
-
img_np = np.array(image)
|
| 175 |
-
img_np = (img_np - img_np.min()) / (img_np.max() - img_np.min())
|
| 176 |
-
visualization = show_cam_on_image(img_np, constrained_map, use_rgb=True)
|
| 177 |
-
|
| 178 |
-
return {
|
| 179 |
-
"heatmap_array": visualization, # RGB HxW
|
| 180 |
-
"heatmap_raw": constrained_map, # 0..1 Map
|
| 181 |
-
"reliability_score": round(reliability, 2),
|
| 182 |
-
"confidence_label": explainability_confidence
|
| 183 |
-
}
|
| 184 |
|
| 185 |
-
def
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 186 |
try:
|
| 187 |
-
#
|
| 188 |
-
inputs = self.processor(text=
|
| 189 |
-
inputs = {k: v.to(self.
|
| 190 |
|
| 191 |
-
#
|
| 192 |
-
# Robust get for attention_mask (some processors might not return it for image-only flows, though text is here)
|
| 193 |
input_ids = inputs.get('input_ids')
|
| 194 |
attention_mask = inputs.get('attention_mask')
|
|
|
|
|
|
|
| 195 |
|
| 196 |
-
|
| 197 |
-
|
| 198 |
-
return None
|
| 199 |
-
|
| 200 |
-
model_wrapper_cam = HuggingFaceWeirdCLIPWrapper(
|
| 201 |
-
self.model, input_ids, attention_mask
|
| 202 |
-
)
|
| 203 |
|
| 204 |
-
|
|
|
|
|
|
|
| 205 |
|
| 206 |
cam = GradCAMPlusPlus(
|
| 207 |
model=model_wrapper_cam,
|
| 208 |
target_layers=target_layers,
|
| 209 |
-
reshape_transform=reshape_transform
|
| 210 |
)
|
| 211 |
|
| 212 |
-
# GradCAM needs pixel_values
|
| 213 |
pixel_values = inputs.get('pixel_values')
|
| 214 |
-
if pixel_values is None:
|
| 215 |
-
logger.error("Explainability: Missing pixel_values")
|
| 216 |
-
return None
|
| 217 |
-
|
| 218 |
-
grayscale_cam = cam(input_tensor=pixel_values, targets=None)
|
| 219 |
-
grayscale_cam = grayscale_cam[0, :]
|
| 220 |
|
| 221 |
-
#
|
| 222 |
-
|
|
|
|
|
|
|
| 223 |
|
| 224 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 225 |
|
| 226 |
except Exception as e:
|
| 227 |
-
logger.error(f"Grad-CAM
|
| 228 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 5 |
import cv2
|
| 6 |
from PIL import Image
|
| 7 |
import logging
|
| 8 |
+
from typing import List, Dict, Any, Optional, Tuple, Union
|
| 9 |
from pytorch_grad_cam import GradCAMPlusPlus
|
| 10 |
from pytorch_grad_cam.utils.image import show_cam_on_image
|
| 11 |
+
from dataclasses import dataclass
|
| 12 |
|
| 13 |
logger = logging.getLogger(__name__)
|
| 14 |
|
| 15 |
+
# =========================================================================
|
| 16 |
+
# CONFIGURATION & EXPERT KNOWLEDGE
|
| 17 |
+
# =========================================================================
|
| 18 |
+
|
| 19 |
+
@dataclass
|
| 20 |
+
class ExpertSegConfig:
|
| 21 |
+
modality: str
|
| 22 |
+
target_organ: str
|
| 23 |
+
anatomical_prompts: List[str] # For Segmentation Mask
|
| 24 |
+
threshold_percentile: int # Top X% activation
|
| 25 |
+
min_area_ratio: float
|
| 26 |
+
max_area_ratio: float
|
| 27 |
+
morphology_kernel: int
|
| 28 |
+
|
| 29 |
+
# Expert Knowledge Base
|
| 30 |
+
EXPERT_KNOWLEDGE = {
|
| 31 |
+
"Thoracic": ExpertSegConfig(
|
| 32 |
+
modality="CXR/CT",
|
| 33 |
+
target_organ="Lung Parenchyma",
|
| 34 |
+
anatomical_prompts=[
|
| 35 |
+
"lung parenchyma",
|
| 36 |
+
"bilateral lungs",
|
| 37 |
+
"pulmonary fields",
|
| 38 |
+
"chest x-ray lungs excluding heart"
|
| 39 |
+
],
|
| 40 |
+
threshold_percentile=75, # Top 25%
|
| 41 |
+
min_area_ratio=0.15,
|
| 42 |
+
max_area_ratio=0.60,
|
| 43 |
+
morphology_kernel=7
|
| 44 |
+
),
|
| 45 |
+
"Orthopedics": ExpertSegConfig(
|
| 46 |
+
modality="X-Ray",
|
| 47 |
+
target_organ="Bone Structure",
|
| 48 |
+
anatomical_prompts=[
|
| 49 |
+
"bone structure",
|
| 50 |
+
"knee joint",
|
| 51 |
+
"cortical bone",
|
| 52 |
+
"skeletal anatomy"
|
| 53 |
+
],
|
| 54 |
+
threshold_percentile=85, # Top 15%
|
| 55 |
+
min_area_ratio=0.05,
|
| 56 |
+
max_area_ratio=0.50,
|
| 57 |
+
morphology_kernel=5
|
| 58 |
+
),
|
| 59 |
+
"Default": ExpertSegConfig(
|
| 60 |
+
modality="General",
|
| 61 |
+
target_organ="Body Part",
|
| 62 |
+
anatomical_prompts=["medical image body part"],
|
| 63 |
+
threshold_percentile=80,
|
| 64 |
+
min_area_ratio=0.05,
|
| 65 |
+
max_area_ratio=0.90,
|
| 66 |
+
morphology_kernel=5
|
| 67 |
+
)
|
| 68 |
+
}
|
| 69 |
+
|
| 70 |
# =========================================================================
|
| 71 |
# WRAPPERS AND UTILS
|
| 72 |
# =========================================================================
|
| 73 |
|
| 74 |
class HuggingFaceWeirdCLIPWrapper(nn.Module):
|
| 75 |
+
"""
|
| 76 |
+
Wraps SigLIP to act like a standard classifier for Grad-CAM.
|
| 77 |
+
Target: Cosine Similarity Score.
|
| 78 |
+
"""
|
| 79 |
def __init__(self, model, text_input_ids, attention_mask):
|
| 80 |
super(HuggingFaceWeirdCLIPWrapper, self).__init__()
|
| 81 |
self.model = model
|
|
|
|
| 88 |
input_ids=self.text_input_ids,
|
| 89 |
attention_mask=self.attention_mask
|
| 90 |
)
|
| 91 |
+
# outputs.logits_per_image is (Batch, Num_Prompts)
|
| 92 |
+
# This IS the similarity score (scaled).
|
| 93 |
+
# Grad-CAM++ will derive gradients relative to this score.
|
| 94 |
return outputs.logits_per_image
|
| 95 |
|
| 96 |
def reshape_transform(tensor, width=32, height=32):
|
| 97 |
"""Reshape Transformer attention/embeddings for Grad-CAM."""
|
| 98 |
+
# Squeeze CLS if present logic (usually SigLIP doesn't have it in last layers same way)
|
| 99 |
+
# Tensor: (Batch, Num_Tokens, Dim)
|
|
|
|
|
|
|
|
|
|
|
|
|
| 100 |
num_tokens = tensor.size(1)
|
| 101 |
side = int(np.sqrt(num_tokens))
|
| 102 |
result = tensor.reshape(tensor.size(0), side, side, tensor.size(2))
|
| 103 |
+
# Bring channels first: (B, C, H, W)
|
|
|
|
| 104 |
result = result.transpose(2, 3).transpose(1, 2)
|
| 105 |
return result
|
| 106 |
|
| 107 |
# =========================================================================
|
| 108 |
+
# EXPERT+ EXPLAINABILITY ENGINE
|
| 109 |
# =========================================================================
|
| 110 |
|
| 111 |
class ExplainabilityEngine:
|
| 112 |
def __init__(self, model_wrapper):
|
|
|
|
|
|
|
|
|
|
| 113 |
self.wrapper = model_wrapper
|
| 114 |
self.model = model_wrapper.model
|
| 115 |
self.processor = model_wrapper.processor
|
| 116 |
+
self.device = self.model.device
|
| 117 |
|
| 118 |
+
def _get_expert_config(self, anatomical_context: str) -> ExpertSegConfig:
|
| 119 |
+
if "lung" in anatomical_context.lower():
|
| 120 |
+
return EXPERT_KNOWLEDGE["Thoracic"]
|
| 121 |
+
elif "bone" in anatomical_context.lower() or "knee" in anatomical_context.lower():
|
| 122 |
+
return EXPERT_KNOWLEDGE["Orthopedics"]
|
| 123 |
+
else:
|
| 124 |
+
base = EXPERT_KNOWLEDGE["Default"]
|
| 125 |
+
base.anatomical_prompts = [anatomical_context]
|
| 126 |
+
return base
|
| 127 |
+
|
| 128 |
+
def generate_expert_mask(self, image: Image.Image, config: ExpertSegConfig) -> Dict[str, Any]:
|
| 129 |
"""
|
| 130 |
+
Expert Segmentation:
|
| 131 |
+
Multi-Prompt Ensembling -> Patch Similarity -> Adaptive Threshold -> Morphology -> Validation.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 132 |
"""
|
| 133 |
+
audit = {
|
| 134 |
+
"seg_prompts": config.anatomical_prompts,
|
| 135 |
+
"seg_status": "INIT"
|
| 136 |
+
}
|
| 137 |
try:
|
| 138 |
+
w, h = image.size
|
| 139 |
+
inputs = self.processor(text=config.anatomical_prompts, images=image, padding="max_length", return_tensors="pt")
|
| 140 |
+
inputs = {k: v.to(self.device) for k, v in inputs.items()}
|
|
|
|
|
|
|
| 141 |
|
| 142 |
with torch.no_grad():
|
| 143 |
+
# Vision Features (1, Token, Dim)
|
| 144 |
+
vision_outputs = self.model.vision_model(
|
| 145 |
+
pixel_values=inputs["pixel_values"],
|
| 146 |
+
output_hidden_states=True
|
| 147 |
+
)
|
| 148 |
+
last_hidden_state = vision_outputs.last_hidden_state
|
| 149 |
+
|
| 150 |
+
# Text Features (Prompts, Dim)
|
| 151 |
text_outputs = self.model.text_model(
|
| 152 |
input_ids=inputs["input_ids"],
|
| 153 |
attention_mask=inputs["attention_mask"]
|
|
|
|
| 155 |
text_embeds = text_outputs.pooler_output
|
| 156 |
text_embeds = text_embeds / text_embeds.norm(p=2, dim=-1, keepdim=True)
|
| 157 |
|
| 158 |
+
# Similarity: (1, T, D) @ (D, P) -> (1, T, P)
|
| 159 |
+
sim_map = torch.matmul(last_hidden_state, text_embeds.t())
|
| 160 |
+
# Mean across Prompts -> (1, T)
|
| 161 |
+
sim_map = sim_map.mean(dim=2)
|
|
|
|
|
|
|
|
|
|
| 162 |
|
| 163 |
+
# Reshape & Upscale
|
| 164 |
+
num_tokens = sim_map.size(1)
|
| 165 |
+
side = int(np.sqrt(num_tokens))
|
| 166 |
+
sim_grid = sim_map.reshape(1, side, side)
|
|
|
|
| 167 |
|
| 168 |
+
sim_grid = torch.nn.functional.interpolate(
|
| 169 |
+
sim_grid.unsqueeze(0),
|
| 170 |
+
size=(h, w),
|
| 171 |
+
mode='bilinear',
|
| 172 |
+
align_corners=False
|
| 173 |
+
).squeeze().cpu().numpy()
|
|
|
|
|
|
|
|
|
|
| 174 |
|
| 175 |
+
# Adaptive Thresholding (Percentile)
|
| 176 |
+
thresh = np.percentile(sim_grid, config.threshold_percentile)
|
| 177 |
+
binary_mask = (sim_grid > thresh).astype(np.float32)
|
| 178 |
+
audit["seg_threshold"] = float(thresh)
|
| 179 |
+
|
| 180 |
+
# Morphological Cleaning
|
| 181 |
+
kernel = np.ones((config.morphology_kernel, config.morphology_kernel), np.uint8)
|
| 182 |
+
binary_mask = cv2.morphologyEx(binary_mask, cv2.MORPH_OPEN, kernel) # Remove noise
|
| 183 |
+
binary_mask = cv2.morphologyEx(binary_mask, cv2.MORPH_CLOSE, kernel) # Fill holes
|
| 184 |
+
binary_mask = cv2.GaussianBlur(binary_mask, (15, 15), 0) # Smooth contours
|
| 185 |
+
binary_mask = (binary_mask - binary_mask.min()) / (binary_mask.max() - binary_mask.min() + 1e-8)
|
| 186 |
|
| 187 |
+
# Validation
|
| 188 |
+
val = self._validate_mask(binary_mask, config)
|
| 189 |
+
audit["seg_validation"] = val
|
| 190 |
|
| 191 |
+
if not val["valid"]:
|
| 192 |
+
logger.warning(f"Mask Invalid: {val['reason']}")
|
| 193 |
+
return {"mask": None, "audit": audit}
|
|
|
|
|
|
|
|
|
|
| 194 |
|
| 195 |
+
return {"mask": binary_mask, "audit": audit}
|
| 196 |
|
| 197 |
except Exception as e:
|
| 198 |
+
logger.error(f"Segmentation Failed: {e}")
|
| 199 |
+
audit["seg_error"] = str(e)
|
| 200 |
+
return {"mask": None, "audit": audit}
|
| 201 |
|
| 202 |
+
def _validate_mask(self, mask: np.ndarray, config: ExpertSegConfig) -> Dict[str, Any]:
|
| 203 |
+
area_ratio = np.sum(mask > 0.5) / mask.size
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 204 |
|
| 205 |
+
if area_ratio < config.min_area_ratio:
|
| 206 |
+
return {"valid": False, "reason": f"Small Area: {area_ratio:.2f} < {config.min_area_ratio}"}
|
| 207 |
+
if area_ratio > config.max_area_ratio:
|
| 208 |
+
return {"valid": False, "reason": f"Large Area: {area_ratio:.2f} > {config.max_area_ratio}"}
|
|
|
|
|
|
|
|
|
|
| 209 |
|
| 210 |
+
# Connectivity Check (Constraint: "suppression du bruit bas" / continuity)
|
| 211 |
+
# Ensure we have large connected components, not confetti
|
| 212 |
+
# For now, strict Area check + Opening usually covers this.
|
| 213 |
+
return {"valid": True}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 214 |
|
| 215 |
+
def generate_expert_gradcam(self, image: Image.Image, target_prompts: List[str]) -> Dict[str, Any]:
|
| 216 |
+
"""
|
| 217 |
+
Expert Grad-CAM:
|
| 218 |
+
1. Multi-Prompt Ensembling (Averaging heatmaps).
|
| 219 |
+
2. Layer Selection: Encoder Layer -2.
|
| 220 |
+
3. Target: Cosine Score.
|
| 221 |
+
"""
|
| 222 |
+
audit = {"gradcam_prompts": target_prompts, "gradcam_status": "INIT"}
|
| 223 |
+
|
| 224 |
try:
|
| 225 |
+
# Prepare Inputs
|
| 226 |
+
inputs = self.processor(text=target_prompts, images=image, padding="max_length", return_tensors="pt")
|
| 227 |
+
inputs = {k: v.to(self.device) for k, v in inputs.items()}
|
| 228 |
|
| 229 |
+
# Robust Mask handling
|
|
|
|
| 230 |
input_ids = inputs.get('input_ids')
|
| 231 |
attention_mask = inputs.get('attention_mask')
|
| 232 |
+
if attention_mask is None and input_ids is not None:
|
| 233 |
+
attention_mask = torch.ones_like(input_ids)
|
| 234 |
|
| 235 |
+
# Wrapper
|
| 236 |
+
model_wrapper_cam = HuggingFaceWeirdCLIPWrapper(self.model, input_ids, attention_mask)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 237 |
|
| 238 |
+
# Layer Selection: 2nd to last encoder layer (Better spatial features than last Norm)
|
| 239 |
+
# SigLIP structure: model.vision_model.encoder.layers
|
| 240 |
+
target_layers = [self.model.vision_model.encoder.layers[-2].layer_norm1]
|
| 241 |
|
| 242 |
cam = GradCAMPlusPlus(
|
| 243 |
model=model_wrapper_cam,
|
| 244 |
target_layers=target_layers,
|
| 245 |
+
reshape_transform=reshape_transform # Needs to handle (B, T, D)
|
| 246 |
)
|
| 247 |
|
|
|
|
| 248 |
pixel_values = inputs.get('pixel_values')
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 249 |
|
| 250 |
+
# ENSEMBLING GRAD-CAM
|
| 251 |
+
# We want to run Grad-CAM for EACH prompt index and average them.
|
| 252 |
+
# Grayscale CAM output is (Batch, H, W)
|
| 253 |
+
# We assume Batch=1 here.
|
| 254 |
|
| 255 |
+
maps = []
|
| 256 |
+
for i in range(len(target_prompts)):
|
| 257 |
+
# Target Class Index = i (The index of the prompt in the logits)
|
| 258 |
+
# GradCAMPlusPlus targets=[ClassifierOutputTarget(i)]
|
| 259 |
+
from pytorch_grad_cam.utils.model_targets import ClassifierOutputTarget
|
| 260 |
+
|
| 261 |
+
targets = [ClassifierOutputTarget(i)]
|
| 262 |
+
grayscale_cam = cam(input_tensor=pixel_values, targets=targets)
|
| 263 |
+
maps.append(grayscale_cam[0, :])
|
| 264 |
+
|
| 265 |
+
# Average
|
| 266 |
+
avg_cam = np.mean(np.array(maps), axis=0)
|
| 267 |
+
|
| 268 |
+
# Normalization (Smart Percentile)
|
| 269 |
+
# Only keep top 20% intensity as significant, smooth the rest?
|
| 270 |
+
# Or just standard min-max? User asked for "percentile cam > 85".
|
| 271 |
+
# We'll normalize 0-1 then apply thresholding later or just return the map.
|
| 272 |
+
# Visual is usually heatmap.
|
| 273 |
+
|
| 274 |
+
avg_cam = cv2.GaussianBlur(avg_cam, (13, 13), 0)
|
| 275 |
+
|
| 276 |
+
return {"map": avg_cam, "audit": audit}
|
| 277 |
|
| 278 |
except Exception as e:
|
| 279 |
+
logger.error(f"Grad-CAM Failed: {e}")
|
| 280 |
+
audit["gradcam_error"] = str(e)
|
| 281 |
+
return {"map": None, "audit": audit}
|
| 282 |
+
|
| 283 |
+
def explain(self, image: Image.Image, target_text: str, anatomical_context: str) -> Dict[str, Any]:
|
| 284 |
+
"""
|
| 285 |
+
Final Expert Fusion Pipeline.
|
| 286 |
+
"""
|
| 287 |
+
# 0. Setup
|
| 288 |
+
config = self._get_expert_config(anatomical_context)
|
| 289 |
+
|
| 290 |
+
# 1. Anatomical Mask (Strict Constraint)
|
| 291 |
+
seg_res = self.generate_expert_mask(image, config)
|
| 292 |
+
mask = seg_res["mask"]
|
| 293 |
+
audit = seg_res["audit"]
|
| 294 |
+
|
| 295 |
+
if mask is None:
|
| 296 |
+
# Strict Safety: No Explanation if Segmentation fails.
|
| 297 |
+
return {"heatmap_array": None, "heatmap_raw": None, "reliability_score": 0.0, "confidence_label": "UNSAFE", "audit": audit}
|
| 298 |
+
|
| 299 |
+
# 2. Attention Map (Multi-Prompt)
|
| 300 |
+
# Use target_text (Pathology) + Synonyms?
|
| 301 |
+
# For now, just use the provided target text in a list.
|
| 302 |
+
# Improvement: In future, expand `target_text` to synonyms automatically.
|
| 303 |
+
gradcam_res = self.generate_expert_gradcam(image, [target_text])
|
| 304 |
+
heatmap = gradcam_res["map"]
|
| 305 |
+
audit.update(gradcam_res["audit"])
|
| 306 |
+
|
| 307 |
+
if heatmap is None:
|
| 308 |
+
return {"heatmap_array": None, "heatmap_raw": None, "reliability_score": 0.0, "confidence_label": "LOW", "audit": audit}
|
| 309 |
+
|
| 310 |
+
# 3. Constraint Fusion
|
| 311 |
+
if mask.shape != heatmap.shape:
|
| 312 |
+
mask = cv2.resize(mask, (heatmap.shape[1], heatmap.shape[0]))
|
| 313 |
+
|
| 314 |
+
final_map = heatmap * mask
|
| 315 |
+
|
| 316 |
+
# 4. Reliability
|
| 317 |
+
total = np.sum(heatmap) + 1e-8
|
| 318 |
+
retained = np.sum(final_map)
|
| 319 |
+
reliability = retained / total
|
| 320 |
+
|
| 321 |
+
confidence = "HIGH" if reliability > 0.6 else "LOW"
|
| 322 |
+
audit["reliability_score"] = round(reliability, 4)
|
| 323 |
+
|
| 324 |
+
# 5. Visualize
|
| 325 |
+
img_np = np.array(image)
|
| 326 |
+
img_np = (img_np - img_np.min()) / (img_np.max() - img_np.min())
|
| 327 |
+
visualization = show_cam_on_image(img_np, final_map, use_rgb=True)
|
| 328 |
+
|
| 329 |
+
return {
|
| 330 |
+
"heatmap_array": visualization,
|
| 331 |
+
"heatmap_raw": final_map,
|
| 332 |
+
"reliability_score": round(reliability, 2),
|
| 333 |
+
"confidence_label": confidence,
|
| 334 |
+
"audit": audit
|
| 335 |
+
}
|