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feat(api): expose MedSAM chained call as named endpoint /medsam for remote invocation
594a845
import os
import sys
import gradio as gr
from PIL import Image
import torch
import numpy as np
import cv2
import time
import json
import traceback
# Simple timestamped logger
def log(msg: str) -> None:
print(f"[{time.strftime('%H:%M:%S')}] {msg}", flush=True)
# Writable cache directory for HF downloads
HF_CACHE_DIR = os.getenv("HF_CACHE_DIR", "/data/hf-cache")
try:
os.makedirs(HF_CACHE_DIR, exist_ok=True)
except Exception:
pass
# Add custom modules to path - try multiple possible locations
possible_paths = [
"./custom_models",
"../custom_models",
"./Dense-Captioning-Platform/custom_models"
]
for path in possible_paths:
if os.path.exists(path):
sys.path.insert(0, os.path.abspath(path))
break
# Add mmcv to path if it exists
if os.path.exists('./mmcv'):
sys.path.insert(0, os.path.abspath('./mmcv'))
print("βœ… Added local mmcv to path")
# Import and register custom modules
try:
from custom_models import register
print("βœ… Custom modules registered successfully")
except Exception as e:
print(f"⚠️ Warning: Could not register custom modules: {e}")
# ----------------------
# Optional MedSAM integration
# ----------------------
class MedSAMIntegrator:
def __init__(self):
self.device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
self.medsam_model = None
self.current_image = None
self.current_image_path = None
self.embedding = None
self._load_medsam_model()
def _ensure_segment_anything(self):
try:
import segment_anything # noqa: F401
return True
except Exception as e:
print(f"⚠ segment_anything not available: {e}. Install it in Dockerfile to enable MedSAM.")
return False
def _load_medsam_model(self):
try:
# Ensure library is present
if not self._ensure_segment_anything():
print("MedSAM features disabled (segment_anything not available)")
return
from segment_anything import sam_model_registry as _reg
import torch as _torch
# Preferred local path in HF cache
medsam_ckpt_path = os.path.join(HF_CACHE_DIR, "medsam_vit_b.pth")
# If not present, fetch from HF Hub using provided repo or default
if not os.path.exists(medsam_ckpt_path):
try:
from huggingface_hub import hf_hub_download, list_repo_files
repo_id = os.environ.get("HF_MEDSAM_REPO", "Aniketg6/Fine-Tuned-MedSAM")
print(f"πŸ”„ Trying to download MedSAM checkpoint from {repo_id} ...")
files = list_repo_files(repo_id)
candidate = None
for f in files:
lf = f.lower()
if lf.endswith(".pth") or lf.endswith(".pt"):
candidate = f
break
if candidate is None:
candidate = "medsam_vit_b.pth"
ckpt_path = hf_hub_download(repo_id=repo_id, filename=candidate, cache_dir=HF_CACHE_DIR)
medsam_ckpt_path = ckpt_path
print(f"βœ… Downloaded MedSAM checkpoint: {medsam_ckpt_path}")
except Exception as dl_err:
print(f"⚠ Could not fetch MedSAM checkpoint from HF Hub: {dl_err}")
print("MedSAM features disabled (no checkpoint)")
return
# Load checkpoint
checkpoint = _torch.load(medsam_ckpt_path, map_location='cpu')
self.medsam_model = _reg["vit_b"](checkpoint=None)
self.medsam_model.load_state_dict(checkpoint)
self.medsam_model.to(self.device)
self.medsam_model.eval()
print("βœ“ MedSAM model loaded successfully")
except Exception as e:
print(f"⚠ MedSAM model not available: {e}. MedSAM features disabled.")
def is_available(self):
return self.medsam_model is not None
def load_image(self, image_path, precomputed_embedding=None):
try:
from skimage import transform, io # local import to avoid hard dep if unused
img_np = io.imread(image_path)
if len(img_np.shape) == 2:
img_3c = np.repeat(img_np[:, :, None], 3, axis=-1)
else:
img_3c = img_np
self.current_image = img_3c
self.current_image_path = image_path
if precomputed_embedding is not None:
if not self.set_precomputed_embedding(precomputed_embedding):
self.get_embeddings()
else:
self.get_embeddings()
return True
except Exception as e:
print(f"Error loading image for MedSAM: {e}")
return False
@torch.no_grad()
def get_embeddings(self):
if self.current_image is None or self.medsam_model is None:
return None
from skimage import transform
img_1024 = transform.resize(
self.current_image, (1024, 1024), order=3, preserve_range=True, anti_aliasing=True
).astype(np.uint8)
img_1024 = (img_1024 - img_1024.min()) / np.clip(img_1024.max() - img_1024.min(), a_min=1e-8, a_max=None)
img_1024_tensor = (
torch.tensor(img_1024).float().permute(2, 0, 1).unsqueeze(0).to(self.device)
)
self.embedding = self.medsam_model.image_encoder(img_1024_tensor)
return self.embedding
def set_precomputed_embedding(self, embedding_array):
try:
if isinstance(embedding_array, np.ndarray):
embedding_tensor = torch.tensor(embedding_array).to(self.device)
self.embedding = embedding_tensor
return True
return False
except Exception as e:
print(f"Error setting precomputed embedding: {e}")
return False
@torch.no_grad()
def medsam_inference(self, box_1024, height, width):
if self.embedding is None or self.medsam_model is None:
return None
box_torch = torch.as_tensor(box_1024, dtype=torch.float, device=self.embedding.device)
if len(box_torch.shape) == 2:
box_torch = box_torch[:, None, :]
sparse_embeddings, dense_embeddings = self.medsam_model.prompt_encoder(
points=None, boxes=box_torch, masks=None,
)
low_res_logits, _ = self.medsam_model.mask_decoder(
image_embeddings=self.embedding,
image_pe=self.medsam_model.prompt_encoder.get_dense_pe(),
sparse_prompt_embeddings=sparse_embeddings,
dense_prompt_embeddings=dense_embeddings,
multimask_output=False,
)
low_res_pred = torch.sigmoid(low_res_logits)
low_res_pred = torch.nn.functional.interpolate(
low_res_pred, size=(height, width), mode="bilinear", align_corners=False,
)
low_res_pred = low_res_pred.squeeze().cpu().numpy()
medsam_seg = (low_res_pred > 0.5).astype(np.uint8)
return medsam_seg
def segment_with_box(self, bbox):
if self.embedding is None or self.current_image is None:
return None
try:
H, W, _ = self.current_image.shape
x1, y1, x2, y2 = bbox
x1 = max(0, min(int(x1), W - 1))
y1 = max(0, min(int(y1), H - 1))
x2 = max(0, min(int(x2), W - 1))
y2 = max(0, min(int(y2), H - 1))
if x2 <= x1:
x2 = min(x1 + 10, W - 1)
if y2 <= y1:
y2 = min(y1 + 10, H - 1)
box_np = np.array([[x1, y1, x2, y2]], dtype=float)
box_1024 = box_np / np.array([W, H, W, H]) * 1024.0
medsam_mask = self.medsam_inference(box_1024, H, W)
if medsam_mask is not None:
return {"mask": medsam_mask, "confidence": 1.0, "method": "medsam_box"}
return None
except Exception as e:
print(f"Error in MedSAM box-based segmentation: {e}")
return None
# Single global instance
_medsam = MedSAMIntegrator()
def _extract_bboxes_from_mmdet_result(det_result):
"""Extract Nx4 xyxy bboxes from various MMDet result formats."""
boxes = []
try:
# MMDet 3.x: list of DetDataSample
if isinstance(det_result, list) and len(det_result) > 0:
sample = det_result[0]
if hasattr(sample, 'pred_instances'):
inst = sample.pred_instances
if hasattr(inst, 'bboxes'):
b = inst.bboxes
# mmengine structures may use .tensor for boxes
if hasattr(b, 'tensor'):
b = b.tensor
boxes = b.detach().cpu().numpy().tolist()
# Single DetDataSample
elif hasattr(det_result, 'pred_instances'):
inst = det_result.pred_instances
if hasattr(inst, 'bboxes'):
b = inst.bboxes
if hasattr(b, 'tensor'):
b = b.tensor
boxes = b.detach().cpu().numpy().tolist()
# MMDet 2.x: tuple of (bbox_result, segm_result)
elif isinstance(det_result, tuple) and len(det_result) >= 1:
bbox_result = det_result[0]
# bbox_result is list per class, each Nx5 [x1,y1,x2,y2,score]
if isinstance(bbox_result, (list, tuple)):
for arr in bbox_result:
try:
arr_np = np.array(arr)
if arr_np.ndim == 2 and arr_np.shape[1] >= 4:
boxes.extend(arr_np[:, :4].tolist())
except Exception:
continue
except Exception as e:
print(f"Failed to parse MMDet result for boxes: {e}")
return boxes
def _overlay_masks_on_image(image_pil, mask_list, alpha=0.4):
"""Overlay binary masks on an image with random colors."""
if image_pil is None or not mask_list:
return image_pil
img = np.array(image_pil.convert('RGB'))
overlay = img.copy()
for idx, m in enumerate(mask_list):
if m is None or 'mask' not in m or m['mask'] is None:
continue
mask = m['mask'].astype(bool)
color = np.random.RandomState(seed=idx + 1234).randint(0, 255, size=3)
overlay[mask] = (0.5 * overlay[mask] + 0.5 * color).astype(np.uint8)
blended = (alpha * overlay + (1 - alpha) * img).astype(np.uint8)
return Image.fromarray(blended)
def _mask_to_polygons(mask: np.ndarray):
"""Convert a binary mask (H,W) to a list of polygons ([[x,y], ...]) using OpenCV contours."""
try:
mask_u8 = (mask.astype(np.uint8) * 255)
contours, _ = cv2.findContours(mask_u8, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
polygons = []
for cnt in contours:
if cnt is None or len(cnt) < 3:
continue
# Simplify contour slightly
epsilon = 0.002 * cv2.arcLength(cnt, True)
approx = cv2.approxPolyDP(cnt, epsilon, True)
poly = approx.reshape(-1, 2).tolist()
polygons.append(poly)
return polygons
except Exception as e:
print(f"_mask_to_polygons failed: {e}")
return []
def _find_largest_foreground_bbox(pil_img: Image.Image):
"""Heuristic: find largest foreground region bbox via Otsu threshold on grayscale.
Returns [x1, y1, x2, y2] or full-image bbox if none found."""
try:
img = np.array(pil_img.convert('RGB'))
gray = cv2.cvtColor(img, cv2.COLOR_RGB2GRAY)
# Otsu threshold (invert if needed by checking mean)
_, th = cv2.threshold(gray, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)
# Assume foreground is darker; invert if threshold yields background as white majority
if th.mean() > 127:
th = 255 - th
# Morph close to connect regions
kernel = np.ones((5, 5), np.uint8)
th = cv2.morphologyEx(th, cv2.MORPH_CLOSE, kernel, iterations=2)
contours, _ = cv2.findContours(th, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
if not contours:
W, H = pil_img.size
return [0, 0, W - 1, H - 1]
# Largest contour by area
cnt = max(contours, key=cv2.contourArea)
x, y, w, h = cv2.boundingRect(cnt)
# Pad a little
pad = int(0.02 * max(w, h))
x1 = max(0, x - pad)
y1 = max(0, y - pad)
x2 = min(img.shape[1] - 1, x + w + pad)
y2 = min(img.shape[0] - 1, y + h + pad)
return [x1, y1, x2, y2]
except Exception as e:
print(f"_find_largest_foreground_bbox failed: {e}")
W, H = pil_img.size
return [0, 0, W - 1, H - 1]
def _find_topk_foreground_bboxes(pil_img: Image.Image, max_regions: int = 20, min_area: int = 100):
"""Find top-K foreground bboxes via Otsu threshold + morphology. Returns list of [x1,y1,x2,y2]."""
try:
img = np.array(pil_img.convert('RGB'))
gray = cv2.cvtColor(img, cv2.COLOR_RGB2GRAY)
_, th = cv2.threshold(gray, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)
if th.mean() > 127:
th = 255 - th
kernel = np.ones((3, 3), np.uint8)
th = cv2.morphologyEx(th, cv2.MORPH_OPEN, kernel, iterations=1)
th = cv2.morphologyEx(th, cv2.MORPH_CLOSE, kernel, iterations=2)
contours, _ = cv2.findContours(th, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
if not contours:
return []
contours = sorted(contours, key=cv2.contourArea, reverse=True)
bboxes = []
H, W = img.shape[:2]
for cnt in contours:
area = cv2.contourArea(cnt)
if area < min_area:
continue
x, y, w, h = cv2.boundingRect(cnt)
# Filter very thin shapes
if w < 5 or h < 5:
continue
pad = int(0.01 * max(w, h))
x1 = max(0, x - pad)
y1 = max(0, y - pad)
x2 = min(W - 1, x + w + pad)
y2 = min(H - 1, y + h + pad)
bboxes.append([x1, y1, x2, y2])
if len(bboxes) >= max_regions:
break
return bboxes
except Exception as e:
print(f"_find_topk_foreground_bboxes failed: {e}")
return []
# Try to import mmdet for inference
try:
from mmdet.apis import init_detector, inference_detector
MM_DET_AVAILABLE = True
print("βœ… MMDetection available for inference")
except ImportError as e:
print(f"⚠️ MMDetection import failed: {e}")
print("❌ MMDetection not available - install in Dockerfile")
MM_DET_AVAILABLE = False
# === Chart Type Classification (DocFigure) ===
print("πŸ”„ Loading Chart Classification Model...")
# Chart type labels from DocFigure dataset (28 classes)
CHART_TYPE_LABELS = [
'Line graph', 'Natural image', 'Table', '3D object', 'Bar plot', 'Scatter plot',
'Medical image', 'Sketch', 'Geographic map', 'Flow chart', 'Heat map', 'Mask',
'Block diagram', 'Venn diagram', 'Confusion matrix', 'Histogram', 'Box plot',
'Vector plot', 'Pie chart', 'Surface plot', 'Algorithm', 'Contour plot',
'Tree diagram', 'Bubble chart', 'Polar plot', 'Area chart', 'Pareto chart', 'Radar chart'
]
try:
# Load the chart_type.pth model file from Hugging Face Hub
from huggingface_hub import hf_hub_download
from torchvision import transforms
print("πŸ”„ Downloading chart_type.pth from Hugging Face Hub...")
chart_type_path = hf_hub_download(
repo_id="hanszhu/ChartTypeNet-DocFigure",
filename="chart_type.pth",
cache_dir=HF_CACHE_DIR
)
print(f"βœ… Downloaded to: {chart_type_path}")
# Load the PyTorch model
loaded_data = torch.load(chart_type_path, map_location='cpu')
# Check if it's a state dict or a complete model
if isinstance(loaded_data, dict):
# Check if it's a checkpoint with model_state_dict
if "model_state_dict" in loaded_data:
print("πŸ”„ Loading checkpoint, extracting model_state_dict...")
state_dict = loaded_data["model_state_dict"]
else:
# It's a direct state dict
print("πŸ”„ Loading state dict, creating model architecture...")
state_dict = loaded_data
# Strip "backbone." prefix from state dict keys if present
cleaned_state_dict = {}
for key, value in state_dict.items():
if key.startswith("backbone."):
# Remove "backbone." prefix
new_key = key[9:]
cleaned_state_dict[new_key] = value
else:
cleaned_state_dict[key] = value
print(f"πŸ”„ Cleaned state dict: {len(cleaned_state_dict)} keys")
# Create the model architecture
from torchvision.models import resnet50
chart_type_model = resnet50(pretrained=False)
# Create the correct classifier structure to match the state dict
import torch.nn as nn
in_features = chart_type_model.fc.in_features
dropout = nn.Dropout(0.5)
chart_type_model.fc = nn.Sequential(
nn.Linear(in_features, 512),
nn.ReLU(inplace=True),
dropout,
nn.Linear(512, 28)
)
# Load the cleaned state dict
chart_type_model.load_state_dict(cleaned_state_dict)
else:
# It's a complete model
chart_type_model = loaded_data
chart_type_model.eval()
# Create a simple processor for the model
chart_type_processor = transforms.Compose([
transforms.Resize((224, 224)),
transforms.ToTensor(),
transforms.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225])
])
CHART_TYPE_AVAILABLE = True
print("βœ… Chart classification model loaded")
except Exception as e:
print(f"⚠️ Failed to load chart classification model: {e}")
import traceback
print("πŸ” Full traceback:")
traceback.print_exc()
CHART_TYPE_AVAILABLE = False
# === Chart Element Detection (Cascade R-CNN) ===
element_model = None
datapoint_model = None
print(f"πŸ” MM_DET_AVAILABLE: {MM_DET_AVAILABLE}")
if MM_DET_AVAILABLE:
# Check if config files exist
element_config = "models/chart_elementnet_swin.py"
point_config = "models/chart_pointnet_swin.py"
print(f"πŸ” Checking config files...")
print(f"πŸ” Element config exists: {os.path.exists(element_config)}")
print(f"πŸ” Point config exists: {os.path.exists(point_config)}")
print(f"πŸ” Current working directory: {os.getcwd()}")
print(f"πŸ” Files in models directory: {os.listdir('models') if os.path.exists('models') else 'models directory not found'}")
try:
print("πŸ”„ Loading ChartElementNet-MultiClass (Cascade R-CNN)...")
print(f"πŸ” Config path: {element_config}")
print(f"πŸ” Weights path: hanszhu/ChartElementNet-MultiClass")
print(f"πŸ” About to call init_detector...")
# Download model from Hugging Face Hub
from huggingface_hub import hf_hub_download
print("πŸ”„ Downloading ChartElementNet weights from Hugging Face Hub...")
element_checkpoint = hf_hub_download(
repo_id="hanszhu/ChartElementNet-MultiClass",
filename="chart_label+.pth",
cache_dir=HF_CACHE_DIR
)
print(f"βœ… Downloaded to: {element_checkpoint}")
# Use local config with downloaded weights
element_model = init_detector(element_config, element_checkpoint, device="cpu")
print("βœ… ChartElementNet loaded successfully")
except Exception as e:
print(f"❌ Failed to load ChartElementNet: {e}")
print(f"πŸ” Error type: {type(e).__name__}")
print(f"πŸ” Error details: {str(e)}")
import traceback
print("πŸ” Full traceback:")
traceback.print_exc()
try:
print("πŸ”„ Loading ChartPointNet-InstanceSeg (Mask R-CNN)...")
print(f"πŸ” Config path: {point_config}")
print(f"πŸ” Weights path: hanszhu/ChartPointNet-InstanceSeg")
print(f"πŸ” About to call init_detector...")
# Download model from Hugging Face Hub
print("πŸ”„ Downloading ChartPointNet weights from Hugging Face Hub...")
datapoint_checkpoint = hf_hub_download(
repo_id="hanszhu/ChartPointNet-InstanceSeg",
filename="chart_datapoint.pth",
cache_dir=HF_CACHE_DIR
)
print(f"βœ… Downloaded to: {datapoint_checkpoint}")
# Use local config with downloaded weights
datapoint_model = init_detector(point_config, datapoint_checkpoint, device="cpu")
print("βœ… ChartPointNet loaded successfully")
except Exception as e:
print(f"❌ Failed to load ChartPointNet: {e}")
print(f"πŸ” Error type: {type(e).__name__}")
print(f"πŸ” Error details: {str(e)}")
import traceback
print("πŸ” Full traceback:")
traceback.print_exc()
else:
print("❌ MMDetection not available - cannot load custom models")
print(f"πŸ” MM_DET_AVAILABLE was False")
print(f"πŸ” Final model status:")
print(f"πŸ” element_model: {element_model is not None}")
print(f"πŸ” datapoint_model: {datapoint_model is not None}")
# === Main prediction function ===
def analyze(image):
try:
log("analyze: start")
start_time = time.time()
# Handle filepath input
if isinstance(image, str):
image = Image.open(image).convert("RGB")
elif image is None:
return {"error": "No image provided"}
if not isinstance(image, Image.Image):
return {"error": "Invalid image format"}
result = {
"chart_type_id": "Model not available",
"chart_type_label": "Model not available",
"element_result": "MMDetection models not available",
"datapoint_result": "MMDetection models not available",
"status": "Basic chart classification only",
"processing_time": 0.0,
"medsam": {"available": False}
}
# Chart Type Classification
if CHART_TYPE_AVAILABLE:
try:
processed_image = chart_type_processor(image).unsqueeze(0)
with torch.no_grad():
outputs = chart_type_model(processed_image)
logits = outputs if isinstance(outputs, torch.Tensor) else getattr(outputs, 'logits', outputs)
predicted_class = logits.argmax(dim=-1).item()
result["chart_type_id"] = predicted_class
result["chart_type_label"] = CHART_TYPE_LABELS[predicted_class] if 0 <= predicted_class < len(CHART_TYPE_LABELS) else f"Unknown ({predicted_class})"
result["status"] = "Chart classification completed"
log(f"analyze: chart_type={result['chart_type_label']} ({result['chart_type_id']})")
except Exception:
log("analyze: chart classification error")
traceback.print_exc()
is_medical = str(result.get("chart_type_label", "")).strip().lower() == "medical image"
# Element Detection (skip for medical images)
if element_model is not None and not is_medical:
try:
np_img = np.array(image.convert("RGB"))[:, :, ::-1]
element_result = inference_detector(element_model, np_img)
if isinstance(element_result, tuple):
bbox_result, segm_result = element_result
element_data = {
"bboxes": bbox_result.tolist() if hasattr(bbox_result, 'tolist') else str(bbox_result),
"segments": segm_result.tolist() if hasattr(segm_result, 'tolist') else str(segm_result)
}
else:
element_data = str(element_result)
result["element_result"] = element_data
result["status"] = "Chart classification + element detection completed"
log("analyze: element detection done")
except Exception:
log("analyze: element detection error")
traceback.print_exc()
elif is_medical:
result["element_result"] = "skipped for medical image"
# Datapoint Segmentation (skip for medical images)
if datapoint_model is not None and not is_medical:
try:
np_img = np.array(image.convert("RGB"))[:, :, ::-1]
datapoint_result = inference_detector(datapoint_model, np_img)
if isinstance(datapoint_result, tuple):
bbox_result, segm_result = datapoint_result
datapoint_data = {
"bboxes": bbox_result.tolist() if hasattr(bbox_result, 'tolist') else str(bbox_result),
"segments": segm_result.tolist() if hasattr(segm_result, 'tolist') else str(segm_result)
}
else:
datapoint_data = str(datapoint_result)
result["datapoint_result"] = datapoint_data
result["status"] = "Full analysis completed"
log("analyze: datapoint segmentation done")
except Exception:
log("analyze: datapoint segmentation error")
traceback.print_exc()
elif is_medical:
result["datapoint_result"] = "skipped for medical image"
# MedSAM availability info
try:
label_lower = str(result.get("chart_type_label", "")).strip().lower()
if label_lower == "medical image":
if _medsam.is_available():
result["medsam"] = {"available": True}
else:
result["medsam"] = {"available": False, "reason": "segment_anything or checkpoint missing"}
except Exception:
log("analyze: medsam availability annotation error")
traceback.print_exc()
result["processing_time"] = round(time.time() - start_time, 3)
log(f"analyze: end in {result['processing_time']}s")
return result
except Exception:
log("analyze: fatal error")
traceback.print_exc()
return {"error": "Internal error in analyze"}
def analyze_with_medsam(base_result, image, include_raw_masks=False, bboxes_json="", points_json=""):
try:
log("analyze_with_medsam: start")
if not isinstance(base_result, dict):
return base_result, None
label = str(base_result.get("chart_type_label", "")).strip().lower()
if label != "medical image" or not _medsam.is_available():
log("analyze_with_medsam: skip (non-medical or MedSAM unavailable)")
return base_result, None
pil_img = Image.open(image).convert("RGB") if isinstance(image, str) else image
if pil_img is None:
return base_result, None
img_path = image if isinstance(image, str) else None
if img_path is None:
tmp_path = "./_tmp_input_image.png"
pil_img.save(tmp_path)
img_path = tmp_path
_medsam.load_image(img_path)
# Parse prompts
parsed_bboxes = []
parsed_points = []
try:
if bboxes_json:
parsed_bboxes = json.loads(bboxes_json)
if points_json:
parsed_points = json.loads(points_json)
except Exception:
log("analyze_with_medsam: failed to parse prompts JSON")
# If no prompts provided, skip (follow original behavior)
if not parsed_bboxes and not parsed_points:
log("analyze_with_medsam: no prompts provided; skipping segmentation")
return base_result, None
segmentations = []
masks_for_overlay = []
# Run MedSAM for provided boxes
for bbox in parsed_bboxes:
if not isinstance(bbox, (list, tuple)) or len(bbox) != 4:
continue
m = _medsam.segment_with_box(bbox)
if m is None or not isinstance(m.get('mask'), np.ndarray):
continue
mask_np = m['mask'].astype(np.uint8)
seg_entry = {
"confidence": float(m.get('confidence', 1.0)),
"method": m.get("method", "medsam_box"),
"polygons": _mask_to_polygons(mask_np)
}
if include_raw_masks:
seg_entry["mask"] = mask_np.tolist()
segmentations.append(seg_entry)
masks_for_overlay.append(m)
# Run MedSAM for provided points by converting to bbox
for item in parsed_points:
try:
# Expect item like {"points": [[x,y],...]} or [ [x,y], ... ]
pts = item.get("points") if isinstance(item, dict) else item
pts_np = np.array(pts)
x_min, y_min = pts_np.min(axis=0)
x_max, y_max = pts_np.max(axis=0)
pad = 20
H, W = _medsam.current_image.shape[:2]
bbox = [max(0, x_min - pad), max(0, y_min - pad), min(W - 1, x_max + pad), min(H - 1, y_max + pad)]
m = _medsam.segment_with_box(bbox)
if m is None or not isinstance(m.get('mask'), np.ndarray):
continue
mask_np = m['mask'].astype(np.uint8)
seg_entry = {
"confidence": float(m.get('confidence', 1.0)),
"method": m.get("method", "medsam_points_box"),
"polygons": _mask_to_polygons(mask_np)
}
if include_raw_masks:
seg_entry["mask"] = mask_np.tolist()
segmentations.append(seg_entry)
masks_for_overlay.append(m)
except Exception:
continue
W, H = pil_img.size
base_result["medsam"] = {
"available": True,
"height": H,
"width": W,
"segmentations": segmentations,
"num_segments": len(segmentations)
}
log(f"analyze_with_medsam: segments={len(segmentations)}")
overlay_img = _overlay_masks_on_image(pil_img, masks_for_overlay) if masks_for_overlay else None
log("analyze_with_medsam: end")
return base_result, overlay_img
except Exception:
log("analyze_with_medsam: fatal error")
traceback.print_exc()
return base_result, None
# === Gradio UI with API enhancements ===
# Create Blocks interface with explicit API name for stable API surface
with gr.Blocks(
title="πŸ“Š Dense Captioning Platform"
) as demo:
gr.Markdown("# πŸ“Š Dense Captioning Platform")
gr.Markdown("""
**Comprehensive Chart Analysis API**
Upload a chart image to get:
- **Chart Type Classification**: Identifies the type of chart (line, bar, scatter, etc.)
- **Element Detection**: Detects chart elements like titles, axes, legends, data points
- **Data Point Segmentation**: Segments individual data points and regions
Masks will be automatically generated for medical images when supported.
**API Usage:**
```python
from gradio_client import Client, handle_file
client = Client("hanszhu/Dense-Captioning-Platform")
result = client.predict(
image=handle_file('path/to/your/chart.png'),
api_name="/predict"
)
print(result)
```
**Supported Chart Types:** Line graphs, Bar plots, Scatter plots, Pie charts, Heat maps, and 23+ more
""")
with gr.Row():
with gr.Column():
# Input
image_input = gr.Image(
type="filepath", # βœ… REQUIRED for gradio_client
label="Upload Chart Image",
height=400,
elem_id="image-input"
)
include_raw_masks_cb = gr.Checkbox(value=False, visible=False, elem_id="include-raw-masks")
bboxes_tb = gr.Textbox(value="", visible=False, elem_id="bboxes-json")
points_tb = gr.Textbox(value="", visible=False, elem_id="points-json")
# Analyze button (single)
analyze_btn = gr.Button(
"πŸ” Analyze",
variant="primary",
size="lg",
elem_id="analyze-btn"
)
with gr.Column():
# Output JSON
result_output = gr.JSON(
label="Analysis Results",
height=400,
elem_id="result-output"
)
# Overlay image output (populated only for medical images)
overlay_output = gr.Image(
label="MedSAM Overlay (Medical images)",
height=400,
elem_id="overlay-output"
)
# Single API endpoint for JSON
analyze_event = analyze_btn.click(
fn=analyze,
inputs=image_input,
outputs=result_output,
api_name="/predict" # βœ… Standard API name that gradio_client expects
)
# MedSAM step (prompt-only). If no prompts, it will skip
analyze_event.then(
fn=analyze_with_medsam,
inputs=[result_output, image_input, include_raw_masks_cb, bboxes_tb, points_tb],
outputs=[result_output, overlay_output],
api_name="/medsam"
)
# Add some examples
gr.Examples(
examples=[
["https://raw.githubusercontent.com/gradio-app/gradio/main/test/test_files/bus.png"]
],
inputs=image_input,
label="Try with this example"
)
# Launch with API-friendly settings
if __name__ == "__main__":
launch_kwargs = {
"server_name": "0.0.0.0", # Allow external connections
"server_port": 7860,
"share": False, # Set to True if you want a public link
"show_error": True, # Show detailed errors for debugging
"quiet": False, # Show startup messages
"show_api": True, # Enable API documentation
"ssr_mode": False # Disable experimental SSR in Docker env
}
# Enable queue for gradio_client compatibility
demo.queue().launch(**launch_kwargs) # βœ… required for gradio_client to work