First commit

README.md

@@ -1,13 +1,13 @@
 ---
-title: Skin Lesion Base
+title: Skin Lesion Base Demo
 emoji: 📊
 colorFrom: pink
 colorTo: purple
 sdk: streamlit
-sdk_version: 1.37.1
+sdk_version: 1.29.0
 app_file: app.py
 pinned: false
 license: apache-2.0
 ---
 
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference

app.py

@@ -0,0 +1,151 @@
+import pandas as pd
+import numpy as np
+import streamlit as st 
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib.backends.backend_agg import FigureCanvasAgg
+from PIL import Image
+from streamlit_image_select import image_select
+from tqdm import tqdm
+import os
+import shutil
+from PIL import Image
+import torch
+import matplotlib.pyplot as plt
+from datasets import load_dataset
+from transformers import AutoProcessor, AutoModelForMaskGeneration
+
+def show_mask(image, mask, ax=None):
+    fig, axes = plt.subplots()
+    axes.imshow(np.array(image))
+    color = np.array([30/255, 144/255, 255/255, 0.6])
+    h, w = mask.shape[-2:]
+    mask_image = mask.reshape(h, w, 1) * color.reshape(1, 1, -1)
+    axes.imshow(mask_image)
+    canvas = FigureCanvasAgg(fig)
+    canvas.draw()
+    pil_image = Image.frombytes('RGB', canvas.get_width_height(), canvas.tostring_rgb())
+    plt.close(fig) 
+    return pil_image 
+def get_bounding_box(ground_truth_map):
+  y_indices, x_indices = np.where(ground_truth_map > 0)
+  x_min, x_max = np.min(x_indices), np.max(x_indices)
+  y_min, y_max = np.min(y_indices), np.max(y_indices)
+  H, W = ground_truth_map.shape
+  x_min = max(0, x_min - np.random.randint(0, 20))
+  x_max = min(W, x_max + np.random.randint(0, 20))
+  y_min = max(0, y_min - np.random.randint(0, 20))
+  y_max = min(H, y_max + np.random.randint(0, 20))
+  bbox = [x_min, y_min, x_max, y_max]
+  return bbox
+def get_output(image,prompt):
+  inputs = processor(image,input_boxes=[[prompt]],return_tensors='pt').to(device)
+  model.eval()
+  with torch.no_grad():
+    outputs = model(**inputs,multimask_output=False)
+  output_proba = torch.sigmoid(outputs.pred_masks.squeeze(1))
+  output_proba = output_proba.cpu().numpy().squeeze()
+  output = (output_proba > 0.5).astype(np.uint8)
+  return output
+def generate_image(np_array):
+  return Image.fromarray((np_array*255).astype('uint8'),mode='L')
+def iou_calculation(result1, result2):
+  intersection = np.logical_and(result1, result2)
+  union = np.logical_or(result1, result2)
+  iou_score = np.sum(intersection) / np.sum(union)
+  iou_score = "{:.4f}".format(iou_score)
+  return float(iou_score)
+def calculate_pixel_accuracy(image1, image2):
+    if image1.size != image2.size or image1.mode != image2.mode:
+        image1 = image1.resize(image2.size, Image.BILINEAR)
+        if image1.mode != image2.mode:
+            image1 = image1.convert(image2.mode)
+    width, height = image1.size
+    total_pixels = width * height
+    image1 = image1.convert("RGB")
+    image2 = image2.convert("RGB")
+    pixels1 = image1.load()
+    pixels2 = image2.load()
+    num_correct_pixels = 0
+    for y in range(height):
+        for x in range(width):
+            if pixels1[x, y] == pixels2[x, y]:
+                num_correct_pixels += 1
+    accuracy = num_correct_pixels / total_pixels
+    return accuracy
+def calculate_f1_score(image1, image2):
+    if image1.size != image2.size or image1.mode != image2.mode:
+        image1 = image1.resize(image2.size, Image.BILINEAR)
+        if image1.mode != image2.mode:
+            image1 = image1.convert(image2.mode)
+    width, height = image1.size
+    image1 = image1.convert("L")
+    image2 = image2.convert("L")
+    np_image1 = np.array(image1)
+    np_image2 = np.array(image2)
+    np_image1_flat = np_image1.flatten()
+    np_image2_flat = np_image2.flatten()
+    true_positives = np.sum(np.logical_and(np_image1_flat == 255, np_image2_flat == 255))
+    false_positives = np.sum(np.logical_and(np_image1_flat != 255, np_image2_flat == 255))
+    false_negatives = np.sum(np.logical_and(np_image1_flat == 255, np_image2_flat != 255))
+    precision = true_positives / (true_positives + false_positives + 1e-7)
+    recall = true_positives / (true_positives + false_negatives + 1e-7)
+    f1_score = 2 * (precision * recall) / (precision + recall + 1e-7)
+    return f1_score
+def calculate_dice_coefficient(image1, image2):
+    if image1.size != image2.size or image1.mode != image2.mode:
+        image1 = image1.resize(image2.size, Image.BILINEAR)
+        if image1.mode != image2.mode:
+            image1 = image1.convert(image2.mode)
+    width, height = image1.size
+    image1 = image1.convert("L")
+    image2 = image2.convert("L")
+    np_image1 = np.array(image1)
+    np_image2 = np.array(image2)
+    np_image1_flat = np_image1.flatten()
+    np_image2_flat = np_image2.flatten()
+    true_positives = np.sum(np.logical_and(np_image1_flat == 255, np_image2_flat == 255))
+    false_positives = np.sum(np.logical_and(np_image1_flat != 255, np_image2_flat == 255))
+    false_negatives = np.sum(np.logical_and(np_image1_flat == 255, np_image2_flat != 255))
+    dice_coefficient = (2 * true_positives) / (2 * true_positives + false_positives + false_negatives)
+    return dice_coefficient
+device = "cuda" if torch.cuda.is_available() else "cpu"
+st.set_page_config(layout='wide')
+ds = load_dataset('yanranxiaoxi/skin-lesion-mask',split='train')
+s1 = ds[7]['image']
+s2 = ds[8]['image']
+s3 = ds[9]['image']
+s4 = ds[10]['image']
+s1_label = ds[7]['label']
+s2_label = ds[8]['label']
+s3_label = ds[9]['label']
+s4_label = ds[10]['label']
+image_arr = [s1,s2,s3,s4]
+label_arr = [s1_label,s2_label,s3_label,s4_label]
+img = image_select(
+    label="选择一个皮肤病变图像",
+    images=[
+        s1,s2,s3,s4
+    ],
+    captions=["例 1","例 2","例 3","例 4"],
+    return_value='index'
+)
+processor = AutoProcessor.from_pretrained('yanranxiaoxi/skin-lesion-base')
+model = AutoModelForMaskGeneration.from_pretrained('yanranxiaoxi/skin-lesion-focalloss-base-combined')
+model.to(device)
+p = get_bounding_box(np.array(label_arr[img])) 
+predicted_mask_array = get_output(image_arr[img],p)
+predicted_mask = generate_image(predicted_mask_array)
+result_image = show_mask(image_arr[img],predicted_mask_array)
+with st.container(): 
+    tab1, tab2 = st.tabs(['可视化','指标'])
+    with tab1: 
+        col1, col2 = st.columns(2) 
+        with col1: 
+            st.image(image_arr[img],caption='原始皮肤病变图像',use_column_width=True)
+        with col2:
+                st.image(result_image,caption='叠加标注遮罩区域',use_column_width=True)
+    with tab2: 
+            st.write(f'IOU 得分：{iou_calculation(label_arr[img],predicted_mask)}')
+            st.write(f'像素精确度：{calculate_pixel_accuracy(label_arr[img],predicted_mask)}')
+            st.write(f'骰子系数（DC）得分：{calculate_dice_coefficient(label_arr[img],predicted_mask)}')

requirements.txt

@@ -0,0 +1,9 @@
+streamlit-image-select
+streamlit 
+tqdm
+torch
+matplotlib
+Pillow
+transformers
+datasets
+accelerate