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Colony_Analyzer_AI2_HF.py

@@ -0,0 +1,305 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Mar 20 14:23:27 2025
+
+@author: mattc
+"""
+
+import os
+import cv2
+
+#this is the huggingface version
+def cut_img(img):
+    img_map = {}
+    name = x.split(".")[0]
+    i_num = img.shape[0]/512
+    j_num = img.shape[1]/512
+    count = 1
+    for i in range(int(i_num)):
+        for j in range(int(j_num)):
+            img_map[count] = img[(512*i):(512*(i+1)), (512*j):(512*(j+1))]
+            count +=1
+    return(img_map)
+    
+import numpy as np
+
+def stitch(img_map):
+    rows = [
+        np.hstack([img_map[1], img_map[2], img_map[3], img_map[4]]),  # First row (images 0 to 3)
+        np.hstack([img_map[5], img_map[6], img_map[7], img_map[8]]),  # Second row (images 4 to 7)
+        np.hstack([img_map[9], img_map[10], img_map[11], img_map[12]])  # Third row (images 8 to 11)
+    ]
+    # Stack rows vertically
+    return(np.vstack(rows))
+
+
+
+from PIL import Image
+
+
+
+import matplotlib.pyplot as plt
+
+def visualize_segmentation(mask, image=0):
+    plt.figure(figsize=(10, 5))
+
+    if(not np.isscalar(image)):
+        # Show original image if it is entered
+        plt.subplot(1, 2, 1)
+        plt.imshow(image)
+        plt.title("Original Image")
+        plt.axis("off")
+
+    # Show segmentation mask
+    plt.subplot(1, 2, 2)
+    plt.imshow(mask, cmap="gray")  # Show as grayscale
+    plt.title("Segmentation Mask")
+    plt.axis("off")
+
+    plt.show()
+
+import torch
+from transformers import SegformerForSemanticSegmentation
+# Load fine-tuned model
+model = SegformerForSemanticSegmentation.from_pretrained("ReyaLabColumbia/Segformer_Colony_Counter")
+device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+model.to(device)
+model.eval()  # Set to evaluation mode
+
+# Load image processor
+from transformers import SegformerForSemanticSegmentation, SegformerImageProcessor
+image_processor = SegformerImageProcessor.from_pretrained("nvidia/segformer-b3-finetuned-cityscapes-1024-1024")
+
+def preprocess_image(image):
+    image = image.convert("RGB")  # Open and convert to RGB
+    inputs = image_processor(image, return_tensors="pt")  # Preprocess for model
+    return image, inputs["pixel_values"]
+
+def postprocess_mask(logits):
+    mask = torch.argmax(logits, dim=1)  # Take argmax across the class dimension
+    return mask.squeeze().cpu().numpy()  # Convert to NumPy array
+
+
+def eval_img(image):
+    # Load and preprocess image
+    image, pixel_values = preprocess_image(image)
+    pixel_values = pixel_values.to(device)
+    with torch.no_grad():  # No gradient calculation for inference
+        outputs = model(pixel_values=pixel_values)  # Run model
+        logits = outputs.logits
+    # Convert logits to segmentation mask
+    segmentation_mask = postprocess_mask(logits)
+    #visualize_segmentation(segmentation_mask,image)
+    segmentation_mask = cv2.resize(segmentation_mask, (512, 512), interpolation=cv2.INTER_LINEAR_EXACT)
+    return(segmentation_mask)
+
+
+# for x in img_map:
+#     mask = eval_img(img_map[x])
+#     cv2.imwrite(img_map[x], mask)
+# del mask,x
+# p = stitch(img_map)
+# visualize_segmentation(p)
+
+# num_colony = np.count_nonzero(p == 1)  # Counts number of 1s
+# num_necrosis = np.count_nonzero(p == 2)
+
+# num_necrosis/num_colony
+
+def find_colonies(mask, size_cutoff, circ_cutoff):
+    binary_mask = np.where(mask == 1, 255, 0).astype(np.uint8)
+    contours, _ = cv2.findContours(binary_mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
+    contoursf = []
+    for x in contours:
+        area = cv2.contourArea(x)
+        if (area < size_cutoff):
+            continue
+        perimeter = cv2.arcLength(x, True)
+
+        # Avoid division by zero
+        if perimeter == 0:
+            continue
+        
+        # Calculate circularity
+        circularity = (4 * np.pi * area) / (perimeter ** 2)
+        if circularity >= circ_cutoff:
+            contoursf.append(x)
+    return(contoursf)
+
+def find_necrosis(mask):
+    binary_mask = np.where(mask == 2, 255, 0).astype(np.uint8)
+    contours, _ = cv2.findContours(binary_mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
+    return(contours)
+
+# contour_image = np.zeros_like(p)
+# contours =  find_necrosis(p)
+# cv2.drawContours(contour_image, contours, -1, (255), 2)
+# visualize_segmentation(contour_image)
+import pandas as pd
+def compute_centroid(contour):
+    M = cv2.moments(contour)
+    if M["m00"] == 0:  # Avoid division by zero
+        return None
+    cx = int(M["m10"] / M["m00"])
+    cy = int(M["m01"] / M["m00"])
+    return (cx, cy)
+
+
+def contours_overlap_using_mask(contour1, contour2, image_shape=(1536, 2048)):
+    """Check if two contours overlap using a bitwise AND mask."""
+    import numpy as np
+    import cv2
+    mask1 = np.zeros(image_shape, dtype=np.uint8)
+    mask2 = np.zeros(image_shape, dtype=np.uint8)
+
+
+    # Draw each contour as a white shape on its respective mask
+    cv2.drawContours(mask1, [contour1], -1, 255, thickness=cv2.FILLED)
+    cv2.drawContours(mask2, [contour2], -1, 255, thickness=cv2.FILLED)
+
+
+    # Compute bitwise AND to find overlapping regions
+    overlap = cv2.bitwise_and(mask1, mask2)
+    
+    return np.any(overlap)
+
+def analyze_colonies(mask, size_cutoff, circ_cutoff):
+    colonies = find_colonies(mask, size_cutoff, circ_cutoff)
+    necrosis = find_necrosis(mask)
+    
+    data = []
+    
+    for colony in colonies:
+        colony_area = cv2.contourArea(colony)
+        centroid = compute_centroid(colony)
+        if colony_area <= 50:
+            continue
+        
+        # Check if any necrosis contour is inside the colony
+        necrosis_area = 0
+        nec_list =[]
+        for nec in necrosis:
+            # Check if the first point of the necrosis contour is inside the colony
+            if contours_overlap_using_mask(colony, nec):
+                nec_area = cv2.contourArea(nec)
+                necrosis_area += nec_area
+                nec_list.append(nec)
+
+        data.append({
+            "colony_area": colony_area,
+            "necrosis_area": necrosis_area,
+            "centroid": centroid,
+            "percent_necrosis": necrosis_area/colony_area,
+            "contour": colony,
+            "nec_contours": nec_list
+        })
+
+    # Convert results to a DataFrame
+    df = pd.DataFrame(data)
+    df.index = range(1,len(df.index)+1)
+    return(df)
+
+
+def contour_overlap(contour1, contour2, centroid1, centroid2, area1, area2, centroid_thresh=25, area_thresh = 85, img_shape = (1536, 2048)):
+    """
+    Determines the overlap between two contours.
+    Returns:
+        0: No overlap
+        1: Overlap but does not meet strict conditions
+        2: Overlap >= 80% of the larger contour and centroids are close
+    """
+    # Create blank images
+    img1 = np.zeros(img_shape, dtype=np.uint8)
+    img2 = np.zeros(img_shape, dtype=np.uint8)
+    
+    # Draw filled contours
+    cv2.drawContours(img1, [contour1], -1, 255, thickness=cv2.FILLED)
+    cv2.drawContours(img2, [contour2], -1, 255, thickness=cv2.FILLED)
+    
+    # Compute overlap
+    intersection = cv2.bitwise_and(img1, img2)
+    intersection_area = np.count_nonzero(intersection)
+    
+    if intersection_area == 0:
+        return 0  # No overlap
+    
+    # Compute centroid distance
+    centroid_distance = float(np.sqrt(abs(centroid1[0]-centroid2[0])**2 + abs(centroid1[1]-centroid2[1])**2))
+    # Check percentage overlap relative to the larger contour
+    overlap_ratio = intersection_area/max(area1, area2)
+    
+    if overlap_ratio >= area_thresh and centroid_distance <= centroid_thresh:
+        if area1 > area2:
+            return(2)
+        else:
+            return(3)
+    else:
+        return 1  # Some overlap but not meeting strict criteria
+    
+def compare_frames(frame1, frame2):
+    for i in range(1, len(frame1)+1):
+        for j in range(1, len(frame2)+1):
+            temp = contour_overlap(frame1.loc[i, "contour"], frame2.loc[j, "contour"], frame1.loc[i, "centroid"], frame2.loc[j, "centroid"], frame1.loc[i, "colony_area"], frame2.loc[j, "colony_area"])
+            if temp ==2:
+                frame2.loc[j,"exclude"] = True
+            elif temp ==3:
+                frame1.loc[j, "exclude"] = True
+                break
+    frame1 = frame1[frame1["exclude"]==False]
+    frame2 = frame2[frame2["exclude"]==False]
+    df = pd.concat([frame1, frame2], axis=0)
+    df.index = range(1,len(df.index)+1)  
+    return(df)
+    
+def main(args):
+    min_size = args[1]
+    min_circ = args[2]
+    colonies = {}
+    img_map = cut_img(args[0])
+    for z in img_map:
+        mask = eval_img(img_map[z])
+        cv2.imwrite(img_map[z], mask)
+    del mask,z
+    p = stitch(img_map)
+    colonies = analyze_colonies(p, min_size, min_circ)
+    
+    img = args[0]
+    img = cv2.copyMakeBorder(img,top=0, bottom=10,left=0,right=10, borderType=cv2.BORDER_CONSTANT,  value=[255, 255, 255]) 
+    
+    
+    colonies = colonies.sort_values(by=["colony_area"], ascending=False)
+    colonies = colonies[colonies["colony_area"]>= min_size]
+    colonies.index = range(1,len(colonies.index)+1) 
+    
+    for i in range(len(colonies)): 
+        cv2.drawContours(img, [list(colonies["contour"])[i]], -1, (0, 255, 0), 2)
+        cv2.drawContours(img, list(colonies['nec_contours'])[i], -1, (0, 0, 255), 2)
+        coords = list(list(colonies["centroid"])[i])
+        if coords[0] > 1950:
+            #if a colony is too close to the right edge, makes the label move to left
+            coords[0] = 1950
+        cv2.putText(img, str(colonies.index[i]), tuple(coords), cv2.FONT_HERSHEY_SIMPLEX, 2, (0, 0, 0), 2)
+    img = cv2.copyMakeBorder(img,top=10, bottom=0,left=10,right=0, borderType=cv2.BORDER_CONSTANT,  value=[255, 255, 255]) 
+    colonies = colonies.drop('contour', axis=1)
+    colonies = colonies.drop('nec_contours', axis=1)
+    
+    colonies.insert(loc=0, column="Colony Number", value=[str(x) for x in range(1, len(colonies)+1)])
+    total_area_dark = sum(colonies['necrosis_area'])
+    total_area_light = sum(colonies['colony_area'])
+    ratio = total_area_dark/(abs(total_area_light)+1)
+
+    colonies.loc[len(colonies)+1] = ["Total", total_area_light, total_area_dark, None, ratio]
+    Parameters = pd.DataFrame({"Minimum colony size in pixels":[min_size], "Minimum colony circularity":[min_circ]})
+    with pd.ExcelWriter('results.xlsx') as writer:
+        colonies.to_excel(writer, sheet_name="Colony data", index=False)
+        Parameters.to_excel(writer, sheet_name="Parameters", index=False)
+    caption = np.ones((150, 2068, 3), dtype=np.uint8) * 255  # Multiply by 255 to make it white
+    cv2.putText(caption, "Total area necrotic: "+str(total_area_dark)+ ", Total area living: "+str(total_area_light)+", Ratio: "+str(ratio), (40, 40), cv2.FONT_HERSHEY_SIMPLEX, 1, (0, 0, 0), 3)
+
+
+
+    #cv2.imwrite('results.png', np.vstack((img, caption)))
+
+    return(np.vstack((img, caption)))
+

app.py

@@ -1,5 +1,5 @@
 import gradio as gr
-import Colony_Analyzer_AI2 as analyzer
+import Colony_Analyzer_AI2_HF as analyzer
 from PIL import Image
 import cv2
 import numpy as np
@@ -25,7 +25,7 @@ iface = gr.Interface(
         gr.Number(label="Minimum Colony Size (pixels)", value=1000),
         gr.Number(label="Minimum Circularity", value=0.25)
     ],
-    outputs=gr.Image(type="pil", label="Analyzed Image"),
+    outputs=[gr.Image(type="pil", label="Analyzed Image"), gr.File(label="Download results (Excel)")],
     title="AI Colony Analyzer",
     description="Upload an image to run the colony analysis."
 )