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README.md

@@ -4,8 +4,11 @@ Refactored pipeline combining all steps into a single class.
 
 ### Usage
 ```bash
-python pipeline.py
+python pipeline.py --pixel_ratio 2.54
 ```
+Arguments:
+- `--root_dir`: Root directory of the project (default: `.`)
+- `--pixel_ratio`: Pixel to micrometer ratio (default: `2.54`)
 
 ### Dependencies (Files)
 The pipeline requires the following files and directories to exist:

alopecia/count_result/density.json

@@ -1,47 +1,47 @@
 {
-  "test_step7_merged_foreground_230219_A200_4.jpg": {
+  "230219_A200_4.jpg": {
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-    "avg_thickness": 54.45850448608398,
-    "avg_length": 238.0105888366699
+  "IMG_02C458E4D7CE-9.jpg": {
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+    "avg_thickness": 53.351995121348985,
+    "avg_length": 255.6298835060813
   },
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-    "count": 14,
-    "avg_thickness": 51.27924510410854,
-    "avg_length": 175.85291181291853
+  "IMG_02C458E4D7CE-5.jpg": {
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+    "avg_thickness": 101.57754105788011,
+    "avg_length": 978.6184944739708
   },
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-    "count": 8,
-    "avg_thickness": 54.27548885345459,
-    "avg_length": 192.99601650238037
+  "IMG_02C458E4D7CE-4.jpg": {
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+    "avg_length": 239.54402330186633
   },
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-    "avg_length": 262.84897232055664
+  "IMG_02C458E4D7CE-6.jpg": {
+    "count": 11,
+    "avg_thickness": 78.9173205982555,
+    "avg_length": 223.1366219954057
   },
-  "test_step7_merged_foreground_IMG_02C458E4D7CE-4.jpeg": {
+  "230219_A191_1.jpg": {
     "count": 10,
-    "avg_thickness": 56.64297752380371,
-    "avg_length": 114.51317901611328
+    "avg_thickness": 60.46284160614014,
+    "avg_length": 235.29658203125
   },
-  "test_step7_merged_foreground_IMG_02C458E4D7CE-9.jpeg": {
-    "count": 11,
-    "avg_thickness": 57.8118123141202,
-    "avg_length": 165.69457591663706
+  "IMG_02C458E4D7CE-7.jpg": {
+    "count": 10,
+    "avg_thickness": 64.95570011138916,
+    "avg_length": 254.72664947509764
   },
-  "test_step7_merged_foreground_IMG_02C458E4D7CE-5.jpeg": {
-    "count": 11,
-    "avg_thickness": 47.383614626797765,
-    "avg_length": 199.2529823996804
+  "IMG_02C458E4D7CE-3.jpg": {
+    "count": 13,
+    "avg_thickness": 102.3023825425368,
+    "avg_length": 1053.9209119356597
   }
 }

alopecia/count_result/hair_count.csv

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+image_name,hair_count
+230219_A200_4.jpg,8
+230219_A191_1_test.jpg,10
+IMG_02C458E4D7CE-9.jpg,11
+IMG_02C458E4D7CE-5.jpg,13
+IMG_02C458E4D7CE-4.jpg,9
+IMG_02C458E4D7CE-6.jpg,11
+230219_A191_1.jpg,10
+IMG_02C458E4D7CE-7.jpg,10
+IMG_02C458E4D7CE-3.jpg,13

alopecia/thickness_result/230219_A191_1.npy

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datasets/train_bbox_points.json

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datasets/train_seg_points.json

@@ -1 +1 @@
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pipeline.py

@@ -1,4 +1,5 @@
 import os
+import argparse
 import csv
 import sys
 import glob
@@ -43,8 +44,9 @@ sys.path.append(os.path.join(os.getcwd(), 'alopecia'))
 # It's better to copy the helper functions to avoid running their main blocks if they are not guarded properly (they seem to be guarded).
 
 class ScalpPipeline:
-    def __init__(self, root_dir="."):
+    def __init__(self, root_dir=".", pixel_ratio=2.54):
         self.root_dir = os.path.abspath(root_dir)
+        self.pixel_ratio = pixel_ratio
         self.device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
         
         # Default Paths
@@ -526,7 +528,7 @@ class ScalpPipeline:
             for center_point, perp_slope in zip(center_points, perpendicular_slope):
                 intersection, dst = find_intersection_points2(center_point, perp_slope, re_copy, 200)
                 if dst != 0:
-                    thicknesses.append(dst)
+                    thicknesses.append(dst * self.pixel_ratio)
                 if intersection[0] != (-1, -1) and intersection[1] != (-1, -1):
                     cv2.line(filtered_image, 
                              (int(intersection[0][0]), int(intersection[0][1])), 
@@ -537,7 +539,7 @@ class ScalpPipeline:
 
             if len(thicknesses) > 0:
                 avg_thickness = np.mean(thicknesses)
-                cv2.putText(filtered_image, f"Avg thickness: {avg_thickness:.2f}px",
+                cv2.putText(filtered_image, f"Avg thickness: {avg_thickness:.2f} um",
                             (10, 30), cv2.FONT_HERSHEY_SIMPLEX, 0.8, (255, 0, 0), 2)
 
             save_img_path = os.path.join(save_path, f"{img_name}_vis.png")
@@ -780,5 +782,10 @@ class ScalpPipeline:
         print("🎉 Pipeline Completed Successfully!")
 
 if __name__ == "__main__":
-    pipeline = ScalpPipeline()
+    parser = argparse.ArgumentParser(description="ScalpVision Pipeline")
+    parser.add_argument("--root_dir", type=str, default=".", help="Root directory of the project")
+    parser.add_argument("--pixel_ratio", type=float, default=2.54, help="Pixel to micrometer ratio (default: 2.54)")
+    args = parser.parse_args()
+
+    pipeline = ScalpPipeline(root_dir=args.root_dir, pixel_ratio=args.pixel_ratio)
     pipeline.run_pipeline()