Final validation - 20 patients

validation/validation_report.txt

@@ -6,9 +6,9 @@
   Method   : HU threshold (-400 HU) + morphology + flood-fill
   Dataset  : Yousra0x0/validation_20
   Patients : 20
-  Valid    : 10
-  Failing  : 1 (Dice < 0.92)
-  Date     : 2026-05-05 11:55
+  Valid    : 20
+  Failing  : 8 (Dice < 0.95)
+  Date     : 2026-05-05 12:43
 
   HYPERPARAMETERS
 ------------------------------------------------------------
@@ -22,29 +22,27 @@
 
   GLOBAL METRICS
 ------------------------------------------------------------
-  dice           : mean=0.9676  std=0.0216  min=0.9090  max=0.9833  CI95=[0.9535, 0.9817]  n=10
-  iou            : mean=0.9380  std=0.0389  min=0.8331  max=0.9672  CI95=[0.9126, 0.9634]  n=10
-  f1             : mean=0.9676  std=0.0216  min=0.9090  max=0.9833  CI95=[0.9535, 0.9817]  n=10
-  precision      : mean=0.9709  std=0.0039  min=0.9649  max=0.9773  CI95=[0.9684, 0.9735]  n=10
-  recall         : mean=0.9651  std=0.0395  min=0.8575  max=0.9937  CI95=[0.9392, 0.9909]  n=10
-  sensitivity    : mean=0.9651  std=0.0395  min=0.8575  max=0.9937  CI95=[0.9392, 0.9909]  n=10
-  specificity    : mean=0.9969  std=0.0009  min=0.9955  max=0.9980  CI95=[0.9964, 0.9975]  n=10
-  hd95           : mean=9.8269  std=5.4066  min=3.6056  max=20.4939  CI95=[6.2946, 13.3592]  n=10
-  vol_error      : mean=0.0240  std=0.0318  min=0.0011  max=0.1133  CI95=[0.0032, 0.0447]  n=10
+  dice           : mean=0.9501  std=0.0317  min=0.8794  max=0.9833  CI95=[0.9358, 0.9644]  n=20
+  iou            : mean=0.9067  std=0.0564  min=0.7847  max=0.9672  CI95=[0.8813, 0.9320]  n=20
+  f1             : mean=0.9501  std=0.0317  min=0.8794  max=0.9833  CI95=[0.9358, 0.9644]  n=20
+  precision      : mean=0.9695  std=0.0061  min=0.9493  max=0.9787  CI95=[0.9667, 0.9722]  n=20
+  recall         : mean=0.9332  std=0.0573  min=0.8056  max=0.9937  CI95=[0.9074, 0.9589]  n=20
+  sensitivity    : mean=0.9332  std=0.0573  min=0.8056  max=0.9937  CI95=[0.9074, 0.9589]  n=20
+  specificity    : mean=0.9966  std=0.0012  min=0.9941  max=0.9981  CI95=[0.9961, 0.9971]  n=20
+  hd95           : mean=9.5158  std=5.3898  min=2.0000  max=20.4939  CI95=[7.0923, 11.9393]  n=20
+  vol_error      : mean=0.0491  std=0.0474  min=0.0011  max=0.1678  CI95=[0.0278, 0.0704]  n=20
 
 ============================================================
   FAILURE CASE REPORT
-  Total failing cases: 11
-  Dice threshold: 0.92
+  Total failing cases: 9
+  Dice threshold: 0.95
 ============================================================
-  radiopaedia_10_85902_1                              ERROR: mask_too_small
-  radiopaedia_10_85902_3                              ERROR: mask_too_small
-  radiopaedia_14_85914_0                              ERROR: mask_too_small
-  radiopaedia_27_86410_0                              ERROR: mask_too_small
-  radiopaedia_29_86490_1                              ERROR: mask_too_small
-  radiopaedia_29_86491_1                              ERROR: mask_too_small
-  radiopaedia_36_86526_0                              ERROR: mask_too_small
-  radiopaedia_40_86625_0                              ERROR: mask_too_small
-  radiopaedia_4_85506_1                               ERROR: mask_too_small
-  radiopaedia_7_85703_0                               ERROR: mask_too_small
+  radiopaedia_40_86625_0                              Dice=0.8794  HD95=14.0  VolErr=0.1678
+  radiopaedia_7_85703_0                               Dice=0.8980  HD95=12.8  VolErr=0.1024
+  radiopaedia_4_85506_1                               Dice=0.9032  HD95=8.0  VolErr=0.1222
   coronacases_003                                     Dice=0.9090  HD95=20.5  VolErr=0.1133
+  radiopaedia_29_86490_1                              Dice=0.9250  HD95=4.9  VolErr=0.0914
+  radiopaedia_10_85902_1                              Dice=0.9320  HD95=4.5  VolErr=0.0706
+  radiopaedia_27_86410_0                              Dice=0.9350  HD95=9.1  VolErr=0.0704
+  radiopaedia_14_85914_0                              Dice=0.9422  HD95=17.3  VolErr=0.0663
+  coronacases_010                                     Dice=0.9499  HD95=16.0  VolErr=0.0369

validation/validation_results.csv

@@ -1,21 +1,21 @@
-uid,subset,failure_case,dice,iou,f1,precision,recall,sensitivity,specificity,hd95,vol_error,tp,fp,fn,tn,pred_voxels,gt_voxels,error
-coronacases_001,,False,0.9760178824227209,0.9531591086101815,0.9760178824227209,0.964853866861702,0.98744327277614,0.98744327277614,0.9975390384893877,6.164414002968976,0.02341225618747537,4989461.0,181748.0,63448.0,73670687.0,5171209.0,5052909.0,
-coronacases_002,,False,0.9783828749732614,0.9576805742637267,0.9783828749732614,0.9710258518612581,0.9858522308441074,0.9858522308441074,0.9957607574845938,5.477225575051661,0.015268778842944771,6510438.0,194263.0,93430.0,45630669.0,6704701.0,6603868.0,
-coronacases_003,,True,0.9089790463790003,0.8331453611062204,0.9089790463790003,0.9670353880994862,0.8574987772497311,0.8574987772497311,0.9973818365212598,20.493901531919196,0.11327052990796194,3695782.0,125983.0,614174.0,47992861.0,3821765.0,4309956.0,
-coronacases_004,,False,0.9818130434804757,0.9642758014074508,0.9818130434804757,0.9720224703467554,0.9918028520013522,0.9918028520013522,0.9954554274693856,3.7416573867739413,0.02034971645001426,9640653.0,277485.0,79679.0,60781063.0,9918138.0,9720332.0,
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-coronacases_006,,False,0.9796287932466904,0.9600709886392693,0.9796287932466904,0.9772917337763539,0.9819770570265477,0.9819770570265477,0.9976937788011436,6.782329983125268,0.004794191016115646,5033200.0,116951.0,92378.0,50594143.0,5150151.0,5125578.0,
-coronacases_007,,False,0.9741074721254315,0.9495219486036999,0.9741074721254315,0.9735844026887623,0.9746311039143972,0.9746311039143972,0.9974463405693121,9.695359714832659,0.0010751006515144742,5602471.0,152008.0,145828.0,59373549.0,5754479.0,5748299.0,
-coronacases_008,,False,0.9760092915584545,0.9531427224021274,0.9760092915584545,0.9753917430282032,0.9766276225595406,0.9766276225595406,0.997493911053334,13.74772708486752,0.0012670596610759547,7114324.0,179488.0,170258.0,71441274.0,7293812.0,7284582.0,
-coronacases_009,,False,0.967813314398884,0.9376339841423771,0.967813314398884,0.9667880618524726,0.9688407437588495,0.9688407437588495,0.9969353015130883,12.529964086141668,0.00212319740734516,5482134.0,188327.0,176313.0,61262090.0,5670461.0,5658447.0,
-coronacases_010,,False,0.949898414722514,0.904577640906538,0.949898414722514,0.9681027247935012,0.9323661000717179,0.9323661000717179,0.9979755619310705,16.0312195418814,0.036914083398963016,4548438.0,149863.0,329944.0,73877099.0,4698301.0,4878382.0,
-radiopaedia_10_85902_1,,True,,,,,,,,,,,,,,,,mask_too_small
-radiopaedia_10_85902_3,,True,,,,,,,,,,,,,,,,mask_too_small
-radiopaedia_14_85914_0,,True,,,,,,,,,,,,,,,,mask_too_small
-radiopaedia_27_86410_0,,True,,,,,,,,,,,,,,,,mask_too_small
-radiopaedia_29_86490_1,,True,,,,,,,,,,,,,,,,mask_too_small
-radiopaedia_29_86491_1,,True,,,,,,,,,,,,,,,,mask_too_small
-radiopaedia_36_86526_0,,True,,,,,,,,,,,,,,,,mask_too_small
-radiopaedia_40_86625_0,,True,,,,,,,,,,,,,,,,mask_too_small
-radiopaedia_4_85506_1,,True,,,,,,,,,,,,,,,,mask_too_small
-radiopaedia_7_85703_0,,True,,,,,,,,,,,,,,,,mask_too_small
+uid,subset,failure_case,dice,iou,f1,precision,recall,sensitivity,specificity,hd95,vol_error,tp,fp,fn,tn,pred_voxels,gt_voxels
+coronacases_001,,False,0.9760178824227209,0.9531591086101815,0.9760178824227209,0.964853866861702,0.98744327277614,0.98744327277614,0.9975390384893877,6.164414002968976,0.02341225618747537,4989461,181748,63448,73670687,5171209,5052909
+coronacases_002,,False,0.9783828749732614,0.9576805742637267,0.9783828749732614,0.9710258518612581,0.9858522308441074,0.9858522308441074,0.9957607574845938,5.477225575051661,0.015268778842944771,6510438,194263,93430,45630669,6704701,6603868
+coronacases_003,,True,0.9089790463790003,0.8331453611062204,0.9089790463790003,0.9670353880994862,0.8574987772497311,0.8574987772497311,0.9973818365212598,20.493901531919196,0.11327052990796194,3695782,125983,614174,47992861,3821765,4309956
+coronacases_004,,False,0.9818130434804757,0.9642758014074508,0.9818130434804757,0.9720224703467554,0.9918028520013522,0.9918028520013522,0.9954554274693856,3.7416573867739413,0.02034971645001426,9640653,277485,79679,60781063,9918138,9720332
+coronacases_005,,False,0.9833353954010368,0.967217104788386,0.9833353954010368,0.9731710720448583,0.9937142831295428,0.9937142831295428,0.9957693438196048,3.605551275463989,0.021109557892550753,10105641,278598,63923,65573598,10384239,10169564
+coronacases_006,,False,0.9796287932466904,0.9600709886392693,0.9796287932466904,0.9772917337763539,0.9819770570265477,0.9819770570265477,0.9976937788011436,6.782329983125268,0.004794191016115646,5033200,116951,92378,50594143,5150151,5125578
+coronacases_007,,False,0.9741074721254315,0.9495219486036999,0.9741074721254315,0.9735844026887623,0.9746311039143972,0.9746311039143972,0.9974463405693121,9.695359714832659,0.0010751006515144742,5602471,152008,145828,59373549,5754479,5748299
+coronacases_008,,False,0.9760092915584545,0.9531427224021274,0.9760092915584545,0.9753917430282032,0.9766276225595406,0.9766276225595406,0.997493911053334,13.74772708486752,0.0012670596610759547,7114324,179488,170258,71441274,7293812,7284582
+coronacases_009,,False,0.967813314398884,0.9376339841423771,0.967813314398884,0.9667880618524726,0.9688407437588495,0.9688407437588495,0.9969353015130883,12.529964086141668,0.00212319740734516,5482134,188327,176313,61262090,5670461,5658447
+coronacases_010,,False,0.949898414722514,0.904577640906538,0.949898414722514,0.9681027247935012,0.9323661000717179,0.9323661000717179,0.9979755619310705,16.0312195418814,0.036914083398963016,4548438,149863,329944,73877099,4698301,4878382
+radiopaedia_10_85902_1,,True,0.9320394564863881,0.8727283626228356,0.9320394564863881,0.9674560838894993,0.8991243180210186,0.8991243180210186,0.9963873370065524,4.47213595499958,0.07063035419014099,1485018,49954,166609,13777519,1534972,1651627
+radiopaedia_10_85902_3,,False,0.9663251482925468,0.9348444016958968,0.9663251482925468,0.9787412880488462,0.9542200802633501,0.9542200802633501,0.9975523127359182,16.431676725154983,0.02505381972224892,16721100,363190,802216,148017694,17084290,17523316
+radiopaedia_14_85914_0,,True,0.9421648139993933,0.8906536920571534,0.9421648139993933,0.9756121822954966,0.9109348102687125,0.9109348102687125,0.9956747714513079,17.291616465790582,0.06629414146369175,4040772,101009,395080,23252439,4141781,4435852
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+radiopaedia_29_86490_1,,True,0.9250090755604247,0.860480823168553,0.9250090755604247,0.9715107970007523,0.8827556517741525,0.8827556517741525,0.9981278191827389,4.898979485566356,0.09135785778262429,992476,29104,131817,15516403,1021580,1124293
+radiopaedia_29_86491_1,,False,0.9734242977918107,0.9482245641485221,0.9734242977918107,0.9673170454304648,0.9796091576259068,0.9796091576259068,0.9953616211269929,3.0,0.012707428503937853,2007179,67817,41780,14553024,2074996,2048959
+radiopaedia_36_86526_0,,False,0.9718592078914323,0.9452588744176772,0.9718592078914323,0.9656406904175405,0.9781583363010922,0.9781583363010922,0.9946096123407059,2.0,0.012963047236694496,2342878,83364,52315,15381943,2426242,2395193
+radiopaedia_40_86625_0,,True,0.8793602784210874,0.7846949037128261,0.8793602784210874,0.9680206912122301,0.8055778998193277,0.8055778998193277,0.9979900456545566,14.035668847618199,0.1678092140670482,2088070,68981,503945,34250704,2157051,2592015
+radiopaedia_4_85506_1,,True,0.90320386067586,0.8234929247950066,0.90320386067586,0.9660915894964042,0.8480031015850841,0.8480031015850841,0.9956450761500717,8.0,0.12223322218645546,1675454,58806,300310,13444530,1734260,1975764
+radiopaedia_7_85703_0,,True,0.8980429949367631,0.8149528437230412,0.8980429949367631,0.9492609533726224,0.852069083597547,0.852069083597547,0.9940946064700706,12.806248474865697,0.10238688258461551,1746774,93367,303264,15717095,1840141,2050038

validation/validation_results.json

@@ -1,6 +1,18 @@
 {
   "method": "algorithmic_HU_threshold_morphology",
   "n_patients": 20,
+  "n_valid": 20,
+  "timestamp": "2026-05-05T12:43:38.279519",
+  "hyperparams": {
+    "HU_THRESHOLD": -400,
+    "DISK_CLOSING_RADIUS": 3,
+    "DISK_CLOSING_TOUCHING": 5,
+    "SEAM_HEAL_RADIUS": 2,
+    "MIN_BLOB_VOXELS": 50,
+    "MAX_LUNG_REGIONS": 3,
+    "CLOSING_RADIUS": 3,
+    "DICE_FAIL_THR": 0.95
+  },
   "summary": {
     "dice": {
       "mean": 0.9501202973399325,