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blueyo0
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organmnist3d

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  1. data_description.md +38 -0
  2. sample_submission.csv +610 -610
  3. test.csv +610 -610
  4. train.csv +971 -971
  5. val.csv +161 -161
data_description.md ADDED
@@ -0,0 +1,38 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ # Introduction
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+ Predict the category of each given 3D Abdominal CT image by selecting the most appropriate one from the 11 available classes.
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+ 0 class-1
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+ 1 class-2
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+ 2 class-3
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+ 3 class-4
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+ 4 class-5
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+ 5 class-6
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+ 6 class-7
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+ 7 class-8
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+ 8 class-9
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+ 9 class-10
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+ 10 class-11
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+
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+ # Example Prediction Code
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+ ``` python
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+ # Load best model and predict on test set
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+ test_transforms = Compose(
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+ [
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+ LoadImaged(keys=["image"]),
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+ EnsureChannelFirstd(keys=["image"]),
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+ ScaleIntensityd(keys=["image"]),
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+ ]
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+ )
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+ test_ds = Dataset(data=test_df.to_dict(orient="records"), transform=test_transforms)
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+ test_loader = DataLoader(test_ds, batch_size=1, shuffle=False, num_workers=4)
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+ predictions = []
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+ with torch.no_grad():
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+ for test_data in test_loader:
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+ test_images = test_data["image"].to(device)
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+ test_outputs = model(test_images)
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+ test_outputs = torch.argmax(test_outputs, dim=1)
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+ predictions.extend(test_outputs.cpu().numpy())
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+
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+ # Save predictions
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+ submission_df = pd.DataFrame({"Id": test_df["Id"], "class": predictions})
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+ submission_df.to_csv("./working/submission.csv", index=False)
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+ ```
sample_submission.csv CHANGED
@@ -1,611 +1,611 @@
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  Id,class,path
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- 1,10,test_nii/1.nii.gz
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1
  Id,class,path
2
+ 1,10,input/test_nii/1.nii.gz
3
+ 2,2,input/test_nii/2.nii.gz
4
+ 3,3,input/test_nii/3.nii.gz
5
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6
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7
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8
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10
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11
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14
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15
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610
+ 609,4,input/test_nii/609.nii.gz
611
+ 610,3,input/test_nii/610.nii.gz
test.csv CHANGED
@@ -1,611 +1,611 @@
1
  Id,class,path
2
- 1,10,test_nii/1.nii.gz
3
- 2,2,test_nii/2.nii.gz
4
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16
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17
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19
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22
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24
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27
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28
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30
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33
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40
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41
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42
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202
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203
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205
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206
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207
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214
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233
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234
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611
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1
  Id,class,path
2
+ 1,10,input/test_nii/1.nii.gz
3
+ 2,2,input/test_nii/2.nii.gz
4
+ 3,3,input/test_nii/3.nii.gz
5
+ 4,4,input/test_nii/4.nii.gz
6
+ 5,9,input/test_nii/5.nii.gz
7
+ 6,7,input/test_nii/6.nii.gz
8
+ 7,5,input/test_nii/7.nii.gz
9
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train.csv CHANGED
@@ -1,972 +1,972 @@
1
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+ 947,1,input/train_nii/947.nii.gz
949
+ 948,4,input/train_nii/948.nii.gz
950
+ 949,2,input/train_nii/949.nii.gz
951
+ 950,0,input/train_nii/950.nii.gz
952
+ 951,5,input/train_nii/951.nii.gz
953
+ 952,0,input/train_nii/952.nii.gz
954
+ 953,10,input/train_nii/953.nii.gz
955
+ 954,6,input/train_nii/954.nii.gz
956
+ 955,0,input/train_nii/955.nii.gz
957
+ 956,5,input/train_nii/956.nii.gz
958
+ 957,9,input/train_nii/957.nii.gz
959
+ 958,0,input/train_nii/958.nii.gz
960
+ 959,0,input/train_nii/959.nii.gz
961
+ 960,1,input/train_nii/960.nii.gz
962
+ 961,0,input/train_nii/961.nii.gz
963
+ 962,10,input/train_nii/962.nii.gz
964
+ 963,0,input/train_nii/963.nii.gz
965
+ 964,5,input/train_nii/964.nii.gz
966
+ 965,4,input/train_nii/965.nii.gz
967
+ 966,1,input/train_nii/966.nii.gz
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+ 967,9,input/train_nii/967.nii.gz
969
+ 968,0,input/train_nii/968.nii.gz
970
+ 969,3,input/train_nii/969.nii.gz
971
+ 970,4,input/train_nii/970.nii.gz
972
+ 971,7,input/train_nii/971.nii.gz
val.csv CHANGED
@@ -1,162 +1,162 @@
1
  Id,class,path
2
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3
- 2,1,val_nii/2.nii.gz
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- 159,6,val_nii/159.nii.gz
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162
- 161,2,val_nii/161.nii.gz
 
1
  Id,class,path
2
+ 1,9,input/val_nii/1.nii.gz
3
+ 2,1,input/val_nii/2.nii.gz
4
+ 3,4,input/val_nii/3.nii.gz
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8
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9
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11
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13
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14
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15
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16
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17
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18
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19
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