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hecktor22 update for latest monai ver #1438

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Merged
merged 1 commit into from
Jun 27, 2023
Merged

hecktor22 update for latest monai ver #1438

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35 changes: 35 additions & 0 deletions auto3dseg/tasks/hecktor22/hecktor22_folds.json
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,41 @@
"image": "imagesTr/CHUP-049__CT.nii.gz",
"image2": "imagesTr/CHUP-049__PT.nii.gz",
"fold": 0
},
{
"image": "imagesTr/CHUP-034__CT.nii.gz",
"image2": "imagesTr/CHUP-034__PT.nii.gz",
"fold": 0
},
{
"image": "imagesTr/CHUS-089__CT.nii.gz",
"image2": "imagesTr/CHUS-089__PT.nii.gz",
"fold": 0
},
{
"image": "imagesTr/CHUP-061__CT.nii.gz",
"image2": "imagesTr/CHUP-061__PT.nii.gz",
"fold": 0
},
{
"image": "imagesTr/CHUP-010__CT.nii.gz",
"image2": "imagesTr/CHUP-010__PT.nii.gz",
"fold": 0
},
{
"image": "imagesTr/HGJ-013__CT.nii.gz",
"image2": "imagesTr/HGJ-013__PT.nii.gz",
"fold": 0
},
{
"image": "imagesTr/CHUM-040__CT.nii.gz",
"image2": "imagesTr/CHUM-040__PT.nii.gz",
"fold": 0
},
{
"image": "imagesTr/HGJ-062__CT.nii.gz",
"image2": "imagesTr/HGJ-062__PT.nii.gz",
"fold": 0
}
],
"training": [
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2 changes: 1 addition & 1 deletion auto3dseg/tasks/hecktor22/hecktor_crop_neck_region.py
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Expand Up @@ -36,7 +36,7 @@ def __init__(
super().__init__(keys=keys, source_key=source_key, allow_missing_keys=allow_missing_keys, **kwargs)
self.box_size = box_size

def __call__(self, data):
def __call__(self, data, **kwargs):
d = dict(data)

im_pet = d["image2"][0]
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5 changes: 3 additions & 2 deletions auto3dseg/tasks/hecktor22/input.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,11 @@ extra_modalities: {image2 : pet} # a second modality
custom_data_transforms:
- key: after_resample_transforms
path: '.'
transform: {_target_: hecktor_crop_neck_region.HecktorCropNeckRegion}
transform: {_target_: hecktor_crop_neck_region.HecktorCropNeckRegion, box_size: [200, 200, 310]}

# indicate the new avg image size (to correctly determine amount of caching required)
image_size: [200, 200, 310]
image_size_mm_90: [200, 200, 310]
resample_resolution: [1, 1, 1]

# update the random crop size (for training) to be slightly smaller, since the automatically
# determined size was based on the whole image
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