Closed sarthakpati closed 5 days ago
the relevant part of the config yaml file (plan.yaml in FeTS Challenge) to reproduce this bug is this:
task_runner :
template : src.fets_challenge_model.FeTSChallengeModel
settings :
train_csv : cla_test_train.csv
val_csv : cla_test_val.csv
device : cpu
fets_config_dict :
problem_type: classification
batch_size: 1
data_augmentation: {}
data_postprocessing: {}
data_preprocessing:
resize_image: [128,128,64]
normalize: null
in_memory: false
learning_rate: 0.001
loss_function: cel
metrics:
- cel
- classification_accuracy
- f1: {
average: weighted,
}
- accuracy
- balanced_accuracy
- precision: {
average: weighted,
}
- recall
- iou: {
reduction: sum,
}
model:
amp: false
architecture: vgg16
base_filters: 32
norm_type: batch
class_list:
- 0
- 1
- 2
- 3
dimension: 2
final_layer: softmax
type: torch
nested_training:
testing: -5
validation: -5
num_epochs: 1
optimizer:
type: adam
parallel_compute_command: ''
patch_sampler: uniform
enable_padding: True
verbose: False
patch_size:
- 128
- 128
- 64
patience: 1
q_max_length: 1
q_num_workers: 0
q_samples_per_volume: 1
q_verbose: false
save_output: false
scaling_factor: 1
scheduler:
{
type: triangle,
min_lr: 0.00001,
max_lr: 1,
}
version:
maximum: 0.0.14
minimum: 0.0.13
weighted_loss: False
which_model: resunet
pin_memory_dataloader: false
print_rgb_label_warning: true
save_training: false
scaling_factor: 1
output_dir: "/home/locolinux2/FETS2024/Challenge/Task_1/temp"
medcam_enabled: False
Please assign to me.
A few notes:
problem_type
is not segmentation. else
block of that logic [ref] does a grid aggregation (i.e., extract patches from the entire image and then average it [ref], which seems to be doing what I'd expect. I used the following csv:
SubjectID,Channel_0,ValueToPredict
1,C:/Projects/GaNDLF/testing/data/2d_rad_segmentation/001/image.png,0
2,C:/Projects/GaNDLF/testing/data/2d_rad_segmentation/002/image.png,1
3,C:/Projects/GaNDLF/testing/data/2d_rad_segmentation/003/image.png,2
4,C:/Projects/GaNDLF/testing/data/2d_rad_segmentation/004/image.png,2
5,C:/Projects/GaNDLF/testing/data/2d_rad_segmentation/005/image.png,0
6,C:/Projects/GaNDLF/testing/data/2d_rad_segmentation/006/image.png,0
7,C:/Projects/GaNDLF/testing/data/2d_rad_segmentation/007/image.png,1
8,C:/Projects/GaNDLF/testing/data/2d_rad_segmentation/008/image.png,0
9,C:/Projects/GaNDLF/testing/data/2d_rad_segmentation/009/image.png,1
10,C:/Projects/GaNDLF/testing/data/2d_rad_segmentation/010/image.png,1
And passed that instead of what the test expects for the 2d classification test [ref], and the current code seems to be working as expected. As in, multiple predictions were done for the image on which the final result was needed, and the average was done appropriately.
Stale issue message
Describe the bug
When the image size is larger than the
patch_size
, GaNDLF tries to extract multiple patches and perform classification for each, after which it takes an average to generate the final prediction [ref].To Reproduce
Steps to reproduce the behavior:
channel_0
header apart fromsubjectid
and avaluetopredict
header).patch_size
to[128,128,64]
.Expected behavior
The classification should work.
Media
N.A.
Environment information
This is using an older version of GaNDLF [ref], but we want to ensure that the error is either reproducible in the current master or completely resolved.
Additional context
Related to the FeTS Challenge.