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Fix TypeError in test_ma.py by casting patient[0] to string #29

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Fix TypeError in test_ma.py by casting patient[0] to string #29

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5e8bbe9
Update test_ma.py
SaiKrishnaChaitanya24 Oct 1, 2025
b64a93b
Update test_ma.py
SaiKrishnaChaitanya24 Oct 1, 2025
694a04f
Merge pull request #1 from SaiKrishnaChaitanya24/SaiKrishnaChaitanya2…
SaiKrishnaChaitanya24 Oct 1, 2025
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27 changes: 14 additions & 13 deletions BrainMaGe/tester/test_ma.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
@author: siddhesh
"""


from __future__ import print_function, division
import os
import sys
Expand Down Expand Up @@ -90,7 +91,7 @@ def infer_ma(cfg, device, save_brain, weights):
print("Resampling the images to isotropic resolution of 1mm x 1mm x 1mm")
print("Also Converting the images to RAI and brats for smarter use.")
for patient in tqdm.tqdm(test_df.values):
os.makedirs(os.path.join(temp_dir, patient[0]), exist_ok=True)
os.makedirs(os.path.join(temp_dir, str(patient[0])), exist_ok=True)
patient_path = patient[1]
image = nib.load(patient_path)
old_spacing = image.header.get_zooms()
Expand Down Expand Up @@ -119,7 +120,7 @@ def infer_ma(cfg, device, save_brain, weights):
temp_image = nib.Nifti1Image(new_image, new_affine)
nib.save(
temp_image,
os.path.join(temp_dir, patient[0], patient[0] + "_resamp111.nii.gz"),
os.path.join(temp_dir, str(patient[0]), str(patient[0]) + "_resamp111.nii.gz"),
)

temp_dict = {}
Expand All @@ -132,7 +133,7 @@ def infer_ma(cfg, device, save_brain, weights):
temp_dict["new_shape"] = new_shape

patient_path = os.path.join(
temp_dir, patient[0], patient[0] + "_resamp111.nii.gz"
temp_dir, str(patient[0]), str(patient[0]) + "_resamp111.nii.gz"
)
patient_nib = nib.load(patient_path)
patient_data = patient_nib.get_fdata()
Expand All @@ -141,10 +142,10 @@ def infer_ma(cfg, device, save_brain, weights):
temp_image = nib.Nifti1Image(patient_data, patient_affine)
nib.save(
temp_image,
os.path.join(temp_dir, patient[0], patient[0] + "_bratsized.nii.gz"),
os.path.join(temp_dir, str(patient[0]), str(patient[0]) + "_bratsized.nii.gz"),
)
temp_dict["pad_info"] = pad_info
patients_dict[patient[0]] = temp_dict
patients_dict[str(patient[0])] = temp_dict

model = fetch_model(
params["model"],
Expand All @@ -164,7 +165,7 @@ def infer_ma(cfg, device, save_brain, weights):
print("Running the model on the subjects")
for patient in tqdm.tqdm(test_df.values):
patient_path = os.path.join(
temp_dir, patient[0], patient[0] + "_bratsized.nii.gz"
temp_dir, str(patient[0]), str(patient[0]) + "_bratsized.nii.gz"
)
patient_nib = nib.load(patient_path)
image = patient_nib.get_fdata()
Expand All @@ -186,16 +187,16 @@ def infer_ma(cfg, device, save_brain, weights):
nib.save(
to_save_nib,
os.path.join(
temp_dir, patient[0], patient[0] + "_bratsized_mask.nii.gz"
temp_dir, str(patient[0]), str(patient[0]) + "_bratsized_mask.nii.gz"
),
)
current_patient_dict = patients_dict[patient[0]]
current_patient_dict = patients_dict[str(patient[0])]
new_image = padder_and_cropper(to_save, current_patient_dict["pad_info"])
to_save_new_nib = nib.Nifti1Image(new_image, patient_nib.affine)
nib.save(
to_save_new_nib,
os.path.join(
temp_dir, patient[0], patient[0] + "_resample111_mask.nii.gz"
temp_dir, str(patient[0]), str(patient[0]) + "_resample111_mask.nii.gz"
),
)
to_save_final = resize(
Expand All @@ -215,12 +216,12 @@ def infer_ma(cfg, device, save_brain, weights):
to_save_final, current_patient_dict["old_affine"]
)

os.makedirs(os.path.join(params["results_dir"], patient[0]), exist_ok=True)
os.makedirs(os.path.join(params["results_dir"], str(patient[0])), exist_ok=True)

nib.save(
to_save_final_nib,
os.path.join(
params["results_dir"], patient[0], patient[0] + "_mask.nii.gz"
params["results_dir"], str(patient[0]), str(patient[0]) + "_mask.nii.gz"
),
)

Expand All @@ -232,7 +233,7 @@ def infer_ma(cfg, device, save_brain, weights):
image_data = image.get_fdata()
mask = nib.load(
os.path.join(
params["results_dir"], patient[0], patient[0] + "_mask.nii.gz"
params["results_dir"], str(patient[0]), str(patient[0]) + "_mask.nii.gz"
)
)
mask_data = mask.get_fdata().astype(np.int8)
Expand All @@ -241,7 +242,7 @@ def infer_ma(cfg, device, save_brain, weights):
nib.save(
to_save_brain,
os.path.join(
params["results_dir"], patient[0], patient[0] + "_brain.nii.gz"
params["results_dir"], str(patient[0]), str(patient[0]) + "_brain.nii.gz"
),
)

Expand Down