def test_seg_no_basedir(self):
tempdir = tempfile.mkdtemp()
test_data = {
"name":
"Spleen",
"description":
"Spleen Segmentation",
"labels": {
"0": "background",
"1": "spleen"
},
"training": [
{
"image": os.path.join(tempdir, "spleen_19.nii.gz"),
"label": os.path.join(tempdir, "spleen_19.nii.gz"),
},
{
"image": os.path.join(tempdir, "spleen_31.nii.gz"),
"label": os.path.join(tempdir, "spleen_31.nii.gz"),
},
],
"test": [
os.path.join(tempdir, "spleen_15.nii.gz"),
os.path.join(tempdir, "spleen_23.nii.gz")
],
}
json_str = json.dumps(test_data)
file_path = os.path.join(tempdir, "test_data.json")
with open(file_path, "w") as json_file:
json_file.write(json_str)
result = load_decathalon_datalist(file_path, True, "training", None)
self.assertEqual(result[0]["image"],
os.path.join(tempdir, "spleen_19.nii.gz"))
self.assertEqual(result[0]["label"],
os.path.join(tempdir, "spleen_19.nii.gz"))
def test_cls_values(self):
tempdir = tempfile.mkdtemp()
test_data = {
"name":
"ChestXRay",
"description":
"Chest X-ray classification",
"labels": {
"0": "background",
"1": "chest"
},
"training": [{
"image": "chest_19.nii.gz",
"label": 0
}, {
"image": "chest_31.nii.gz",
"label": 1
}],
"test": ["chest_15.nii.gz", "chest_23.nii.gz"],
}
json_str = json.dumps(test_data)
file_path = os.path.join(tempdir, "test_data.json")
with open(file_path, "w") as json_file:
json_file.write(json_str)
result = load_decathalon_datalist(file_path, False, "training",
tempdir)
self.assertEqual(result[0]["image"],
os.path.join(tempdir, "chest_19.nii.gz"))
self.assertEqual(result[0]["label"], 0)
shutil.rmtree(tempdir)
def test_seg_values(self):
with tempfile.TemporaryDirectory() as tempdir:
test_data = {
"name":
"Spleen",
"description":
"Spleen Segmentation",
"labels": {
"0": "background",
"1": "spleen"
},
"training": [
{
"image": "spleen_19.nii.gz",
"label": "spleen_19.nii.gz"
},
{
"image": "spleen_31.nii.gz",
"label": "spleen_31.nii.gz"
},
],
"test": ["spleen_15.nii.gz", "spleen_23.nii.gz"],
}
json_str = json.dumps(test_data)
file_path = os.path.join(tempdir, "test_data.json")
with open(file_path, "w") as json_file:
json_file.write(json_str)
result = load_decathalon_datalist(file_path, True, "training",
tempdir)
self.assertEqual(result[0]["image"],
os.path.join(tempdir, "spleen_19.nii.gz"))
self.assertEqual(result[0]["label"],
os.path.join(tempdir, "spleen_19.nii.gz"))
def _generate_data_list(self, dataset_dir: str) -> List[Dict]:
section = "training" if self.section in ["training", "validation"] else "test"
datalist = load_decathalon_datalist(os.path.join(dataset_dir, "dataset.json"), True, section)
if section == "test":
return datalist
else:
data = list()
for i in datalist:
self.randomize()
if self.section == "training":
if self.rann < self.val_frac:
continue
else:
if self.rann >= self.val_frac:
continue
data.append(i)
return data
def test_seg_no_labels(self):
tempdir = tempfile.mkdtemp()
test_data = {
"name": "Spleen",
"description": "Spleen Segmentation",
"labels": {
"0": "background",
"1": "spleen"
},
"test": ["spleen_15.nii.gz", "spleen_23.nii.gz"],
}
json_str = json.dumps(test_data)
file_path = os.path.join(tempdir, "test_data.json")
with open(file_path, "w") as json_file:
json_file.write(json_str)
result = load_decathalon_datalist(file_path, True, "test", tempdir)
self.assertEqual(result[0]["image"],
os.path.join(tempdir, "spleen_15.nii.gz"))
shutil.rmtree(tempdir)