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simpler example
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Signed-off-by: neuronflow <[email protected]>
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@neuronflow
neuronflow committed Feb 15, 2024
1 parent c2cc450 commit 5a4bc89
Showing 1 changed file with 98 additions and 117 deletions.
215 changes: 98 additions & 117 deletions example/example_modality_centric_preprocessor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,128 +13,109 @@

def preprocess(inputDir):
inputDir = turbopath(inputDir)
try:
print("*** start ***")

# where are the raw mr files?
btk_raw_dir = turbopath(inputDir)

# is the exam already processed?
brainles_dir = turbopath(inputDir) + "/" + inputDir.name + "_brainles"
raw_bet_dir = brainles_dir / "raw_bet"
norm_bet_dir = brainles_dir / "normalized_bet"
raw_skull_dir = brainles_dir / "raw_skull"
norm_skull_dir = brainles_dir / "normalized_skull"

# if not os.path.exists(prep_dir):
# if os.path.exists(prep_dir):
t1_file = btk_raw_dir.files("*t1.nii.gz")
t1c_file = btk_raw_dir.files("*t1c.nii.gz")
t2_file = btk_raw_dir.files("*t2.nii.gz")
flair_file = btk_raw_dir.files("*fla.nii.gz")

if len(t1_file) == len(t1c_file) == len(t2_file) == len(flair_file) == 1:
# print(t1_file)
# print(t1c_file)
# print(t2_file)
# print(flair_file)

t1File = t1_file[0]
t1cFile = t1c_file[0]
t2File = t2_file[0]
flaFile = flair_file[0]

# normalizer
percentile_normalizer = PercentileNormalizer(
lower_percentile=0.1,
upper_percentile=99.9,
lower_limit=0,
upper_limit=1,
)

# define modalities
center = Modality(
modality_name="t1c",
input_path=t1cFile,
raw_bet_output_path=raw_bet_dir / inputDir.name + "_t1c_bet_raw.nii.gz",
print("*** start ***")

# where are the raw mr files?
btk_raw_dir = turbopath(inputDir)
# is the exam already processed?
brainles_dir = turbopath(inputDir) + "/" + inputDir.name + "_brainles"
raw_bet_dir = brainles_dir / "raw_bet"
norm_bet_dir = brainles_dir / "normalized_bet"
raw_skull_dir = brainles_dir / "raw_skull"
norm_skull_dir = brainles_dir / "normalized_skull"
# if not os.path.exists(prep_dir):
# if os.path.exists(prep_dir):
t1_file = btk_raw_dir.files("*t1.nii.gz")
t1c_file = btk_raw_dir.files("*t1c.nii.gz")
t2_file = btk_raw_dir.files("*t2.nii.gz")
flair_file = btk_raw_dir.files("*fla.nii.gz")
if len(t1_file) == len(t1c_file) == len(t2_file) == len(flair_file) == 1:
# print(t1_file)
# print(t1c_file)
# print(t2_file)
# print(flair_file)
t1File = t1_file[0]
t1cFile = t1c_file[0]
t2File = t2_file[0]
flaFile = flair_file[0]
# normalizer
percentile_normalizer = PercentileNormalizer(
lower_percentile=0.1,
upper_percentile=99.9,
lower_limit=0,
upper_limit=1,
)
# define modalities
center = Modality(
modality_name="t1c",
input_path=t1cFile,
raw_bet_output_path=raw_bet_dir / inputDir.name + "_t1c_bet_raw.nii.gz",
raw_skull_output_path=raw_skull_dir / inputDir.name
+ "_t1c_skull_raw.nii.gz",
# normalized_bet_output_path=norm_bet_dir / inputDir.name
# + "_t1c_bet_normalized.nii.gz",
normalized_skull_output_path=norm_skull_dir / inputDir.name
+ "_t1c_skull_normalized.nii.gz",
atlas_correction=True,
normalizer=percentile_normalizer,
)
moving_modalities = [
Modality(
modality_name="t1",
input_path=t1File,
raw_bet_output_path=raw_bet_dir / inputDir.name + "_t1_bet_raw.nii.gz",
raw_skull_output_path=raw_skull_dir / inputDir.name
+ "_t1c_skull_raw.nii.gz",
+ "_t1_skull_raw.nii.gz",
normalized_bet_output_path=norm_bet_dir / inputDir.name
+ "_t1c_bet_normalized.nii.gz",
+ "_t1_bet_normalized.nii.gz",
normalized_skull_output_path=norm_skull_dir / inputDir.name
+ "_t1c_skull_normalized.nii.gz",
+ "_t1_skull_normalized.nii.gz",
atlas_correction=True,
normalizer=percentile_normalizer,
)

moving_modalities = [
Modality(
modality_name="t1",
input_path=t1File,
raw_bet_output_path=raw_bet_dir / inputDir.name
+ "_t1_bet_raw.nii.gz",
raw_skull_output_path=raw_skull_dir / inputDir.name
+ "_t1_skull_raw.nii.gz",
normalized_bet_output_path=norm_bet_dir / inputDir.name
+ "_t1_bet_normalized.nii.gz",
normalized_skull_output_path=norm_skull_dir / inputDir.name
+ "_t1_skull_normalized.nii.gz",
atlas_correction=True,
normalizer=percentile_normalizer,
),
Modality(
modality_name="t2",
input_path=t2File,
raw_bet_output_path=raw_bet_dir / inputDir.name
+ "_t2_bet_raw.nii.gz",
raw_skull_output_path=raw_skull_dir / inputDir.name
+ "_t2_skull_raw.nii.gz",
normalized_bet_output_path=norm_bet_dir / inputDir.name
+ "_t2_bet_normalized.nii.gz",
normalized_skull_output_path=norm_skull_dir / inputDir.name
+ "_t2_skull_normalized.nii.gz",
atlas_correction=True,
normalizer=percentile_normalizer,
),
Modality(
modality_name="flair",
input_path=flaFile,
raw_bet_output_path=raw_bet_dir / inputDir.name
+ "_fla_bet_raw.nii.gz",
raw_skull_output_path=raw_skull_dir / inputDir.name
+ "_fla_skull_raw.nii.gz",
normalized_bet_output_path=norm_bet_dir / inputDir.name
+ "_fla_bet_normalized.nii.gz",
normalized_skull_output_path=norm_skull_dir / inputDir.name
+ "_fla_skull_normalized.nii.gz",
atlas_correction=True,
normalizer=percentile_normalizer,
),
]

preprocessor = Preprocessor(
center_modality=center,
moving_modalities=moving_modalities,
registrator=NiftyRegRegistrator(),
brain_extractor=HDBetExtractor(),
temp_folder="tempo",
limit_cuda_visible_devices="1",
)

preprocessor.run(
save_dir_coregistration=brainles_dir + "/co-registration",
save_dir_atlas_registration=brainles_dir + "/atlas-registration",
save_dir_atlas_correction=brainles_dir + "/atlas-correction",
save_dir_brain_extraction=brainles_dir + "/brain-extraction",
)

except Exception as e:
print("error: " + str(e))
print("conversion error for:", inputDir)

time = str(datetime.datetime.now().time())

print("** finished:", inputDir.name, "at:", time)
),
Modality(
modality_name="t2",
input_path=t2File,
raw_bet_output_path=raw_bet_dir / inputDir.name + "_t2_bet_raw.nii.gz",
raw_skull_output_path=raw_skull_dir / inputDir.name
+ "_t2_skull_raw.nii.gz",
normalized_bet_output_path=norm_bet_dir / inputDir.name
+ "_t2_bet_normalized.nii.gz",
normalized_skull_output_path=norm_skull_dir / inputDir.name
+ "_t2_skull_normalized.nii.gz",
atlas_correction=True,
normalizer=percentile_normalizer,
),
Modality(
modality_name="flair",
input_path=flaFile,
raw_bet_output_path=raw_bet_dir / inputDir.name + "_fla_bet_raw.nii.gz",
raw_skull_output_path=raw_skull_dir / inputDir.name
+ "_fla_skull_raw.nii.gz",
normalized_bet_output_path=norm_bet_dir / inputDir.name
+ "_fla_bet_normalized.nii.gz",
normalized_skull_output_path=norm_skull_dir / inputDir.name
+ "_fla_skull_normalized.nii.gz",
atlas_correction=True,
normalizer=percentile_normalizer,
),
]

preprocessor = Preprocessor(
center_modality=center,
moving_modalities=moving_modalities,
registrator=NiftyRegRegistrator(),
brain_extractor=HDBetExtractor(),
temp_folder="tempo",
limit_cuda_visible_devices="1",
)

preprocessor.run(
save_dir_coregistration=brainles_dir + "/co-registration",
save_dir_atlas_registration=brainles_dir + "/atlas-registration",
save_dir_atlas_correction=brainles_dir + "/atlas-correction",
save_dir_brain_extraction=brainles_dir + "/brain-extraction",
)


### *** GOGOGO *** ###
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