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Merged
MahdiAll99 merged 3 commits into from
Feb 14, 2025
Merged

new version #10

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MahdiAll99 Feb 12, 2025
d3a4ceb
New features and improvements
MahdiAll99 Feb 14, 2025
d4dcdb8
changed version to 0.9.8
MahdiAll99 Feb 14, 2025
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93 changes: 46 additions & 47 deletions MEDimage/MEDscan.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,15 +60,9 @@ def __init__(self, medscan=None) -> None:
self.data = medscan.data
except:
self.data = self.data()
try:
self.params = medscan.params
except:
self.params = self.Params()
try:
self.radiomics = medscan.radiomics
except:
self.radiomics = self.Radiomics()

self.params = self.Params()
self.radiomics = self.Radiomics()
self.skip = False

def __init_process_params(self, im_params: Dict) -> None:
Expand All @@ -90,6 +84,8 @@ def __init_process_params(self, im_params: Dict) -> None:
raise ValueError(f"The given parameters dict is not valid, no params found for {self.type} modality")

# re-segmentation range processing
if(im_params['reSeg']['range'] and (im_params['reSeg']['range'][0] == "inf" or im_params['reSeg']['range'][0] == "-inf")):
im_params['reSeg']['range'][0] = -np.inf
if(im_params['reSeg']['range'] and im_params['reSeg']['range'][1] == "inf"):
im_params['reSeg']['range'][1] = np.inf

Expand Down Expand Up @@ -218,6 +214,22 @@ def __init_extraction_params(self, im_params: Dict):
self.params.radiomics.ngtdm.dist_correction = False
else:
self.params.radiomics.ngtdm.dist_correction = False

# Features to extract
features = [
"Morph", "LocalIntensity", "Stats", "IntensityHistogram", "IntensityVolumeHistogram",
"GLCM", "GLRLM", "GLSZM", "GLDZM", "NGTDM", "NGLDM"
]
if "extract" in im_params.keys():
self.params.radiomics.extract = im_params['extract']
for key in self.params.radiomics.extract:
if key not in features:
raise ValueError(f"Invalid key in 'extract' parameter: {key} (Modality {self.type}).")

# Ensure each feature is in the extract dictionary with a default value of True
for feature in features:
if feature not in self.params.radiomics.extract:
self.params.radiomics.extract[feature] = True

def __init_filter_params(self, filter_params: Dict) -> None:
"""Initializes the filtering params from a given Dict.
Expand Down Expand Up @@ -351,54 +363,41 @@ def init_ntf_calculation(self, vol_obj: image_volume_obj) -> None:
'_' + ih_val_name + min_val_name

# IVH name
if not self.params.process.ivh: # CT case
if self.params.process.im_range: # The im_range defines the computation.
min_val_name = ((str(self.params.process.im_range[0])).replace('.', 'dot')).replace('-', 'M')
max_val_name = ((str(self.params.process.im_range[1])).replace('.', 'dot')).replace('-', 'M')
if max_val_name == 'inf':
# In this case, the maximum value of the ROI is used,
# so no need to report it.
range_name = '_min' + min_val_name
elif min_val_name == '-inf' or min_val_name == 'inf':
# In this case, the minimum value of the ROI is used,
# so no need to report it.
range_name = '_max' + max_val_name
else:
range_name = '_min' + min_val_name + '_max' + max_val_name
else:
# min-max of ROI will be used, no need to report it.
range_name = ''
if not self.params.process.ivh: # CT case for example
ivh_algo_name = 'algoNone'
ivh_val_name = 'bin1'
if self.params.process.im_range: # The im_range defines the computation.
min_val_name = ((str(self.params.process.im_range[0])).replace(
'.', 'dot')).replace('-', 'M')
max_val_name = ((str(self.params.process.im_range[1])).replace(
'.', 'dot')).replace('-', 'M')
range_name = '_min' + min_val_name + '_max' + max_val_name
else:
range_name = ''
else:
ivh_algo_name = 'algo' + self.params.process.ivh['type']
if 'val' in self.params.process.ivh:
ivh_algo_name = 'algo' + self.params.process.ivh['type'] if 'type' in self.params.process.ivh else 'algoNone'
if 'val' in self.params.process.ivh and self.params.process.ivh['val']:
ivh_val_name = 'bin' + (str(self.params.process.ivh['val'])).replace('.', 'dot')
else:
ivh_val_name = 'binNone'
# The im_range defines the computation.
if 'type' in self.params.process.ivh and self.params.process.ivh['type'].find('FBS') >=0:
if self.params.process.im_range:
min_val_name = ((str(self.params.process.im_range[0])).replace(
'.', 'dot')).replace('-', 'M')
max_val_name = ((str(self.params.process.im_range[1])).replace(
'.', 'dot')).replace('-', 'M')
if max_val_name == 'inf':
# In this case, the maximum value of the ROI is used,
# so no need to report it.
range_name = '_min' + min_val_name
elif min_val_name == '-inf':
# In this case, the minimum value of the ROI is used,
# so no need to report it.
range_name = '_max' + max_val_name
else:
range_name = '_min' + min_val_name + '_max' + max_val_name
else: # min-max of ROI will be used, no need to report it.
range_name = ''
else: # min-max of ROI will be used, no need to report it.
range_name = ''
self.params.radiomics.ivh_name = self.params.radiomics.scale_name + '_' + ivh_algo_name + '_' + ivh_val_name + range_name

# Now initialize the attribute that will hold the computation results
self.radiomics.image.update({
'morph_3D': {self.params.radiomics.scale_name: {}},
'locInt_3D': {self.params.radiomics.scale_name: {}},
'stats_3D': {self.params.radiomics.scale_name: {}},
'intHist_3D': {self.params.radiomics.ih_name: {}},
'intVolHist_3D': {self.params.radiomics.ivh_name: {}}
})
'morph_3D': {self.params.radiomics.scale_name: {}},
'locInt_3D': {self.params.radiomics.scale_name: {}},
'stats_3D': {self.params.radiomics.scale_name: {}},
'intHist_3D': {self.params.radiomics.ih_name: {}},
'intVolHist_3D': {self.params.radiomics.ivh_name: {}}
})

except Exception as e:
message = f"\n PROBLEM WITH PRE-PROCESSING OF FEATURES IN init_ntf_calculation(): \n {e}"
Expand Down Expand Up @@ -1037,7 +1036,7 @@ def __init__(self, **kwargs) -> None:
self.name_text_types = kwargs['name_text_types'] if 'name_text_types' in kwargs else None
self.processing_name = kwargs['processing_name'] if 'processing_name' in kwargs else None
self.scale_name = kwargs['scale_name'] if 'scale_name' in kwargs else None

self.extract = kwargs['extract'] if 'extract' in kwargs else {}

class GLCM:
"""Organizes the GLCM features extraction parameters"""
Expand Down
2 changes: 1 addition & 1 deletion MEDimage/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
logging.getLogger(__name__).addHandler(stream_handler)

__author__ = "MEDomicsLab consortium"
__version__ = "0.9.7"
__version__ = "0.9.8"
__copyright__ = "Copyright (C) MEDomicsLab consortium"
__license__ = "GNU General Public License 3.0"
__maintainer__ = "MAHDI AIT LHAJ LOUTFI"
Expand Down
131 changes: 87 additions & 44 deletions MEDimage/biomarkers/BatchExtractor.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,8 @@ def __init__(
path_csv: Union[str, Path],
path_params: Union[str, Path],
path_save: Union[str, Path],
n_batch: int = 4
n_batch: int = 4,
skip_existing: bool = False
) -> None:
"""
constructor of the BatchExtractor class
Expand All @@ -41,6 +42,7 @@ def __init__(
self.roi_types = []
self.roi_type_labels = []
self.n_bacth = n_batch
self.skip_existing = skip_existing

def __load_and_process_params(self) -> Dict:
"""Load and process the computing & batch parameters from JSON file"""
Expand Down Expand Up @@ -82,6 +84,14 @@ def __compute_radiomics_one_patient(
# Setting up logging settings
logging.basicConfig(filename=log_file, level=logging.DEBUG, force=True)

# Check if features are already computed for the current scan
if self.skip_existing:
modality = name_patient.split('.')[1]
name_save = name_patient.split('.')[0] + f'({roi_type_label})' + f'.{modality}.json'
if Path(self._path_save / f'features({roi_type})' / name_save).exists():
logging.info("Skipping existing features for scan: {name_patient}")
return log_file

# start timer
t_start = time()

Expand All @@ -94,7 +104,7 @@ def __compute_radiomics_one_patient(
with open(self._path_read / name_patient, 'rb') as f: medscan = pickle.load(f)
medscan = MEDimage.MEDscan(medscan)
except Exception as e:
logging.error(f"\n ERROR LOADING PATIENT {name_patient}:\n {e}")
print(f"\n ERROR LOADING PATIENT {name_patient}:\n {e}")
return None

# Init processing & computation parameters
Expand Down Expand Up @@ -197,35 +207,44 @@ def __compute_radiomics_one_patient(

# Morphological features extraction
try:
morph = MEDimage.biomarkers.morph.extract_all(
vol=vol_obj.data,
mask_int=roi_obj_int.data,
mask_morph=roi_obj_morph.data,
res=medscan.params.process.scale_non_text,
intensity_type=medscan.params.process.intensity_type
)
if medscan.params.radiomics.extract['Morph']:
morph = MEDimage.biomarkers.morph.extract_all(
vol=vol_obj.data,
mask_int=roi_obj_int.data,
mask_morph=roi_obj_morph.data,
res=medscan.params.process.scale_non_text,
intensity_type=medscan.params.process.intensity_type
)
else:
morph = None
except Exception as e:
logging.error(f'PROBLEM WITH COMPUTATION OF MORPHOLOGICAL FEATURES {e}')
morph = None

# Local intensity features extraction
try:
local_intensity = MEDimage.biomarkers.local_intensity.extract_all(
img_obj=vol_obj.data,
roi_obj=roi_obj_int.data,
res=medscan.params.process.scale_non_text,
intensity_type=medscan.params.process.intensity_type
)
if medscan.params.radiomics.extract['LocalIntensity']:
local_intensity = MEDimage.biomarkers.local_intensity.extract_all(
img_obj=vol_obj.data,
roi_obj=roi_obj_int.data,
res=medscan.params.process.scale_non_text,
intensity_type=medscan.params.process.intensity_type
)
else:
local_intensity = None
except Exception as e:
logging.error(f'PROBLEM WITH COMPUTATION OF LOCAL INTENSITY FEATURES {e}')
local_intensity = None

# statistical features extraction
try:
stats = MEDimage.biomarkers.stats.extract_all(
vol=vol_int_re,
intensity_type=medscan.params.process.intensity_type
)
if medscan.params.radiomics.extract['Stats']:
stats = MEDimage.biomarkers.stats.extract_all(
vol=vol_int_re,
intensity_type=medscan.params.process.intensity_type
)
else:
stats = None
except Exception as e:
logging.error(f'PROBLEM WITH COMPUTATION OF STATISTICAL FEATURES {e}')
stats = None
Expand All @@ -240,9 +259,12 @@ def __compute_radiomics_one_patient(

# Intensity histogram features extraction
try:
int_hist = MEDimage.biomarkers.intensity_histogram.extract_all(
vol=vol_quant_re
)
if medscan.params.radiomics.extract['IntensityHistogram']:
int_hist = MEDimage.biomarkers.intensity_histogram.extract_all(
vol=vol_quant_re
)
else:
int_hist = None
except Exception as e:
logging.error(f'PROBLEM WITH COMPUTATION OF INTENSITY HISTOGRAM FEATURES {e}')
int_hist = None
Expand All @@ -262,12 +284,15 @@ def __compute_radiomics_one_patient(
wd = 1

# Intensity volume histogram features extraction
int_vol_hist = MEDimage.biomarkers.int_vol_hist.extract_all(
medscan=medscan,
vol=vol_quant_re,
vol_int_re=vol_int_re,
wd=wd
)
if medscan.params.radiomics.extract['IntensityVolumeHistogram']:
int_vol_hist = MEDimage.biomarkers.int_vol_hist.extract_all(
medscan=medscan,
vol=vol_quant_re,
vol_int_re=vol_int_re,
wd=wd
)
else:
int_vol_hist = None

# End of Non-Texture features extraction
logging.info(f"End of non-texture features extraction: {time() - start}\n")
Expand Down Expand Up @@ -372,52 +397,70 @@ def __compute_radiomics_one_patient(

# GLCM features extraction
try:
glcm = MEDimage.biomarkers.glcm.extract_all(
vol=vol_quant_re,
dist_correction=medscan.params.radiomics.glcm.dist_correction)
if medscan.params.radiomics.extract['GLCM']:
glcm = MEDimage.biomarkers.glcm.extract_all(
vol=vol_quant_re,
dist_correction=medscan.params.radiomics.glcm.dist_correction)
else:
glcm = None
except Exception as e:
logging.error(f'PROBLEM WITH COMPUTATION OF GLCM FEATURES {e}')
glcm = None

# GLRLM features extraction
try:
glrlm = MEDimage.biomarkers.glrlm.extract_all(
vol=vol_quant_re,
dist_correction=medscan.params.radiomics.glrlm.dist_correction)
if medscan.params.radiomics.extract['GLRLM']:
glrlm = MEDimage.biomarkers.glrlm.extract_all(
vol=vol_quant_re,
dist_correction=medscan.params.radiomics.glrlm.dist_correction)
else:
glrlm = None
except Exception as e:
logging.error(f'PROBLEM WITH COMPUTATION OF GLRLM FEATURES {e}')
glrlm = None

# GLSZM features extraction
try:
glszm = MEDimage.biomarkers.glszm.extract_all(
vol=vol_quant_re)
if medscan.params.radiomics.extract['GLSZM']:
glszm = MEDimage.biomarkers.glszm.extract_all(
vol=vol_quant_re)
else:
glszm = None
except Exception as e:
logging.error(f'PROBLEM WITH COMPUTATION OF GLSZM FEATURES {e}')
glszm = None

# GLDZM features extraction
try:
gldzm = MEDimage.biomarkers.gldzm.extract_all(
vol_int=vol_quant_re,
mask_morph=roi_obj_morph.data)
if medscan.params.radiomics.extract['GLDZM']:
gldzm = MEDimage.biomarkers.gldzm.extract_all(
vol_int=vol_quant_re,
mask_morph=roi_obj_morph.data)
else:
gldzm = None
except Exception as e:
logging.error(f'PROBLEM WITH COMPUTATION OF GLDZM FEATURES {e}')
gldzm = None

# NGTDM features extraction
try:
ngtdm = MEDimage.biomarkers.ngtdm.extract_all(
vol=vol_quant_re,
dist_correction=medscan.params.radiomics.ngtdm.dist_correction)
if medscan.params.radiomics.extract['NGTDM']:
ngtdm = MEDimage.biomarkers.ngtdm.extract_all(
vol=vol_quant_re,
dist_correction=medscan.params.radiomics.ngtdm.dist_correction)
else:
ngtdm = None
except Exception as e:
logging.error(f'PROBLEM WITH COMPUTATION OF NGTDM FEATURES {e}')
ngtdm = None

# NGLDM features extraction
try:
ngldm = MEDimage.biomarkers.ngldm.extract_all(
vol=vol_quant_re)
if medscan.params.radiomics.extract['NGLDM']:
ngldm = MEDimage.biomarkers.ngldm.extract_all(
vol=vol_quant_re)
else:
ngldm = None
except Exception as e:
logging.error(f'PROBLEM WITH COMPUTATION OF NGLDM FEATURES {e}')
ngldm = None
Expand Down
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