from .mod_glcm import glcm, glcm_units
from .mod_gldm import gldm, gldm_units
from .mod_glrlm import glrlm, glrlm_units
from .mod_glszm import glszm, glszm_units
from .mod_ngtdm import ngtdm, ngtdm_units
[docs]
def texture(image, mask, binWidth=25, distances=[1], distance=1, alpha=0, levels=None, connectivity=None, symmetricalGLCM=True, weightingNorm=None):
"""
Wrapper to compute all texture features (GLCM, GLDM, GLRLM, GLSZM, NGTDM) in a single call.
This function aggregates the 5 standard texture matrices, handling the prefixing of keys
(e.g., 'Contrast' becomes 'glcm_Contrast', 'gldm_Contrast', etc.) to avoid name collisions.
Args:
image (np.ndarray): 3D image array containing voxel intensities.
mask (np.ndarray): 3D mask array (same shape as image), where non-zero values indicate the ROI.
binWidth (float, optional): Bin width for discretization (used by all matrices). Default is 25.
distances (list, optional): List of pixel distances for GLCM. Default is [1].
distance (int, optional): Integer pixel distance for NGTDM. Default is 1.
alpha (int, optional): Alpha cutoff for GLDM dependence. Default is 0.
levels (int, optional): Manual number of levels (overrides binWidth if set). Default is None.
connectivity (int, optional): Connectivity kernel for GLSZM (e.g., 6, 18, 26). Default is None (26).
symmetricalGLCM (bool, optional): Whether to symmetrize the GLCM. Default is True.
weightingNorm (str, optional): GLCM weighting norm ('manhattan', 'euclidean', 'infinity'). Default is None.
Returns:
dict: Combined dictionary of all texture features (~75 features) with standard prefixes:
- **glcm_**: Features from Gray Level Co-occurrence Matrix.
- **gldm_**: Features from Gray Level Dependence Matrix.
- **glrlm_**: Features from Gray Level Run Length Matrix.
- **glszm_**: Features from Gray Level Size Zone Matrix.
- **ngtdm_**: Features from Neighborhood Gray Tone Difference Matrix.
Example:
>>> import numpyradiomics as npr
>>> # Generate a noisy ellipsoid
>>> img, mask = npr.dro.noisy_ellipsoid(radii_mm=(15, 15, 15), intensity_range=(0, 100))
>>>
>>> # Compute all texture features
>>> feats = npr.texture(img, mask, binWidth=10)
>>>
>>> print(f"GLCM Contrast: {feats['glcm_Contrast']:.4f}")
GLCM Contrast: 12.4501
>>> print(f"GLSZM Zone %: {feats['glszm_ZonePercentage']:.4f}")
GLSZM Zone %: 0.8912
"""
results = {}
# --- 1. GLCM ---
# Signature: glcm(img, mask, binWidth, distances, symmetricalGLCM, weightingNorm)
try:
res = glcm(image, mask,
binWidth=binWidth,
distances=distances,
symmetricalGLCM=symmetricalGLCM,
weightingNorm=weightingNorm)
results.update({f"glcm_{k}": v for k, v in res.items()})
except Exception as e:
print(f"GLCM failed: {e}")
# --- 2. GLDM ---
try:
res = gldm(image, mask, binWidth=binWidth, alpha=alpha, levels=levels)
results.update({f"gldm_{k}": v for k, v in res.items()})
except Exception as e:
print(f"GLDM failed: {e}")
# --- 3. GLRLM ---
try:
res = glrlm(image, mask, binWidth=binWidth, levels=levels)
results.update({f"glrlm_{k}": v for k, v in res.items()})
except Exception as e:
print(f"GLRLM failed: {e}")
# --- 4. GLSZM ---
try:
res = glszm(image, mask, binWidth=binWidth, levels=levels, connectivity=connectivity)
results.update({f"glszm_{k}": v for k, v in res.items()})
except Exception as e:
print(f"GLSZM failed: {e}")
# --- 5. NGTDM ---
try:
res = ngtdm(image, mask, binWidth=binWidth, distance=distance)
results.update({f"ngtdm_{k}": v for k, v in res.items()})
except Exception as e:
print(f"NGTDM failed: {e}")
return results
[docs]
def texture_units(intensity_unit='HU'):
"""
Returns units of returned texture metrics with correct prefixes.
Args:
intensity_unit (str, optional): units of signal intensity (e.g., 'HU', 'SUV'). Default is 'HU'.
Returns:
dict: Dictionary mapping prefixed feature names to their units.
Example:
>>> from numpyradiomics import texture_units
>>> units = texture_units(intensity_unit='HU')
>>> print(units['glcm_Contrast'])
HU^2
>>> print(units['ngtdm_Coarseness'])
HU^-1
"""
units = {}
# --- 1. GLCM ---
glcm_u = glcm_units(intensity_unit)
units.update({f"glcm_{k}": v for k, v in glcm_u.items()})
# --- 2. GLDM ---
gldm_u = gldm_units(intensity_unit)
units.update({f"gldm_{k}": v for k, v in gldm_u.items()})
# --- 3. GLRLM ---
glrlm_u = glrlm_units(intensity_unit)
units.update({f"glrlm_{k}": v for k, v in glrlm_u.items()})
# --- 4. GLSZM ---
glszm_u = glszm_units(intensity_unit)
units.update({f"glszm_{k}": v for k, v in glszm_u.items()})
# --- 5. NGTDM ---
ngtdm_u = ngtdm_units(intensity_unit)
units.update({f"ngtdm_{k}": v for k, v in ngtdm_u.items()})
return units
