radiomicsj 2.1.18

Python wrapper for RadiomicsJ (Java-based radiomics feature extraction)

RadiomicsJ (Python Wrapper)

RadiomicsJ is a Python wrapper for the Java-based radiomics feature extraction library RadiomicsJ. It provides highly accurate, IBSI-compliant feature calculations directly from Python, utilizing JPype to run on the JVM.

Prerequisites

• Java 8 or higher must be installed and available in your system path.
• Note: If you are using Google Colab, the JDK is pre-installed, so no additional setup is required.

Installation

pip install radiomicsj

Quick Start

You can compute features by passing file paths or NumPy arrays directly.

1. Using File Paths

from radiomicsj import calculate_features

'''
path to folders

# pattern1 : series folder
image_folder/images
mask_folder/masks

# pattern2 : NIfTI or Tiff, also specify parent folder.
image_folder/image.nii.gz
mask_folder/mask.nii.gz
image_folder/image.tif
mask_folder/mask.tif
'''

df = calculate_features(payh_to_image_folder, path_to_mask_folder)
print(df.head())

2. Using NumPy Arrays (In-Memory Processing)

import numpy as np
from radiomicsj import calculate_features

# z,y,z order
image_np = np.random.rand(5, 10, 10)
mask_np = np.ones((5, 10, 10)) # radiomicsj default label is 1.

# Specify voxel spacing (Width, Height, Depth)
df = calculate_features(image_np, mask_np, spacing=(1.0, 1.0, 1.0))

Using a Configuration file

from radiomicsj.core import RadiomicsJExtractor

# Initialize with a properties file
extractor = RadiomicsJExtractor("path/to/params.properties")

results = []
for path_to_image, path_to_mask in my_image_list:
    df = extractor.execute(path_to_image, path_to_mask)
    results.append(df)

# To update properties dynamically:
# extractor.load_settings("path/to/another_params.properties")

Advanced Usage

1. Specific Feature Calculation (Texture & Non-Texture)

You can directly access individual feature classes (e.g., GLCM, GLSZM, Morphological, IntensityBasedStatistical) to extract specific features or retrieve raw texture matrices as NumPy arrays.

import numpy as np
from radiomicsj import GLCM, IntensityBasedStatistical

image_np = np.random.rand(5, 20, 20)
mask_np = np.ones((5, 20, 20))
spacing = (1.0, 1.0, 1.0)

# --- Texture Features ---
glcm = GLCM(image_np, mask_np, spacing, n_bins=16)

# Calculate ONLY specific features using IDE-friendly constants
features = glcm.calculate_features([GLCM.JointEntropy, GLCM.Contrast])
print(features) 
# -> {'JointEntropy': 2.45, 'Contrast': 5.12}

# Get the raw GLCM matrix as a NumPy array for specific angle (Z, Y, X)
matrix = glcm.get_matrix(angle=(0, 1, 0))
print(matrix.shape) 
# -> (16, 16)

# --- Non-Texture Features ---
stats = IntensityBasedStatistical(image_np, mask_np, spacing)
stat_features = stats.calculate_features([IntensityBasedStatistical.Mean, IntensityBasedStatistical.Skewness])

Note regarding Discretized Intensity-Based Statistics: Discretized IntensityBasedStatisticalFeatures are obtained by passing pre-discretized image data to the standard IntensityBasedStatisticalFeature class.

2. Feature Map Generation (Visualization Texture Feature)

Generate 2D/3D parametric feature maps using a sliding window. RadiomicsJ optimizes this heavily by supporting strided calculations in Java followed by fast scipy-based linear interpolation in Python, drastically reducing computation time while keeping boundaries smooth and clean.

import numpy as np
import matplotlib.pyplot as plt
from radiomicsj.features import generate_feature_map
from radiomicsj import GLCM

# ... load your image_np and mask_np ...

settings = {
    "label": 1,
    "useBinCount": True,
    "nBins": 16
}

# Generate Feature Map
fmap = generate_feature_map(
    image_np=image_np,
    mask_np=mask_np,
    mask_label=1,
    spacing=(1.0, 1.0, 1.0),
    feature_class=GLCM,           # Target texture class
    feature_id=GLCM.JointEntropy, # Target feature
    settings=settings,
    filter_size=5,                # Sliding window size
    d2_mode=True,                 # 2D (True) or 3D (False) mode
    stride=2,                     # Skip pixels to speed up calculation, then interpolate
    slice_idx=-1                  # Calculate for all slices
)

# Plot the result
target_z = fmap.shape[0] // 2
fmap_slice = fmap[target_z, :, :].copy()
fmap_slice[mask_np[target_z, :, :] == 0] = np.nan # Make background transparent

plt.imshow(image_np[target_z, :, :], cmap='gray')
plt.imshow(fmap_slice, cmap='jet', alpha=0.6)
plt.title("GLCM Joint Entropy Feature Map")
plt.colorbar()
plt.show()

Citation

If you use RadiomicsJ in your research, please cite:

Kobayashi T. RadiomicsJ: a library to compute radiomic features. Radiol Phys Technol. 2022 Sep;15(3):255-263. doi: 10.1007/s12194-022-00664-4. Epub 2022 Jul 6. PMID: 35792994.