radiomicsj 2.1.16__tar.gz

radiomicsj-2.1.16/PKG-INFO

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+Metadata-Version: 2.4
+Name: radiomicsj
+Version: 2.1.16
+Summary: Python wrapper for RadiomicsJ
+Author: Tatsuaki Kobayashi
+Requires-Dist: jpype1>=1.3.0
+Requires-Dist: numpy
+Requires-Dist: pandas
+Dynamic: author
+Dynamic: requires-dist
+Dynamic: summary

radiomicsj-2.1.16/README.md

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+# RadiomicsJ (Python Wrapper)
+
+RadiomicsJ(Python wrapper) is an image feature extraction tool implemented in Java.
+
+## Main Function
+- Radiomics Feature calculation.
+- Calculation results will return by Pandas DataFrame.
+
+## Install Requirements
+
+### When use : pip
+You need install Java (>= JDK 8), and add it's jdk/bin to environment path.
+
+```bash
+pip install radiomicsj
+
+## Example
+
+```python
+from radiomicsj.core import RadiomicsJExtractor
+
+# init
+extractor = RadiomicsJExtractor("path/to/params.properties")
+
+results = []
+for image_path, mask_path in my_image_list:
+    df = extractor.execute(image_path, mask_path)
+    results.append(df)
+
+# If you want to set properties case by case.
+# extractor.load_settings("path/to/another_params.properties")

radiomicsj-2.1.16/radiomicsj/__init__.py

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+'''
+@Copy right Visionary Imaging Services, Inc.
+@since 2026
+'''
+
+from .core import start_jvm, calculate_features
+
+__all__ = ["start_jvm", "calculate_features"]

radiomicsj-2.1.16/radiomicsj/core.py

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+'''
+@CopyRight : Visionary Imaging Services, Inc.
+'''
+
+import os
+import math
+import jpype
+import jpype.imports
+import pandas as pd
+import numpy as np
+
+# Mavenのビルド時に自動置換されるバージョン情報
+__version__ = "2.1.16"
+if __version__.startswith("${"):
+    __version__ = "0.0.0.dev0"
+
+def start_jvm():
+    """JVMを起動し、jarsフォルダ内のすべてのJARをクラスパスに追加する"""
+    if jpype.isJVMStarted():
+        return
+    
+    package_dir = os.path.dirname(os.path.abspath(__file__))
+    jars_dir = os.path.join(package_dir, "jars")
+    
+    if not os.path.exists(jars_dir):
+        raise FileNotFoundError(f"Jars directory not found at: {jars_dir}")
+    
+    jar_path = os.path.join(jars_dir, "*")
+    jpype.startJVM(classpath=[jar_path])
+
+
+class RadiomicsJExtractor:
+    """
+    RadiomicsJの機能を利用して特徴量を抽出するクラス。
+    インスタンス化時に一度だけ設定を読み込むことで、連続処理を高速化します。
+    """
+    
+    def __init__(self, config_prop_path: str = None):
+        """
+        Args:
+            config_prop_path (str, optional): 設定プロパティファイルのパス。
+        """
+        if not jpype.isJVMStarted():
+            start_jvm()
+            
+        self._RadiomicsJClass = jpype.JClass("io.github.tatsunidas.radiomics.main.RadiomicsJ")
+        self.radj = self._RadiomicsJClass()
+        
+        # ImageJのパッケージを取得
+        self.ij = jpype.JPackage("ij")
+        
+        if config_prop_path is not None:
+            self.load_settings(config_prop_path)
+
+    def load_settings(self, config_prop_path: str):
+        """プロパティファイルを読み込み、設定を更新します。"""
+        if not os.path.exists(config_prop_path):
+            raise FileNotFoundError(f"Config file not found: {config_prop_path}")
+        self.radj.loadSettings(config_prop_path)
+
+    def _numpy_to_imageplus(self, arr: np.ndarray, spacing: tuple, title: str) -> "ij.ImagePlus":
+       """
+       NumPy ndarray to ImagePlus directly.
+       arr : (Z, Y, X) 3d-array, if ndarray sorted by ordered (X, Y, Z), do np.transpose(arr, (2, 1, 0)) before input. 
+       spacing : (x,y,z) voxel size
+       """
+       # ImageJは内部的にfloat配列を扱うため、float32に変換
+       arr_f = arr.astype(np.float32)
+       
+       if arr.ndim == 2:
+           h, w = arr_f.shape
+             # メモリコピーを最小限にJArrayへ変換
+           jarr = jpype.JArray(jpype.JFloat)(arr_f.ravel())
+           proc = self.ij.process.FloatProcessor(w, h, jarr)
+           img_plus = self.ij.ImagePlus(title, proc)
+            
+           cal = img_plus.getCalibration()
+           cal.pixelWidth = spacing[0]
+           cal.pixelHeight = spacing[1]
+            
+       elif arr.ndim == 3:
+           d, h, w = arr_f.shape
+           stack = self.ij.ImageStack(w, h)
+           
+           for i in range(d):
+                 # 1スライスごとにJArrayに変換してスタックに追加
+               slice_arr = arr_f[i, :, :]
+               jarr = jpype.JArray(jpype.JFloat)(slice_arr.ravel())
+               proc = self.ij.process.FloatProcessor(w, h, jarr)
+               stack.addSlice(str(i), proc)
+                
+           img_plus = self.ij.ImagePlus(title, stack)
+            
+           cal = img_plus.getCalibration()
+           cal.pixelWidth = spacing[0]
+           cal.pixelHeight = spacing[1]
+           cal.pixelDepth = spacing[2]
+       else:
+           raise ValueError("NumPy array must be 2D or 3D.")
+            
+       return img_plus
+
+    def execute(self, image, mask, spacing=(1.0, 1.0, 1.0)) -> pd.DataFrame:
+       """
+        特徴量を計算し、Pandas DataFrameとして返します。
+       Args:
+           image: ファイルパス(str) または NumPy配列(np.ndarray)
+           mask: ファイルパス(str) または NumPy配列(np.ndarray)
+           spacing (tuple): NumPy配列の場合のピクセル間隔 (x, y, z)。デフォルトは(1.0, 1.0, 1.0)
+            
+       Returns:
+           pd.DataFrame: 計算された特徴量
+       """
+       # Imageの変換
+       if isinstance(image, np.ndarray):
+           target_image = self._numpy_to_imageplus(image, spacing, title="target_image")
+       else:
+           target_image = image
+
+       # Maskの変換
+       if isinstance(mask, np.ndarray):
+           target_mask = self._numpy_to_imageplus(mask, spacing, title="target_mask")
+       else:
+           target_mask = mask
+
+       # Java側の実行 (JPypeが自動で String と ImagePlus のオーバーロードを判別してくれます)
+       res_table = self.radj.execute(target_image, target_mask, self._RadiomicsJClass.targetLabel)
+        
+       if res_table is None or res_table.size() == 0:
+           return pd.DataFrame()
+
+       # DataFrameへの変換処理
+       headings = [str(h) for h in res_table.getHeadings()]
+       num_rows = res_table.size()
+       data_list = []
+       for i in range(num_rows):
+           row_dict = {}
+           for h in headings:
+               val = res_table.getValue(h, i)
+               if math.isnan(val):
+                   str_val = res_table.getStringValue(h, i)
+                   row_dict[h] = str(str_val) if str_val is not None else float('nan')
+               else:
+                   row_dict[h] = val
+           data_list.append(row_dict)
+        
+       return pd.DataFrame(data_list)
+
+def calculate_features(image, mask, config_prop_path: str = None, spacing=(1.0, 1.0, 1.0)) -> pd.DataFrame:
+    """単一処理用の簡易ラッパー関数"""
+    extractor = RadiomicsJExtractor(config_prop_path)
+    return extractor.execute(image, mask, spacing=spacing)
+    

radiomicsj-2.1.16/radiomicsj.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: radiomicsj
+Version: 2.1.16
+Summary: Python wrapper for RadiomicsJ
+Author: Tatsuaki Kobayashi
+Requires-Dist: jpype1>=1.3.0
+Requires-Dist: numpy
+Requires-Dist: pandas
+Dynamic: author
+Dynamic: requires-dist
+Dynamic: summary

radiomicsj-2.1.16/radiomicsj.egg-info/SOURCES.txt

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+README.md
+setup.py
+radiomicsj/__init__.py
+radiomicsj/core.py
+radiomicsj.egg-info/PKG-INFO
+radiomicsj.egg-info/SOURCES.txt
+radiomicsj.egg-info/dependency_links.txt
+radiomicsj.egg-info/requires.txt
+radiomicsj.egg-info/top_level.txt
+radiomicsj/jars/SparseBitSet-1.2.jar
+radiomicsj/jars/commons-cli-1.5.0.jar
+radiomicsj/jars/commons-codec-1.13.jar
+radiomicsj/jars/commons-collections4-4.4.jar
+radiomicsj/jars/commons-compress-1.19.jar
+radiomicsj/jars/commons-math3-3.6.1.jar
+radiomicsj/jars/curvesapi-1.06.jar
+radiomicsj/jars/ij-1.54p.jar
+radiomicsj/jars/poi-4.1.2.jar
+radiomicsj/jars/poi-ooxml-4.1.2.jar
+radiomicsj/jars/poi-ooxml-schemas-4.1.2.jar
+radiomicsj/jars/radiomicsj-2.1.16.jar
+radiomicsj/jars/vecmath-1.5.2.jar
+radiomicsj/jars/xmlbeans-3.1.0.jar

radiomicsj-2.1.16/radiomicsj.egg-info/dependency_links.txt

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+

radiomicsj-2.1.16/radiomicsj.egg-info/requires.txt

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+jpype1>=1.3.0
+numpy
+pandas

radiomicsj-2.1.16/radiomicsj.egg-info/top_level.txt

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+radiomicsj

radiomicsj-2.1.16/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

radiomicsj-2.1.16/setup.py

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+
+'''
+@Copy right Visionary Imaging Services, Inc.
+@since 2026
+'''
+
+from setuptools import setup
+
+version_str = "2.1.16"
+if version_str.startswith("${"):
+    version_str = "0.0.0.dev0"
+
+setup(
+    name="radiomicsj",
+    version=version_str,
+    description="Python wrapper for RadiomicsJ",
+    author="Tatsuaki Kobayashi",
+    packages=["radiomicsj", "radiomicsj.jars"],
+    package_data={
+        "radiomicsj": ["jars/*.jar"],
+    },
+    include_package_data=True,
+    install_requires=[
+        "jpype1>=1.3.0",
+        "numpy",
+        "pandas"
+    ],
+)