z-rad 24.9.1__tar.gz

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Files changed (20) hide show
  1. z_rad-24.9.1/LICENSE +21 -0
  2. z_rad-24.9.1/PKG-INFO +141 -0
  3. z_rad-24.9.1/README.md +118 -0
  4. z_rad-24.9.1/pyproject.toml +37 -0
  5. z_rad-24.9.1/zrad/__init__.py +1 -0
  6. z_rad-24.9.1/zrad/gui/__init__.py +0 -0
  7. z_rad-24.9.1/zrad/gui/_base_tab.py +420 -0
  8. z_rad-24.9.1/zrad/gui/filt_tab.py +698 -0
  9. z_rad-24.9.1/zrad/gui/prep_tab.py +473 -0
  10. z_rad-24.9.1/zrad/gui/rad_tab.py +654 -0
  11. z_rad-24.9.1/zrad/gui/toolbox_gui.py +180 -0
  12. z_rad-24.9.1/zrad/logic/__init__.py +2 -0
  13. z_rad-24.9.1/zrad/logic/exceptions.py +13 -0
  14. z_rad-24.9.1/zrad/logic/filtering.py +82 -0
  15. z_rad-24.9.1/zrad/logic/filtering_definitions.py +518 -0
  16. z_rad-24.9.1/zrad/logic/image.py +476 -0
  17. z_rad-24.9.1/zrad/logic/preprocessing.py +119 -0
  18. z_rad-24.9.1/zrad/logic/radiomics.py +724 -0
  19. z_rad-24.9.1/zrad/logic/radiomics_definitions.py +2409 -0
  20. z_rad-24.9.1/zrad/logic/toolbox_logic.py +182 -0
z_rad-24.9.1/LICENSE ADDED
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+ MIT License
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+
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+ Copyright (c) 2024 Z-Rad developers
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
z_rad-24.9.1/PKG-INFO ADDED
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+ Metadata-Version: 2.1
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+ Name: z-rad
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+ Version: 24.9.1
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+ Summary: Z-Rad is a radiomic feature extraction software with GUI and API.
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+ Author: Radiomics Team of Radiation Oncology Department at University Hospital Zurich
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+ Author-email: zrad@usz.ch
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+ Requires-Python: >=3.12,<4.0
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: Programming Language :: Python :: 3.12
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+ Requires-Dist: joblib (>=1.4.2,<2.0.0)
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+ Requires-Dist: numpy (>=2.1.1,<3.0.0)
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+ Requires-Dist: opencv-python-headless (>=4.10.0.84,<5.0.0.0)
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+ Requires-Dist: openpyxl (>=3.1.5,<4.0.0)
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+ Requires-Dist: pandas (>=2.2.2,<3.0.0)
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+ Requires-Dist: pydicom (>=3.0.0,<4.0.0)
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+ Requires-Dist: pyqt5 (>=5.15.11,<6.0.0)
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+ Requires-Dist: pywavelets (>=1.7.0,<2.0.0)
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+ Requires-Dist: scikit-image (>=0.24.0,<0.25.0)
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+ Requires-Dist: scikit-learn (>=1.5.2,<2.0.0)
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+ Requires-Dist: scipy (>=1.14.1,<2.0.0)
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+ Requires-Dist: simpleitk (>=2.4.0,<3.0.0)
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+ Description-Content-Type: text/markdown
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+
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+ # Z-RAD
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+
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+ <img src="https://raw.githubusercontent.com/radiomics-usz/z-rad/master/doc/logos/ZRadLogo.jpg" width="600" alt="Z-Rad logo"/>
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+
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+ Radiomics is the high-throughput extraction of quantitative features from medical images,
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+ revolutionizing personalized medicine and enhancing clinical decision-making.
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+ Despite its potential, radiomics faces several challenges, including the need for programming skills
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+ and lack of standardization.
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+
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+ **Z-Rad (Zurich Radiomics)**, developed by the Radiation Oncology Department at the University Hospital Zurich,
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+ addresses these issues by offering a user-friendly, IBSI-compliant, and open-source solution for radiomics analysis.
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+
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+ ## Z-Rad Features
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+
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+ ### User-Friendly Interface
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+ - **Graphical User Interface (GUI)**: Designed for medical professionals with no programming skills.
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+ - **Application Programming Interface (API)**: Allows researchers to customize, automate, and extend Z-Rad functionalities using Python.
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+
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+ ### Compatibility
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+ - **Medical Data Formats**: Supports CT, PET, and MR imaging modalities in both DICOM and NIfTI formats.
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+ - **Operating Systems**: Windows, macOS, and Linux.
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+
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+ ### Standard Compliance
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+ - **IBSI Compliance**: Adheres to [IBSI I](https://arxiv.org/abs/1612.07003) and [IBSI II](https://arxiv.org/abs/2006.05470) standards for reproducible and comparable radiomics features.
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+
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+
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+ ## Software Architecture and Design
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+
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+ ### Backend
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+ - **Programming Language**: Python.
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+ - **Dependencies**:
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+ - Joblib
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+ - NumPy
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+ - OpenCV
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+ - OpenPyXL
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+ - Pandas
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+ - PyDicom
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+ - PyQt5
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+ - PyWavelets
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+ - Scikit-image
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+ - Scikit-learn
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+ - SciPy
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+ - SimpleITK
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+
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+ ### Radiomics Extraction Pathways
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+ <img src="https://raw.githubusercontent.com/radiomics-usz/z-rad/master/doc/images/ZRadExtractionPathways.png" width="600" alt="Z-Rad Pathways"/>
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+
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+ ## Graphical User Interface (GUI) and Application Programming Interface (API)
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+
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+ Both GUI and API are structured into three primary classes: **Resampling**, **Filtering**, and **Radiomics**:
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+
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+ ### Resampling
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+ Z-Rad supports image resampling alone, alongside regions of interest (ROI) masks, or converting DICOM files to NIfTI
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+ images and masks without resampling. Resampling can be performed in 3D or 2D (axial slice-wise), with nearest
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+ neighbors, linear, B-spline, and Gaussian strategies.
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+
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+ ### Filtering
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+ This tab requires users to define the desired filter settings.
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+ The current version of Z-Rad supports mean, Laplace of Gaussian, Laws kernels,
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+ and wavelet (Daubechies 2, Daubechies 3, first-order Coiflet, and Haar) filters.
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+
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+ ### Radiomics Feature Extraction
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+ Parameters for radiomics feature extraction include the intensity re-segmentation
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+ (e.g., HU for CT or SUV for PET within ROIs) and intensity outlier filtering,
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+ discretisation strategies, and a variety of radiomics feature aggregation methods covering 2D, 2.5D, and 3D options.
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+ Radiomic features include shape, intensity, grey level co-occurrence matrix (GLCM),
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+ grey level run length matrix (GLRLM), grey level distance zone matrix (GLDZM),
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+ neighbouring gray tone difference matrix (NGTDM),
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+ and neighbouring gray level dependance matrix (NGLDM) features families.
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+
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+ ## Error and Warning Handling
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+
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+ - **GUI**: Uses warning pop-up messages for immediate feedback.
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+ - **API**: Records processes in log files for comprehensive documentation.
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+
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+ ## Installation and Get Started
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+
101
+ ### Windows executable file:
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+ The simplest way to run Z-Rad on Windows is to start the `main.exe` attached to every Z-Rad release.
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+
104
+ An executable can be also generated from the source files by running
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+ ```sh
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+ python generate_executable.py
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+ ```
108
+ Creating an executable requires [PyInstaller](https://pyinstaller.readthedocs.io).
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+ The executable is going to be saved in *dist/* directory.
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+
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+ ### Windows, Linux, and macOS
112
+ For users familiar with Python programming langauage, we recommend:
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+
114
+ 1. Download the Z-Rad repository
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+ 2. Open the terminal and navigate to the project directory
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+ 3. Install requirements by typing in the terminal:
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+
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+ ```sh
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+ pip install -r requirements.txt
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+ ```
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+
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+ 4. Run the `main.py` file:
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+
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+ ```sh
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+ python main.py
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+ ```
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+
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+ ### API
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+ ```sh
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+ pip install z-rad
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+ ```
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+
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+ ## License
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+
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+ Z-Rad is an open-source project licensed under the MIT License.
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+
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+ ## Contact
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+
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+ For any questions or feedback, please contact us at [zrad@usz.ch](mailto:zrad@usz.ch).
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+
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+ ---
z_rad-24.9.1/README.md ADDED
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+ # Z-RAD
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+
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+ <img src="https://raw.githubusercontent.com/radiomics-usz/z-rad/master/doc/logos/ZRadLogo.jpg" width="600" alt="Z-Rad logo"/>
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+
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+ Radiomics is the high-throughput extraction of quantitative features from medical images,
6
+ revolutionizing personalized medicine and enhancing clinical decision-making.
7
+ Despite its potential, radiomics faces several challenges, including the need for programming skills
8
+ and lack of standardization.
9
+
10
+ **Z-Rad (Zurich Radiomics)**, developed by the Radiation Oncology Department at the University Hospital Zurich,
11
+ addresses these issues by offering a user-friendly, IBSI-compliant, and open-source solution for radiomics analysis.
12
+
13
+ ## Z-Rad Features
14
+
15
+ ### User-Friendly Interface
16
+ - **Graphical User Interface (GUI)**: Designed for medical professionals with no programming skills.
17
+ - **Application Programming Interface (API)**: Allows researchers to customize, automate, and extend Z-Rad functionalities using Python.
18
+
19
+ ### Compatibility
20
+ - **Medical Data Formats**: Supports CT, PET, and MR imaging modalities in both DICOM and NIfTI formats.
21
+ - **Operating Systems**: Windows, macOS, and Linux.
22
+
23
+ ### Standard Compliance
24
+ - **IBSI Compliance**: Adheres to [IBSI I](https://arxiv.org/abs/1612.07003) and [IBSI II](https://arxiv.org/abs/2006.05470) standards for reproducible and comparable radiomics features.
25
+
26
+
27
+ ## Software Architecture and Design
28
+
29
+ ### Backend
30
+ - **Programming Language**: Python.
31
+ - **Dependencies**:
32
+ - Joblib
33
+ - NumPy
34
+ - OpenCV
35
+ - OpenPyXL
36
+ - Pandas
37
+ - PyDicom
38
+ - PyQt5
39
+ - PyWavelets
40
+ - Scikit-image
41
+ - Scikit-learn
42
+ - SciPy
43
+ - SimpleITK
44
+
45
+ ### Radiomics Extraction Pathways
46
+ <img src="https://raw.githubusercontent.com/radiomics-usz/z-rad/master/doc/images/ZRadExtractionPathways.png" width="600" alt="Z-Rad Pathways"/>
47
+
48
+ ## Graphical User Interface (GUI) and Application Programming Interface (API)
49
+
50
+ Both GUI and API are structured into three primary classes: **Resampling**, **Filtering**, and **Radiomics**:
51
+
52
+ ### Resampling
53
+ Z-Rad supports image resampling alone, alongside regions of interest (ROI) masks, or converting DICOM files to NIfTI
54
+ images and masks without resampling. Resampling can be performed in 3D or 2D (axial slice-wise), with nearest
55
+ neighbors, linear, B-spline, and Gaussian strategies.
56
+
57
+ ### Filtering
58
+ This tab requires users to define the desired filter settings.
59
+ The current version of Z-Rad supports mean, Laplace of Gaussian, Laws kernels,
60
+ and wavelet (Daubechies 2, Daubechies 3, first-order Coiflet, and Haar) filters.
61
+
62
+ ### Radiomics Feature Extraction
63
+ Parameters for radiomics feature extraction include the intensity re-segmentation
64
+ (e.g., HU for CT or SUV for PET within ROIs) and intensity outlier filtering,
65
+ discretisation strategies, and a variety of radiomics feature aggregation methods covering 2D, 2.5D, and 3D options.
66
+ Radiomic features include shape, intensity, grey level co-occurrence matrix (GLCM),
67
+ grey level run length matrix (GLRLM), grey level distance zone matrix (GLDZM),
68
+ neighbouring gray tone difference matrix (NGTDM),
69
+ and neighbouring gray level dependance matrix (NGLDM) features families.
70
+
71
+ ## Error and Warning Handling
72
+
73
+ - **GUI**: Uses warning pop-up messages for immediate feedback.
74
+ - **API**: Records processes in log files for comprehensive documentation.
75
+
76
+ ## Installation and Get Started
77
+
78
+ ### Windows executable file:
79
+ The simplest way to run Z-Rad on Windows is to start the `main.exe` attached to every Z-Rad release.
80
+
81
+ An executable can be also generated from the source files by running
82
+ ```sh
83
+ python generate_executable.py
84
+ ```
85
+ Creating an executable requires [PyInstaller](https://pyinstaller.readthedocs.io).
86
+ The executable is going to be saved in *dist/* directory.
87
+
88
+ ### Windows, Linux, and macOS
89
+ For users familiar with Python programming langauage, we recommend:
90
+
91
+ 1. Download the Z-Rad repository
92
+ 2. Open the terminal and navigate to the project directory
93
+ 3. Install requirements by typing in the terminal:
94
+
95
+ ```sh
96
+ pip install -r requirements.txt
97
+ ```
98
+
99
+ 4. Run the `main.py` file:
100
+
101
+ ```sh
102
+ python main.py
103
+ ```
104
+
105
+ ### API
106
+ ```sh
107
+ pip install z-rad
108
+ ```
109
+
110
+ ## License
111
+
112
+ Z-Rad is an open-source project licensed under the MIT License.
113
+
114
+ ## Contact
115
+
116
+ For any questions or feedback, please contact us at [zrad@usz.ch](mailto:zrad@usz.ch).
117
+
118
+ ---
z_rad-24.9.1/pyproject.toml ADDED
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+ [tool.poetry]
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+ name = "z-rad"
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+ version = "24.9.1"
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+ description = "Z-Rad is a radiomic feature extraction software with GUI and API."
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+ authors = ["Radiomics Team of Radiation Oncology Department at University Hospital Zurich <zrad@usz.ch>"]
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+ readme = "README.md"
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+
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+ packages = [
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+ { include = "zrad" }
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+ ]
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+
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+ [tool.poetry.dependencies]
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+ python = "^3.12"
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+ pydicom = "^3.0.0"
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+ pyqt5 = "^5.15.11"
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+ numpy = "^2.1.1"
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+ pandas = "^2.2.2"
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+ simpleitk = "^2.4.0"
19
+ scipy = "^1.14.1"
20
+ pywavelets = "^1.7.0"
21
+ openpyxl = "^3.1.5"
22
+ scikit-image = "^0.24.0"
23
+ scikit-learn = "^1.5.2"
24
+ opencv-python-headless = "^4.10.0.84"
25
+ joblib = "^1.4.2"
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+
27
+
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+ [build-system]
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+ requires = ["poetry-core", "poetry-dynamic-versioning"]
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+ build-backend = "poetry_dynamic_versioning.backend"
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+
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+ [tool.poetry-dynamic-versioning]
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+ enable = false
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+
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+ [tool.poetry-dynamic-versioning.from-file]
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+ source = "zrad/__init__.py"
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+ pattern = "^__version__ = [\"'](?P<version>.+?)[\"']$"
z_rad-24.9.1/zrad/__init__.py ADDED
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+ __version__ = "24.9.1"
z_rad-24.9.1/zrad/gui/__init__.py ADDED
File without changes