ctkit 0.1.0__py3-none-any.whl

ctkit-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: ctkit
+Version: 0.1.0
+Summary: A toolkit for reproducible CT image processing for AI and radiomics.
+Author-email: Joseph Rich <josephrich98@gmail.com>
+Maintainer-email: Joseph Rich <josephrich98@gmail.com>
+License: BSD 2-Clause License
+        
+        Copyright (c) 2026, Pachter Lab
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: Homepage, https://github.com/pachterlab/ctkit
+Project-URL: Source, https://github.com/pachterlab/ctkit
+Project-URL: Issues, https://github.com/pachterlab/ctkit/issues
+Keywords: AI,bioinformatics,deep learning,medicine,radiology,radiomics,CT,DICOM,NIfTI,TCIA,medical imaging
+Classifier: Environment :: Console
+Classifier: Framework :: Jupyter
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Utilities
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: matplotlib
+Requires-Dist: tqdm
+Requires-Dist: requests
+Requires-Dist: pydicom
+Requires-Dist: highdicom
+Requires-Dist: nibabel
+Requires-Dist: scipy
+Requires-Dist: simpleitk
+Requires-Dist: pyyaml
+Requires-Dist: openpyxl
+Requires-Dist: pydantic>=2
+Provides-Extra: segmentation
+Requires-Dist: TotalSegmentator; extra == "segmentation"
+Provides-Extra: radiomics
+Requires-Dist: pyradiomics; extra == "radiomics"
+Provides-Extra: notebook
+Requires-Dist: ipython; extra == "notebook"
+Requires-Dist: ipykernel; extra == "notebook"
+Requires-Dist: ipywidgets; extra == "notebook"
+Provides-Extra: dicom
+Requires-Dist: dcm2niix; extra == "dicom"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Provides-Extra: all
+Requires-Dist: TotalSegmentator; extra == "all"
+Requires-Dist: pyradiomics; extra == "all"
+Requires-Dist: ipython; extra == "all"
+Requires-Dist: ipykernel; extra == "all"
+Requires-Dist: ipywidgets; extra == "all"
+Requires-Dist: dcm2niix; extra == "all"
+Dynamic: license-file
+
+# ctkit
+
+CT image processing for AI and radiomics. Makes CT processing simple and reproducible.
+
+![pipeline](https://github.com/pachterlab/ctkit/blob/main/figures/Fig1.png?raw=true)
+
+## Installation
+
+```sh
+pip install ctkit
+```
+
+To install pyradiomics and TotalSegmentator:
+
+```sh
+pip install 'ctkit[all]'
+```
+
+## Quick start
+
+```python
+import ctkit
+
+ctkit.download("tcga-kirc", "data/tcga_kirc_raw", limit=20)
+
+data = ctkit.Dataset("data/tcga_kirc_raw")
+data.filter(min_slices=25).process("tcga-kirc", out_dir="data/processed")
+# the tcga-kirc protocol segments the kidneys, so this one needs ctkit[all]
+```
+
+## The pipeline
+
+| Step | What it does | Why it matters |
+| --- | --- | --- |
+| `filter` | Drop series that fail quality control, keeping a pass/fail table | Localizers, reformats and 4D series are not the acquisition you meant to analyze, and finding that out after processing wastes the expensive part |
+| `check` | Run the same quality control without dropping anything: a result for one series, the whole table for a cohort | The measurements behind every pass and fail, which is what an exclusion criterion has to cite |
+| `orient` | Reorient to canonical RAS | Archives disagree on storage order, so two scans of the same anatomy can arrive mirrored or transposed |
+| `segment` | TotalSegmentator organ masks, merged with any tumor mask | Gives a region of interest when the collection ships without one |
+| `clip` | Clamp to an intensity window (e.g. −200/300 HU) | Spends the dynamic range on the tissue you care about; caps metal artifacts |
+| `resample` | Resample to a fixed voxel size in mm | Until scans share a voxel grid, a millimeter of anatomy is a different number of voxels in each one |
+| `select_slice` | Keep one axial slice: the one with the most mask, or the one you name (2D mode) | How a 3D series becomes a 2D training example |
+| `apply_mask` | Blank outside the ROI, crop to its bounding box | Removes irrelevant anatomy and makes volumes small enough to hold a cohort in memory |
+| `crop_to_content` | Crop to the voxels above a threshold — air, once intensities are clipped | Trims the air around the body when there is no mask to crop to |
+| `standardize_size` | Center-crop/pad to a common array shape | Fixed-size tensors, without rescaling the anatomy |
+| `normalize` | Z-score, per volume or per dataset | Stops a model keying on per-scan intensity offsets |
+| `save` | Write the processed series to disk | Makes the processed dataset available for training and sharing |
+| `process` | Run the whole pipeline, with a saved configuration | Reproducibility and collaboration |
+| `radiomics` | Extract radiomics features | For radiomic analysis. Does not require many steps above. |
+
+## Reproducibility
+
+Every run that writes a cohort to disk writes `processing_config.yaml` next to
+it. To reproduce a dataset, or to hand one to a collaborator:
+
+```python
+ctkit.Dataset("data/raw").process(
+    "data/processed/processing_config.yaml", out_dir="rerun"
+)
+```
+
+`process` takes a protocol as a `ProcessingConfig`, a path to a saved one, or
+the name of a collection whose curated protocol to use.
+
+## Notebooks
+
+[`notebooks/quickstart.ipynb`](notebooks/quickstart.ipynb) walks through the
+package end to end: pick a collection, download it, filter it, process it, and
+extract features.
+
+## Relationship to tcia-radiology-processing
+
+This package grew out of the protocol in
+[pachterlab/tcia-radiology-processing](https://github.com/pachterlab/tcia-radiology-processing),
+which documents the same pipeline as a step-by-step notebook. That repository
+remains the written protocol; `ctkit` is the library implementation of it.
+
+## License
+
+BSD 2-Clause. See [LICENSE](LICENSE).
+
+---
+
+Issues and pull requests welcome.

ctkit-0.1.0.dist-info/RECORD

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ctkit-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (84.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

ctkit-0.1.0.dist-info/entry_points.txt

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+[console_scripts]
+ctkit = ctkit.cli:main

ctkit-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,24 @@
+BSD 2-Clause License
+
+Copyright (c) 2026, Pachter Lab
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

ctkit-0.1.0.dist-info/top_level.txt

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+ctkit