segprobe 0.1.0__tar.gz

segprobe-0.1.0/CITATION.cff

@@ -0,0 +1,17 @@
+cff-version: 1.2.0
+message: "If you use SegProbe in your research, please cite this software."
+title: "SegProbe"
+type: software
+version: 0.1.0
+authors:
+  - family-names: "Ebou"
+    given-names: "Elhaj Samitt"
+    orcid: "https://orcid.org/0009-0004-5324-2385"
+repository-code: "https://github.com/hajteyib/segprobe"
+license: "Apache-2.0"
+keywords:
+  - medical image segmentation
+  - prompt evaluation
+  - interactive segmentation
+  - bounding boxes
+  - reproducibility

segprobe-0.1.0/LICENSE

@@ -0,0 +1,201 @@
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segprobe-0.1.0/MANIFEST.in

@@ -0,0 +1,2 @@
+include CITATION.cff
+recursive-include examples *.py

segprobe-0.1.0/PKG-INFO

@@ -0,0 +1,247 @@
+Metadata-Version: 2.4
+Name: segprobe
+Version: 0.1.0
+Summary: Reproducible, model-agnostic prompt evaluation for medical segmentation.
+Author: Elhaj Samitt Ebou
+License-Expression: Apache-2.0
+Project-URL: Repository, https://github.com/hajteyib/segprobe
+Project-URL: Issues, https://github.com/hajteyib/segprobe/issues
+Classifier: Development Status :: 3 - Alpha
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.23
+Provides-Extra: dev
+Requires-Dist: build>=1.2; extra == "dev"
+Requires-Dist: pytest>=8; extra == "dev"
+Requires-Dist: ruff>=0.6; extra == "dev"
+Dynamic: license-file
+
+# SegProbe
+
+SegProbe makes box-prompt experiments reproducible across medical image
+segmentation models. It generates prompt protocols, records the manual effort,
+and evaluates the resulting masks through one small API.
+
+![SegProbe overview](https://raw.githubusercontent.com/hajteyib/segprobe/main/docs/assets/segprobe-overview.png)
+
+It started as code i used while testing MedSAM. i wanted to answer simple
+questions without rewriting the evaluation each time:
+
+- How many boxes must be drawn manually?
+- What happens if boxes are sparse, larger, or slightly misplaced?
+- Can the same protocol be compared across different models?
+
+SegProbe has one runtime dependency: NumPy. It does not download a model or a
+dataset.
+
+## Install
+
+```bash
+python -m pip install segprobe
+```
+
+For development, install it from a local clone:
+
+```bash
+python -m pip install -e .
+```
+
+## Quick start
+
+```python
+from segprobe import evaluate, sparse_boxes
+
+plan = sparse_boxes(target_mask, every=3, padding=5)
+
+def predictor(volume, z_index, box_xyxy):
+    image_slice = volume[z_index]
+    return my_model.predict(image_slice, box=box_xyxy)
+
+result = evaluate(predictor, image_volume, target_mask, plan)
+
+print(result.dice)
+print(result.manual_boxes)
+print(result.generated_boxes)
+```
+
+The `predictor` function is the only model-specific part. It can call MedSAM,
+SAM2, nnInteractive, or your own slice-based model.
+
+## Prompt protocols
+
+```python
+from segprobe import global_box, slice_boxes, sparse_boxes
+
+dense = slice_boxes(mask, padding=5)
+global_prompt = global_box(mask, padding=5)
+sparse = sparse_boxes(mask, every=3, padding=5)
+```
+
+| Protocol | Manual effort | Boxes sent to the model |
+| --- | ---: | --- |
+| `slice_boxes` | one per positive slice | one manual box on each slice |
+| `global_box` | one per volume | the same box reused on all positive slices |
+| `sparse_boxes` | one every N positive slices, plus the last | manual anchors and interpolated boxes |
+
+Each plan reports `manual_boxes`, `generated_boxes`, and `manual_fraction`.
+`plan.to_dict()` returns plain Python values ready for JSON.
+
+### Sparse prompts
+
+Here, only five boxes are drawn manually. The other fifteen are interpolated.
+
+![Sparse box interpolation through a CT volume](https://raw.githubusercontent.com/hajteyib/segprobe/main/docs/assets/sparse-prompts.gif)
+
+Blue boxes are manual anchors. Orange dashed boxes are generated between them.
+The green line is the reference-mask contour.
+
+## Prompt robustness
+
+Box size and placement can change a promptable model's result. SegProbe can add
+padding or apply deterministic perturbations, so the same stress test can be
+run again with the same seed.
+
+```python
+from segprobe import jitter_plan
+
+noisy = jitter_plan(
+    dense,
+    max_translate=5,
+    max_expand=10,
+    seed=42,
+    sample_key="case-001",
+)
+```
+
+![Box size, translation, and expansion](https://raw.githubusercontent.com/hajteyib/segprobe/main/docs/assets/prompt-geometry.gif)
+
+## Public MedSAM example
+
+[`examples/medsam_lidc.py`](examples/medsam_lidc.py) connects SegProbe to the
+official [MedSAM ViT-B model](https://github.com/bowang-lab/MedSAM). It expects
+one folder per case containing
+`image.nii.gz` and `mask.nii.gz`.
+
+Run it from an environment where MedSAM, PyTorch, NiBabel, and scikit-image are
+available:
+
+```bash
+python examples/medsam_lidc.py \
+  --cases-root /path/to/lidc_crops \
+  --one-per-patient \
+  --limit 5 \
+  --medsam-repo /path/to/MedSAM \
+  --checkpoint /path/to/medsam_vit_b.pth \
+  --output-dir medsam_results \
+  --device cpu
+```
+
+The script saves `results.csv` and `results.json` after every protocol. Running
+the same command again resumes from the saved results.
+
+We used it for a small public check with five LIDC-IDRI nodules, one per
+patient. The run used the official MedSAM checkpoint, no private fine-tuning,
+no postprocessing, and an oracle positive z-range from the reference mask.
+
+### Prompt density with padding=5
+
+| Protocol | Mean manual boxes | Mean generated boxes | Mean Dice ± SD |
+| --- | ---: | ---: | ---: |
+| Global | 1.0 | 16.0 | 0.372 ± 0.173 |
+| Sparse every 5 slices | 4.4 | 12.6 | 0.515 ± 0.267 |
+| Sparse every 3 slices | 7.0 | 10.0 | 0.508 ± 0.270 |
+| Sparse every 2 slices | 9.2 | 7.8 | 0.510 ± 0.270 |
+| Dense | 17.0 | 0.0 | 0.511 ± 0.271 |
+
+In this small run, sparse prompting every five slices used about 74% fewer
+manual boxes than dense prompting, with nearly the same mean Dice.
+
+### Dense prompt geometry
+
+| Box | Mean Dice ± SD |
+| --- | ---: |
+| Tight, `padding=0` | 0.843 ± 0.031 |
+| `padding=5` | 0.511 ± 0.271 |
+| Large, `padding=10` | 0.310 ± 0.224 |
+| `padding=5` with deterministic jitter | 0.363 ± 0.263 |
+
+The tight box is derived directly from the reference mask, so it is a strong
+oracle prompt. These five cases are a reproducibility example, not a model
+comparison or a clinical result.
+
+## Inputs and image formats
+
+SegProbe works with arrays, not a specific medical file format. CT, MRI, PET,
+and other 3D images can use the same API after they are loaded into NumPy.
+
+- The mask must have shape `(z, y, x)`.
+- The image must start with the same dimensions: `(z, y, x)` or
+  `(z, y, x, channels)`.
+- Boxes use `(x_min, y_min, x_max, y_max)`, with exclusive maximum coordinates.
+
+NIfTI, DICOM, NRRD, and other files can be loaded with tools such as NiBabel,
+SimpleITK, or pydicom. File loading stays outside SegProbe so the core package
+remains small and does not impose an imaging stack.
+
+## Evaluation output
+
+`evaluate` returns the predicted 3D mask together with:
+
+- Dice and IoU;
+- target and prediction voxel counts;
+- manual and generated box counts;
+- number of prompted slices.
+
+The scalar values are available with `result.to_dict()` for a CSV or JSON
+report.
+
+## Scope
+
+The current prompt generators use a reference mask. They are made for
+controlled oracle-prompt evaluation, not automatic lesion localization.
+
+Only reference-positive slices receive a box, so the positive z-range is known.
+Results should be described as prompt-effort or prompt-robustness experiments,
+not end-to-end detection results.
+
+The manual-box count is an effort proxy. It is not a measurement of annotation
+time. SegProbe is a research evaluation tool and is not intended for clinical
+decision-making.
+
+## Development
+
+```bash
+python -m pip install -e ".[dev]"
+ruff check .
+pytest -q
+python -m build
+```
+
+Tests use small synthetic masks. They do not download images, checkpoints, or
+patient data.
+
+## Citation
+
+If SegProbe supports your work, please cite the software using
+[`CITATION.cff`](CITATION.cff).
+
+The images in this README use a cropped, windowed, and annotated case from the
+public [LIDC-IDRI collection](https://www.cancerimagingarchive.net/collection/lidc-idri/):
+
+> Armato III, S. G., McLennan, G., Bidaut, L., et al. (2015). Data From
+> LIDC-IDRI. The Cancer Imaging Archive.
+> [https://doi.org/10.7937/K9/TCIA.2015.LO9QL9SX](https://doi.org/10.7937/K9/TCIA.2015.LO9QL9SX)
+
+LIDC-IDRI is available under the
+[Creative Commons Attribution 3.0 license](https://creativecommons.org/licenses/by/3.0/).
+
+## License
+
+SegProbe is released under the [Apache-2.0 license](LICENSE).

segprobe-0.1.0/README.md

@@ -0,0 +1,222 @@
+# SegProbe
+
+SegProbe makes box-prompt experiments reproducible across medical image
+segmentation models. It generates prompt protocols, records the manual effort,
+and evaluates the resulting masks through one small API.
+
+![SegProbe overview](https://raw.githubusercontent.com/hajteyib/segprobe/main/docs/assets/segprobe-overview.png)
+
+It started as code i used while testing MedSAM. i wanted to answer simple
+questions without rewriting the evaluation each time:
+
+- How many boxes must be drawn manually?
+- What happens if boxes are sparse, larger, or slightly misplaced?
+- Can the same protocol be compared across different models?
+
+SegProbe has one runtime dependency: NumPy. It does not download a model or a
+dataset.
+
+## Install
+
+```bash
+python -m pip install segprobe
+```
+
+For development, install it from a local clone:
+
+```bash
+python -m pip install -e .
+```
+
+## Quick start
+
+```python
+from segprobe import evaluate, sparse_boxes
+
+plan = sparse_boxes(target_mask, every=3, padding=5)
+
+def predictor(volume, z_index, box_xyxy):
+    image_slice = volume[z_index]
+    return my_model.predict(image_slice, box=box_xyxy)
+
+result = evaluate(predictor, image_volume, target_mask, plan)
+
+print(result.dice)
+print(result.manual_boxes)
+print(result.generated_boxes)
+```
+
+The `predictor` function is the only model-specific part. It can call MedSAM,
+SAM2, nnInteractive, or your own slice-based model.
+
+## Prompt protocols
+
+```python
+from segprobe import global_box, slice_boxes, sparse_boxes
+
+dense = slice_boxes(mask, padding=5)
+global_prompt = global_box(mask, padding=5)
+sparse = sparse_boxes(mask, every=3, padding=5)
+```
+
+| Protocol | Manual effort | Boxes sent to the model |
+| --- | ---: | --- |
+| `slice_boxes` | one per positive slice | one manual box on each slice |
+| `global_box` | one per volume | the same box reused on all positive slices |
+| `sparse_boxes` | one every N positive slices, plus the last | manual anchors and interpolated boxes |
+
+Each plan reports `manual_boxes`, `generated_boxes`, and `manual_fraction`.
+`plan.to_dict()` returns plain Python values ready for JSON.
+
+### Sparse prompts
+
+Here, only five boxes are drawn manually. The other fifteen are interpolated.
+
+![Sparse box interpolation through a CT volume](https://raw.githubusercontent.com/hajteyib/segprobe/main/docs/assets/sparse-prompts.gif)
+
+Blue boxes are manual anchors. Orange dashed boxes are generated between them.
+The green line is the reference-mask contour.
+
+## Prompt robustness
+
+Box size and placement can change a promptable model's result. SegProbe can add
+padding or apply deterministic perturbations, so the same stress test can be
+run again with the same seed.
+
+```python
+from segprobe import jitter_plan
+
+noisy = jitter_plan(
+    dense,
+    max_translate=5,
+    max_expand=10,
+    seed=42,
+    sample_key="case-001",
+)
+```
+
+![Box size, translation, and expansion](https://raw.githubusercontent.com/hajteyib/segprobe/main/docs/assets/prompt-geometry.gif)
+
+## Public MedSAM example
+
+[`examples/medsam_lidc.py`](examples/medsam_lidc.py) connects SegProbe to the
+official [MedSAM ViT-B model](https://github.com/bowang-lab/MedSAM). It expects
+one folder per case containing
+`image.nii.gz` and `mask.nii.gz`.
+
+Run it from an environment where MedSAM, PyTorch, NiBabel, and scikit-image are
+available:
+
+```bash
+python examples/medsam_lidc.py \
+  --cases-root /path/to/lidc_crops \
+  --one-per-patient \
+  --limit 5 \
+  --medsam-repo /path/to/MedSAM \
+  --checkpoint /path/to/medsam_vit_b.pth \
+  --output-dir medsam_results \
+  --device cpu
+```
+
+The script saves `results.csv` and `results.json` after every protocol. Running
+the same command again resumes from the saved results.
+
+We used it for a small public check with five LIDC-IDRI nodules, one per
+patient. The run used the official MedSAM checkpoint, no private fine-tuning,
+no postprocessing, and an oracle positive z-range from the reference mask.
+
+### Prompt density with padding=5
+
+| Protocol | Mean manual boxes | Mean generated boxes | Mean Dice ± SD |
+| --- | ---: | ---: | ---: |
+| Global | 1.0 | 16.0 | 0.372 ± 0.173 |
+| Sparse every 5 slices | 4.4 | 12.6 | 0.515 ± 0.267 |
+| Sparse every 3 slices | 7.0 | 10.0 | 0.508 ± 0.270 |
+| Sparse every 2 slices | 9.2 | 7.8 | 0.510 ± 0.270 |
+| Dense | 17.0 | 0.0 | 0.511 ± 0.271 |
+
+In this small run, sparse prompting every five slices used about 74% fewer
+manual boxes than dense prompting, with nearly the same mean Dice.
+
+### Dense prompt geometry
+
+| Box | Mean Dice ± SD |
+| --- | ---: |
+| Tight, `padding=0` | 0.843 ± 0.031 |
+| `padding=5` | 0.511 ± 0.271 |
+| Large, `padding=10` | 0.310 ± 0.224 |
+| `padding=5` with deterministic jitter | 0.363 ± 0.263 |
+
+The tight box is derived directly from the reference mask, so it is a strong
+oracle prompt. These five cases are a reproducibility example, not a model
+comparison or a clinical result.
+
+## Inputs and image formats
+
+SegProbe works with arrays, not a specific medical file format. CT, MRI, PET,
+and other 3D images can use the same API after they are loaded into NumPy.
+
+- The mask must have shape `(z, y, x)`.
+- The image must start with the same dimensions: `(z, y, x)` or
+  `(z, y, x, channels)`.
+- Boxes use `(x_min, y_min, x_max, y_max)`, with exclusive maximum coordinates.
+
+NIfTI, DICOM, NRRD, and other files can be loaded with tools such as NiBabel,
+SimpleITK, or pydicom. File loading stays outside SegProbe so the core package
+remains small and does not impose an imaging stack.
+
+## Evaluation output
+
+`evaluate` returns the predicted 3D mask together with:
+
+- Dice and IoU;
+- target and prediction voxel counts;
+- manual and generated box counts;
+- number of prompted slices.
+
+The scalar values are available with `result.to_dict()` for a CSV or JSON
+report.
+
+## Scope
+
+The current prompt generators use a reference mask. They are made for
+controlled oracle-prompt evaluation, not automatic lesion localization.
+
+Only reference-positive slices receive a box, so the positive z-range is known.
+Results should be described as prompt-effort or prompt-robustness experiments,
+not end-to-end detection results.
+
+The manual-box count is an effort proxy. It is not a measurement of annotation
+time. SegProbe is a research evaluation tool and is not intended for clinical
+decision-making.
+
+## Development
+
+```bash
+python -m pip install -e ".[dev]"
+ruff check .
+pytest -q
+python -m build
+```
+
+Tests use small synthetic masks. They do not download images, checkpoints, or
+patient data.
+
+## Citation
+
+If SegProbe supports your work, please cite the software using
+[`CITATION.cff`](CITATION.cff).
+
+The images in this README use a cropped, windowed, and annotated case from the
+public [LIDC-IDRI collection](https://www.cancerimagingarchive.net/collection/lidc-idri/):
+
+> Armato III, S. G., McLennan, G., Bidaut, L., et al. (2015). Data From
+> LIDC-IDRI. The Cancer Imaging Archive.
+> [https://doi.org/10.7937/K9/TCIA.2015.LO9QL9SX](https://doi.org/10.7937/K9/TCIA.2015.LO9QL9SX)
+
+LIDC-IDRI is available under the
+[Creative Commons Attribution 3.0 license](https://creativecommons.org/licenses/by/3.0/).
+
+## License
+
+SegProbe is released under the [Apache-2.0 license](LICENSE).