nnInteractive 1.1.2__tar.gz → 1.1.3__tar.gz

{nninteractive-1.1.2 → nninteractive-1.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nnInteractive
-Version: 1.1.2
+Version: 1.1.3
 Summary: Inference code for nnInteractive
 Author: Helmholtz Imaging Applied Computer Vision Lab
 Author-email: Fabian Isensee <f.isensee@dkfz-heidelberg.de>
@@ -220,7 +220,7 @@ Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: nnunetv2>=2.6
-Requires-Dist: torch>=2.6
+Requires-Dist: torch<2.9.0,>=2.6
 Requires-Dist: acvl-utils<0.3,>=0.2.3
 Requires-Dist: batchgenerators>=0.25.1
 Provides-Extra: dev
@@ -231,29 +231,36 @@ Dynamic: license-file
 
 <img src="imgs/nnInteractive_header_white.png">
 
+
 # Python backend for `nnInteractive: Redefining 3D Promptable Segmentation`
 
 This repository provides the official Python backend for `nnInteractive`, a state-of-the-art framework for 3D promptable segmentation. It is designed for seamless integration into Python-based workflows—ideal for researchers, developers, and power users working directly with code.
 
+> ⚠️ **Temporary Compatibility Warning**  
+> There is a known issue with **PyTorch 2.9.0** causing **OOM errors during inference** in `nnInteractive` (related to 3D convolutions — see the PyTorch issue [here](https://github.com/pytorch/pytorch/issues/166122)).  
+> **Until this is resolved, please use PyTorch 2.8.0 or earlier.**
+
+
 `nnInteractive` is also available through graphical viewers (GUI) for those who prefer a visual workflow. The napari and MITK integrations are developed and maintained by our team. Thanks to the community for contributing the 3D Slicer extension!
 
 
 <div align="center">
 
-| **<div align="center">[napari plugin](https://github.com/MIC-DKFZ/napari-nninteractive)</div>** | **<div align="center">[MITK integration](https://www.mitk.org/wiki/MITK-nnInteractive)</div>** | **<div align="center">[3D Slicer extension](https://github.com/coendevente/SlicerNNInteractive)</div>** | **<div align="center">[ITK-SNAP extension](https://itksnap-dls.readthedocs.io/en/latest/quick_start.html)</div>** |
-|-------------------|----------------------|-------------------------|-------------------------|
-| [<img src="imgs/Logos/napari.jpg" height="200">](https://github.com/MIC-DKFZ/napari-nninteractive) | [<img src="imgs/Logos/mitk.jpg" height="200">](https://www.mitk.org/wiki/MITK-nnInteractive) | [<img src="imgs/Logos/3DSlicer.png" height="200">](https://github.com/coendevente/SlicerNNInteractive) | [<img src="imgs/Logos/snaplogo_sq.png" height="200">](https://itksnap-dls.readthedocs.io/en/latest/quick_start.html) |
+| **<div align="center">[napari plugin](https://github.com/MIC-DKFZ/napari-nninteractive)</div>** | **<div align="center">[MITK integration](https://www.mitk.org/wiki/MITK-nnInteractive)</div>** | **<div align="center">[3D Slicer extension](https://github.com/coendevente/SlicerNNInteractive)</div>** | **<div align="center">[ITK-SNAP extension](https://itksnap-dls.readthedocs.io/en/latest/quick_start.html)</div>** | **<div align="center">[OHIF integration](https://github.com/CCI-Bonn/OHIF-AI)</div>** |
+|-------------------|----------------------|-------------------------|-------------------------|-------------------------|
+| [<img src="imgs/Logos/napari.jpg" height="200">](https://github.com/MIC-DKFZ/napari-nninteractive) | [<img src="imgs/Logos/mitk.jpg" height="200">](https://www.mitk.org/wiki/MITK-nnInteractive) | [<img src="imgs/Logos/3DSlicer.png" height="200">](https://github.com/coendevente/SlicerNNInteractive) | [<img src="imgs/Logos/snaplogo_sq.png" height="200">](https://itksnap-dls.readthedocs.io/en/latest/quick_start.html) | [<img src="imgs/Logos/ohif.png" height="200">](https://github.com/CCI-Bonn/OHIF-AI) |
 
 </div>
 
 
 ## 📰 News
 
+- **11/2025**: 🌐 New community driven **OHIF integration** released by our colleagues at [CCI Bonn](https://ccibonn.ai/). Try nnInteractive directly in OHIF 👉 [OHIF-AI](https://github.com/CCI-Bonn/OHIF-AI)
 - **07/2025**: 🧩 New ITK-SNAP extension released! Try nnInteractive directly in ITK-SNAP 👉 [Quick Start](https://itksnap-dls.readthedocs.io/en/latest/quick_start.html)
 - **06/2025**: 🏆 We’re thrilled to announce that `nnInteractive` **won the 1st place** in the [CVPR 2025 Challenge on Interactive 3D Segmentation](https://www.codabench.org/competitions/5263/). Huge shoutout to the organizers and all contributors!
-- **05/2025**: `nnInteractive` presents an **official baseline** at **CVPR 2025** in the _Foundation Models for Interactive 3D Biomedical Image Segmentation Challenge_ ([Codabench link](https://www.codabench.org/competitions/5263/)) → see [`nnInteractive/inference/cvpr2025_challenge_baseline`](nnInteractive/inference/cvpr2025_challenge_baseline)
-- **04/2025**: 🎉 The **community contributed a 3D Slicer integration** – thank you! 👉 [SlicerNNInteractive](https://github.com/coendevente/SlicerNNInteractive)
-- **03/2025**: 🚀 `nnInteractive` **launched** with native support for **napari** and **MITK**
+- **05/2025**: `nnInteractive` presents an official baseline at CVPR 2025 in the _Foundation Models for Interactive 3D Biomedical Image Segmentation Challenge_ ([Codabench link](https://www.codabench.org/competitions/5263/)) → see [`nnInteractive/inference/cvpr2025_challenge_baseline`](nnInteractive/inference/cvpr2025_challenge_baseline)
+- **04/2025**: 🎉 The community contributed a 3D Slicer integration – thank you! 👉 [SlicerNNInteractive](https://github.com/coendevente/SlicerNNInteractive)
+- **03/2025**: 🚀 `nnInteractive` launched with native support for napari and MITK
 
 ---
 
@@ -361,6 +368,10 @@ model_path = os.path.join(DOWNLOAD_DIR, MODEL_NAME)
 session.initialize_from_trained_model_folder(model_path)
 
 # --- Load Input Image (Example with SimpleITK) ---
+# DO NOT preprocess the image in any way. Give it to nnInteractive as it is! DO NOT apply level window, DO NOT normalize 
+# intensities and never ever convert an image with higher precision (float32, uint16, etc) to uint8!
+# The ONLY instance where some preprocesing makes sense is if your original image is too large to be reasonably used. 
+# This may be the case, for example, for some microCT images. In this case you can consider downsampling.
 input_image = sitk.ReadImage("FILENAME")
 img = sitk.GetArrayFromImage(input_image)[None]  # Ensure shape (1, x, y, z)
 

{nninteractive-1.1.2 → nninteractive-1.1.3}/nnInteractive/inference/inference_session.py

@@ -363,6 +363,9 @@ class nnInteractiveInferenceSession():
         """
         assert self.pad_mode_data == 'constant', 'pad modes other than constant are not implemented here'
         assert len(self.new_interaction_centers) == len(self.new_interaction_zoom_out_factors)
+        if len(self.new_interaction_centers) == 0:
+            print('No patch queued for prediction. Nothing to do.')
+            return
 
         if len(self.new_interaction_centers) > 1:
             print('It seems like more than one interaction was added since the last prediction. This is not '

{nninteractive-1.1.2 → nninteractive-1.1.3}/nnInteractive.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nnInteractive
-Version: 1.1.2
+Version: 1.1.3
 Summary: Inference code for nnInteractive
 Author: Helmholtz Imaging Applied Computer Vision Lab
 Author-email: Fabian Isensee <f.isensee@dkfz-heidelberg.de>
@@ -220,7 +220,7 @@ Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: nnunetv2>=2.6
-Requires-Dist: torch>=2.6
+Requires-Dist: torch<2.9.0,>=2.6
 Requires-Dist: acvl-utils<0.3,>=0.2.3
 Requires-Dist: batchgenerators>=0.25.1
 Provides-Extra: dev
@@ -231,29 +231,36 @@ Dynamic: license-file
 
 <img src="imgs/nnInteractive_header_white.png">
 
+
 # Python backend for `nnInteractive: Redefining 3D Promptable Segmentation`
 
 This repository provides the official Python backend for `nnInteractive`, a state-of-the-art framework for 3D promptable segmentation. It is designed for seamless integration into Python-based workflows—ideal for researchers, developers, and power users working directly with code.
 
+> ⚠️ **Temporary Compatibility Warning**  
+> There is a known issue with **PyTorch 2.9.0** causing **OOM errors during inference** in `nnInteractive` (related to 3D convolutions — see the PyTorch issue [here](https://github.com/pytorch/pytorch/issues/166122)).  
+> **Until this is resolved, please use PyTorch 2.8.0 or earlier.**
+
+
 `nnInteractive` is also available through graphical viewers (GUI) for those who prefer a visual workflow. The napari and MITK integrations are developed and maintained by our team. Thanks to the community for contributing the 3D Slicer extension!
 
 
 <div align="center">
 
-| **<div align="center">[napari plugin](https://github.com/MIC-DKFZ/napari-nninteractive)</div>** | **<div align="center">[MITK integration](https://www.mitk.org/wiki/MITK-nnInteractive)</div>** | **<div align="center">[3D Slicer extension](https://github.com/coendevente/SlicerNNInteractive)</div>** | **<div align="center">[ITK-SNAP extension](https://itksnap-dls.readthedocs.io/en/latest/quick_start.html)</div>** |
-|-------------------|----------------------|-------------------------|-------------------------|
-| [<img src="imgs/Logos/napari.jpg" height="200">](https://github.com/MIC-DKFZ/napari-nninteractive) | [<img src="imgs/Logos/mitk.jpg" height="200">](https://www.mitk.org/wiki/MITK-nnInteractive) | [<img src="imgs/Logos/3DSlicer.png" height="200">](https://github.com/coendevente/SlicerNNInteractive) | [<img src="imgs/Logos/snaplogo_sq.png" height="200">](https://itksnap-dls.readthedocs.io/en/latest/quick_start.html) |
+| **<div align="center">[napari plugin](https://github.com/MIC-DKFZ/napari-nninteractive)</div>** | **<div align="center">[MITK integration](https://www.mitk.org/wiki/MITK-nnInteractive)</div>** | **<div align="center">[3D Slicer extension](https://github.com/coendevente/SlicerNNInteractive)</div>** | **<div align="center">[ITK-SNAP extension](https://itksnap-dls.readthedocs.io/en/latest/quick_start.html)</div>** | **<div align="center">[OHIF integration](https://github.com/CCI-Bonn/OHIF-AI)</div>** |
+|-------------------|----------------------|-------------------------|-------------------------|-------------------------|
+| [<img src="imgs/Logos/napari.jpg" height="200">](https://github.com/MIC-DKFZ/napari-nninteractive) | [<img src="imgs/Logos/mitk.jpg" height="200">](https://www.mitk.org/wiki/MITK-nnInteractive) | [<img src="imgs/Logos/3DSlicer.png" height="200">](https://github.com/coendevente/SlicerNNInteractive) | [<img src="imgs/Logos/snaplogo_sq.png" height="200">](https://itksnap-dls.readthedocs.io/en/latest/quick_start.html) | [<img src="imgs/Logos/ohif.png" height="200">](https://github.com/CCI-Bonn/OHIF-AI) |
 
 </div>
 
 
 ## 📰 News
 
+- **11/2025**: 🌐 New community driven **OHIF integration** released by our colleagues at [CCI Bonn](https://ccibonn.ai/). Try nnInteractive directly in OHIF 👉 [OHIF-AI](https://github.com/CCI-Bonn/OHIF-AI)
 - **07/2025**: 🧩 New ITK-SNAP extension released! Try nnInteractive directly in ITK-SNAP 👉 [Quick Start](https://itksnap-dls.readthedocs.io/en/latest/quick_start.html)
 - **06/2025**: 🏆 We’re thrilled to announce that `nnInteractive` **won the 1st place** in the [CVPR 2025 Challenge on Interactive 3D Segmentation](https://www.codabench.org/competitions/5263/). Huge shoutout to the organizers and all contributors!
-- **05/2025**: `nnInteractive` presents an **official baseline** at **CVPR 2025** in the _Foundation Models for Interactive 3D Biomedical Image Segmentation Challenge_ ([Codabench link](https://www.codabench.org/competitions/5263/)) → see [`nnInteractive/inference/cvpr2025_challenge_baseline`](nnInteractive/inference/cvpr2025_challenge_baseline)
-- **04/2025**: 🎉 The **community contributed a 3D Slicer integration** – thank you! 👉 [SlicerNNInteractive](https://github.com/coendevente/SlicerNNInteractive)
-- **03/2025**: 🚀 `nnInteractive` **launched** with native support for **napari** and **MITK**
+- **05/2025**: `nnInteractive` presents an official baseline at CVPR 2025 in the _Foundation Models for Interactive 3D Biomedical Image Segmentation Challenge_ ([Codabench link](https://www.codabench.org/competitions/5263/)) → see [`nnInteractive/inference/cvpr2025_challenge_baseline`](nnInteractive/inference/cvpr2025_challenge_baseline)
+- **04/2025**: 🎉 The community contributed a 3D Slicer integration – thank you! 👉 [SlicerNNInteractive](https://github.com/coendevente/SlicerNNInteractive)
+- **03/2025**: 🚀 `nnInteractive` launched with native support for napari and MITK
 
 ---
 
@@ -361,6 +368,10 @@ model_path = os.path.join(DOWNLOAD_DIR, MODEL_NAME)
 session.initialize_from_trained_model_folder(model_path)
 
 # --- Load Input Image (Example with SimpleITK) ---
+# DO NOT preprocess the image in any way. Give it to nnInteractive as it is! DO NOT apply level window, DO NOT normalize 
+# intensities and never ever convert an image with higher precision (float32, uint16, etc) to uint8!
+# The ONLY instance where some preprocesing makes sense is if your original image is too large to be reasonably used. 
+# This may be the case, for example, for some microCT images. In this case you can consider downsampling.
 input_image = sitk.ReadImage("FILENAME")
 img = sitk.GetArrayFromImage(input_image)[None]  # Ensure shape (1, x, y, z)
 

{nninteractive-1.1.2 → nninteractive-1.1.3}/nnInteractive.egg-info/requires.txt

@@ -1,5 +1,5 @@
 nnunetv2>=2.6
-torch>=2.6
+torch<2.9.0,>=2.6
 acvl-utils<0.3,>=0.2.3
 batchgenerators>=0.25.1
 

{nninteractive-1.1.2 → nninteractive-1.1.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nnInteractive"
-version = "1.1.2"
+version = "1.1.3"
 requires-python = ">=3.10"
 description = "Inference code for nnInteractive"
 readme = "readme.md"
@@ -31,7 +31,7 @@ keywords = [
 ]
 dependencies = [
     "nnunetv2>=2.6",
-    "torch>=2.6",
+    "torch>=2.6,<2.9.0",
     "acvl-utils>=0.2.3,<0.3",  # 0.3 may bring breaking changes. Careful!
     "batchgenerators>=0.25.1",
 ]

{nninteractive-1.1.2 → nninteractive-1.1.3}/readme.md

@@ -1,28 +1,35 @@
 <img src="imgs/nnInteractive_header_white.png">
 
+
 # Python backend for `nnInteractive: Redefining 3D Promptable Segmentation`
 
 This repository provides the official Python backend for `nnInteractive`, a state-of-the-art framework for 3D promptable segmentation. It is designed for seamless integration into Python-based workflows—ideal for researchers, developers, and power users working directly with code.
 
+> ⚠️ **Temporary Compatibility Warning**  
+> There is a known issue with **PyTorch 2.9.0** causing **OOM errors during inference** in `nnInteractive` (related to 3D convolutions — see the PyTorch issue [here](https://github.com/pytorch/pytorch/issues/166122)).  
+> **Until this is resolved, please use PyTorch 2.8.0 or earlier.**
+
+
 `nnInteractive` is also available through graphical viewers (GUI) for those who prefer a visual workflow. The napari and MITK integrations are developed and maintained by our team. Thanks to the community for contributing the 3D Slicer extension!
 
 
 <div align="center">
 
-| **<div align="center">[napari plugin](https://github.com/MIC-DKFZ/napari-nninteractive)</div>** | **<div align="center">[MITK integration](https://www.mitk.org/wiki/MITK-nnInteractive)</div>** | **<div align="center">[3D Slicer extension](https://github.com/coendevente/SlicerNNInteractive)</div>** | **<div align="center">[ITK-SNAP extension](https://itksnap-dls.readthedocs.io/en/latest/quick_start.html)</div>** |
-|-------------------|----------------------|-------------------------|-------------------------|
-| [<img src="imgs/Logos/napari.jpg" height="200">](https://github.com/MIC-DKFZ/napari-nninteractive) | [<img src="imgs/Logos/mitk.jpg" height="200">](https://www.mitk.org/wiki/MITK-nnInteractive) | [<img src="imgs/Logos/3DSlicer.png" height="200">](https://github.com/coendevente/SlicerNNInteractive) | [<img src="imgs/Logos/snaplogo_sq.png" height="200">](https://itksnap-dls.readthedocs.io/en/latest/quick_start.html) |
+| **<div align="center">[napari plugin](https://github.com/MIC-DKFZ/napari-nninteractive)</div>** | **<div align="center">[MITK integration](https://www.mitk.org/wiki/MITK-nnInteractive)</div>** | **<div align="center">[3D Slicer extension](https://github.com/coendevente/SlicerNNInteractive)</div>** | **<div align="center">[ITK-SNAP extension](https://itksnap-dls.readthedocs.io/en/latest/quick_start.html)</div>** | **<div align="center">[OHIF integration](https://github.com/CCI-Bonn/OHIF-AI)</div>** |
+|-------------------|----------------------|-------------------------|-------------------------|-------------------------|
+| [<img src="imgs/Logos/napari.jpg" height="200">](https://github.com/MIC-DKFZ/napari-nninteractive) | [<img src="imgs/Logos/mitk.jpg" height="200">](https://www.mitk.org/wiki/MITK-nnInteractive) | [<img src="imgs/Logos/3DSlicer.png" height="200">](https://github.com/coendevente/SlicerNNInteractive) | [<img src="imgs/Logos/snaplogo_sq.png" height="200">](https://itksnap-dls.readthedocs.io/en/latest/quick_start.html) | [<img src="imgs/Logos/ohif.png" height="200">](https://github.com/CCI-Bonn/OHIF-AI) |
 
 </div>
 
 
 ## 📰 News
 
+- **11/2025**: 🌐 New community driven **OHIF integration** released by our colleagues at [CCI Bonn](https://ccibonn.ai/). Try nnInteractive directly in OHIF 👉 [OHIF-AI](https://github.com/CCI-Bonn/OHIF-AI)
 - **07/2025**: 🧩 New ITK-SNAP extension released! Try nnInteractive directly in ITK-SNAP 👉 [Quick Start](https://itksnap-dls.readthedocs.io/en/latest/quick_start.html)
 - **06/2025**: 🏆 We’re thrilled to announce that `nnInteractive` **won the 1st place** in the [CVPR 2025 Challenge on Interactive 3D Segmentation](https://www.codabench.org/competitions/5263/). Huge shoutout to the organizers and all contributors!
-- **05/2025**: `nnInteractive` presents an **official baseline** at **CVPR 2025** in the _Foundation Models for Interactive 3D Biomedical Image Segmentation Challenge_ ([Codabench link](https://www.codabench.org/competitions/5263/)) → see [`nnInteractive/inference/cvpr2025_challenge_baseline`](nnInteractive/inference/cvpr2025_challenge_baseline)
-- **04/2025**: 🎉 The **community contributed a 3D Slicer integration** – thank you! 👉 [SlicerNNInteractive](https://github.com/coendevente/SlicerNNInteractive)
-- **03/2025**: 🚀 `nnInteractive` **launched** with native support for **napari** and **MITK**
+- **05/2025**: `nnInteractive` presents an official baseline at CVPR 2025 in the _Foundation Models for Interactive 3D Biomedical Image Segmentation Challenge_ ([Codabench link](https://www.codabench.org/competitions/5263/)) → see [`nnInteractive/inference/cvpr2025_challenge_baseline`](nnInteractive/inference/cvpr2025_challenge_baseline)
+- **04/2025**: 🎉 The community contributed a 3D Slicer integration – thank you! 👉 [SlicerNNInteractive](https://github.com/coendevente/SlicerNNInteractive)
+- **03/2025**: 🚀 `nnInteractive` launched with native support for napari and MITK
 
 ---
 
@@ -130,6 +137,10 @@ model_path = os.path.join(DOWNLOAD_DIR, MODEL_NAME)
 session.initialize_from_trained_model_folder(model_path)
 
 # --- Load Input Image (Example with SimpleITK) ---
+# DO NOT preprocess the image in any way. Give it to nnInteractive as it is! DO NOT apply level window, DO NOT normalize 
+# intensities and never ever convert an image with higher precision (float32, uint16, etc) to uint8!
+# The ONLY instance where some preprocesing makes sense is if your original image is too large to be reasonably used. 
+# This may be the case, for example, for some microCT images. In this case you can consider downsampling.
 input_image = sitk.ReadImage("FILENAME")
 img = sitk.GetArrayFromImage(input_image)[None]  # Ensure shape (1, x, y, z)