Pull request changes

.github/workflows/build-main.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.9, '3.10', 3.11]
+        python-version: ['3.10', '3.11']
         os: [
           ubuntu-latest,
           windows-latest,
@@ -36,17 +36,17 @@ jobs:
       run: |
         pytest --cov-report xml --cov=mmv_im2im mmv_im2im/tests/
     - name: Upload codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v4
 
   lint:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9.15
+        python-version: 3.11
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip
@@ -68,7 +68,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.11
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/test-and-lint.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.9, '3.10', 3.11]
+        python-version: ['3.10', '3.11']
         os: [
           ubuntu-latest,
           windows-latest,
@@ -28,17 +28,17 @@ jobs:
       run: |
         pytest mmv_im2im/tests/
     - name: Upload codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v4
 
   lint:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9.15
+        python-version: 3.11
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip

README.md

@@ -19,14 +19,19 @@ The overall package is designed with a generic image-to-image transformation fra
 
 ## Installation
 
-Before starting, we recommend to [create a new conda environment](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-with-commands) or [a virtual environment](https://docs.python.org/3/library/venv.html) with Python 3.9+.
+Before starting, we recommend to [create a new conda environment](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-with-commands) or [a virtual environment](https://docs.python.org/3/library/venv.html) with Python 3.10+.
+
+```bash
+conda create -y -n im2im -c conda-forge python=3.11
+conda activate im2im
+```
 
 Please note that the proper setup of hardware is beyond the scope of this pacakge. This package was tested with GPU/CPU on Linux/Windows and CPU on MacOS. [Special note for MacOS users: Directly pip install in MacOS may need [additional setup of xcode](https://developer.apple.com/forums/thread/673827).]
 
 ### Install MONAI
 
 To reproduce our results, we need to install MONAI's code version of a specific commit. To do this:
-```
+```bash
 git clone https://github.com/Project-MONAI/MONAI.git
 cd ./MONAI
 git checkout 37b58fcec48f3ec1f84d7cabe9c7ad08a93882c0
@@ -49,7 +54,7 @@ For MacOS users, additional ' ' marks are need when using installation tags in z
 ### Install MMV_Im2Im for customization or extension:
 
 
-```
+```bash
 git clone https://github.com/MMV-Lab/mmv_im2im.git
 cd mmv_im2im
 pip install -e .[all]
@@ -71,10 +76,10 @@ You can try out on a simple example following [the quick start guide](tutorials/
 
 Basically, you can specify your training configuration in a yaml file and run training with `run_im2im --config /path/to/train_config.yaml`. Then, you can specify the inference configuration in another yaml file and run inference with `run_im2im --config /path/to/inference_config.yaml`. You can also run the inference as a function with the provided API. This will be useful if you want to run the inference within another python script or workflow.  Here is an example:
 
-```
+```python
 from pathlib import Path
-from aicsimageio import AICSImage
-from aicsimageio.writers import OmeTiffWriter
+from bioio import BioImage
+from bioio.writers import OmeTiffWriter
 from mmv_im2im.configs.config_base import ProgramConfig, parse_adaptor, configuration_validation
 from mmv_im2im import ProjectTester
 
@@ -89,9 +94,9 @@ executor.setup_data_processing()
 
 # get the data, run inference, and save the result
 fn = Path("./data/img_00_IM.tiff")
-img = AICSImage(fn).get_image_data("YX", Z=0, C=0, T=0)
+img = BioImage(fn).get_image_data("YX", Z=0, C=0, T=0)
 # or using delayed loading if the data is large
-# img = AICSImage(fn).get_image_dask_data("YX", Z=0, C=0, T=0)
+# img = BioImage(fn).get_image_dask_data("YX", Z=0, C=0, T=0)
 seg = executor.process_one_image(img)
 OmeTiffWriter.save(seg, "output.tiff", dim_orders="YX")
 ```

mmv_im2im/configs/config_base.py

@@ -405,9 +405,9 @@ def configuration_validation(cfg):
                 cfg.data.dataloader.train.dataset_params["cache_dir"]
                 != cfg.data.dataloader.val.dataset_params["cache_dir"]
             ):
-                cfg.data.dataloader.val.dataset_params[
-                    "cache_dir"
-                ] = cfg.data.dataloader.train.dataset_params["cache_dir"]
+                cfg.data.dataloader.val.dataset_params["cache_dir"] = (
+                    cfg.data.dataloader.train.dataset_params["cache_dir"]
+                )
                 warnings.warn(
                     UserWarning(
                         "The cache dir of PersistentDataset for validation was"

mmv_im2im/data_modules/data_loader_basic.py

@@ -106,7 +106,7 @@ def train_dataloader(self):
             train_dataset = train_dataset_func(
                 data=train_data,
                 transform=self.transform,
-                **train_loader_info.dataset_params
+                **train_loader_info.dataset_params,
             )
         else:
             train_dataset = train_dataset_func(
@@ -117,7 +117,7 @@ def train_dataloader(self):
             train_dataset,
             shuffle=True,
             collate_fn=list_data_collate,
-            **train_loader_info.dataloader_params
+            **train_loader_info.dataloader_params,
         )
         return train_dataloader
 
@@ -130,14 +130,14 @@ def val_dataloader(self):
             val_dataset = val_dataset_func(
                 data=self.val_data,
                 transform=self.preproc,
-                **val_loader_info.dataset_params
+                **val_loader_info.dataset_params,
             )
         else:
             val_dataset = val_dataset_func(data=self.val_data, transform=self.preproc)
         val_dataloader = DataLoader(
             val_dataset,
             shuffle=False,
             collate_fn=list_data_collate,
-            **val_loader_info.dataloader_params
+            **val_loader_info.dataloader_params,
         )
         return val_dataloader

mmv_im2im/models/nets/BranchedERFNet_2d.py

@@ -1,9 +1,10 @@
 """
 Author: Davy Neven
-Licensed under the CC BY-NC 4.0 license 
+Licensed under the CC BY-NC 4.0 license
 (https://creativecommons.org/licenses/by-nc/4.0/)
 https://github.com/davyneven/SpatialEmbeddings
 """
+
 import torch
 import torch.nn as nn
 import mmv_im2im.models.nets.erfnet as erfnet