188 setuptools

README.md

@@ -19,6 +19,16 @@ MONAI is a [PyTorch](https://pytorch.org/)-based, [open-source](https://github.c
 - customizable design for varying user expertise;
 - multi-GPU data parallelism support.
 
+## Installation
+Clone and build this repository from source
+
+```bash
+git clone https://github.com/Project-MONAI/MONAI.git
+pip install -e MONAI/
+```
+
+Run some of the examples in [Getting Started](##getting-started)
+
 ## Getting Started
 
 Tutorials & examples are located at [monai/examples](https://github.com/Project-MONAI/MONAI/tree/master/examples).

examples/classification_3d/densenet_evaluation_array.py

@@ -16,8 +16,6 @@
 from ignite.engine import create_supervised_evaluator, _prepare_batch
 from torch.utils.data import DataLoader
 
-# assumes the framework is found here, change as necessary
-sys.path.append("../..")
 import monai
 import monai.transforms.compose as transforms
 from monai.data.nifti_reader import NiftiDataset

examples/classification_3d/densenet_evaluation_dict.py

@@ -17,8 +17,6 @@
 from ignite.engine import create_supervised_evaluator, _prepare_batch
 from torch.utils.data import DataLoader
 
-# assumes the framework is found here, change as necessary
-sys.path.append("../..")
 from monai.handlers.classification_saver import ClassificationSaver
 from monai.handlers.checkpoint_loader import CheckpointLoader
 from monai.handlers.stats_handler import StatsHandler

examples/classification_3d/densenet_training_array.py

@@ -17,8 +17,6 @@
 from ignite.handlers import ModelCheckpoint, EarlyStopping
 from torch.utils.data import DataLoader
 
-# assumes the framework is found here, change as necessary
-sys.path.append("../..")
 import monai
 import monai.transforms.compose as transforms
 from monai.data.nifti_reader import NiftiDataset

examples/classification_3d/densenet_training_dict.py

@@ -17,8 +17,6 @@
 from ignite.handlers import ModelCheckpoint, EarlyStopping
 from torch.utils.data import DataLoader
 
-# assumes the framework is found here, change as necessary
-sys.path.append("../..")
 import monai
 import monai.transforms.compose as transforms
 from monai.transforms.composables import \

examples/integrate_to_spleen_program.ipynb

@@ -67,8 +67,6 @@
     "import torch\n",
     "from torch.utils.data import DataLoader\n",
     "import matplotlib.pyplot as plt\n",
-    "# assumes the framework is found here, change as necessary\n",
-    "sys.path.append(\"..\")\n",
     "import monai\n",
     "import monai.transforms.compose as transforms\n",
     "from monai.transforms.composables import \\\n",

examples/multi_gpu_test.ipynb

@@ -24,9 +24,6 @@
     "from ignite.engine.engine import Events\n",
     "from ignite.handlers import ModelCheckpoint\n",
     "\n",
-    "# assumes the framework is found here, change as necessary\n",
-    "sys.path.append(\"..\")\n",
-    "\n",
     "import monai\n",
     "\n",
     "\n",

examples/nifti_read_example.ipynb

@@ -37,8 +37,6 @@
     "from torch.utils.data import DataLoader\n",
     "import monai.transforms.compose as transforms\n",
     "\n",
-    "sys.path.append('..') # assumes this is where MONAI is\n",
-    "\n",
     "import monai\n",
     "\n",
     "from monai.transforms.utils import rescale_array\n",

examples/segmentation_3d/unet_evaluation_array.py

@@ -20,9 +20,6 @@
 from ignite.engine import Engine
 from torch.utils.data import DataLoader
 
-# assumes the framework is found here, change as necessary
-sys.path.append("../..")
-
 from monai import config
 from monai.handlers.checkpoint_loader import CheckpointLoader
 from monai.handlers.segmentation_saver import SegmentationSaver

examples/segmentation_3d/unet_evaluation_dict.py

@@ -20,9 +20,6 @@
 from ignite.engine import Engine
 from torch.utils.data import DataLoader
 
-# assumes the framework is found here, change as necessary
-sys.path.append("../..")
-
 import monai
 from monai.data.utils import list_data_collate
 from monai.utils.sliding_window_inference import sliding_window_inference

examples/segmentation_3d/unet_training_array.py

@@ -21,9 +21,6 @@
 from ignite.handlers import ModelCheckpoint, EarlyStopping
 from torch.utils.data import DataLoader
 
-# assumes the framework is found here, change as necessary
-sys.path.append("../..")
-
 import monai
 import monai.transforms.compose as transforms
 

examples/segmentation_3d/unet_training_dict.py

@@ -21,9 +21,6 @@
 from ignite.handlers import ModelCheckpoint, EarlyStopping
 from torch.utils.data import DataLoader
 
-# assumes the framework is found here, change as necessary
-sys.path.append("../..")
-
 import monai
 import monai.transforms.compose as transforms
 from monai.transforms.composables import \

examples/transform_speed.ipynb

@@ -46,8 +46,6 @@
     "except RuntimeError:\n",
     "    pass\n",
     "\n",
-    "sys.path.append('..') # assumes this is where MONAI is\n",
-    "\n",
     "import monai\n",
     "from monai.transforms.compose import Compose\n",
     "from monai.data.nifti_reader import NiftiDataset\n",

examples/transforms_demo_2d.ipynb

@@ -55,8 +55,6 @@
     "import matplotlib.pyplot as plt\n",
     "from PIL import Image\n",
     "\n",
-    "sys.path.append('..') # assumes this is where MONAI is\n",
-    "\n",
     "import monai\n",
     "from monai.transforms import Affine, Rand2DElastic\n",
     "\n",

examples/unet_segmentation_3d.ipynb

@@ -39,9 +39,6 @@
     "from ignite.handlers import ModelCheckpoint, EarlyStopping\n",
     "from torch.utils.data import DataLoader\n",
     "\n",
-    "# assumes the framework is found here, change as necessary\n",
-    "sys.path.append(\"..\")\n",
-    "\n",
     "import monai\n",
     "import monai.transforms.compose as transforms\n",
     "\n",

monai/__init__.py

@@ -15,8 +15,7 @@
 from .utils.module import load_submodules
 
 __copyright__ = "(c) 2020 MONAI Consortium"
-__version__tuple__ = (0, 0, 1)
-__version__ = "%i.%i.%i" % __version__tuple__
+__version__ = "0.0.1"
 
 __basedir__ = os.path.dirname(__file__)
 

setup.py

@@ -0,0 +1,55 @@
+import os
+import io
+import re
+from setuptools import setup, find_packages
+
+# inspired by https://github.com/pytorch/ignite/blob/master/setup.py
+def read(*names, **kwargs):
+    print(os.path.join(os.path.dirname(__file__), *names))
+    with io.open(
+        os.path.join(os.path.dirname(__file__), *names), 
+        encoding=kwargs.get("encoding", "utf8")
+    ) as fp:
+        return fp.read()
+
+def find_version(*file_paths):
+    version_file = read(*file_paths)
+    version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
+                              version_file, re.M)
+    if version_match:
+        return version_match.group(1)
+    raise RuntimeError("Unable to find version string.")
+
+readme = read("README.md")
+VERSION = find_version("monai", "__init__.py")
+requirements = [
+    "torch",
+    "pytorch-ignite",
+    "numpy",
+    "pillow",
+    "coverage",
+    "nibabel",
+    "parameterized",
+    "tensorboard",
+    "scikit-image",
+    "scipy"
+]
+
+if __name__ == '__main__':
+    setup(
+        # Metadata
+        name="monai",
+        version=VERSION,
+        author="MONAI Consortium",
+        url="https://github.com/Project-MONAI/MONAI",
+        author_email="monai.miccai2019@gmail.com",
+        description="AI Toolkit for Healthcare Imaging",
+        long_description_content_type="text/markdown",
+        long_description=readme,
+        license="Apache License 2.0",
+
+        # Package info
+        packages=find_packages(exclude=('docs', 'examples', 'tests')),
+        zip_safe=True,
+        install_requires=requirements
+    )