909 IO factory - develop ITKReader, NibabelReader, LoadImage

.github/workflows/pythonapp.yml

@@ -76,7 +76,7 @@ jobs:
         python -m pip install torch==1.4 -f https://download.pytorch.org/whl/cpu/torch_stable.html
         python -m pip install torchvision==0.5.0
         # min. requirements for windows instances
-        python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines(txt[1:11]); f.close()"
+        python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines(txt[1:12]); f.close()"
     - name: Install the dependencies
       run: |
         python -m pip install torch==1.4
@@ -205,6 +205,7 @@ jobs:
         # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
         # fresh torch installation according to pyproject.toml
         python -m pip install torch>=1.4 torchvision
+        python -m pip install -r requirements-dev.txt
     - name: Test source archive and wheel file
       run: |
         git fetch --depth=1 origin +refs/tags/*:refs/tags/*

docs/requirements.txt

@@ -2,6 +2,7 @@
 torch>=1.4.0
 pytorch-ignite==0.3.0
 numpy>=1.17
+itk
 nibabel
 parameterized
 scikit-image>=0.14.2

docs/source/data.rst

@@ -49,6 +49,20 @@ Patch-based dataset
   :members:
 
 
+Image reader
+------------
+
+ITKReader
+~~~~~~~~~
+.. autoclass:: ITKReader
+  :members:
+
+NibabelReader
+~~~~~~~~~~~~~
+.. autoclass:: NibabelReader
+  :members:
+
+
 Nifti format handling
 ---------------------
 

docs/source/installation.md

@@ -129,9 +129,9 @@ Since MONAI v0.2.0, the extras syntax such as `pip install 'monai[nibabel]'` is
 
 - The options are
 ```
-[nibabel, skimage, pillow, tensorboard, gdown, ignite]
+[nibabel, skimage, pillow, tensorboard, gdown, ignite, itk]
 ```
 which correspond to `nibabel`, `scikit-image`, `pillow`, `tensorboard`,
-`gdown`, and `pytorch-ignite` respectively.
+`gdown`, `pytorch-ignite`, and `itk` respectively.
 
 - `pip install 'monai[all]'` installs all the optional dependencies.

docs/source/transforms.rst

@@ -195,6 +195,12 @@ Intensity
 IO
 ^^
 
+`LoadImage`
+"""""""""""
+.. autoclass:: LoadImage
+    :members:
+    :special-members: __call__
+
 `LoadNifti`
 """""""""""
 .. autoclass:: LoadNifti
@@ -630,6 +636,12 @@ IO (Dict)
     :members:
     :special-members: __call__
 
+`LoadImaged`
+""""""""""""
+.. autoclass:: LoadImaged
+    :members:
+    :special-members: __call__
+
 `LoadNiftid`
 """"""""""""
 .. autoclass:: LoadNiftid

monai/config/deviceconfig.py

@@ -58,6 +58,22 @@
 except (ImportError, AttributeError):
     tensorboard_version = "NOT INSTALLED or UNKNOWN VERSION."
 
+try:
+    import gdown
+
+    gdown_version = gdown.__version__
+    del gdown
+except (ImportError, AttributeError):
+    gdown_version = "NOT INSTALLED or UNKNOWN VERSION."
+
+try:
+    import itk
+
+    itk_version = itk.Version.GetITKVersion()
+    del itk
+except (ImportError, AttributeError):
+    itk_version = "NOT INSTALLED or UNKNOWN VERSION."
+
 
 def get_config_values():
     """
@@ -84,6 +100,8 @@ def get_optional_config_values():
     output["scikit-image"] = skimage_version
     output["Pillow"] = PIL_version
     output["Tensorboard"] = tensorboard_version
+    output["gdown"] = gdown_version
+    output["ITK"] = itk_version
 
     return output
 

monai/data/__init__.py

@@ -14,6 +14,7 @@
 from .dataset import ArrayDataset, CacheDataset, Dataset, PersistentDataset, ZipDataset
 from .decathalon_datalist import load_decathalon_datalist
 from .grid_dataset import GridPatchDataset
+from .image_reader import *
 from .nifti_reader import NiftiDataset
 from .nifti_saver import NiftiSaver
 from .nifti_writer import write_nifti