Mqin/fix mednist app error missing nibabel pkg (#308)

* Change to use optional import and explicitly add dependencies to dev and example requirements files.

Signed-off-by: mmelqin <mingmelvinq@nvidia.com>

* Formatting

Signed-off-by: mmelqin <mingmelvinq@nvidia.com>

* Add comments

Signed-off-by: mmelqin <mingmelvinq@nvidia.com>

Author: MMelQin

monai/deploy/operators/stl_conversion_operator.py

@@ -16,11 +16,11 @@
 from pathlib import Path
 from typing import Dict, Optional
 
-import nibabel as nib
 import numpy as np
 
 from monai.deploy.utils.importutil import optional_import
 
+nib, _ = optional_import("nibabel")
 sitk, _ = optional_import("SimpleITK")
 label, _ = optional_import("skimage.measure", name="label")
 measure, _ = optional_import("skimage", name="measure")
@@ -36,7 +36,10 @@
 
 @md.input("image", Image, IOType.IN_MEMORY)
 @md.output("stl_output", DataPath, IOType.DISK)
-@md.env(pip_packages=["numpy>=1.21", "numpy-stl>=2.12.0", "scikit-image>=0.17.2", "trimesh>=3.8.11"])
+# nibabel is required by the dependent class STLConverter.
+@md.env(
+    pip_packages=["numpy>=1.21", "nibabel >= 3.2.1", "numpy-stl>=2.12.0", "scikit-image>=0.17.2", "trimesh>=3.8.11"]
+)
 class STLConversionOperator(Operator):
     """Converts volumetric image to surface mesh in STL format, file output only."""
 

requirements-dev.txt

@@ -29,3 +29,7 @@ pydicom>=1.4.2
 SimpleITK>=2.0.0
 Pillow>=8.0.0
 bump2version==1.0.1
+scikit-image >= 0.17.2
+nibabel >= 3.2.1
+numpy-stl >= 2.12.0
+trimesh >= 3.8.11

requirements-examples.txt

@@ -3,3 +3,5 @@ pydicom >= 1.4.2
 SimpleITK >= 2.0.0
 Pillow >= 8.0.0
 nibabel >= 3.2.1
+numpy-stl >= 2.12.0
+trimesh >= 3.8.11