Accept only folder input path on App Runner

Signed-off-by: Gigon Bae <gbae@nvidia.com>

Author: gigony

README.md

@@ -44,8 +44,12 @@ python examples/apps/simple_imaging_app/app.py -i examples/apps/simple_imaging_a
 # Package app (creating MAP Docker image), using `-l DEBUG` option to see progress.
 monai-deploy package examples/apps/simple_imaging_app -t simple_app:latest -l DEBUG
 
-# Run the app with docker image and input file locally
-monai-deploy run simple_app:latest examples/apps/simple_imaging_app/brain_mr_input.jpg output
+# Run the app with docker image and an input file locally
+## Copy a test input file to 'input' folder
+mkdir -p input && rm -rf input/*
+cp examples/apps/simple_imaging_app/brain_mr_input.jpg input/
+## Launch the app
+monai-deploy run simple_app:latest input output
 ```
 
 [MedNIST demo](TBD) is available on Colab.

docs/source/developing_with_sdk/executing_packaged_app_locally.md

@@ -17,7 +17,7 @@ usage: monai-deploy run [-h] [-l <LEVEL>G,INFO,WARN,ERROR,CRITICAL}] [-q] <map-i
 
 positional arguments:
   <map-image[:tag]>     MAP image name
-  <input>               Input data path
+  <input>               Input data directory path
   <output>              Output data directory path
 
 optional arguments:
@@ -40,14 +40,14 @@ monai-deploy run <container-image-name>[:tag] <input> <output> [-q|--quiet]
 | Name     | Format                           | Description                                                   |
 | -------- | -------------------------------- | ------------------------------------------------------------- |
 | MAP      | `container-image-name[:tag]`     | MAP container image name with or without image tag.           |
-| input    | file or directory path           | Local file or folder that contains input dataset for the MAP. |
-| output   | path                             | Local path to store output from the executing MAP.            |
+| input    | directory path                   | Local folder path that contains input dataset for the MAP.    |
+| output   | directory path                   | Local folder path to store output from the executing MAP.     |
 
 #### Optional arguments
 
 | Name                | Shorthand  | Default    | Description                                                       |
 | ------------------- | ---------- | ---------- | --------------------------------------------------------------    |
-| quiet               | -q         | False      | Suppress the STDOUT and print only STDERR from the application    |
+| quiet               | -q         | False      | Suppress the STDOUT and print only STDERR from the application.   |
 
 ## Example
 

examples/apps/mednist_classifier_monaideploy/mednist_classifier_monaideploy.py

@@ -39,6 +39,8 @@ def compute(self, input: InputContext, output: OutputContext, context: Execution
         from PIL import Image as PILImage
 
         input_path = input.get().path
+        if input_path.is_dir():
+            input_path = next(input_path.glob("*.*"))  # take the first file
 
         image = PILImage.open(input_path)
         image = image.convert("L")  # convert to greyscale image

examples/apps/simple_imaging_app/sobel_operator.py

@@ -37,6 +37,8 @@ def compute(self, input: InputContext, output: OutputContext, context: Execution
         from skimage import filters, io
 
         input_path = input.get().path
+        if input_path.is_dir():
+            input_path = next(input_path.glob("*.*"))  # take the first file
 
         data_in = io.imread(input_path)[:, :, :3]  # discard alpha channel if exists
         data_out = filters.sobel(data_in)

monai/deploy/runner/README.md

@@ -1,23 +1,25 @@
-# MONAI APPLICATION RUNNER
+# MONAI Application Runner
 
-The MONAI Application Runner (MAR) allows users to run and test their MONAI Application Package (MAP) locally. MAR allows the users to specify input and output path on local file system which it maps to the input and output of MAP during execution.
+The MONAI Application Runner (MAR) is a command-line utility that allows users to run and test their MONAI Application Package (MAP) locally. MAR is developed to make the running and testing of MAPs locally an easy process for developers and scientists by abstracting away the need to understand the internal details of the MAP. MAR allows the users to specify input and output paths on the local file system which it maps to the input and output of MAP during execution.
 
 ## Syntax
-```
+
+```bash
 monai-deploy run <container-image-name>[:tag] <input> <output> [-q|--quiet]
 ```
+
 ### Arguments
 
-#### Positional arguments:
+#### Positional arguments
 
 | Name     | Format                           | Description                                                   |
 | -------- | -------------------------------- | ------------------------------------------------------------- |
 | MAP      | `container-image-name[:tag]`     | MAP container image name with or without image tag.           |
-| input    | file or directory path           | Local file or folder that contains input dataset for the MAP. |
-| output   | path                             | Local path to store output from the executing MAP.       |
+| input    | directory path                   | Local folder path that contains input dataset for the MAP.    |
+| output   | directory path                   | Local folder path to store output from the executing MAP.     |
 
-#### Optional arguments:
+#### Optional arguments
 
 | Name                | Shorthand  | Default    | Description                                                       |
 | ------------------- | ---------- | ---------- | --------------------------------------------------------------    |
-| quiet               | -q         | False      | Supress the STDOUT and print only STDERR from the application |
+| quiet               | -q         | False      | Suppress the STDOUT and print only STDERR from the application.   |

monai/deploy/runner/run_command.py

@@ -24,7 +24,7 @@ def create_run_parser(subparser: _SubParsersAction, command: str, parents: List[
 
     parser.add_argument("map", metavar="<map-image[:tag]>", help="MAP image name")
 
-    parser.add_argument("input", metavar="<input>", type=argparse_types.valid_existing_path, help="Input data path")
+    parser.add_argument("input", metavar="<input>", type=argparse_types.valid_existing_path, help="Input data directory path")
 
     parser.add_argument(
         "output", metavar="<output>", type=argparse_types.valid_dir_path, help="Output data directory path"