[BUG]
reghbali opened this issue · 1 comments
reghbali commented
Describe the bug
I am trying to run the simple app example in
https://docs.monai.io/projects/monai-deploy-app-sdk/en/stable/notebooks/tutorials/01_simple_app.html
and I get this error
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/monai/deploy/core/io_context.py", line 112, in set
check_type("value", value, data_type)
TypeError: check_type() takes 2 positional arguments but 3 were given
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/lebgali/Repos/monai-deploy/app.py", line 114, in <module>
app.run(input='./normal-brain-mri-4.png', output="output")
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/monai/deploy/core/application.py", line 429, in run
executor_obj.run()
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/monai/deploy/core/executors/single_process_executor.py", line 93, in run
op_exec_context.input_context.set(DataPath(input_path, read_only=True), input_label)
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/monai/deploy/core/io_context.py", line 114, in set
raise IOMappingError(
monai.deploy.exceptions.IOMappingError: The data type of 'image' in the input of '<__main__.SobelOperator object at 0x136f42850>' is <class 'monai.deploy.core.domain.datapath.DataPath'>, but the value to set is the data type of <class 'monai.deploy.core.domain.datapath.DataPath'>.
Which does not make sense. It is complaining that monai.deploy.core.domain.datapath.DataPath is not the same as itself.
Steps/Code to reproduce bug
from skimage import io
import monai.deploy.core as md # 'md' stands for MONAI Deploy (or can use 'core' instead)
from monai.deploy.core import (
Application,
DataPath,
ExecutionContext,
Image,
InputContext,
IOType,
Operator,
OutputContext,
)
@md.input("image", DataPath, IOType.DISK)
@md.output("image", Image, IOType.IN_MEMORY)
# If `pip_packages` is specified, the definition will be aggregated with the package dependency list of other
# operators and the application in packaging time.
# @md.env(pip_packages=["scikit-image >= 0.17.2"])
class SobelOperator(Operator):
"""This Operator implements a Sobel edge detector.
It has a single input and single output.
"""
def compute(self, op_input: InputContext, op_output: OutputContext, context: ExecutionContext):
from skimage import filters, io
input_path = op_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)
op_output.set(Image(data_out))
@md.input("image", Image, IOType.IN_MEMORY)
@md.output("image", Image, IOType.IN_MEMORY)
# If `pip_packages` is specified, the definition will be aggregated with the package dependency list of other
# operators and the application in packaging time.
# @md.env(pip_packages=["scikit-image >= 0.17.2"])
class MedianOperator(Operator):
"""This Operator implements a noise reduction.
The algorithm is based on the median operator.
It ingests a single input and provides a single output.
"""
def compute(self, op_input: InputContext, op_output: OutputContext, context: ExecutionContext):
from skimage.filters import median
data_in = op_input.get().asnumpy()
data_out = median(data_in)
op_output.set(Image(data_out))
@md.input("image", Image, IOType.IN_MEMORY)
@md.output("image", DataPath, IOType.DISK)
# If `pip_packages` is specified, the definition will be aggregated with the package dependency list of other
# operators and the application in packaging time.
# @md.env(pip_packages=["scikit-image >= 0.17.2"])
class GaussianOperator(Operator):
"""This Operator implements a smoothening based on Gaussian.
It ingests a single input and provides a single output.
"""
def compute(self, op_input: InputContext, op_output: OutputContext, context: ExecutionContext):
from skimage.filters import gaussian
from skimage.io import imsave
data_in = op_input.get().asnumpy()
data_out = gaussian(data_in, sigma=0.2)
output_folder = op_output.get().path
output_path = output_folder / "final_output.png"
imsave(output_path, data_out)
@md.resource(cpu=1)
# pip_packages can be a string that is a path(str) to requirements.txt file or a list of packages.
@md.env(pip_packages=["scikit-image >= 0.17.2"])
class App(Application):
"""This is a very basic application.
This showcases the MONAI Deploy application framework.
"""
# App's name. <class name>('App') if not specified.
name = "simple_imaging_app"
# App's description. <class docstring> if not specified.
description = "This is a very simple application."
# App's version. <git version tag> or '0.0.0' if not specified.
version = "0.1.0"
def compose(self):
"""This application has three operators.
Each operator has a single input and a single output port.
Each operator performs some kind of image processing function.
"""
sobel_op = SobelOperator()
median_op = MedianOperator()
gaussian_op = GaussianOperator()
self.add_flow(sobel_op, median_op)
# self.add_flow(sobel_op, median_op, {"image": "image"})
# self.add_flow(sobel_op, median_op, {"image": {"image"}})
self.add_flow(median_op, gaussian_op)
if __name__ == '__main__':
app = App()
app.run(input='./normal-brain-mri-4.png', output="output")
Expected behavior
This is copy pasted tutorial code. I expect no error.
Environment details (please complete the following information)
- OS/Platform: macOS 12.4
- Python Version: 3.11.0
- Method of MONAI Deploy App SDK install: pip
- SDK Version: 0.5.0