Parse callables (functions, methods) similarly to objects

[ibro45]

Is your feature request related to a problem? Please describe.
Support for functions/methods in config by making Monai call them instead of attempting to instantiate them.

calculate:
    _target_: "math.isclose"
    a: 0.001
    b: 0.002

Describe the solution you'd like
A solution like Hydra's (https://hydra.cc/docs/advanced/instantiate_objects/overview/) that can both instantiate or call would be perfect.

Describe alternatives you've considered
None

Additional context
While you could do calculate: "$math.isclose(0.001, 0.002)", it does not allow argument overriding from CLI.

[wyli]

thanks for reporting, it's possible to use @ to refer to an object, so that it supports overriding:

from monai.bundle import ConfigParser

config = {"import statements": "$import math",
          "calculate": "$math.isclose(@a, @b)",
          "a": 0.001,
          "b": 0.005}
parser = ConfigParser(config)
print(parser.get_parsed_content("calculate"))  # False
parser["b"] = 0.001
print(parser.get_parsed_content("calculate"))  # True

[ibro45]

Hi, yes, thank you, but you still have to refer the arguments manually in"$math.isclose(@a, @b)". With _target_ and instantiation that's not necessary.

Do you think you're interested in adding support for calling functions/methods in the same fashion as object instantiation?

[wyli]

I took another look, actually it's a supported use case, but there's bug in the code. I'm create a pull request to fix it.

[ibro45]

Awesome, thank you so much. I love what you did; I switched from OmegaConf/Hydra, Monai Bundle Config solves quite a few problems I had there, and the error messages are way better. Super simple to integrate it too. Looking forward to learning more about Bundle Specification!

[ibro45]

Hi, so I just installed monai from your branch and tried this:

config.yaml

imports: $import torch

forward:
    _target_: "@model.forward"
    input: $torch.rand(1, 3, 256, 256)

model:
    _target_: monai.networks.nets.resnet.resnet18
    spatial_dim: 2

Command:
python -m monai.bundle run forward --config_file config.yaml

And it raises:

Traceback (most recent call last):
  File "/home/ibro/anaconda3/envs/lighter/lib/python3.9/site-packages/monai/bundle/config_item.py", line 286, in instantiate
    return instantiate(modname, **args)
  File "/home/ibro/anaconda3/envs/lighter/lib/python3.9/site-packages/monai/utils/module.py", line 232, in instantiate
    raise ModuleNotFoundError(f"Cannot locate class or function path: '{path}'.")
ModuleNotFoundError: Cannot locate class or function path: '@model.forward'.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/ibro/anaconda3/envs/lighter/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/home/ibro/anaconda3/envs/lighter/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/home/ibro/anaconda3/envs/lighter/lib/python3.9/site-packages/monai/bundle/__main__.py", line 20, in <module>
    fire.Fire()
  File "/home/ibro/anaconda3/envs/lighter/lib/python3.9/site-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/home/ibro/anaconda3/envs/lighter/lib/python3.9/site-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/home/ibro/anaconda3/envs/lighter/lib/python3.9/site-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/home/ibro/anaconda3/envs/lighter/lib/python3.9/site-packages/monai/bundle/scripts.py", line 744, in run
    return [parser.get_parsed_content(i, lazy=True, eval_expr=True, instantiate=True) for i in ensure_tuple(runner_id_)]
  File "/home/ibro/anaconda3/envs/lighter/lib/python3.9/site-packages/monai/bundle/scripts.py", line 744, in <listcomp>
    return [parser.get_parsed_content(i, lazy=True, eval_expr=True, instantiate=True) for i in ensure_tuple(runner_id_)]
  File "/home/ibro/anaconda3/envs/lighter/lib/python3.9/site-packages/monai/bundle/config_parser.py", line 287, in get_parsed_content
    return self.ref_resolver.get_resolved_content(id=id, **kwargs)
  File "/home/ibro/anaconda3/envs/lighter/lib/python3.9/site-packages/monai/bundle/reference_resolver.py", line 188, in get_resolved_content
    return self._resolve_one_item(id=id, **kwargs)
  File "/home/ibro/anaconda3/envs/lighter/lib/python3.9/site-packages/monai/bundle/reference_resolver.py", line 166, in _resolve_one_item
    self.resolved_content[id] = item.instantiate() if kwargs.get("instantiate", True) else item
  File "/home/ibro/anaconda3/envs/lighter/lib/python3.9/site-packages/monai/bundle/config_item.py", line 288, in instantiate
    raise RuntimeError(f"Failed to instantiate {self}.") from e
RuntimeError: Failed to instantiate {'_target_': '@model.forward', 'input': tensor([[[[0.3608, 0.3325, 0.4329,  ..., 0.0211, 0.4916, 0.6840],
          [0.0417, 0.7033, 0.3991,  ..., 0.3597, 0.1550, 0.3324],
          [0.6108, 0.8000, 0.8778,  ..., 0.7984, 0.9651, 0.8256],
          ...,
          [0.7286, 0.7389, 0.3762,  ..., 0.5201, 0.3182, 0.0289],
          [0.4781, 0.3437, 0.1659,  ..., 0.1252, 0.5990, 0.7619],
          [0.0707, 0.7495, 0.2894,  ..., 0.3977, 0.8704, 0.3102]],

         [[0.5390, 0.2731, 0.1640,  ..., 0.6009, 0.2121, 0.9602],
          [0.8667, 0.7630, 0.8089,  ..., 0.0607, 0.2541, 0.7719],
          [0.8204, 0.3814, 0.4954,  ..., 0.6606, 0.3937, 0.6057],
          ...,
          [0.8998, 0.0648, 0.3001,  ..., 0.5004, 0.6388, 0.1619],
          [0.6452, 0.4225, 0.1998,  ..., 0.4859, 0.4119, 0.0660],
          [0.2361, 0.5676, 0.9900,  ..., 0.6868, 0.3248, 0.9527]],

         [[0.6602, 0.6643, 0.8554,  ..., 0.7943, 0.4970, 0.1568],
          [0.2356, 0.6178, 0.7380,  ..., 0.8589, 0.4696, 0.2227],
          [0.5740, 0.3209, 0.6339,  ..., 0.3270, 0.3660, 0.3420],
          ...,
          [0.7360, 0.1710, 0.9990,  ..., 0.1324, 0.6394, 0.5160],
          [0.0786, 0.9697, 0.0510,  ..., 0.3566, 0.4310, 0.2636],
          [0.0938, 0.4502, 0.2579,  ..., 0.5274, 0.5545, 0.3955]]]])}.

Am I doing something wrong, or is referencing a method of an object from the config not supported?

[wyli]

that's a good question, at the moment the usage would be

imports: $import torch

x: "$torch.rand(1, 3, 256, 256)"
forward: "$@model().forward(@x)"

model:
    _target_: monai.networks.nets.resnet.resnet18
    pretrained: False
    spatial_dims: 2

if you want to delay the forward call, it's also possible to add the partial wrapper:

imports:
    - $import torch
    - $import functools

x: "$torch.rand(1, 3, 256, 256)"
forward: "$functools.partial(@model().forward, @x)"

model:
    _target_: monai.networks.nets.resnet.resnet18
    pretrained: False
    spatial_dims: 2

[ibro45]

Alright, thanks! Do you think that's something that the bundle config will support?

[wyli]

sure, it seems that is doable with minor code changes, I'm creating a pull request and getting more comments from @Nic-Ma @ericspod.

[ericspod]

The way that we do searching when referring to something by name should perhaps be revisited. Currently our code traverses all known libraries looking for names, this a problem if multiple definitions use the same name in different modules as well as also forcing a lot of things to get loaded that don't need to be. The solution to your specific use case above works but there's a number of extra syntax that we've introduce with the "$@" sigils that isn't obvious. I feel we need a bit of a smarter name searching system that will look at some target like "X.Y.Z" and search for "X" first in currently known objects and imported modules, then for "X.Y" if not found, etc. It would then resolve the rest of the name looking for definitions or members of definitions, so a target "model.forward" should find the object "model" and that "forward" is a callable member and not try to instantiate it.

[wyli]

I've updated #5854 for this.
Previously the check of _target_ was too restrictive:

MONAI/monai/bundle/config_item.py

Lines 237 to 239 in 33d41d7

	target = config.get("_target_")
	if not isinstance(target, str):
	raise ValueError("must provide a string for the `_target_` of component to instantiate.")

please see the new test cases in PR #5854 for the newly supported cases.