Merge branch 'Project-MONAI:dev' into dev

.github/workflows/release.yml

@@ -78,12 +78,13 @@ jobs:
         rm dist/monai*.tar.gz
         ls -al dist/
 
-    - if: matrix.python-version == '3.9' && startsWith(github.ref, 'refs/tags/')
-      name: Publish to Test PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        password: ${{ secrets.TEST_PYPI }}
-        repository-url: https://test.pypi.org/legacy/
+    # remove publishing to Test PyPI as it is moved to blossom
+    # - if: matrix.python-version == '3.9' && startsWith(github.ref, 'refs/tags/')
+    #   name: Publish to Test PyPI
+    #   uses: pypa/gh-action-pypi-publish@release/v1
+    #   with:
+    #     password: ${{ secrets.TEST_PYPI }}
+    #     repository-url: https://test.pypi.org/legacy/
 
   versioning:
     # compute versioning file from python setup.py

Dockerfile

@@ -56,4 +56,5 @@ RUN apt-get update \
   && rm -rf /var/lib/apt/lists/*
 # append /opt/tools to runtime path for NGC CLI to be accessible from all file system locations
 ENV PATH=${PATH}:/opt/tools
+ENV POLYGRAPHY_AUTOINSTALL_DEPS=1
 WORKDIR /opt/monai

docs/source/config_syntax.md

@@ -16,6 +16,7 @@ Content:
   - [`$` to evaluate as Python expressions](#to-evaluate-as-python-expressions)
   - [`%` to textually replace configuration elements](#to-textually-replace-configuration-elements)
   - [`_target_` (`_disabled_`, `_desc_`, `_requires_`, `_mode_`) to instantiate a Python object](#instantiate-a-python-object)
+  - [`+` to alter semantics of merging config keys from multiple configuration files](#multiple-config-files)
 - [The command line interface](#the-command-line-interface)
 - [Recommendations](#recommendations)
 
@@ -175,6 +176,47 @@ _Description:_ `_requires_`, `_disabled_`, `_desc_`, and `_mode_` are optional k
   - `"debug"` -- execute with debug prompt and return the return value of ``pdb.runcall(_target_, **kwargs)``,
     see also [`pdb.runcall`](https://docs.python.org/3/library/pdb.html#pdb.runcall).
 
+## Multiple config files
+
+_Description:_ Multiple config files may be specified on the command line.
+The content of those config files is being merged. When same keys are specifiled in more than one config file,
+the value associated with the key is being overridden, in the order config files are specified.
+If the desired behaviour is to merge values from both files, the key in second config file should be prefixed with `+`.
+The value types for the merged contents must match and be both of `dict` or both of `list` type.
+`dict` values will be merged via update(), `list` values - concatenated via extend().
+Here's an example. In this case, "amp" value will be overridden by extra_config.json.
+`imports` and `preprocessing#transforms` lists will be merged. An error would be thrown if the value type in `"+imports"` is not `list`:
+
+config.json:
+```json
+{
+    "amp": "$True"
+    "imports": [
+	"$import torch"
+    ],
+    "preprocessing": {
+        "_target_": "Compose",
+        "transforms": [
+	  "$@t1",
+	  "$@t2"
+        ]
+    },
+}
+```
+
+extra_config.json:
+```json
+{
+    "amp": "$False"
+    "+imports": [
+	"$from monai.networks import trt_compile"
+    ],
+    "+preprocessing#transforms": [
+        "$@t3"
+    ]
+}
+```
+
 ## The command line interface
 
 In addition to the Pythonic APIs, a few command line interfaces (CLI) are provided to interact with the bundle.

docs/source/transforms.rst

@@ -976,6 +976,18 @@ Spatial
     :members:
     :special-members: __call__
 
+`ConvertBoxToPoints`
+""""""""""""""""""""
+.. autoclass:: ConvertBoxToPoints
+    :members:
+    :special-members: __call__
+
+`ConvertPointsToBoxes`
+""""""""""""""""""""""
+.. autoclass:: ConvertPointsToBoxes
+    :members:
+    :special-members: __call__
+
 
 Smooth Field
 ^^^^^^^^^^^^
@@ -1222,6 +1234,12 @@ Utility
     :members:
     :special-members: __call__
 
+`ApplyTransformToPoints`
+""""""""""""""""""""""""
+.. autoclass:: ApplyTransformToPoints
+    :members:
+    :special-members: __call__
+
 Dictionary Transforms
 ---------------------
 
@@ -1973,6 +1991,18 @@ Spatial (Dict)
     :members:
     :special-members: __call__
 
+`ConvertBoxToPointsd`
+"""""""""""""""""""""
+.. autoclass:: ConvertBoxToPointsd
+    :members:
+    :special-members: __call__
+
+`ConvertPointsToBoxesd`
+"""""""""""""""""""""""
+.. autoclass:: ConvertPointsToBoxesd
+    :members:
+    :special-members: __call__
+
 
 Smooth Field (Dict)
 ^^^^^^^^^^^^^^^^^^^
@@ -2277,6 +2307,12 @@ Utility (Dict)
     :members:
     :special-members: __call__
 
+`ApplyTransformToPointsd`
+"""""""""""""""""""""""""
+.. autoclass:: ApplyTransformToPointsd
+    :members:
+    :special-members: __call__
+
 
 MetaTensor
 ^^^^^^^^^^

monai/__init__.py

@@ -13,9 +13,51 @@
 
 import os
 import sys
-
+import logging
+import warnings
 from ._version import get_versions
 
+
+old_showwarning = warnings.showwarning
+
+
+def custom_warning_handler(message, category, filename, lineno, file=None, line=None):
+    ignore_files = ["ignite/handlers/checkpoint", "modelopt/torch/quantization/tensor_quant"]
+    if any(ignore in filename for ignore in ignore_files):
+        return
+    old_showwarning(message, category, filename, lineno, file, line)
+
+
+class DeprecatedTypesWarningFilter(logging.Filter):
+    def filter(self, record):
+        message_bodies_to_ignore = [
+            "np.bool8",
+            "np.object0",
+            "np.int0",
+            "np.uint0",
+            "np.void0",
+            "np.str0",
+            "np.bytes0",
+            "@validator",
+            "@root_validator",
+            "class-based `config`",
+            "pkg_resources",
+            "Implicitly cleaning up",
+        ]
+        for message in message_bodies_to_ignore:
+            if message in record.getMessage():
+                return False
+        return True
+
+
+# workaround for https://github.com/Project-MONAI/MONAI/issues/8060
+# TODO: remove this workaround after upstream fixed the warning
+# Set the custom warning handler to filter warning
+warnings.showwarning = custom_warning_handler
+# Get the logger for warnings and add the filter to the logger
+logging.getLogger("py.warnings").addFilter(DeprecatedTypesWarningFilter())
+
+
 PY_REQUIRED_MAJOR = 3
 PY_REQUIRED_MINOR = 9
 

monai/apps/vista3d/inferer.py

@@ -100,7 +100,7 @@ def point_based_window_inferer(
                         point_labels=point_labels,
                         class_vector=class_vector,
                         prompt_class=prompt_class,
-                        patch_coords=unravel_slice,
+                        patch_coords=[unravel_slice],
                         prev_mask=prev_mask,
                         **kwargs,
                     )

monai/bundle/config_parser.py

@@ -20,7 +20,7 @@
 
 from monai.bundle.config_item import ComponentLocator, ConfigComponent, ConfigExpression, ConfigItem
 from monai.bundle.reference_resolver import ReferenceResolver
-from monai.bundle.utils import ID_REF_KEY, ID_SEP_KEY, MACRO_KEY
+from monai.bundle.utils import ID_REF_KEY, ID_SEP_KEY, MACRO_KEY, merge_kv
 from monai.config import PathLike
 from monai.utils import ensure_tuple, look_up_option, optional_import
 from monai.utils.misc import CheckKeyDuplicatesYamlLoader, check_key_duplicates
@@ -423,8 +423,10 @@ def load_config_files(cls, files: PathLike | Sequence[PathLike] | dict, **kwargs
         if isinstance(files, str) and not Path(files).is_file() and "," in files:
             files = files.split(",")
         for i in ensure_tuple(files):
-            for k, v in (cls.load_config_file(i, **kwargs)).items():
-                parser[k] = v
+            config_dict = cls.load_config_file(i, **kwargs)
+            for k, v in config_dict.items():
+                merge_kv(parser, k, v)
+
         return parser.get()  # type: ignore
 
     @classmethod

monai/bundle/scripts.py

@@ -32,7 +32,7 @@
 from monai.apps.utils import _basename, download_url, extractall, get_logger
 from monai.bundle.config_item import ConfigComponent
 from monai.bundle.config_parser import ConfigParser
-from monai.bundle.utils import DEFAULT_INFERENCE, DEFAULT_METADATA
+from monai.bundle.utils import DEFAULT_INFERENCE, DEFAULT_METADATA, merge_kv
 from monai.bundle.workflows import BundleWorkflow, ConfigWorkflow
 from monai.config import IgniteInfo, PathLike
 from monai.data import load_net_with_metadata, save_net_with_metadata
@@ -105,7 +105,7 @@ def update_kwargs(args: str | dict | None = None, ignore_none: bool = True, **kw
         if isinstance(v, dict) and isinstance(args_.get(k), dict):
             args_[k] = update_kwargs(args_[k], ignore_none, **v)
         else:
-            args_[k] = v
+            merge_kv(args_, k, v)
     return args_
 
 
@@ -255,6 +255,7 @@ def _download_from_ngc_private(
     else:
         raise ValueError("NGC API requires requests package. Please install it.")
 
+    os.makedirs(download_path, exist_ok=True)
     zip_path = download_path / f"{filename}_v{version}.zip"
     with open(zip_path, "wb") as f:
         f.write(response.content)

monai/bundle/utils.py

@@ -13,6 +13,7 @@
 
 import json
 import os
+import warnings
 import zipfile
 from typing import Any
 
@@ -21,12 +22,21 @@
 
 yaml, _ = optional_import("yaml")
 
-__all__ = ["ID_REF_KEY", "ID_SEP_KEY", "EXPR_KEY", "MACRO_KEY", "DEFAULT_MLFLOW_SETTINGS", "DEFAULT_EXP_MGMT_SETTINGS"]
+__all__ = [
+    "ID_REF_KEY",
+    "ID_SEP_KEY",
+    "EXPR_KEY",
+    "MACRO_KEY",
+    "MERGE_KEY",
+    "DEFAULT_MLFLOW_SETTINGS",
+    "DEFAULT_EXP_MGMT_SETTINGS",
+]
 
 ID_REF_KEY = "@"  # start of a reference to a ConfigItem
 ID_SEP_KEY = "::"  # separator for the ID of a ConfigItem
 EXPR_KEY = "$"  # start of a ConfigExpression
 MACRO_KEY = "%"  # start of a macro of a config
+MERGE_KEY = "+"  # prefix indicating merge instead of override in case of multiple configs.
 
 _conf_values = get_config_values()
 
@@ -233,3 +243,27 @@ def load_bundle_config(bundle_path: str, *config_names: str, **load_kw_args: Any
             parser.read_config(f=cdata)
 
     return parser
+
+
+def merge_kv(args: dict | Any, k: str, v: Any) -> None:
+    """
+    Update the `args` dict-like object with the key/value pair `k` and `v`.
+    """
+    if k.startswith(MERGE_KEY):
+        """
+        Both values associated with `+`-prefixed key pair must be of `dict` or `list` type.
+        `dict` values will be merged, `list` values - concatenated.
+        """
+        id = k[1:]
+        if id in args:
+            if isinstance(v, dict) and isinstance(args[id], dict):
+                args[id].update(v)
+            elif isinstance(v, list) and isinstance(args[id], list):
+                args[id].extend(v)
+            else:
+                raise ValueError(ValueError(f"config must be dict or list for key `{k}`, but got {type(v)}: {v}."))
+        else:
+            warnings.warn(f"Can't merge entry ['{k}'], '{id}' is not in target dict - copying instead.")
+            args[id] = v
+    else:
+        args[k] = v

monai/bundle/workflows.py

@@ -26,7 +26,7 @@
 from monai.bundle.properties import InferProperties, MetaProperties, TrainProperties
 from monai.bundle.utils import DEFAULT_EXP_MGMT_SETTINGS, EXPR_KEY, ID_REF_KEY, ID_SEP_KEY
 from monai.config import PathLike
-from monai.utils import BundleProperty, BundlePropertyConfig, deprecated_arg, deprecated_arg_default, ensure_tuple
+from monai.utils import BundleProperty, BundlePropertyConfig, deprecated_arg, ensure_tuple
 
 __all__ = ["BundleWorkflow", "ConfigWorkflow"]
 
@@ -43,7 +43,7 @@ class BundleWorkflow(ABC):
         workflow_type: specifies the workflow type: "train" or "training" for a training workflow,
             or "infer", "inference", "eval", "evaluation" for a inference workflow,
             other unsupported string will raise a ValueError.
-            default to `None` for common workflow.
+            default to `train` for train workflow.
         workflow: specifies the workflow type: "train" or "training" for a training workflow,
             or "infer", "inference", "eval", "evaluation" for a inference workflow,
             other unsupported string will raise a ValueError.
@@ -274,7 +274,6 @@ class ConfigWorkflow(BundleWorkflow):
         new_name="workflow_type",
         msg_suffix="please use `workflow_type` instead.",
     )
-    @deprecated_arg_default("workflow_type", None, "train", since="1.2", replaced="1.4")
     def __init__(
         self,
         config_file: str | Sequence[str],
@@ -284,7 +283,7 @@ def __init__(
         run_id: str = "run",
         final_id: str = "finalize",
         tracking: str | dict | None = None,
-        workflow_type: str | None = None,
+        workflow_type: str | None = "train",
         workflow: str | None = None,
         properties_path: PathLike | None = None,
         **override: Any,

monai/data/image_reader.py

@@ -1359,7 +1359,7 @@ def _get_affine(self, header: dict) -> np.ndarray:
         x, y = direction.shape
         affine_diam = min(x, y) + 1
         affine: np.ndarray = np.eye(affine_diam)
-        affine[:x, :y] = direction
+        affine[:x, :y] = direction.T
         affine[: (affine_diam - 1), -1] = origin  # len origin is always affine_diam - 1
         return affine
 

monai/handlers/__init__.py

@@ -20,7 +20,7 @@
 from .earlystop_handler import EarlyStopHandler
 from .garbage_collector import GarbageCollector
 from .hausdorff_distance import HausdorffDistance
-from .ignite_metric import IgniteMetric, IgniteMetricHandler
+from .ignite_metric import IgniteMetricHandler
 from .logfile_handler import LogfileHandler
 from .lr_schedule_handler import LrScheduleHandler
 from .mean_dice import MeanDice
@@ -40,5 +40,6 @@
 from .stats_handler import StatsHandler
 from .surface_distance import SurfaceDistance
 from .tensorboard_handlers import TensorBoardHandler, TensorBoardImageHandler, TensorBoardStatsHandler
+from .trt_handler import TrtHandler
 from .utils import from_engine, ignore_data, stopping_fn_from_loss, stopping_fn_from_metric, write_metrics_reports
 from .validation_handler import ValidationHandler