monai-weekly 1.4.dev2427__py3-none-any.whl → 1.4.dev2429__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- monai/__init__.py +2 -2
- monai/_version.py +3 -3
- monai/apps/auto3dseg/auto_runner.py +1 -1
- monai/apps/detection/utils/anchor_utils.py +2 -2
- monai/apps/generation/maisi/networks/autoencoderkl_maisi.py +0 -2
- monai/apps/pathology/transforms/post/array.py +1 -0
- monai/auto3dseg/utils.py +1 -1
- monai/bundle/scripts.py +106 -8
- monai/bundle/utils.py +1 -0
- monai/data/dataset_summary.py +1 -0
- monai/data/utils.py +9 -6
- monai/data/wsi_reader.py +2 -2
- monai/engines/__init__.py +3 -1
- monai/engines/trainer.py +281 -2
- monai/engines/utils.py +76 -1
- monai/handlers/mlflow_handler.py +21 -4
- monai/inferers/__init__.py +5 -0
- monai/inferers/inferer.py +1279 -1
- monai/networks/blocks/__init__.py +3 -0
- monai/networks/blocks/attention_utils.py +128 -0
- monai/networks/blocks/crossattention.py +166 -0
- monai/networks/blocks/rel_pos_embedding.py +56 -0
- monai/networks/blocks/selfattention.py +72 -5
- monai/networks/blocks/spade_norm.py +95 -0
- monai/networks/blocks/spatialattention.py +82 -0
- monai/networks/blocks/transformerblock.py +24 -4
- monai/networks/blocks/upsample.py +22 -10
- monai/networks/layers/__init__.py +2 -1
- monai/networks/layers/factories.py +12 -1
- monai/networks/layers/utils.py +14 -1
- monai/networks/layers/vector_quantizer.py +233 -0
- monai/networks/nets/__init__.py +9 -0
- monai/networks/nets/autoencoderkl.py +702 -0
- monai/networks/nets/controlnet.py +465 -0
- monai/networks/nets/diffusion_model_unet.py +1913 -0
- monai/networks/nets/patchgan_discriminator.py +230 -0
- monai/networks/nets/quicknat.py +2 -0
- monai/networks/nets/resnet.py +3 -4
- monai/networks/nets/spade_autoencoderkl.py +480 -0
- monai/networks/nets/spade_diffusion_model_unet.py +934 -0
- monai/networks/nets/spade_network.py +435 -0
- monai/networks/nets/swin_unetr.py +4 -3
- monai/networks/nets/transformer.py +157 -0
- monai/networks/nets/vqvae.py +472 -0
- monai/networks/schedulers/__init__.py +17 -0
- monai/networks/schedulers/ddim.py +294 -0
- monai/networks/schedulers/ddpm.py +250 -0
- monai/networks/schedulers/pndm.py +316 -0
- monai/networks/schedulers/scheduler.py +205 -0
- monai/networks/utils.py +22 -0
- monai/transforms/io/array.py +3 -3
- monai/transforms/regularization/array.py +4 -0
- monai/transforms/utils_create_transform_ims.py +2 -4
- monai/utils/__init__.py +1 -0
- monai/utils/misc.py +5 -4
- monai/utils/ordering.py +207 -0
- {monai_weekly-1.4.dev2427.dist-info → monai_weekly-1.4.dev2429.dist-info}/METADATA +3 -3
- {monai_weekly-1.4.dev2427.dist-info → monai_weekly-1.4.dev2429.dist-info}/RECORD +61 -40
- {monai_weekly-1.4.dev2427.dist-info → monai_weekly-1.4.dev2429.dist-info}/WHEEL +1 -1
- {monai_weekly-1.4.dev2427.dist-info → monai_weekly-1.4.dev2429.dist-info}/LICENSE +0 -0
- {monai_weekly-1.4.dev2427.dist-info → monai_weekly-1.4.dev2429.dist-info}/top_level.txt +0 -0
monai/__init__.py
CHANGED
@@ -17,7 +17,7 @@ import sys
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from ._version import get_versions
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PY_REQUIRED_MAJOR = 3
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PY_REQUIRED_MINOR =
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PY_REQUIRED_MINOR = 9
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version_dict = get_versions()
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__version__: str = version_dict.get("version", "0+unknown")
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@@ -93,4 +93,4 @@ except BaseException:
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if MONAIEnvVars.debug():
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raise
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__commit_id__ = "
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__commit_id__ = "d020facccbd3afe979fce68c24703dcda47234f6"
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monai/_version.py
CHANGED
@@ -8,11 +8,11 @@ import json
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version_json = '''
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{
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"date": "2024-07-
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"date": "2024-07-21T02:18:43+0000",
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"dirty": false,
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"error": null,
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"full-revisionid": "
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"version": "1.4.
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"full-revisionid": "023827f344ab6236402ad609f0e938c308f68ca0",
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"version": "1.4.dev2429"
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}
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''' # END VERSION_JSON
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@@ -551,7 +551,7 @@ class AutoRunner:
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cmd_prefix: command line prefix for subprocess running in BundleAlgo and EnsembleRunner.
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Default using env "CMD_PREFIX" or None, examples are:
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- single GPU/CPU or multinode bcprun: "python " or "/opt/conda/bin/python3.
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- single GPU/CPU or multinode bcprun: "python " or "/opt/conda/bin/python3.9 ",
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- single node multi-GPU running "torchrun --nnodes=1 --nproc_per_node=2 "
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If user define this prefix, please make sure --nproc_per_node matches cuda_visible_device or
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@@ -189,7 +189,7 @@ class AnchorGenerator(nn.Module):
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w_ratios = 1 / area_scale
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h_ratios = area_scale
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# if 3d, w:h:d = 1:aspect_ratios[:,0]:aspect_ratios[:,1]
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else:
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area_scale = torch.pow(aspect_ratios_t[:, 0] * aspect_ratios_t[:, 1], 1 / 3.0)
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w_ratios = 1 / area_scale
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h_ratios = aspect_ratios_t[:, 0] / area_scale
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@@ -199,7 +199,7 @@ class AnchorGenerator(nn.Module):
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hs = (h_ratios[:, None] * scales_t[None, :]).view(-1)
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if self.spatial_dims == 2:
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base_anchors = torch.stack([-ws, -hs, ws, hs], dim=1) / 2.0
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elif self.spatial_dims == 3:
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else: # elif self.spatial_dims == 3:
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ds = (d_ratios[:, None] * scales_t[None, :]).view(-1)
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base_anchors = torch.stack([-ws, -hs, -ds, ws, hs, ds], dim=1) / 2.0
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@@ -27,13 +27,11 @@ AttentionBlock, has_attentionblock = optional_import("generative.networks.nets.a
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AutoencoderKL, has_autoencoderkl = optional_import("generative.networks.nets.autoencoderkl", name="AutoencoderKL")
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ResBlock, has_resblock = optional_import("generative.networks.nets.autoencoderkl", name="ResBlock")
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if TYPE_CHECKING:
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from generative.networks.nets.autoencoderkl import AutoencoderKL as AutoencoderKLType
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else:
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AutoencoderKLType = cast(type, AutoencoderKL)
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# Set up logging configuration
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logger = logging.getLogger(__name__)
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monai/auto3dseg/utils.py
CHANGED
@@ -407,7 +407,7 @@ def _prepare_cmd_default(cmd: str, cmd_prefix: str | None = None, **kwargs: Any)
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Args:
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cmd: the command or script to run in the distributed job.
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cmd_prefix: the command prefix to run the script, e.g., "python", "python -m", "python3", "/opt/conda/bin/python3.
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cmd_prefix: the command prefix to run the script, e.g., "python", "python -m", "python3", "/opt/conda/bin/python3.9 ".
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kwargs: the keyword arguments to be passed to the script.
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Returns:
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monai/bundle/scripts.py
CHANGED
@@ -16,6 +16,7 @@ import json
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import os
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import re
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import warnings
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import zipfile
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from collections.abc import Mapping, Sequence
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from pathlib import Path
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from pydoc import locate
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@@ -171,6 +172,10 @@ def _get_ngc_bundle_url(model_name: str, version: str) -> str:
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return f"https://api.ngc.nvidia.com/v2/models/nvidia/monaitoolkit/{model_name.lower()}/versions/{version}/zip"
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def _get_ngc_private_bundle_url(model_name: str, version: str, repo: str) -> str:
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return f"https://api.ngc.nvidia.com/v2/{repo}/models/{model_name.lower()}/versions/{version}/zip"
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def _get_monaihosting_bundle_url(model_name: str, version: str) -> str:
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monaihosting_root_path = "https://api.ngc.nvidia.com/v2/models/nvidia/monaihosting"
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return f"{monaihosting_root_path}/{model_name.lower()}/versions/{version}/files/{model_name}_v{version}.zip"
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extractall(filepath=filepath, output_dir=extract_path, has_base=True)
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def _download_from_ngc_private(
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download_path: Path, filename: str, version: str, remove_prefix: str | None, repo: str, headers: dict | None = None
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) -> None:
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# ensure prefix is contained
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filename = _add_ngc_prefix(filename)
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request_url = _get_ngc_private_bundle_url(model_name=filename, version=version, repo=repo)
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if has_requests:
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headers = {} if headers is None else headers
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response = requests_get(request_url, headers=headers)
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response.raise_for_status()
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else:
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raise ValueError("NGC API requires requests package. Please install it.")
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zip_path = download_path / f"{filename}_v{version}.zip"
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with open(zip_path, "wb") as f:
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f.write(response.content)
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logger.info(f"Downloading: {zip_path}.")
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if remove_prefix:
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filename = _remove_ngc_prefix(filename, prefix=remove_prefix)
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extract_path = download_path / f"{filename}"
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with zipfile.ZipFile(zip_path, "r") as z:
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z.extractall(extract_path)
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logger.info(f"Writing into directory: {extract_path}.")
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def _get_ngc_token(api_key, retry=0):
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"""Try to connect to NGC."""
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url = "https://authn.nvidia.com/token?service=ngc"
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headers = {"Accept": "application/json", "Authorization": "ApiKey " + api_key}
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if has_requests:
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response = requests_get(url, headers=headers)
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if not response.ok:
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# retry 3 times, if failed, raise an error.
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if retry < 3:
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logger.info(f"Retrying {retry} time(s) to GET {url}.")
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return _get_ngc_token(url, retry + 1)
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raise RuntimeError("NGC API response is not ok. Failed to get token.")
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else:
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token = response.json()["token"]
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return token
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def _get_latest_bundle_version_monaihosting(name):
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url = "https://api.ngc.nvidia.com/v2/models/nvidia/monaihosting"
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full_url = f"{url}/{name.lower()}"
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resp = requests_get(full_url)
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resp.raise_for_status()
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else:
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raise ValueError("NGC API requires requests package.
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raise ValueError("NGC API requires requests package. Please install it.")
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model_info = json.loads(resp.text)
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return model_info["model"]["latestVersionIdStr"]
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def
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def _get_latest_bundle_version_private_registry(name, repo, headers=None):
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url = f"https://api.ngc.nvidia.com/v2/{repo}/models"
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full_url = f"{url}/{name.lower()}"
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requests_get, has_requests = optional_import("requests", name="get")
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if has_requests:
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headers = {} if headers is None else headers
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resp = requests_get(full_url, headers=headers)
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resp.raise_for_status()
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else:
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raise ValueError("NGC API requires requests package. Please install it.")
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model_info = json.loads(resp.text)
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return model_info["model"]["latestVersionIdStr"]
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def _get_latest_bundle_version(
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source: str, name: str, repo: str, **kwargs: Any
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) -> dict[str, list[str] | str] | Any | None:
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if source == "ngc":
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name = _add_ngc_prefix(name)
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model_dict = _get_all_ngc_models(name)
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return None
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elif source == "monaihosting":
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return _get_latest_bundle_version_monaihosting(name)
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elif source == "ngc_private":
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headers = kwargs.pop("headers", {})
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name = _add_ngc_prefix(name)
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return _get_latest_bundle_version_private_registry(name, repo, headers)
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elif source == "github":
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repo_owner, repo_name, tag_name = repo.split("/")
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return get_bundle_versions(name, repo=f"{repo_owner}/{repo_name}", tag=tag_name)["latest_version"]
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# Execute this module as a CLI entry, and download bundle via URL:
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python -m monai.bundle download --name <bundle_name> --url <url>
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# Execute this module as a CLI entry, and download bundle from ngc_private with latest version:
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python -m monai.bundle download --name <bundle_name> --source "ngc_private" --bundle_dir "./" --repo "org/org_name"
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# Set default args of `run` in a JSON / YAML file, help to record and simplify the command line.
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# Other args still can override the default args at runtime.
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# The content of the JSON / YAML file is a dictionary. For example:
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Default is `bundle` subfolder under `torch.hub.get_dir()`.
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source: storage location name. This argument is used when `url` is `None`.
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In default, the value is achieved from the environment variable BUNDLE_DOWNLOAD_SRC, and
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it should be "ngc", "monaihosting", "github", or "huggingface_hub".
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it should be "ngc", "monaihosting", "github", "ngc_private", or "huggingface_hub".
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If source is "ngc_private", you need specify the NGC_API_KEY in the environment variable.
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repo: repo name. This argument is used when `url` is `None` and `source` is "github" or "huggingface_hub".
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If `source` is "github", it should be in the form of "repo_owner/repo_name/release_tag".
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If `source` is "huggingface_hub", it should be in the form of "repo_owner/repo_name".
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If `source` is "ngc_private", it should be in the form of "org/org_name" or "org/org_name/team/team_name",
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or you can specify the environment variable NGC_ORG and NGC_TEAM.
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url: url to download the data. If not `None`, data will be downloaded directly
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and `source` will not be checked.
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If `name` is `None`, filename is determined by `monai.apps.utils._basename(url)`.
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bundle_dir_ = _process_bundle_dir(bundle_dir_)
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org_ = os.getenv("NGC_ORG", None)
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team_ = os.getenv("NGC_TEAM", None)
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if org_ is not None and source_ == "ngc_private":
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repo_ = f"org/{org_}/team/{team_}" if team_ is not None else f"org/{org_}"
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else:
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repo_ = "Project-MONAI/model-zoo/hosting_storage_v1"
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if len(repo_.split("/")) not in (2, 4) and source_ == "ngc_private":
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raise ValueError(f"repo should be in the form of `org/org_name/team/team_name` or `org/org_name`, got {repo_}.")
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if len(repo_.split("/")) != 3 and source_ == "github":
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raise ValueError(f"repo should be in the form of `repo_owner/repo_name/release_tag`, got {repo_}.")
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elif len(repo_.split("/")) != 2 and source_ == "huggingface_hub":
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raise ValueError("Hugging Face Hub repo should be in the form of `repo_owner/repo_name
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raise ValueError(f"Hugging Face Hub repo should be in the form of `repo_owner/repo_name`, got {repo_}.")
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if url_ is not None:
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if name_ is not None:
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filepath = bundle_dir_ / f"{name_}.zip"
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download_url(url=url_, filepath=filepath, hash_val=None, progress=progress_)
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extractall(filepath=filepath, output_dir=bundle_dir_, has_base=True)
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else:
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headers = {}
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if name_ is None:
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raise ValueError(f"To download from source: {source_}, `name` must be provided.")
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if source == "ngc_private":
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api_key = os.getenv("NGC_API_KEY", None)
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if api_key is None:
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raise ValueError("API key is required for ngc_private source.")
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else:
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token = _get_ngc_token(api_key)
|
468
|
+
headers = {"Authorization": f"Bearer {token}"}
|
469
|
+
|
381
470
|
if version_ is None:
|
382
|
-
version_ = _get_latest_bundle_version(source=source_, name=name_, repo=repo_)
|
471
|
+
version_ = _get_latest_bundle_version(source=source_, name=name_, repo=repo_, headers=headers)
|
383
472
|
if source_ == "github":
|
384
473
|
if version_ is not None:
|
385
474
|
name_ = "_v".join([name_, version_])
|
@@ -394,6 +483,15 @@ def download(
|
|
394
483
|
remove_prefix=remove_prefix_,
|
395
484
|
progress=progress_,
|
396
485
|
)
|
486
|
+
elif source_ == "ngc_private":
|
487
|
+
_download_from_ngc_private(
|
488
|
+
download_path=bundle_dir_,
|
489
|
+
filename=name_,
|
490
|
+
version=version_,
|
491
|
+
remove_prefix=remove_prefix_,
|
492
|
+
repo=repo_,
|
493
|
+
headers=headers,
|
494
|
+
)
|
397
495
|
elif source_ == "huggingface_hub":
|
398
496
|
extract_path = os.path.join(bundle_dir_, name_)
|
399
497
|
huggingface_hub.snapshot_download(repo_id=repo_, revision=version_, local_dir=extract_path)
|
monai/bundle/utils.py
CHANGED
@@ -221,6 +221,7 @@ def load_bundle_config(bundle_path: str, *config_names: str, **load_kw_args: Any
|
|
221
221
|
raise ValueError(f"Cannot find config file '{full_cname}'")
|
222
222
|
|
223
223
|
ardata = archive.read(full_cname)
|
224
|
+
cdata = {}
|
224
225
|
|
225
226
|
if full_cname.lower().endswith("json"):
|
226
227
|
cdata = json.loads(ardata, **load_kw_args)
|
monai/data/dataset_summary.py
CHANGED
monai/data/utils.py
CHANGED
@@ -53,10 +53,6 @@ from monai.utils import (
|
|
53
53
|
pytorch_after,
|
54
54
|
)
|
55
55
|
|
56
|
-
if pytorch_after(1, 13):
|
57
|
-
# import private code for reuse purposes, comment in case things break in the future
|
58
|
-
from torch.utils.data._utils.collate import collate_tensor_fn, default_collate_fn_map
|
59
|
-
|
60
56
|
pd, _ = optional_import("pandas")
|
61
57
|
DataFrame, _ = optional_import("pandas", name="DataFrame")
|
62
58
|
nib, _ = optional_import("nibabel")
|
@@ -454,8 +450,13 @@ def collate_meta_tensor_fn(batch, *, collate_fn_map=None):
|
|
454
450
|
Collate a sequence of meta tensor into a single batched metatensor. This is called by `collage_meta_tensor`
|
455
451
|
and so should not be used as a collate function directly in dataloaders.
|
456
452
|
"""
|
457
|
-
|
458
|
-
|
453
|
+
if pytorch_after(1, 13):
|
454
|
+
from torch.utils.data._utils.collate import collate_tensor_fn # imported here for pylint/mypy issues
|
455
|
+
|
456
|
+
collated = collate_tensor_fn(batch)
|
457
|
+
else:
|
458
|
+
collated = default_collate(batch)
|
459
|
+
|
459
460
|
meta_dicts = [i.meta or TraceKeys.NONE for i in batch]
|
460
461
|
common_ = set.intersection(*[set(d.keys()) for d in meta_dicts if isinstance(d, dict)])
|
461
462
|
if common_:
|
@@ -496,6 +497,8 @@ def list_data_collate(batch: Sequence):
|
|
496
497
|
|
497
498
|
if pytorch_after(1, 13):
|
498
499
|
# needs to go here to avoid circular import
|
500
|
+
from torch.utils.data._utils.collate import default_collate_fn_map
|
501
|
+
|
499
502
|
from monai.data.meta_tensor import MetaTensor
|
500
503
|
|
501
504
|
default_collate_fn_map.update({MetaTensor: collate_meta_tensor_fn})
|
monai/data/wsi_reader.py
CHANGED
@@ -1097,8 +1097,8 @@ class TiffFileWSIReader(BaseWSIReader):
|
|
1097
1097
|
):
|
1098
1098
|
unit = wsi.pages[level].tags.get("ResolutionUnit")
|
1099
1099
|
if unit is not None:
|
1100
|
-
unit = str(unit.value)
|
1101
|
-
|
1100
|
+
unit = str(unit.value.name)
|
1101
|
+
if unit is None or len(unit) == 0:
|
1102
1102
|
warnings.warn("The resolution unit is missing. `micrometer` will be used as default.")
|
1103
1103
|
unit = "micrometer"
|
1104
1104
|
|
monai/engines/__init__.py
CHANGED
@@ -12,12 +12,14 @@
|
|
12
12
|
from __future__ import annotations
|
13
13
|
|
14
14
|
from .evaluator import EnsembleEvaluator, Evaluator, SupervisedEvaluator
|
15
|
-
from .trainer import GanTrainer, SupervisedTrainer, Trainer
|
15
|
+
from .trainer import AdversarialTrainer, GanTrainer, SupervisedTrainer, Trainer
|
16
16
|
from .utils import (
|
17
|
+
DiffusionPrepareBatch,
|
17
18
|
IterationEvents,
|
18
19
|
PrepareBatch,
|
19
20
|
PrepareBatchDefault,
|
20
21
|
PrepareBatchExtraInput,
|
22
|
+
VPredictionPrepareBatch,
|
21
23
|
default_make_latent,
|
22
24
|
default_metric_cmp_fn,
|
23
25
|
default_prepare_batch,
|