monai-weekly 1.5.dev2513__py3-none-any.whl → 1.5.dev2515__py3-none-any.whl

monai/bundle/scripts.py

@@ -312,21 +312,6 @@ def _get_ngc_token(api_key, retry=0):
         return token
 
 
-def _get_latest_bundle_version_monaihosting(name):
-    full_url = f"{MONAI_HOSTING_BASE_URL}/{name.lower()}"
-    if has_requests:
-        resp = requests.get(full_url)
-        try:
-            resp.raise_for_status()
-            model_info = json.loads(resp.text)
-            return model_info["model"]["latestVersionIdStr"]
-        except requests.exceptions.HTTPError:
-            # for monaihosting bundles, if cannot find the version, get from model zoo model_info.json
-            return get_bundle_versions(name)["latest_version"]
-
-    raise ValueError("NGC API requires requests package. Please install it.")
-
-
 def _examine_monai_version(monai_version: str) -> tuple[bool, str]:
     """Examine if the package version is compatible with the MONAI version in the metadata."""
     version_dict = get_versions()
@@ -430,7 +415,7 @@ def _get_latest_bundle_version(
         name = _add_ngc_prefix(name)
         return _get_latest_bundle_version_ngc(name)
     elif source == "monaihosting":
-        return _get_latest_bundle_version_monaihosting(name)
+        return get_bundle_versions(name, repo="Project-MONAI/model-zoo", tag="dev")["latest_version"]
     elif source == "ngc_private":
         headers = kwargs.pop("headers", {})
         name = _add_ngc_prefix(name)
@@ -528,7 +513,9 @@ def download(
             If source is "ngc_private", you need specify the NGC_API_KEY in the environment variable.
         repo: repo name. This argument is used when `url` is `None` and `source` is "github" or "huggingface_hub".
             If `source` is "github", it should be in the form of "repo_owner/repo_name/release_tag".
-            If `source` is "huggingface_hub", it should be in the form of "repo_owner/repo_name".
+            If `source` is "huggingface_hub", it should be in the form of "repo_owner/repo_name". Please note that
+            bundles for "monaihosting" source are also hosted on Hugging Face Hub, but the "repo_id" is always in the form
+            of "MONAI/bundle_name", therefore, this argument is not required for "monaihosting" source.
             If `source` is "ngc_private", it should be in the form of "org/org_name" or "org/org_name/team/team_name",
             or you can specify the environment variable NGC_ORG and NGC_TEAM.
         url: url to download the data. If not `None`, data will be downloaded directly
@@ -600,11 +587,15 @@ def download(
             _download_from_github(repo=repo_, download_path=bundle_dir_, filename=name_ver, progress=progress_)
         elif source_ == "monaihosting":
             try:
+                extract_path = os.path.join(bundle_dir_, name_)
+                huggingface_hub.snapshot_download(repo_id=f"MONAI/{name_}", revision=version_, local_dir=extract_path)
+            except (huggingface_hub.errors.RevisionNotFoundError, huggingface_hub.errors.RepositoryNotFoundError):
+                # if bundle or version not found from huggingface, download from ngc monaihosting
                 _download_from_monaihosting(
                     download_path=bundle_dir_, filename=name_, version=version_, progress=progress_
                 )
             except urllib.error.HTTPError:
-                # for monaihosting bundles, if cannot download from default host, download according to bundle_info
+                # if also cannot download from ngc monaihosting, download according to bundle_info
                 _download_from_bundle_info(
                     download_path=bundle_dir_, filename=name_, version=version_, progress=progress_
                 )

monai/networks/blocks/fft_utils_t.py

@@ -139,21 +139,17 @@ def ifftn_centered_t(ksp: Tensor, spatial_dims: int, is_complex: bool = True) ->
             output2 = ifftn_centered(ksp, spatial_dims=2, is_complex=True)
     """
     # define spatial dims to perform ifftshift, fftshift, and ifft
-    shift = list(range(-spatial_dims, 0))
+    dims = list(range(-spatial_dims, 0))
     if is_complex:
         if ksp.shape[-1] != 2:
             raise ValueError(f"ksp.shape[-1] is not 2 ({ksp.shape[-1]}).")
-        shift = list(range(-spatial_dims - 1, -1))
-    dims = list(range(-spatial_dims, 0))
-
-    x = ifftshift(ksp, shift)
-
-    if is_complex:
-        x = torch.view_as_real(torch.fft.ifftn(torch.view_as_complex(x), dim=dims, norm="ortho"))
+        x = torch.view_as_complex(ifftshift(ksp, [d - 1 for d in dims]))
     else:
-        x = torch.view_as_real(torch.fft.ifftn(x, dim=dims, norm="ortho"))
+        x = ifftshift(ksp, dims)
+
+    x = torch.view_as_real(torch.fft.ifftn(x, dim=dims, norm="ortho"))
 
-    out: Tensor = fftshift(x, shift)
+    out: Tensor = fftshift(x, [d - 1 for d in dims])
 
     return out
 
@@ -187,20 +183,16 @@ def fftn_centered_t(im: Tensor, spatial_dims: int, is_complex: bool = True) -> T
             output2 = fftn_centered(im, spatial_dims=2, is_complex=True)
     """
     # define spatial dims to perform ifftshift, fftshift, and fft
-    shift = list(range(-spatial_dims, 0))
+    dims = list(range(-spatial_dims, 0))
     if is_complex:
         if im.shape[-1] != 2:
             raise ValueError(f"img.shape[-1] is not 2 ({im.shape[-1]}).")
-        shift = list(range(-spatial_dims - 1, -1))
-    dims = list(range(-spatial_dims, 0))
-
-    x = ifftshift(im, shift)
-
-    if is_complex:
-        x = torch.view_as_real(torch.fft.fftn(torch.view_as_complex(x), dim=dims, norm="ortho"))
+        x = torch.view_as_complex(ifftshift(im, [d - 1 for d in dims]))
     else:
-        x = torch.view_as_real(torch.fft.fftn(x, dim=dims, norm="ortho"))
+        x = ifftshift(im, dims)
+
+    x = torch.view_as_real(torch.fft.fftn(x, dim=dims, norm="ortho"))
 
-    out: Tensor = fftshift(x, shift)
+    out: Tensor = fftshift(x, [d - 1 for d in dims])
 
     return out

monai/transforms/inverse.py

@@ -11,6 +11,7 @@
 
 from __future__ import annotations
 
+import threading
 import warnings
 from collections.abc import Hashable, Mapping
 from contextlib import contextmanager
@@ -66,15 +67,41 @@ class TraceableTransform(Transform):
     The information in the stack of applied transforms must be compatible with the
     default collate, by only storing strings, numbers and arrays.
 
-    `tracing` could be enabled by `self.set_tracing` or setting
+    `tracing` could be enabled by assigning to `self.tracing` or setting
     `MONAI_TRACE_TRANSFORM` when initializing the class.
     """
 
-    tracing = MONAIEnvVars.trace_transform() != "0"
+    def _init_trace_threadlocal(self):
+        """Create a `_tracing` instance member to store the thread-local tracing state value."""
+        # needed since this class is meant to be a trait with no constructor
+        if not hasattr(self, "_tracing"):
+            self._tracing = threading.local()
+
+        # This is True while the above initialising _tracing is False when this is
+        # called from a different thread than the one initialising _tracing.
+        if not hasattr(self._tracing, "value"):
+            self._tracing.value = MONAIEnvVars.trace_transform() != "0"
+
+    def __getstate__(self):
+        """When pickling, remove the `_tracing` member from the output, if present, since it's not picklable."""
+        _dict = dict(getattr(self, "__dict__", {}))  # this makes __dict__ always present in the unpickled object
+        _slots = {k: getattr(self, k) for k in getattr(self, "__slots__", [])}
+        _dict.pop("_tracing", None)  # remove tracing
+        return _dict if len(_slots) == 0 else (_dict, _slots)
+
+    @property
+    def tracing(self) -> bool:
+        """
+        Returns the tracing state, which is thread-local and initialised to `MONAIEnvVars.trace_transform() != "0"`.
+        """
+        self._init_trace_threadlocal()
+        return bool(self._tracing.value)
 
-    def set_tracing(self, tracing: bool) -> None:
-        """Set whether to trace transforms."""
-        self.tracing = tracing
+    @tracing.setter
+    def tracing(self, val: bool):
+        """Sets the thread-local tracing state to `val`."""
+        self._init_trace_threadlocal()
+        self._tracing.value = val
 
     @staticmethod
     def trace_key(key: Hashable = None):
@@ -291,7 +318,7 @@ class TraceableTransform(Transform):
 
     def get_most_recent_transform(self, data, key: Hashable = None, check: bool = True, pop: bool = False):
         """
-        Get most recent transform for the stack.
+        Get most recent matching transform for the current class from the sequence of applied operations.
 
         Args:
             data: dictionary of data or `MetaTensor`.
@@ -316,9 +343,14 @@ class TraceableTransform(Transform):
                 all_transforms = data.get(self.trace_key(key), MetaTensor.get_default_applied_operations())
         else:
             raise ValueError(f"`data` should be either `MetaTensor` or dictionary, got {type(data)}.")
+
+        if not all_transforms:
+            raise ValueError(f"Item of type {type(data)} (key: {key}, pop: {pop}) has empty 'applied_operations'")
+
         if check:
             self.check_transforms_match(all_transforms[-1])
-        return all_transforms.pop() if pop else all_transforms[-1]
+
+        return all_transforms.pop(-1) if pop else all_transforms[-1]
 
     def pop_transform(self, data, key: Hashable = None, check: bool = True):
         """

monai/utils/misc.py

@@ -546,7 +546,7 @@ class MONAIEnvVars:
 
     @staticmethod
     def algo_hash() -> str | None:
-        return os.environ.get("MONAI_ALGO_HASH", "c108ea9")
+        return os.environ.get("MONAI_ALGO_HASH", "4c18daf")
 
     @staticmethod
     def trace_transform() -> str | None:

{monai_weekly-1.5.dev2513.dist-info → monai_weekly-1.5.dev2515.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: monai-weekly
-Version: 1.5.dev2513
+Version: 1.5.dev2515
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium
@@ -49,6 +49,7 @@ Requires-Dist: lmdb; extra == "all"
 Requires-Dist: psutil; extra == "all"
 Requires-Dist: cucim-cu12; (platform_system == "Linux" and python_version >= "3.9" and python_version <= "3.10") and extra == "all"
 Requires-Dist: openslide-python; extra == "all"
+Requires-Dist: openslide-bin; extra == "all"
 Requires-Dist: tifffile; (platform_system == "Linux" or platform_system == "Darwin") and extra == "all"
 Requires-Dist: imagecodecs; (platform_system == "Linux" or platform_system == "Darwin") and extra == "all"
 Requires-Dist: pandas; extra == "all"
@@ -105,6 +106,7 @@ Provides-Extra: cucim
 Requires-Dist: cucim-cu12; (platform_system == "Linux" and python_version >= "3.9" and python_version <= "3.10") and extra == "cucim"
 Provides-Extra: openslide
 Requires-Dist: openslide-python; extra == "openslide"
+Requires-Dist: openslide-bin; extra == "openslide"
 Provides-Extra: tifffile
 Requires-Dist: tifffile; (platform_system == "Linux" or platform_system == "Darwin") and extra == "tifffile"
 Provides-Extra: imagecodecs

{monai_weekly-1.5.dev2513.dist-info → monai_weekly-1.5.dev2515.dist-info}/RECORD

@@ -1,5 +1,5 @@
-monai/__init__.py,sha256=lOVClDZxEDXvMXltT5kiFD_6UM2TYyLqp6gJRLLSWY8,4095
-monai/_version.py,sha256=TaZfkTv96TjOsFZhWyZwFaEDQWRV0aCQUaMZaKfJkOo,503
+monai/__init__.py,sha256=cz2IbPvV5WFZb9B6iwGQYTcCSUfAkFQgg6Z7EyBu82E,4095
+monai/_version.py,sha256=PvcDKbDCwlMsws9Aqn0bDOjHV15xcRqSmMGahjEBO5k,503
 monai/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 monai/_extensions/__init__.py,sha256=NEBPreRhQ8H9gVvgrLr_y52_TmqB96u_u4VQmeNT93I,642
 monai/_extensions/loader.py,sha256=7SiKw36q-nOzH8CRbBurFrz7GM40GCu7rc93Tm8XpnI,3643
@@ -55,8 +55,9 @@ monai/apps/generation/maisi/networks/diffusion_model_unet_maisi.py,sha256=XFOiy6
 monai/apps/mmars/__init__.py,sha256=BolpgEi9jNBgrOQd3Kwp-9QQLeWQwQtlN_MJkK1eu5s,726
 monai/apps/mmars/mmars.py,sha256=24JylLuw-qTDsTnTK4Y5kAbF_nWdivrSRS8EMGy69oQ,13134
 monai/apps/mmars/model_desc.py,sha256=k7WSMRuyQN8xPax8aUmGKiTNZmcVatdqPYCgxDih-x4,9996
-monai/apps/nnunet/__init__.py,sha256=gyqmg1fxPf3RF6LL25gnpMTfNS14uxweuJ93e4UzjB8,745
+monai/apps/nnunet/__init__.py,sha256=u_VSta8R-Ta0oKUxxzDKXo9BK6WL7kAsGPRee2Gp9GY,963
 monai/apps/nnunet/__main__.py,sha256=qrloBLymK98OPcaBKocrlF8io2h4mUuXJPFVLZT-XDo,832
+monai/apps/nnunet/nnunet_bundle.py,sha256=ucqx9P2oDC0G5AYbNYwZvs4TgcoNVmOEIDTGZpi4jbw,24758
 monai/apps/nnunet/nnunetv2_runner.py,sha256=0VZTpzmjkOhamdqYGd9bhTdZcRDeOsMOBIjaW1Upi8w,48001
 monai/apps/nnunet/utils.py,sha256=OwLBcc0LZ_n7-ofE8EgkgmIHT23wq1xySCD6lphSjz0,6761
 monai/apps/nuclick/__init__.py,sha256=s9djSd6kvViPnFvMR11Dgd30Lv4oY6FaPJr4ZZJZLq0,573
@@ -114,7 +115,7 @@ monai/bundle/config_item.py,sha256=rMjXSGkjJZdi04BwSHwCcIwzIb_TflmC3xDhC3SVJRs,1
 monai/bundle/config_parser.py,sha256=cGyEn-cqNk0rEEZ1Qiv6UydmIDvtWZcMVljyfVm5i50,23025
 monai/bundle/properties.py,sha256=iN3K4FVmN9ny1Hw9p5j7_ULcCdSD8PmrR7qXxbNz49k,11582
 monai/bundle/reference_resolver.py,sha256=GXCMK4iogxxE6VocsmAbUrcXosmC5arnjeG9zYhHKpg,16748
-monai/bundle/scripts.py,sha256=VE3hIAcPfncbT1MGyLk0by1ZtA9jit6Hc7djrUUKUX8,91018
+monai/bundle/scripts.py,sha256=69sZ_W9xQzuVnRL0Ma64Ac742UIe9iCvTKHwkuCU0a8,91064
 monai/bundle/utils.py,sha256=t-22uFvLn7Yy-dr1v1U33peNOxgAmU4TJiGAbsBrUKs,10108
 monai/bundle/workflows.py,sha256=CuhmFq1AWsN3ATiYJCSakPOxrOdGutl6vkpo9sxe8gU,34369
 monai/config/__init__.py,sha256=CN28CfTdsp301gv8YXfVvkbztCfbAqrLKrJi_C8oP9s,1048
@@ -263,7 +264,7 @@ monai/networks/blocks/dynunet_block.py,sha256=kg8NNTL4nBqsy6gBcxmS5ZCPxlhWM_iB0B
 monai/networks/blocks/encoder.py,sha256=NwH5VSQLwamJqrSbZSdQqMwZCk80CPbSpMGEE0r0Cwo,3669
 monai/networks/blocks/fcn.py,sha256=mnCMrxhUdj2yZ0DPIj0Xf9OKVdv-qhG1BpnAg5j7q6c,9024
 monai/networks/blocks/feature_pyramid_network.py,sha256=zHMXB_hl92kmuJIe0rTvQlzQn1W77WTQZ7XaoivktEw,10631
-monai/networks/blocks/fft_utils_t.py,sha256=8bOvhLgP5nDLz8QwzD4XnRaxE9-tGba2-b_QDK8IWSs,8263
+monai/networks/blocks/fft_utils_t.py,sha256=rarC7BUw9TeawhDQESC5oJhPvbg_OFFNTa1HsNs3GKg,8017
 monai/networks/blocks/localnet_block.py,sha256=b2-ZZvkMPphHJZYTbwEZDhqA-mMBSFM5WQOoohk_6W4,11456
 monai/networks/blocks/mednext_block.py,sha256=GKaFkRvmho79yxwfYyeSaJtHFtk185dY0tA4_rPnsQA,10487
 monai/networks/blocks/mlp.py,sha256=qw_jgyrYwoQ5WYBM1rtSSaO4C837ZbctoRKhh_BQQFI,3341
@@ -357,7 +358,7 @@ monai/optimizers/utils.py,sha256=GVsJsZWO2aAP9IzwhXgca_9gUNHFClup6qG4ZFs42z4,413
 monai/transforms/__init__.py,sha256=-LmAa_W5fJxm5I_btvAONNebWe2exa7IWwcvYrNxzCc,16744
 monai/transforms/adaptors.py,sha256=LpYChldlOur-VFgu_nBIBze0J841-NWgf0UHvvHRNPU,8796
 monai/transforms/compose.py,sha256=EQPQkxdzrLoVvoeKVa8KABmB_Oc9pg-G0EsSS8aTraw,39189
-monai/transforms/inverse.py,sha256=Wg8UnMJru41G3eHGipUemAWziHGU-qdd-Flfi3eOpeo,18746
+monai/transforms/inverse.py,sha256=BARCRaUYabIajmOfsyNbN47v1v0eQiFAU7Vyvz-IddU,20287
 monai/transforms/inverse_batch_transform.py,sha256=fMbukZq2P99BhqqMuWZFJ9uboZ5dN61MBvvicwf40V0,7055
 monai/transforms/nvtx.py,sha256=1EKEXZIhTUFKoIrJmd_fevwrHwo731dVFUFJQFiOk3w,3386
 monai/transforms/traits.py,sha256=F8kmhnekTyaAdo8wIFjO3-uqpVtmFym3mNxbYbyvkFI,3563
@@ -410,7 +411,7 @@ monai/utils/deprecate_utils.py,sha256=gKeEV4MsI51qeQ5gci2me_C-0e-tDwa3VZzd3XPQqL
 monai/utils/dist.py,sha256=7brB42CvdS8Jvr8Y7hfqov1uk6NNnYea9dYfgMYy0BY,8578
 monai/utils/enums.py,sha256=aupxnORUHqVPF2Ac5nxstsP5aIyewMoqgGb88D62yxg,19931
 monai/utils/jupyter_utils.py,sha256=BYtj80LWQAYg5RWPj5g4j2AMCzLECvAcnZdXns0Ruw8,15651
-monai/utils/misc.py,sha256=9-5zBIDSUYewzoQBkiBm0G_HR8hmwQCT-I15RYOQqEQ,31759
+monai/utils/misc.py,sha256=M0oCfj55pZTrcYF0QgyS91JflqBwxSuNnOifl2HRSZk,31759
 monai/utils/module.py,sha256=R37PpCNCcHQvjjZFbNjNyzWb3FURaKLxQucjhzQk0eU,26087
 monai/utils/nvtx.py,sha256=i9JBxR1uhW1ZCgLPLlTx8b907QlXkFzJyTBLMlFjhtU,6876
 monai/utils/ordering.py,sha256=0nlA5b5QpVCHbtiCbTC-YsqjTmjm0bub0IeJhGFBOes,8270
@@ -425,7 +426,7 @@ monai/visualize/img2tensorboard.py,sha256=n4ztSa5BQAUxSTGvi2tp45v-F7-RNgSlbsdy-9
 monai/visualize/occlusion_sensitivity.py,sha256=OQHEJLyIhB8zWqQsfKaX-1kvCjWFVYtLfS4dFC0nKFI,18160
 monai/visualize/utils.py,sha256=B-MhTVs7sQbIqYS3yPnpBwPw2K82rE2PBtGIfpwZtWM,9894
 monai/visualize/visualizer.py,sha256=qckyaMZCbezYUwE20k5yc-Pb7UozVavMDbrmyQwfYHY,1377
-monai_weekly-1.5.dev2513.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+monai_weekly-1.5.dev2515.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
 tests/apps/__init__.py,sha256=s9djSd6kvViPnFvMR11Dgd30Lv4oY6FaPJr4ZZJZLq0,573
 tests/apps/test_auto3dseg_bundlegen.py,sha256=FpTJo9Lfe8vdhGuWeZ9y1BQmqYwTt-s8mDVtoLGAz_I,5594
 tests/apps/test_check_hash.py,sha256=MuZslW2DDCxHKEo6-PiL7hnbxGuZRRYf6HOh3ZQv1qQ,1761
@@ -507,7 +508,7 @@ tests/apps/vista3d/test_vista3d_sampler.py,sha256=-luQCe3Hhle2PC9AkFCUgK8gozOD0O
 tests/apps/vista3d/test_vista3d_transforms.py,sha256=nAPiDBNWeXLoW7ax3HHL63t5jqzQ3HFa-6wTvdyqVJk,3280
 tests/bundle/__init__.py,sha256=s9djSd6kvViPnFvMR11Dgd30Lv4oY6FaPJr4ZZJZLq0,573
 tests/bundle/test_bundle_ckpt_export.py,sha256=VnpigCoBAAc2lo0rWOpVMg0IYGB6vbHXL8xLtB1Pkio,4622
-tests/bundle/test_bundle_download.py,sha256=sM6bIaCjIdDbHWpMigYx4T7qFLXSeexnRpGubUKbx9U,20404
+tests/bundle/test_bundle_download.py,sha256=QaQOde6MCpUeHhoYNTd1GjDQmT0j01kTMw53qocOzxQ,20695
 tests/bundle/test_bundle_get_data.py,sha256=lQh321mev_7fsLXRg0Tq5uEjuQILethDHRKzB6VV0o4,3667
 tests/bundle/test_bundle_push_to_hf_hub.py,sha256=Zjl6xDwRKgkS6jvO5dzMBaTLEd4EXyMXp0_wzDNSY3g,1740
 tests/bundle/test_bundle_trt_export.py,sha256=png-2SGjBSt46LXSz-PLprOXwJ0WkC_3YLR3Ibk_WBc,6344
@@ -596,6 +597,7 @@ tests/integration/test_integration_determinism.py,sha256=AiSBXHcPwDtKRbt_lejI-ID
 tests/integration/test_integration_fast_train.py,sha256=WxEIJV52F0Cf2wmGlIQDiVs1m2QZrvxmta_UAsa0OCI,9736
 tests/integration/test_integration_gpu_customization.py,sha256=z-w6iBaY72LEi8TBVxZuzvsEBgBecZAP2YPwl6KFUhA,5547
 tests/integration/test_integration_lazy_samples.py,sha256=d_4GNy_ixiizvehIYJBht4dQropRsqQy7rJOpW7OkZ8,9198
+tests/integration/test_integration_nnunet_bundle.py,sha256=V1X57m7cJwFsR5YfgzFLtCRe8vWx_wP5b2OZkb3Ux9Y,6813
 tests/integration/test_integration_nnunetv2_runner.py,sha256=KgyAI0Irl93KDLZyo8fGZjEL8dS5UXPKQz_osRfhtSU,4332
 tests/integration/test_integration_segmentation_3d.py,sha256=TSV8tdiloK4_E03DgM1SqJxMo4fcH-Ta1NutG-3cPFc,13229
 tests/integration/test_integration_sliding_window.py,sha256=N0CYquebXk8N3KiPcGWbD9KAf5UHuXx2pqAZY5PQVSE,3769
@@ -785,7 +787,7 @@ tests/networks/nets/test_spade_diffusion_model_unet.py,sha256=LEN1PAGid0DMdP2NyS
 tests/networks/nets/test_spade_vaegan.py,sha256=ur1SPoXEmpr_8KwVS6-E_1tIPMBKpNqsvHJ7z5-obzA,5632
 tests/networks/nets/test_swin_unetr.py,sha256=gj1Jqg8xTBYdCZWCR4Y9_ZlGNNYVTkCPmB2sdF2xIDM,5690
 tests/networks/nets/test_torchvision_fc_model.py,sha256=oNb-PaOhIAjOrpnsXApC2hKSUK6lMutIEinMrCOKQoA,6397
-tests/networks/nets/test_transchex.py,sha256=vUUsCd_CJrW_q0jcaGQegBoanJQVoufrs_EP3MC46Xo,3220
+tests/networks/nets/test_transchex.py,sha256=G8WHEAlZlovlpJjlWD5cfeGD6FTFzUM6Y7_bVehHNY0,3293
 tests/networks/nets/test_transformer.py,sha256=rsGjemv0JV9SMTTWiZ8Sz_w5t5Rkz15b2rjJit4R2XA,4218
 tests/networks/nets/test_unet.py,sha256=wXwaXkufYDjFXzQ-AygbePAwigZLLaY58sGygizF3Q4,5801
 tests/networks/nets/test_unetr.py,sha256=3_V4VWfsQVB22-T8XTSRra3Her2XrLx5gzIRHis2zPs,5325
@@ -904,10 +906,7 @@ tests/transforms/test_histogram_normalized.py,sha256=dwaZ9ux-sgYKx0cy6aQqt5L07ts
 tests/transforms/test_image_filter.py,sha256=ERomnuZRJkdFL7wAObos22qxry2jpPCtT2QXML6hIWY,11619
 tests/transforms/test_intensity_stats.py,sha256=MjWFd_Oeu0Ay-rd9Asp2ZLiwg75u4SFmHvj-VwBGiHA,2795
 tests/transforms/test_intensity_statsd.py,sha256=tLuq1EQ6aVjGP_0xCCRVDZ1kPvtaqBuRwWy-EuxMhmQ,3595
-tests/transforms/test_inverse.py,sha256=vCj7yrm1L15HBEUEUdUgkXbfPckCnvslIltHncee7dk,18982
 tests/transforms/test_inverse_collation.py,sha256=8iptVqniLP77pfVJnLpE13xcthO-BgXoZCza8sGPAcA,5451
-tests/transforms/test_invert.py,sha256=gBJgAaVs4WKTkaYS8JNXH3qeKM8DBAZvF_t3GoPmVPU,4292
-tests/transforms/test_invertd.py,sha256=J7e_unCTiD1fXzAXLvCCKkVCGqNMJcIPentoOjmwxq4,6094
 tests/transforms/test_k_space_spike_noise.py,sha256=9jP6fFggTKScbR8orjJacSYtzwv1gQMuomPiaz1o1_0,2863
 tests/transforms/test_k_space_spike_noised.py,sha256=_n7b-0S6N5HEJBTLYQVKka8bpKZ2eL1xqOMUqB1cSi0,3511
 tests/transforms/test_keep_largest_connected_component.py,sha256=yXLKF3FdaVN5FFLq0okNunlQc0OI6CrAOhzIM9Gjcg4,14759
@@ -1105,8 +1104,12 @@ tests/transforms/intensity/test_rand_histogram_shiftd.py,sha256=0TFQO5qz5GVFyH95
 tests/transforms/intensity/test_scale_intensity_range_percentiles.py,sha256=y5O_BLLVxDqUmF3BvqNHgt5dg04FrwSK9qHEXI8IzXY,3986
 tests/transforms/intensity/test_scale_intensity_range_percentilesd.py,sha256=ZHSiTTJn5Lp1OaJVff7eq94OAHCc7gJZLSsTSuNFAhM,3980
 tests/transforms/inverse/__init__.py,sha256=s9djSd6kvViPnFvMR11Dgd30Lv4oY6FaPJr4ZZJZLq0,573
+tests/transforms/inverse/test_inverse.py,sha256=vCj7yrm1L15HBEUEUdUgkXbfPckCnvslIltHncee7dk,18982
 tests/transforms/inverse/test_inverse_array.py,sha256=KIFCHhkQSbVbirheLk4c9Kz0Uqpf9m5Do4LkD026ISk,2769
-tests/transforms/inverse/test_traceable_transform.py,sha256=njTHREPWZvGV6mW550fXT8QJlIbGj6hAhNnPGsOruuU,1887
+tests/transforms/inverse/test_inverse_dict.py,sha256=Sd84lHWCr-IpWp8DUNspfSfRyfooBNa301hOS6pKJNE,4817
+tests/transforms/inverse/test_invert.py,sha256=gBJgAaVs4WKTkaYS8JNXH3qeKM8DBAZvF_t3GoPmVPU,4292
+tests/transforms/inverse/test_invertd.py,sha256=J7e_unCTiD1fXzAXLvCCKkVCGqNMJcIPentoOjmwxq4,6094
+tests/transforms/inverse/test_traceable_transform.py,sha256=1NEw_C755p_3Hr96qFYAYqSZQk1sRfuWiOK8N9z8hDs,1887
 tests/transforms/post/__init__.py,sha256=s9djSd6kvViPnFvMR11Dgd30Lv4oY6FaPJr4ZZJZLq0,573
 tests/transforms/post/test_label_filterd.py,sha256=OMIoSlbTu8owWE2WqcRfobUDRZE96mpLaE1fuWpdWdY,2597
 tests/transforms/post/test_probnms.py,sha256=-HMnXkVLqXiMkvgJeD7jDoLkm74gNwE57iigi63waKo,2866
@@ -1186,7 +1189,7 @@ tests/visualize/test_vis_gradcam.py,sha256=WpA-pvTB75eZs7JoIc5qyvOV9PwgkzWI8-Vow
 tests/visualize/utils/__init__.py,sha256=s9djSd6kvViPnFvMR11Dgd30Lv4oY6FaPJr4ZZJZLq0,573
 tests/visualize/utils/test_blend_images.py,sha256=RVs2p_8RWQDfhLHDNNtZaMig27v8o0km7XxNa-zWjKE,2274
 tests/visualize/utils/test_matshow3d.py,sha256=wXYj77L5Jvnp0f6DvL1rsi_-YlCxS0HJ9hiPmrbpuP8,5021
-monai_weekly-1.5.dev2513.dist-info/METADATA,sha256=JtMbpoy1PATNUbzheFGRBPWYUP9Ka18xyiyNHGhad8k,12008
-monai_weekly-1.5.dev2513.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-monai_weekly-1.5.dev2513.dist-info/top_level.txt,sha256=hn2Y6P9xBf2R8faMeVMHhPMvrdDKxMsIOwMDYI0yTjs,12
-monai_weekly-1.5.dev2513.dist-info/RECORD,,
+monai_weekly-1.5.dev2515.dist-info/METADATA,sha256=0PRAJeakVM2LmWoAgV6ooMkk8Z-btuFbcstMou9dQaA,12104
+monai_weekly-1.5.dev2515.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+monai_weekly-1.5.dev2515.dist-info/top_level.txt,sha256=hn2Y6P9xBf2R8faMeVMHhPMvrdDKxMsIOwMDYI0yTjs,12
+monai_weekly-1.5.dev2515.dist-info/RECORD,,

tests/bundle/test_bundle_download.py

@@ -63,6 +63,8 @@ TEST_CASE_5 = [
 
 TEST_CASE_6 = [["models/model.pt", "configs/train.json"], "renalStructures_CECT_segmentation", "0.1.0"]
 
+TEST_CASE_6_HF = [["models/model.pt", "configs/train.yaml"], "mednist_ddpm", "1.0.1"]
+
 TEST_CASE_7 = [
     ["model.pt", "model.ts", "network.json", "test_output.pt", "test_input.pt"],
     "test_bundle",
@@ -193,6 +195,7 @@ class TestDownload(unittest.TestCase):
 
     @parameterized.expand([TEST_CASE_6])
     @skip_if_quick
+    @skipUnless(has_huggingface_hub, "Requires `huggingface_hub`.")
     def test_monaihosting_source_download_bundle(self, bundle_files, bundle_name, version):
         with skip_if_downloading_fails():
             # download a single file from url, also use `args_file`
@@ -239,6 +242,7 @@ class TestDownload(unittest.TestCase):
         self.assertEqual(_list_latest_versions(data), ["1.1", "1.0"])
 
     @skip_if_quick
+    @skipUnless(has_huggingface_hub, "Requires `huggingface_hub`.")
     @patch("monai.bundle.scripts.get_versions", return_value={"version": "1.2"})
     def test_download_monaihosting(self, mock_get_versions):
         """Test checking MONAI version from a metadata file."""
@@ -333,6 +337,7 @@ class TestLoad(unittest.TestCase):
 
     @parameterized.expand([TEST_CASE_8])
     @skip_if_quick
+    @skipUnless(has_huggingface_hub, "Requires `huggingface_hub`.")
     def test_load_weights_with_net_override(self, bundle_name, device, net_override):
         with skip_if_downloading_fails():
             # download bundle, and load weights from the downloaded path

tests/integration/test_integration_nnunet_bundle.py

@@ -0,0 +1,150 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import os
+import tempfile
+import unittest
+from pathlib import Path
+
+import numpy as np
+
+from monai.apps.nnunet import nnUNetV2Runner
+from monai.apps.nnunet.nnunet_bundle import (
+    convert_nnunet_to_monai_bundle,
+    get_nnunet_monai_predictor,
+    get_nnunet_trainer,
+)
+from monai.bundle.config_parser import ConfigParser
+from monai.data import DataLoader, Dataset, create_test_image_3d
+from monai.transforms import Compose, Decollated, EnsureChannelFirstd, LoadImaged, SaveImaged
+from monai.utils import optional_import
+from tests.test_utils import SkipIfBeforePyTorchVersion, skip_if_downloading_fails, skip_if_no_cuda, skip_if_quick
+
+_, has_tb = optional_import("torch.utils.tensorboard", name="SummaryWriter")
+_, has_nnunet = optional_import("nnunetv2")
+
+sim_datalist: dict[str, list[dict]] = {
+    "testing": [{"image": "val_001.fake.nii.gz"}, {"image": "val_002.fake.nii.gz"}],
+    "training": [
+        {"fold": 0, "image": "tr_image_001.fake.nii.gz", "label": "tr_label_001.fake.nii.gz"},
+        {"fold": 0, "image": "tr_image_002.fake.nii.gz", "label": "tr_label_002.fake.nii.gz"},
+        {"fold": 1, "image": "tr_image_003.fake.nii.gz", "label": "tr_label_003.fake.nii.gz"},
+        {"fold": 1, "image": "tr_image_004.fake.nii.gz", "label": "tr_label_004.fake.nii.gz"},
+        {"fold": 2, "image": "tr_image_005.fake.nii.gz", "label": "tr_label_005.fake.nii.gz"},
+        {"fold": 2, "image": "tr_image_006.fake.nii.gz", "label": "tr_label_006.fake.nii.gz"},
+        {"fold": 3, "image": "tr_image_007.fake.nii.gz", "label": "tr_label_007.fake.nii.gz"},
+        {"fold": 3, "image": "tr_image_008.fake.nii.gz", "label": "tr_label_008.fake.nii.gz"},
+        {"fold": 4, "image": "tr_image_009.fake.nii.gz", "label": "tr_label_009.fake.nii.gz"},
+        {"fold": 4, "image": "tr_image_010.fake.nii.gz", "label": "tr_label_010.fake.nii.gz"},
+    ],
+}
+
+
+@skip_if_quick
+@SkipIfBeforePyTorchVersion((1, 13, 0))
+@unittest.skipIf(not has_tb, "no tensorboard summary writer")
+@unittest.skipIf(not has_nnunet, "no nnunetv2")
+class TestnnUNetBundle(unittest.TestCase):
+
+    def setUp(self) -> None:
+
+        import nibabel as nib
+
+        self.test_dir = tempfile.TemporaryDirectory()
+        test_path = self.test_dir.name
+
+        sim_dataroot = os.path.join(test_path, "dataroot")
+        if not os.path.isdir(sim_dataroot):
+            os.makedirs(sim_dataroot)
+
+        self.sim_dataroot = sim_dataroot
+        # Generate a fake dataset
+        for d in sim_datalist["testing"] + sim_datalist["training"]:
+            im, seg = create_test_image_3d(24, 24, 24, rad_max=10, num_seg_classes=2)
+            nib_image = nib.Nifti1Image(im, affine=np.eye(4))
+            image_fpath = os.path.join(sim_dataroot, d["image"])
+            nib.save(nib_image, image_fpath)
+
+            if "label" in d:
+                nib_image = nib.Nifti1Image(seg, affine=np.eye(4))
+                label_fpath = os.path.join(sim_dataroot, d["label"])
+                nib.save(nib_image, label_fpath)
+
+        sim_json_datalist = os.path.join(sim_dataroot, "sim_input.json")
+        ConfigParser.export_config_file(sim_datalist, sim_json_datalist)
+
+        data_src_cfg = os.path.join(test_path, "data_src_cfg.yaml")
+        data_src = {"modality": "CT", "datalist": sim_json_datalist, "dataroot": sim_dataroot}
+
+        ConfigParser.export_config_file(data_src, data_src_cfg)
+        self.data_src_cfg = data_src_cfg
+        self.test_path = test_path
+
+    @skip_if_no_cuda
+    def test_nnunet_bundle(self) -> None:
+        runner = nnUNetV2Runner(
+            input_config=self.data_src_cfg, trainer_class_name="nnUNetTrainer_1epoch", work_dir=self.test_path
+        )
+        with skip_if_downloading_fails():
+            runner.run(run_train=False, run_find_best_configuration=False, run_predict_ensemble_postprocessing=False)
+
+            nnunet_trainer = get_nnunet_trainer(
+                dataset_name_or_id=runner.dataset_name, fold=0, configuration="3d_fullres"
+            )
+
+            print("Max Epochs: ", nnunet_trainer.num_epochs)
+            print("Num Iterations: ", nnunet_trainer.num_iterations_per_epoch)
+            print("Train Batch dims: ", next(nnunet_trainer.dataloader_train.generator)["data"].shape)
+            print("Val Batch dims: ", next(nnunet_trainer.dataloader_val.generator)["data"].shape)
+            print("Network: ", nnunet_trainer.network)
+            print("Optimizer: ", nnunet_trainer.optimizer)
+            print("Loss Function: ", nnunet_trainer.loss)
+            print("LR Scheduler: ", nnunet_trainer.lr_scheduler)
+            print("Device: ", nnunet_trainer.device)
+            runner.train_single_model("3d_fullres", fold=0)
+
+        nnunet_config = {"dataset_name_or_id": "001", "nnunet_trainer": "nnUNetTrainer_1epoch"}
+        self.bundle_root = os.path.join("bundle_root")
+
+        Path(self.bundle_root).joinpath("models").mkdir(parents=True, exist_ok=True)
+        convert_nnunet_to_monai_bundle(nnunet_config, self.bundle_root, 0)
+
+        data_transforms = Compose([LoadImaged(keys="image"), EnsureChannelFirstd(keys="image")])
+        dataset = Dataset(
+            data=[{"image": os.path.join(self.test_path, "dataroot", "val_001.fake.nii.gz")}], transform=data_transforms
+        )
+        data_loader = DataLoader(dataset, batch_size=1)
+        input = next(iter(data_loader))
+
+        predictor = get_nnunet_monai_predictor(Path(self.bundle_root).joinpath("models", "fold_0"))
+        pred_batch = predictor(input["image"])
+        Path(self.sim_dataroot).joinpath("predictions").mkdir(parents=True, exist_ok=True)
+
+        post_processing_transforms = Compose(
+            [
+                Decollated(keys=None, detach=True),
+                # Not needed after reading the data directly from the MONAI LoadImaged Transform
+                # Transposed(keys="pred", indices=[0, 3, 2, 1]),
+                SaveImaged(
+                    keys="pred", output_dir=Path(self.sim_dataroot).joinpath("predictions"), output_postfix="pred"
+                ),
+            ]
+        )
+        post_processing_transforms({"pred": pred_batch})
+
+    def tearDown(self) -> None:
+        self.test_dir.cleanup()
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/networks/nets/test_transchex.py

@@ -18,7 +18,7 @@ from parameterized import parameterized
 
 from monai.networks import eval_mode
 from monai.networks.nets.transchex import Transchex
-from tests.test_utils import skip_if_quick
+from tests.test_utils import skip_if_downloading_fails, skip_if_quick
 
 TEST_CASE_TRANSCHEX = []
 for drop_out in [0.4]:
@@ -49,7 +49,8 @@ for drop_out in [0.4]:
 class TestTranschex(unittest.TestCase):
     @parameterized.expand(TEST_CASE_TRANSCHEX)
     def test_shape(self, input_param, expected_shape):
-        net = Transchex(**input_param)
+        with skip_if_downloading_fails():
+            net = Transchex(**input_param)
         with eval_mode(net):
             result = net(torch.randint(2, (2, 512)), torch.randint(2, (2, 512)), torch.randn((2, 3, 224, 224)))
             self.assertEqual(result.shape, expected_shape)