monai-weekly 1.5.dev2503__tar.gz → 1.5.dev2504__tar.gz

{monai_weekly-1.5.dev2503 → monai_weekly-1.5.dev2504}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: monai-weekly
-Version: 1.5.dev2503
+Version: 1.5.dev2504
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium

{monai_weekly-1.5.dev2503 → monai_weekly-1.5.dev2504}/monai/__init__.py

@@ -136,4 +136,4 @@ except BaseException:
 
     if MONAIEnvVars.debug():
         raise
-__commit_id__ = "56d1f621964ba07b0f50d775a8b46c33c2fb1784"
+__commit_id__ = "bc9352ed33952da6be6d4e6d6af9fe9db9faf756"

{monai_weekly-1.5.dev2503 → monai_weekly-1.5.dev2504}/monai/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-01-19T02:26:43+0000",
+ "date": "2025-01-26T02:25:01+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "bbe25ef2e54a64253c272eb084bf88336ed018fb",
- "version": "1.5.dev2503"
+ "full-revisionid": "5787bf9b5b634509248b453c241610d9d9ee9314",
+ "version": "1.5.dev2504"
 }
 '''  # END VERSION_JSON
 

{monai_weekly-1.5.dev2503 → monai_weekly-1.5.dev2504}/monai/bundle/scripts.py

@@ -174,7 +174,7 @@ def _get_git_release_url(repo_owner: str, repo_name: str, tag_name: str, filenam
 
 
 def _get_ngc_bundle_url(model_name: str, version: str) -> str:
-    return f"{NGC_BASE_URL}/{model_name.lower()}/versions/{version}/zip"
+    return f"{NGC_BASE_URL}/{model_name.lower()}/versions/{version}/files"
 
 
 def _get_ngc_private_base_url(repo: str) -> str:
@@ -218,6 +218,21 @@ def _remove_ngc_prefix(name: str, prefix: str = "monai_") -> str:
     return name
 
 
+def _get_all_download_files(request_url: str, headers: dict | None = None) -> list[str]:
+    if not has_requests:
+        raise ValueError("requests package is required, please install it.")
+    headers = {} if headers is None else headers
+    response = requests_get(request_url, headers=headers)
+    response.raise_for_status()
+    model_info = json.loads(response.text)
+
+    if not isinstance(model_info, dict) or "modelFiles" not in model_info:
+        raise ValueError("The data is not a dictionary or it does not have the key 'modelFiles'.")
+
+    model_files = model_info["modelFiles"]
+    return [f["path"] for f in model_files]
+
+
 def _download_from_ngc(
     download_path: Path,
     filename: str,
@@ -229,12 +244,12 @@ def _download_from_ngc(
     # ensure prefix is contained
     filename = _add_ngc_prefix(filename, prefix=prefix)
     url = _get_ngc_bundle_url(model_name=filename, version=version)
-    filepath = download_path / f"{filename}_v{version}.zip"
     if remove_prefix:
         filename = _remove_ngc_prefix(filename, prefix=remove_prefix)
-    extract_path = download_path / f"{filename}"
-    download_url(url=url, filepath=filepath, hash_val=None, progress=progress)
-    extractall(filepath=filepath, output_dir=extract_path, has_base=True)
+    filepath = download_path / filename
+    filepath.mkdir(parents=True, exist_ok=True)
+    for file in _get_all_download_files(url):
+        download_url(url=f"{url}/{file}", filepath=f"{filepath}/{file}", hash_val=None, progress=progress)
 
 
 def _download_from_ngc_private(

{monai_weekly-1.5.dev2503 → monai_weekly-1.5.dev2504}/monai/inferers/merger.py

@@ -15,12 +15,13 @@ import threading
 from abc import ABC, abstractmethod
 from collections.abc import Sequence
 from contextlib import nullcontext
+from tempfile import TemporaryDirectory
 from typing import TYPE_CHECKING, Any
 
 import numpy as np
 import torch
 
-from monai.utils import ensure_tuple_size, optional_import, require_pkg
+from monai.utils import ensure_tuple_size, get_package_version, optional_import, require_pkg, version_geq
 
 if TYPE_CHECKING:
     import zarr
@@ -233,7 +234,7 @@ class ZarrAvgMerger(Merger):
         store: zarr.storage.Store | str = "merged.zarr",
         value_store: zarr.storage.Store | str | None = None,
         count_store: zarr.storage.Store | str | None = None,
-        compressor: str = "default",
+        compressor: str | None = None,
         value_compressor: str | None = None,
         count_compressor: str | None = None,
         chunks: Sequence[int] | bool = True,
@@ -246,8 +247,22 @@ class ZarrAvgMerger(Merger):
         self.value_dtype = value_dtype
         self.count_dtype = count_dtype
         self.store = store
-        self.value_store = zarr.storage.TempStore() if value_store is None else value_store
-        self.count_store = zarr.storage.TempStore() if count_store is None else count_store
+        self.tmpdir: TemporaryDirectory | None
+        if version_geq(get_package_version("zarr"), "3.0.0"):
+            if value_store is None:
+                self.tmpdir = TemporaryDirectory()
+                self.value_store = zarr.storage.LocalStore(self.tmpdir.name)
+            else:
+                self.value_store = value_store
+            if count_store is None:
+                self.tmpdir = TemporaryDirectory()
+                self.count_store = zarr.storage.LocalStore(self.tmpdir.name)
+            else:
+                self.count_store = count_store
+        else:
+            self.tmpdir = None
+            self.value_store = zarr.storage.TempStore() if value_store is None else value_store
+            self.count_store = zarr.storage.TempStore() if count_store is None else count_store
         self.chunks = chunks
         self.compressor = compressor
         self.value_compressor = value_compressor

{monai_weekly-1.5.dev2503 → monai_weekly-1.5.dev2504}/monai/transforms/intensity/array.py

@@ -821,6 +821,7 @@ class NormalizeIntensity(Transform):
     mean and std on each channel separately.
     When `channel_wise` is True, the first dimension of `subtrahend` and `divisor` should
     be the number of image channels if they are not None.
+    If the input is not of floating point type, it will be converted to float32
 
     Args:
         subtrahend: the amount to subtract by (usually the mean).
@@ -907,6 +908,9 @@ class NormalizeIntensity(Transform):
             if self.divisor is not None and len(self.divisor) != len(img):
                 raise ValueError(f"img has {len(img)} channels, but divisor has {len(self.divisor)} components.")
 
+            if not img.dtype.is_floating_point:
+                img, *_ = convert_data_type(img, dtype=torch.float32)
+
             for i, d in enumerate(img):
                 img[i] = self._normalize(  # type: ignore
                     d,

{monai_weekly-1.5.dev2503 → monai_weekly-1.5.dev2504}/monai_weekly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: monai-weekly
-Version: 1.5.dev2503
+Version: 1.5.dev2504
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium

{monai_weekly-1.5.dev2503 → monai_weekly-1.5.dev2504}/tests/test_normalize_intensity.py

@@ -108,6 +108,27 @@ class TestNormalizeIntensity(NumpyImageTestCase2D):
         normalized = normalizer(input_data)
         assert_allclose(normalized, im_type(expected), type_test="tensor")
 
+    @parameterized.expand([[p] for p in TEST_NDARRAYS])
+    def test_channel_wise_int(self, im_type):
+        normalizer = NormalizeIntensity(nonzero=True, channel_wise=True)
+        input_data = im_type(torch.arange(1, 25).reshape(2, 3, 4))
+        expected = np.array(
+            [
+                [
+                    [-1.593255, -1.3035723, -1.0138896, -0.7242068],
+                    [-0.4345241, -0.1448414, 0.1448414, 0.4345241],
+                    [0.7242068, 1.0138896, 1.3035723, 1.593255],
+                ],
+                [
+                    [-1.593255, -1.3035723, -1.0138896, -0.7242068],
+                    [-0.4345241, -0.1448414, 0.1448414, 0.4345241],
+                    [0.7242068, 1.0138896, 1.3035723, 1.593255],
+                ],
+            ]
+        )
+        normalized = normalizer(input_data)
+        assert_allclose(normalized, im_type(expected), type_test="tensor", rtol=1e-7, atol=1e-7)  # tolerance
+
     @parameterized.expand([[p] for p in TEST_NDARRAYS])
     def test_value_errors(self, im_type):
         input_data = im_type(np.array([[0.0, 3.0, 0.0, 4.0], [0.0, 4.0, 0.0, 5.0]]))

{monai_weekly-1.5.dev2503 → monai_weekly-1.5.dev2504}/tests/test_zarr_avg_merger.py

@@ -287,15 +287,16 @@ class ZarrAvgMergerTests(unittest.TestCase):
         ]
     )
     def test_zarr_avg_merger_patches(self, arguments, patch_locations, expected):
+        codec_reg = numcodecs.registry.codec_registry
         if "compressor" in arguments:
             if arguments["compressor"] != "default":
-                arguments["compressor"] = zarr.codec_registry[arguments["compressor"].lower()]()
+                arguments["compressor"] = codec_reg[arguments["compressor"].lower()]()
         if "value_compressor" in arguments:
             if arguments["value_compressor"] != "default":
-                arguments["value_compressor"] = zarr.codec_registry[arguments["value_compressor"].lower()]()
+                arguments["value_compressor"] = codec_reg[arguments["value_compressor"].lower()]()
         if "count_compressor" in arguments:
             if arguments["count_compressor"] != "default":
-                arguments["count_compressor"] = zarr.codec_registry[arguments["count_compressor"].lower()]()
+                arguments["count_compressor"] = codec_reg[arguments["count_compressor"].lower()]()
         merger = ZarrAvgMerger(**arguments)
         for pl in patch_locations:
             merger.aggregate(pl[0], pl[1])