From 1c2f1448f4170d7275a3dd380f2a904953ab9cd8 Mon Sep 17 00:00:00 2001
From: Nic Ma <nma@nvidia.com>
Date: Mon, 15 Nov 2021 12:00:49 +0800
Subject: [PATCH 1/8] [DLMED] optimize astype

Signed-off-by: Nic Ma <nma@nvidia.com>
---
 monai/apps/deepedit/transforms.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/monai/apps/deepedit/transforms.py b/monai/apps/deepedit/transforms.py
index ab2d4b40fa..98201955c6 100644
--- a/monai/apps/deepedit/transforms.py
+++ b/monai/apps/deepedit/transforms.py
@@ -158,7 +158,7 @@ def _apply(self, guidance, discrepancy):
             guidance[0].append([-1] * len(neg))
             guidance[1].append(neg)
 
-        return json.dumps(np.asarray(guidance).astype(int).tolist())
+        return json.dumps(np.asarray(guidance, dtype=int).tolist())
 
     def __call__(self, data):
         d = dict(data)

From 0550d77ff778cc376b7959b6ad0bb88dd6fbd3cf Mon Sep 17 00:00:00 2001
From: Nic Ma <nma@nvidia.com>
Date: Wed, 17 Nov 2021 19:04:08 +0800
Subject: [PATCH 2/8] [DLMED] improve astype

Signed-off-by: Nic Ma <nma@nvidia.com>
---
 monai/apps/deepedit/transforms.py             |  4 ++--
 monai/apps/deepgrow/transforms.py             | 22 +++++++++----------
 .../apps/pathology/transforms/stain/array.py  |  6 ++---
 monai/data/nifti_writer.py                    | 15 +++++++------
 monai/data/png_writer.py                      |  6 ++---
 monai/data/synthetic.py                       |  4 ++--
 monai/data/test_time_augmentation.py          |  4 +++-
 monai/data/utils.py                           |  4 ++--
 monai/transforms/intensity/array.py           |  7 +++---
 monai/transforms/io/array.py                  |  2 +-
 monai/transforms/spatial/array.py             |  4 ++--
 monai/transforms/utility/array.py             |  2 +-
 monai/utils/type_conversion.py                |  3 ++-
 monai/visualize/img2tensorboard.py            |  3 ++-
 monai/visualize/utils.py                      |  3 ++-
 15 files changed, 48 insertions(+), 41 deletions(-)

diff --git a/monai/apps/deepedit/transforms.py b/monai/apps/deepedit/transforms.py
index 98201955c6..33054f4a13 100644
--- a/monai/apps/deepedit/transforms.py
+++ b/monai/apps/deepedit/transforms.py
@@ -71,8 +71,8 @@ def __call__(self, data):
         factor = np.divide(current_shape, d["image_meta_dict"]["dim"][1:4])
         pos_clicks, neg_clicks = d["foreground"], d["background"]
 
-        pos = np.multiply(pos_clicks, factor).astype(int).tolist() if len(pos_clicks) else []
-        neg = np.multiply(neg_clicks, factor).astype(int).tolist() if len(neg_clicks) else []
+        pos = np.multiply(pos_clicks, factor).astype(int, copy=False).tolist() if len(pos_clicks) else []
+        neg = np.multiply(neg_clicks, factor).astype(int, copy=False).tolist() if len(neg_clicks) else []
 
         d[self.guidance] = [pos, neg]
         return d
diff --git a/monai/apps/deepgrow/transforms.py b/monai/apps/deepgrow/transforms.py
index 1a3c035083..4954c1c5fb 100644
--- a/monai/apps/deepgrow/transforms.py
+++ b/monai/apps/deepgrow/transforms.py
@@ -145,7 +145,7 @@ def _apply(self, label, sid):
     def __call__(self, data):
         d = dict(data)
         self.randomize(data)
-        d[self.guidance] = json.dumps(self._apply(d[self.label], self.sid).astype(int).tolist())
+        d[self.guidance] = json.dumps(self._apply(d[self.label], self.sid).astype(int, copy=False).tolist())
         return d
 
 
@@ -323,7 +323,7 @@ def _apply(self, guidance, discrepancy):
             guidance[0].append([-1] * len(neg))
             guidance[1].append(neg)
 
-        return json.dumps(np.asarray(guidance).astype(int).tolist())
+        return json.dumps(np.asarray(guidance, dtype=int).tolist())
 
     def __call__(self, data):
         d = dict(data)
@@ -420,8 +420,8 @@ def __call__(self, data):
             d[self.source_key], self.select_fn, self.channel_indices, self.margin
         )
 
-        center = list(np.mean([box_start, box_end], axis=0).astype(int))
-        current_size = list(np.subtract(box_end, box_start).astype(int))
+        center = list(np.mean([box_start, box_end], axis=0).astype(int, copy=False))
+        current_size = list(np.subtract(box_end, box_start).astype(int, copy=False))
 
         if np.all(np.less(current_size, self.spatial_size)):
             cropper = SpatialCrop(roi_center=center, roi_size=self.spatial_size)
@@ -528,9 +528,9 @@ def _apply(self, pos_clicks, neg_clicks, factor, slice_num):
             guidance = [pos, neg, slice_idx]
         else:
             if len(pos_clicks):
-                pos = np.multiply(pos_clicks, factor).astype(int).tolist()
+                pos = np.multiply(pos_clicks, factor).astype(int, copy=False).tolist()
             if len(neg_clicks):
-                neg = np.multiply(neg_clicks, factor).astype(int).tolist()
+                neg = np.multiply(neg_clicks, factor).astype(int, copy=False).tolist()
             guidance = [pos, neg]
         return guidance
 
@@ -555,7 +555,7 @@ def __call__(self, data):
         fg_bg_clicks = []
         for key in [self.foreground, self.background]:
             clicks = d[key]
-            clicks = list(np.array(clicks).astype(int))
+            clicks = list(np.array(clicks, dtype=int))
             if self.depth_first:
                 for i in range(len(clicks)):
                     clicks[i] = list(np.roll(clicks[i], 1))
@@ -651,10 +651,10 @@ def __call__(self, data):
         guidance = d[self.guidance]
         original_spatial_shape = d[first_key].shape[1:]  # type: ignore
         box_start, box_end = self.bounding_box(np.array(guidance[0] + guidance[1]), original_spatial_shape)
-        center = list(np.mean([box_start, box_end], axis=0).astype(int))
+        center = list(np.mean([box_start, box_end], axis=0).astype(int, copy=False))
         spatial_size = self.spatial_size
 
-        box_size = list(np.subtract(box_end, box_start).astype(int))
+        box_size = list(np.subtract(box_end, box_start).astype(int, copy=False))
         spatial_size = spatial_size[-len(box_size) :]
 
         if len(spatial_size) < len(box_size):
@@ -738,8 +738,8 @@ def __call__(self, data):
         factor = np.divide(current_shape, cropped_shape)
 
         pos_clicks, neg_clicks = guidance[0], guidance[1]
-        pos = np.multiply(pos_clicks, factor).astype(int).tolist() if len(pos_clicks) else []
-        neg = np.multiply(neg_clicks, factor).astype(int).tolist() if len(neg_clicks) else []
+        pos = np.multiply(pos_clicks, factor).astype(int, copy=False).tolist() if len(pos_clicks) else []
+        neg = np.multiply(neg_clicks, factor).astype(int, copy=False).tolist() if len(neg_clicks) else []
 
         d[self.guidance] = [pos, neg]
         return d
diff --git a/monai/apps/pathology/transforms/stain/array.py b/monai/apps/pathology/transforms/stain/array.py
index bd644a77c2..6c27df3b5e 100644
--- a/monai/apps/pathology/transforms/stain/array.py
+++ b/monai/apps/pathology/transforms/stain/array.py
@@ -67,7 +67,7 @@ def _deconvolution_extract_stain(self, image: np.ndarray) -> np.ndarray:
 
         # reshape image and calculate absorbance
         image = image.reshape((-1, 3))
-        image = image.astype(np.float32) + 1.0
+        image = image.astype(np.float32, copy=False) + 1.0
         absorbance = -np.log(image.clip(max=self.tli) / self.tli)
 
         # remove transparent pixels
@@ -76,7 +76,7 @@ def _deconvolution_extract_stain(self, image: np.ndarray) -> np.ndarray:
             raise ValueError("All pixels of the input image are below the absorbance threshold.")
 
         # compute eigenvectors
-        _, eigvecs = np.linalg.eigh(np.cov(absorbance_hat.T).astype(np.float32))
+        _, eigvecs = np.linalg.eigh(np.cov(absorbance_hat.T).astype(np.float32, copy=False))
 
         # project on the plane spanned by the eigenvectors corresponding to the two largest eigenvalues
         t_hat = absorbance_hat.dot(eigvecs[:, 1:3])
@@ -186,7 +186,7 @@ def __call__(self, image: np.ndarray) -> np.ndarray:
         conc = np.linalg.lstsq(he, y, rcond=None)[0]
 
         # normalize stain concentrations
-        max_conc = np.array([np.percentile(conc[0, :], 99), np.percentile(conc[1, :], 99)], dtype=np.float32)
+        max_conc = np.asarray([np.percentile(conc[0, :], 99), np.percentile(conc[1, :], 99)], dtype=np.float32)
         tmp = np.divide(max_conc, self.max_cref, dtype=np.float32)
         image_c = np.divide(conc, tmp[:, np.newaxis], dtype=np.float32)
 
diff --git a/monai/data/nifti_writer.py b/monai/data/nifti_writer.py
index 210321daca..130830dd53 100644
--- a/monai/data/nifti_writer.py
+++ b/monai/data/nifti_writer.py
@@ -9,6 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from enum import Flag
 from typing import Optional, Sequence, Union
 
 import numpy as np
@@ -116,7 +117,7 @@ def write_nifti(
 
     if np.allclose(affine, target_affine, atol=1e-3):
         # no affine changes, save (data, affine)
-        results_img = nib.Nifti1Image(data.astype(output_dtype), to_affine_nd(3, target_affine))
+        results_img = nib.Nifti1Image(data.astype(output_dtype, copy=False), to_affine_nd(3, target_affine))
         nib.save(results_img, file_name)
         return
 
@@ -128,7 +129,7 @@ def write_nifti(
     data = nib.orientations.apply_orientation(data, ornt_transform)
     _affine = affine @ nib.orientations.inv_ornt_aff(ornt_transform, data_shape)
     if np.allclose(_affine, target_affine, atol=1e-3) or not resample:
-        results_img = nib.Nifti1Image(data.astype(output_dtype), to_affine_nd(3, _affine))  # type: ignore
+        results_img = nib.Nifti1Image(data.astype(output_dtype, copy=False), to_affine_nd(3, _affine))  # type: ignore
         nib.save(results_img, file_name)
         return
 
@@ -147,8 +148,8 @@ def write_nifti(
         data_np: np.ndarray = data.reshape(list(spatial_shape) + [-1])  # type: ignore
         data_np = np.moveaxis(data_np, -1, 0)  # channel first for pytorch
         data_torch = affine_xform(
-            torch.as_tensor(np.ascontiguousarray(data_np).astype(dtype)).unsqueeze(0),
-            torch.as_tensor(np.ascontiguousarray(transform).astype(dtype)),
+            torch.as_tensor(np.ascontiguousarray(data_np).astype(dtype, copy=False)).unsqueeze(0),
+            torch.as_tensor(np.ascontiguousarray(transform).astype(dtype, copy=False)),
             spatial_size=output_spatial_shape_[:3],
         )
         data_np = data_torch.squeeze(0).detach().cpu().numpy()
@@ -158,12 +159,12 @@ def write_nifti(
         while len(output_spatial_shape_) < len(data.shape):
             output_spatial_shape_ = output_spatial_shape_ + [1]
         data_torch = affine_xform(
-            torch.as_tensor(np.ascontiguousarray(data).astype(dtype)[None, None]),
-            torch.as_tensor(np.ascontiguousarray(transform).astype(dtype)),
+            torch.as_tensor(np.ascontiguousarray(data).astype(dtype, copy=False)[None, None]),
+            torch.as_tensor(np.ascontiguousarray(transform).astype(dtype, copy=False)),
             spatial_size=output_spatial_shape_[: len(data.shape)],
         )
         data_np = data_torch.squeeze(0).squeeze(0).detach().cpu().numpy()
 
-    results_img = nib.Nifti1Image(data_np.astype(output_dtype), to_affine_nd(3, target_affine))
+    results_img = nib.Nifti1Image(data_np.astype(output_dtype, copy=False), to_affine_nd(3, target_affine))
     nib.save(results_img, file_name)
     return
diff --git a/monai/data/png_writer.py b/monai/data/png_writer.py
index 52163e40ac..ea028a07be 100644
--- a/monai/data/png_writer.py
+++ b/monai/data/png_writer.py
@@ -70,15 +70,15 @@ def write_png(
     if scale is not None:
         data = np.clip(data, 0.0, 1.0)  # type: ignore # png writer only can scale data in range [0, 1]
         if scale == np.iinfo(np.uint8).max:
-            data = (scale * data).astype(np.uint8)
+            data = (scale * data).astype(np.uint8, copy=False)
         elif scale == np.iinfo(np.uint16).max:
-            data = (scale * data).astype(np.uint16)
+            data = (scale * data).astype(np.uint16, copy=False)
         else:
             raise ValueError(f"Unsupported scale: {scale}, available options are [255, 65535]")
 
     # PNG data must be int number
     if data.dtype not in (np.uint8, np.uint16):  # type: ignore
-        data = data.astype(np.uint8)
+        data = data.astype(np.uint8, copy=False)
 
     data = np.moveaxis(data, 0, 1)
     img = Image.fromarray(data)
diff --git a/monai/data/synthetic.py b/monai/data/synthetic.py
index 6eec9fd277..0a1c179a7f 100644
--- a/monai/data/synthetic.py
+++ b/monai/data/synthetic.py
@@ -73,7 +73,7 @@ def create_test_image_2d(
         else:
             image[circle] = rs.random() * 0.5 + 0.5
 
-    labels = np.ceil(image).astype(np.int32)
+    labels = np.ceil(image).astype(np.int32, copy=False)
 
     norm = rs.uniform(0, num_seg_classes * noise_max, size=image.shape)
     noisyimage: np.ndarray = rescale_array(np.maximum(image, norm))  # type: ignore
@@ -148,7 +148,7 @@ def create_test_image_3d(
         else:
             image[circle] = rs.random() * 0.5 + 0.5
 
-    labels = np.ceil(image).astype(np.int32)
+    labels = np.ceil(image).astype(np.int32, copy=False)
 
     norm = rs.uniform(0, num_seg_classes * noise_max, size=image.shape)
     noisyimage: np.ndarray = rescale_array(np.maximum(image, norm))  # type: ignore
diff --git a/monai/data/test_time_augmentation.py b/monai/data/test_time_augmentation.py
index 948e85e131..a87bf9b7cf 100644
--- a/monai/data/test_time_augmentation.py
+++ b/monai/data/test_time_augmentation.py
@@ -26,6 +26,7 @@
 from monai.transforms.utils import allow_missing_keys_mode, convert_inverse_interp_mode
 from monai.utils.enums import CommonKeys, TraceKeys
 from monai.utils.module import optional_import
+from monai.utils.type_conversion import convert_data_type
 
 if TYPE_CHECKING:
     from tqdm import tqdm
@@ -215,7 +216,8 @@ def __call__(
             return output
 
         # calculate metrics
-        mode = np.array(torch.mode(torch.Tensor(output.astype(np.int64)), dim=0).values)
+        output_t, *_ = convert_data_type(output, output_type=torch.Tensor, dtype=np.int64)
+        mode = np.array(torch.mode(output_t, dim=0).values)
         mean: np.ndarray = np.mean(output, axis=0)  # type: ignore
         std: np.ndarray = np.std(output, axis=0)  # type: ignore
         vvc: float = (np.std(output) / np.mean(output)).item()
diff --git a/monai/data/utils.py b/monai/data/utils.py
index 2e5efce7cd..29dbeeda24 100644
--- a/monai/data/utils.py
+++ b/monai/data/utils.py
@@ -631,7 +631,7 @@ def compute_shape_offset(
         # different orientation, the min is the origin
         corners = corners[:-1] / corners[-1]
         offset = np.min(corners, 1)
-    return out_shape.astype(int), offset
+    return out_shape.astype(int, copy=False), offset
 
 
 def to_affine_nd(r: Union[np.ndarray, int], affine: np.ndarray) -> np.ndarray:
@@ -1143,7 +1143,7 @@ def convert_tables_to_dicts(
         # convert data types
         types = {k: v["type"] for k, v in col_types.items() if v is not None and "type" in v}
         if types:
-            data_ = data_.astype(dtype=types)
+            data_ = data_.astype(dtype=types, copy=False)
     data: List[Dict] = data_.to_dict(orient="records")
 
     # group columns to generate new column
diff --git a/monai/transforms/intensity/array.py b/monai/transforms/intensity/array.py
index cffbc27d19..131bc19f29 100644
--- a/monai/transforms/intensity/array.py
+++ b/monai/transforms/intensity/array.py
@@ -15,6 +15,7 @@
 
 from abc import abstractmethod
 from collections.abc import Iterable
+from copy import copy
 from functools import partial
 from typing import Any, Callable, List, Optional, Sequence, Tuple, Union
 from warnings import warn
@@ -168,8 +169,8 @@ def _add_noise(self, img: NdarrayTensor, mean: float, std: float):
         dtype_np = get_equivalent_dtype(img.dtype, np.ndarray)
         im_shape = img.shape
         _std = self.R.uniform(0, std) if self.sample_std else std
-        self._noise1 = self.R.normal(mean, _std, size=im_shape).astype(dtype_np)
-        self._noise2 = self.R.normal(mean, _std, size=im_shape).astype(dtype_np)
+        self._noise1 = self.R.normal(mean, _std, size=im_shape).astype(dtype_np, copy=False)
+        self._noise2 = self.R.normal(mean, _std, size=im_shape).astype(dtype_np, copy=False)
         if isinstance(img, torch.Tensor):
             n1 = torch.tensor(self._noise1, device=img.device)
             n2 = torch.tensor(self._noise2, device=img.device)
@@ -1942,7 +1943,7 @@ def _transform_holes(self, img: np.ndarray):
             ret = img
         else:
             if isinstance(fill_value, (tuple, list)):
-                ret = self.R.uniform(fill_value[0], fill_value[1], size=img.shape).astype(img.dtype)
+                ret = self.R.uniform(fill_value[0], fill_value[1], size=img.shape).astype(img.dtype, copy=False)
             else:
                 ret = np.full_like(img, fill_value)
             for h in self.hole_coords:
diff --git a/monai/transforms/io/array.py b/monai/transforms/io/array.py
index 170482f504..cd2d93a0c7 100644
--- a/monai/transforms/io/array.py
+++ b/monai/transforms/io/array.py
@@ -212,7 +212,7 @@ def __call__(self, filename: Union[Sequence[PathLike], PathLike], reader: Option
             )
 
         img_array, meta_data = reader.get_data(img)
-        img_array = img_array.astype(self.dtype)
+        img_array = img_array.astype(self.dtype, copy=False)
 
         if self.image_only:
             return img_array
diff --git a/monai/transforms/spatial/array.py b/monai/transforms/spatial/array.py
index 1be621477e..8d1558c230 100644
--- a/monai/transforms/spatial/array.py
+++ b/monai/transforms/spatial/array.py
@@ -1302,7 +1302,7 @@ def __init__(
         self.device = device
 
     def randomize(self, grid_size: Sequence[int]) -> None:
-        self.random_offset = self.R.normal(size=([len(grid_size)] + list(grid_size))).astype(np.float32)
+        self.random_offset = self.R.normal(size=([len(grid_size)] + list(grid_size))).astype(np.float32, copy=False)
         self.rand_mag = self.R.uniform(self.magnitude[0], self.magnitude[1])
 
     def __call__(self, spatial_size: Sequence[int]):
@@ -1978,7 +1978,7 @@ def randomize(self, grid_size: Sequence[int]) -> None:
         super().randomize(None)
         if not self._do_transform:
             return None
-        self.rand_offset = self.R.uniform(-1.0, 1.0, [3] + list(grid_size)).astype(np.float32)
+        self.rand_offset = self.R.uniform(-1.0, 1.0, [3] + list(grid_size)).astype(np.float32, copy=False)
         self.magnitude = self.R.uniform(self.magnitude_range[0], self.magnitude_range[1])
         self.sigma = self.R.uniform(self.sigma_range[0], self.sigma_range[1])
         self.rand_affine_grid.randomize()
diff --git a/monai/transforms/utility/array.py b/monai/transforms/utility/array.py
index 50738978bb..8be270b250 100644
--- a/monai/transforms/utility/array.py
+++ b/monai/transforms/utility/array.py
@@ -1023,7 +1023,7 @@ def __call__(self, img: NdarrayOrTensor):
         img_np, *_ = convert_data_type(img, np.ndarray)
         img_flat = img_np.flatten()
         try:
-            out_flat = np.copy(img_flat).astype(self.dtype)
+            out_flat = np.copy(img_flat).astype(self.dtype, copy=False)
         except ValueError:
             # can't copy unchanged labels as the expected dtype is not supported, must map all the label values
             out_flat = np.zeros(shape=img_flat.shape, dtype=self.dtype)
diff --git a/monai/utils/type_conversion.py b/monai/utils/type_conversion.py
index c9ac49901f..6d6613b6bf 100644
--- a/monai/utils/type_conversion.py
+++ b/monai/utils/type_conversion.py
@@ -10,6 +10,7 @@
 # limitations under the License.
 
 import re
+from copy import copy
 from typing import Any, Optional, Sequence, Tuple, Union
 
 import numpy as np
@@ -157,7 +158,7 @@ def convert_to_numpy(data, dtype: DtypeLike = None, wrap_sequence: bool = False)
     if isinstance(data, torch.Tensor):
         data = data.detach().to(dtype=get_equivalent_dtype(dtype, torch.Tensor), device="cpu").numpy()
     elif has_cp and isinstance(data, cp_ndarray):
-        data = cp.asnumpy(data).astype(dtype)
+        data = cp.asnumpy(data).astype(dtype, copy=False)
     elif isinstance(data, (np.ndarray, float, int, bool)):
         data = np.asarray(data, dtype=dtype)
     elif isinstance(data, list):
diff --git a/monai/visualize/img2tensorboard.py b/monai/visualize/img2tensorboard.py
index eef1b2e764..78c78bc9b8 100644
--- a/monai/visualize/img2tensorboard.py
+++ b/monai/visualize/img2tensorboard.py
@@ -9,6 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from copy import copy
 from typing import TYPE_CHECKING, Dict, List, Optional, Sequence, Union
 
 import numpy as np
@@ -45,7 +46,7 @@ def _image3_animated_gif(tag: str, image: Union[np.ndarray, torch.Tensor], write
     if len(image.shape) != 3:
         raise AssertionError("3D image tensors expected to be in `HWD` format, len(image.shape) != 3")
 
-    ims = [(np.asarray(image[:, :, i]) * scale_factor).astype(np.uint8) for i in range(image.shape[2])]
+    ims = [(np.asarray(image[:, :, i]) * scale_factor).astype(np.uint8, copy=False) for i in range(image.shape[2])]
     ims = [GifImage.fromarray(im) for im in ims]
     img_str = b""
     for b_data in PIL.GifImagePlugin.getheader(ims[0])[0]:
diff --git a/monai/visualize/utils.py b/monai/visualize/utils.py
index c0304e9e68..25abbbd646 100644
--- a/monai/visualize/utils.py
+++ b/monai/visualize/utils.py
@@ -9,6 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from copy import copy
 from typing import Optional
 
 import numpy as np
@@ -108,7 +109,7 @@ def matshow3d(
     cols = max(min(len(vol), frames_per_row), 1)
     rows = int(np.ceil(len(vol) / cols))
     width = [[0, cols * rows - len(vol)]] + [[margin, margin]] * (len(vol.shape) - 1)
-    vol = np.pad(vol.astype(dtype), width, mode="constant", constant_values=fill_value)
+    vol = np.pad(vol.astype(dtype, copy=False), width, mode="constant", constant_values=fill_value)
     im = np.block([[vol[i * cols + j] for j in range(cols)] for i in range(rows)])
 
     # figure related configurations

From f2ba306e2643ee2a7a7b7f5c4bdf10425eb93476 Mon Sep 17 00:00:00 2001
From: Nic Ma <nma@nvidia.com>
Date: Wed, 17 Nov 2021 19:17:46 +0800
Subject: [PATCH 3/8] [DLMED] fix flake8

Signed-off-by: Nic Ma <nma@nvidia.com>
---
 monai/data/nifti_writer.py           | 1 -
 monai/data/test_time_augmentation.py | 2 +-
 monai/transforms/intensity/array.py  | 1 -
 monai/utils/type_conversion.py       | 1 -
 monai/visualize/img2tensorboard.py   | 1 -
 monai/visualize/utils.py             | 1 -
 6 files changed, 1 insertion(+), 6 deletions(-)

diff --git a/monai/data/nifti_writer.py b/monai/data/nifti_writer.py
index 130830dd53..655080824f 100644
--- a/monai/data/nifti_writer.py
+++ b/monai/data/nifti_writer.py
@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from enum import Flag
 from typing import Optional, Sequence, Union
 
 import numpy as np
diff --git a/monai/data/test_time_augmentation.py b/monai/data/test_time_augmentation.py
index a87bf9b7cf..1d81d91a16 100644
--- a/monai/data/test_time_augmentation.py
+++ b/monai/data/test_time_augmentation.py
@@ -217,7 +217,7 @@ def __call__(
 
         # calculate metrics
         output_t, *_ = convert_data_type(output, output_type=torch.Tensor, dtype=np.int64)
-        mode = np.array(torch.mode(output_t, dim=0).values)
+        mode: np.ndarray = np.asarray(torch.mode(output_t, dim=0).values)  # type: ignore
         mean: np.ndarray = np.mean(output, axis=0)  # type: ignore
         std: np.ndarray = np.std(output, axis=0)  # type: ignore
         vvc: float = (np.std(output) / np.mean(output)).item()
diff --git a/monai/transforms/intensity/array.py b/monai/transforms/intensity/array.py
index 131bc19f29..dca5db7a35 100644
--- a/monai/transforms/intensity/array.py
+++ b/monai/transforms/intensity/array.py
@@ -15,7 +15,6 @@
 
 from abc import abstractmethod
 from collections.abc import Iterable
-from copy import copy
 from functools import partial
 from typing import Any, Callable, List, Optional, Sequence, Tuple, Union
 from warnings import warn
diff --git a/monai/utils/type_conversion.py b/monai/utils/type_conversion.py
index 6d6613b6bf..2defbe30c1 100644
--- a/monai/utils/type_conversion.py
+++ b/monai/utils/type_conversion.py
@@ -10,7 +10,6 @@
 # limitations under the License.
 
 import re
-from copy import copy
 from typing import Any, Optional, Sequence, Tuple, Union
 
 import numpy as np
diff --git a/monai/visualize/img2tensorboard.py b/monai/visualize/img2tensorboard.py
index 78c78bc9b8..309e7f4b18 100644
--- a/monai/visualize/img2tensorboard.py
+++ b/monai/visualize/img2tensorboard.py
@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from copy import copy
 from typing import TYPE_CHECKING, Dict, List, Optional, Sequence, Union
 
 import numpy as np
diff --git a/monai/visualize/utils.py b/monai/visualize/utils.py
index 25abbbd646..29def9d0ef 100644
--- a/monai/visualize/utils.py
+++ b/monai/visualize/utils.py
@@ -9,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from copy import copy
 from typing import Optional
 
 import numpy as np

From 268a3f8edde8ad46682a13b77a43bbb8f08bfc47 Mon Sep 17 00:00:00 2001
From: Nic Ma <nma@nvidia.com>
Date: Thu, 18 Nov 2021 16:26:35 +0800
Subject: [PATCH 4/8] [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
---
 monai/data/nifti_writer.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/monai/data/nifti_writer.py b/monai/data/nifti_writer.py
index 655080824f..078ea2e605 100644
--- a/monai/data/nifti_writer.py
+++ b/monai/data/nifti_writer.py
@@ -147,8 +147,8 @@ def write_nifti(
         data_np: np.ndarray = data.reshape(list(spatial_shape) + [-1])  # type: ignore
         data_np = np.moveaxis(data_np, -1, 0)  # channel first for pytorch
         data_torch = affine_xform(
-            torch.as_tensor(np.ascontiguousarray(data_np).astype(dtype, copy=False)).unsqueeze(0),
-            torch.as_tensor(np.ascontiguousarray(transform).astype(dtype, copy=False)),
+            torch.as_tensor(np.ascontiguousarray(data_np, dtype=dtype)).unsqueeze(0),
+            torch.as_tensor(np.ascontiguousarray(transform, dtype=dtype)),
             spatial_size=output_spatial_shape_[:3],
         )
         data_np = data_torch.squeeze(0).detach().cpu().numpy()
@@ -158,8 +158,8 @@ def write_nifti(
         while len(output_spatial_shape_) < len(data.shape):
             output_spatial_shape_ = output_spatial_shape_ + [1]
         data_torch = affine_xform(
-            torch.as_tensor(np.ascontiguousarray(data).astype(dtype, copy=False)[None, None]),
-            torch.as_tensor(np.ascontiguousarray(transform).astype(dtype, copy=False)),
+            torch.as_tensor(np.ascontiguousarray(data, dtype=dtype)[None, None]),
+            torch.as_tensor(np.ascontiguousarray(transform, dtype=dtype)),
             spatial_size=output_spatial_shape_[: len(data.shape)],
         )
         data_np = data_torch.squeeze(0).squeeze(0).detach().cpu().numpy()

From cc6e168f2546d4dc338ad7f03752bec718ee796f Mon Sep 17 00:00:00 2001
From: Nic Ma <nma@nvidia.com>
Date: Thu, 18 Nov 2021 19:34:49 +0800
Subject: [PATCH 5/8] [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
---
 monai/transforms/intensity/array.py      | 16 +++++++++++----
 monai/transforms/intensity/dictionary.py | 26 ++++++++++++++++--------
 tests/test_rand_gaussian_noised.py       |  2 +-
 tests/test_rand_rician_noised.py         |  2 +-
 4 files changed, 31 insertions(+), 15 deletions(-)

diff --git a/monai/transforms/intensity/array.py b/monai/transforms/intensity/array.py
index dca5db7a35..a0d7a02670 100644
--- a/monai/transforms/intensity/array.py
+++ b/monai/transforms/intensity/array.py
@@ -23,7 +23,7 @@
 import torch
 
 from monai.config import DtypeLike
-from monai.config.type_definitions import NdarrayOrTensor, NdarrayTensor
+from monai.config.type_definitions import NdarrayOrTensor
 from monai.data.utils import get_random_patch, get_valid_patch_size
 from monai.networks.layers import GaussianFilter, HilbertTransform, SavitzkyGolayFilter
 from monai.transforms.transform import RandomizableTransform, Transform
@@ -86,15 +86,17 @@ class RandGaussianNoise(RandomizableTransform):
         prob: Probability to add Gaussian noise.
         mean: Mean or “centre” of the distribution.
         std: Standard deviation (spread) of distribution.
+        dtype: output data type, if None, same as input image. defaults to float32.
 
     """
 
     backend = [TransformBackends.TORCH, TransformBackends.NUMPY]
 
-    def __init__(self, prob: float = 0.1, mean: float = 0.0, std: float = 0.1) -> None:
+    def __init__(self, prob: float = 0.1, mean: float = 0.0, std: float = 0.1, dtype: DtypeLike = np.float32) -> None:
         RandomizableTransform.__init__(self, prob)
         self.mean = mean
         self.std = std
+        self.dtype = dtype
         self.noise: Optional[np.ndarray] = None
 
     def randomize(self, img: NdarrayOrTensor, mean: Optional[float] = None) -> None:
@@ -116,6 +118,7 @@ def __call__(self, img: NdarrayOrTensor, mean: Optional[float] = None, randomize
 
         if self.noise is None:
             raise RuntimeError("please call the `randomize()` function first.")
+        img, *_ = convert_data_type(img, dtype=self.dtype)
         noise, *_ = convert_to_dst_type(self.noise, img)
         return img + noise
 
@@ -141,6 +144,8 @@ class RandRicianNoise(RandomizableTransform):
             histogram.
         sample_std: If True, sample the spread of the Gaussian distributions
             uniformly from 0 to std.
+        dtype: output data type, if None, same as input image. defaults to float32.
+
     """
 
     backend = [TransformBackends.TORCH, TransformBackends.NUMPY]
@@ -153,6 +158,7 @@ def __init__(
         channel_wise: bool = False,
         relative: bool = False,
         sample_std: bool = True,
+        dtype: DtypeLike = np.float32,
     ) -> None:
         RandomizableTransform.__init__(self, prob)
         self.prob = prob
@@ -161,10 +167,11 @@ def __init__(
         self.channel_wise = channel_wise
         self.relative = relative
         self.sample_std = sample_std
+        self.dtype = dtype
         self._noise1: NdarrayOrTensor
         self._noise2: NdarrayOrTensor
 
-    def _add_noise(self, img: NdarrayTensor, mean: float, std: float):
+    def _add_noise(self, img: NdarrayOrTensor, mean: float, std: float):
         dtype_np = get_equivalent_dtype(img.dtype, np.ndarray)
         im_shape = img.shape
         _std = self.R.uniform(0, std) if self.sample_std else std
@@ -177,7 +184,7 @@ def _add_noise(self, img: NdarrayTensor, mean: float, std: float):
 
         return np.sqrt((img + self._noise1) ** 2 + self._noise2 ** 2)
 
-    def __call__(self, img: NdarrayTensor, randomize: bool = True) -> NdarrayTensor:
+    def __call__(self, img: NdarrayOrTensor, randomize: bool = True) -> NdarrayOrTensor:
         """
         Apply the transform to `img`.
         """
@@ -187,6 +194,7 @@ def __call__(self, img: NdarrayTensor, randomize: bool = True) -> NdarrayTensor:
         if not self._do_transform:
             return img
 
+        img, *_ = convert_data_type(img, dtype=self.dtype)
         if self.channel_wise:
             _mean = ensure_tuple_rep(self.mean, len(img))
             _std = ensure_tuple_rep(self.std, len(img))
diff --git a/monai/transforms/intensity/dictionary.py b/monai/transforms/intensity/dictionary.py
index 71809d7ea2..fa2de4c7b8 100644
--- a/monai/transforms/intensity/dictionary.py
+++ b/monai/transforms/intensity/dictionary.py
@@ -19,7 +19,7 @@
 
 import numpy as np
 
-from monai.config import DtypeLike, KeysCollection, NdarrayTensor
+from monai.config import DtypeLike, KeysCollection
 from monai.config.type_definitions import NdarrayOrTensor
 from monai.transforms.intensity.array import (
     AdjustContrast,
@@ -156,6 +156,7 @@ class RandGaussianNoised(RandomizableTransform, MapTransform):
         prob: Probability to add Gaussian noise.
         mean: Mean or “centre” of the distribution.
         std: Standard deviation (spread) of distribution.
+        dtype: output data type, if None, same as input image. defaults to float32.
         allow_missing_keys: don't raise exception if key is missing.
     """
 
@@ -167,11 +168,12 @@ def __init__(
         prob: float = 0.1,
         mean: float = 0.0,
         std: float = 0.1,
+        dtype: DtypeLike = np.float32,
         allow_missing_keys: bool = False,
     ) -> None:
         MapTransform.__init__(self, keys, allow_missing_keys)
         RandomizableTransform.__init__(self, prob)
-        self.rand_gaussian_noise = RandGaussianNoise(mean=mean, std=std, prob=1.0)
+        self.rand_gaussian_noise = RandGaussianNoise(mean=mean, std=std, prob=1.0, dtype=dtype)
 
     def set_random_state(
         self, seed: Optional[int] = None, state: Optional[np.random.RandomState] = None
@@ -206,9 +208,7 @@ class RandRicianNoised(RandomizableTransform, MapTransform):
     Args:
         keys: Keys of the corresponding items to be transformed.
             See also: :py:class:`monai.transforms.compose.MapTransform`
-        global_prob: Probability to add Rician noise to the dictionary.
-        prob: Probability to add Rician noise to each item in the dictionary,
-            once asserted that noise will be added to the dictionary at all.
+        prob: Probability to add Rician noise to the dictionary.
         mean: Mean or "centre" of the Gaussian distributions sampled to make up
             the Rician noise.
         std: Standard deviation (spread) of the Gaussian distributions sampled
@@ -219,27 +219,35 @@ class RandRicianNoised(RandomizableTransform, MapTransform):
             histogram.
         sample_std: If True, sample the spread of the Gaussian distributions
             uniformly from 0 to std.
+        dtype: output data type, if None, same as input image. defaults to float32.
         allow_missing_keys: Don't raise exception if key is missing.
     """
 
     backend = RandRicianNoise.backend
 
+    @deprecated_arg("global_prob", since="0.7")
     def __init__(
         self,
         keys: KeysCollection,
-        global_prob: float = 0.1,
         prob: float = 0.1,
         mean: Union[Sequence[float], float] = 0.0,
         std: Union[Sequence[float], float] = 1.0,
         channel_wise: bool = False,
         relative: bool = False,
         sample_std: bool = True,
+        dtype: DtypeLike = np.float32,
         allow_missing_keys: bool = False,
     ) -> None:
         MapTransform.__init__(self, keys, allow_missing_keys)
-        RandomizableTransform.__init__(self, global_prob)
+        RandomizableTransform.__init__(self, prob)
         self.rand_rician_noise = RandRicianNoise(
-            prob=1.0, mean=mean, std=std, channel_wise=channel_wise, relative=relative, sample_std=sample_std
+            prob=1.0,
+            mean=mean,
+            std=std,
+            channel_wise=channel_wise,
+            relative=relative,
+            sample_std=sample_std,
+            dtype=dtype,
         )
 
     def set_random_state(
@@ -249,7 +257,7 @@ def set_random_state(
         self.rand_rician_noise.set_random_state(seed, state)
         return self
 
-    def __call__(self, data: Mapping[Hashable, NdarrayTensor]) -> Dict[Hashable, NdarrayTensor]:
+    def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> Dict[Hashable, NdarrayOrTensor]:
         d = dict(data)
         self.randomize(None)
         if not self._do_transform:
diff --git a/tests/test_rand_gaussian_noised.py b/tests/test_rand_gaussian_noised.py
index d9fd5d023d..3e578075ae 100644
--- a/tests/test_rand_gaussian_noised.py
+++ b/tests/test_rand_gaussian_noised.py
@@ -29,7 +29,7 @@
 class TestRandGaussianNoised(NumpyImageTestCase2D):
     @parameterized.expand(TESTS)
     def test_correct_results(self, _, im_type, keys, mean, std):
-        gaussian_fn = RandGaussianNoised(keys=keys, prob=1.0, mean=mean, std=std)
+        gaussian_fn = RandGaussianNoised(keys=keys, prob=1.0, mean=mean, std=std, dtype=np.float64)
         gaussian_fn.set_random_state(seed)
         im = im_type(self.imt)
         noised = gaussian_fn({k: im for k in keys})
diff --git a/tests/test_rand_rician_noised.py b/tests/test_rand_rician_noised.py
index e8cb84dc99..bb5ebbe8c8 100644
--- a/tests/test_rand_rician_noised.py
+++ b/tests/test_rand_rician_noised.py
@@ -29,7 +29,7 @@
 class TestRandRicianNoisedNumpy(NumpyImageTestCase2D):
     @parameterized.expand(TESTS)
     def test_correct_results(self, _, in_type, keys, mean, std):
-        rician_fn = RandRicianNoised(keys=keys, global_prob=1.0, prob=1.0, mean=mean, std=std)
+        rician_fn = RandRicianNoised(keys=keys, prob=1.0, mean=mean, std=std, dtype=np.float64)
         rician_fn.set_random_state(seed)
         noised = rician_fn({k: in_type(self.imt) for k in keys})
         np.random.seed(seed)

From be4dd9d93baf86dcde5c780a71934746a0e24dcc Mon Sep 17 00:00:00 2001
From: Nic Ma <nma@nvidia.com>
Date: Thu, 18 Nov 2021 20:09:54 +0800
Subject: [PATCH 6/8] [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
---
 monai/transforms/intensity/array.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/monai/transforms/intensity/array.py b/monai/transforms/intensity/array.py
index a0d7a02670..3420b1a36a 100644
--- a/monai/transforms/intensity/array.py
+++ b/monai/transforms/intensity/array.py
@@ -104,7 +104,9 @@ def randomize(self, img: NdarrayOrTensor, mean: Optional[float] = None) -> None:
         if not self._do_transform:
             return None
         rand_std = self.R.uniform(0, self.std)
-        self.noise = self.R.normal(self.mean if mean is None else mean, rand_std, size=img.shape)
+        noise = self.R.normal(self.mean if mean is None else mean, rand_std, size=img.shape)
+        # noise is float64 array, convert to the output dtype to save memory
+        self.noise, *_ = convert_data_type(noise, dtype=self.dtype)  # type: ignore
 
     def __call__(self, img: NdarrayOrTensor, mean: Optional[float] = None, randomize: bool = True) -> NdarrayOrTensor:
         """

From 7ed2a2877aa01790943e0ff82b9c5eaed712fa9c Mon Sep 17 00:00:00 2001
From: Nic Ma <nma@nvidia.com>
Date: Thu, 18 Nov 2021 21:42:20 +0800
Subject: [PATCH 7/8] [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
---
 monai/transforms/utility/array.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/monai/transforms/utility/array.py b/monai/transforms/utility/array.py
index 8be270b250..e7a14ce9ea 100644
--- a/monai/transforms/utility/array.py
+++ b/monai/transforms/utility/array.py
@@ -1023,7 +1023,7 @@ def __call__(self, img: NdarrayOrTensor):
         img_np, *_ = convert_data_type(img, np.ndarray)
         img_flat = img_np.flatten()
         try:
-            out_flat = np.copy(img_flat).astype(self.dtype, copy=False)
+            out_flat = np.array(img_flat, dtype=self.dtype)
         except ValueError:
             # can't copy unchanged labels as the expected dtype is not supported, must map all the label values
             out_flat = np.zeros(shape=img_flat.shape, dtype=self.dtype)

From ec9e835f0005170781e0a3e8d5913dd2ab812bd6 Mon Sep 17 00:00:00 2001
From: Nic Ma <nma@nvidia.com>
Date: Thu, 18 Nov 2021 22:11:10 +0800
Subject: [PATCH 8/8] [DLMED] fix flake8

Signed-off-by: Nic Ma <nma@nvidia.com>
---
 monai/transforms/utility/array.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/monai/transforms/utility/array.py b/monai/transforms/utility/array.py
index e7a14ce9ea..be0800474a 100644
--- a/monai/transforms/utility/array.py
+++ b/monai/transforms/utility/array.py
@@ -1033,8 +1033,8 @@ def __call__(self, img: NdarrayOrTensor):
                 continue
             np.place(out_flat, img_flat == o, t)
 
-        out = out_flat.reshape(img_np.shape)
-        out, *_ = convert_to_dst_type(src=out, dst=img, dtype=self.dtype)
+        reshaped = out_flat.reshape(img_np.shape)
+        out, *_ = convert_to_dst_type(src=reshaped, dst=img, dtype=self.dtype)
         return out