[RELEASE] cucim v22.04 #260
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
[gpuCI] Forward-merge branch-22.02 to branch-22.04 [skip gpuci]
[gpuCI] Forward-merge branch-22.02 to branch-22.04 [skip gpuci]
[gpuCI] Forward-merge branch-22.02 to branch-22.04 [skip gpuci]
[gpuCI] Forward-merge branch-22.02 to branch-22.04 [skip gpuci]
[gpuCI] Forward-merge branch-22.02 to branch-22.04 [skip gpuci]
[gpuCI] Forward-merge branch-22.02 to branch-22.04 [skip gpuci]
[gpuCI] Forward-merge branch-22.02 to branch-22.04 [skip gpuci]
This PR fixes an issue with the doc builds. `get_html_theme_path()` was removed in the commit below. After some local testing, it seems that the lines in this PR can be removed without any issues. - pydata/pydata-sphinx-theme@579d7ce Authors: - AJ Schmidt (https://github.com/ajschmidt8) Approvers: - https://github.com/jakirkham URL: #218
Merge branch-22.02 into branch-22.04
Fixes #192 Signed-off-by: Gigon Bae <gbae@nvidia.com> Authors: - Gigon Bae (https://github.com/gigony) Approvers: - https://github.com/jakirkham URL: #227
In the near future, the [rapidsai/ops-bot](https://github.com/rapidsai/ops-bot) GitHub application that we use for GitHub automation will be enabled on all repositories in the `rapidsai` GitHub organization. Since not all features of the application are applicable to all repositories, this PR adds a new file, `.github/ops-bot.yaml`, which can configure which features are enabled per repository. Authors: - AJ Schmidt (https://github.com/ajschmidt8) Approvers: - Jake Awe (https://github.com/AyodeAwe) URL: #236
Update outdated CHANGELOG.md and README.md files. Authors: - Gigon Bae (https://github.com/gigony) Approvers: - Gregory Lee (https://github.com/grlee77) - https://github.com/jakirkham URL: #226
Do not reference nullptr in CuFileDriver::close() method. ``` pip install --extra-index-url https://test.pypi.org/simple/ cucim==0.0.229 ``` Fixes #228 Signed-off-by: Gigon Bae <gbae@nvidia.com> Authors: - Gigon Bae (https://github.com/gigony) Approvers: - Benjamin Zaitlen (https://github.com/quasiben) - https://github.com/jakirkham URL: #229
I recently committed a config file to be used by the [rapidsai/ops-bot](https://github.com/rapidsai/ops-bot/) and in hindsight, I should've had the new `external_contributors` functionality set to `false` until we're ready to roll it out everywhere. This PR fixes that. Authors: - AJ Schmidt (https://github.com/ajschmidt8) Approvers:
- Close the file descriptor if the file descriptor is owned by the object.
- Update GDS example in the Jupyter notebook.
```python
from cucim.clara.filesystem import CuFileDriver
import cucim.clara.filesystem as fs
import os, cupy as cp, torch
# Create a CuPy array with size 10 (in bytes)
cp_arr = cp.ones(10, dtype=cp.uint8)
# Create a PyTorch array with size 10 (in bytes)
cuda0 = torch.device('cuda:0')
torch_arr = torch.ones(10, dtype=torch.uint8, device=cuda0)
# Using CuFileDriver
# (Opening a file with O_DIRECT flag is required for GDS)
fno = os.open("input.raw", os.O_RDONLY | os.O_DIRECT)
with CuFileDriver(fno) as fd:
# Read 8 bytes starting from file offset 0 into buffer offset 2
read_count = fd.pread(cp_arr, 8, 0, 2)
# Read 10 bytes starting from file offset 3
read_count = fd.pread(torch_arr, 10, 3)
os.close(fno)
# Another way of opening file with cuFile
with fs.open("output.raw", "w") as fd:
# Write 10 bytes from cp_array to file starting from offset 5
write_count = fd.pwrite(cp_arr, 10, 5)
#############################################
# <=== file descriptor created by fs.open() would be closed when exiting the scope
#############################################
```
Fixes #233
Authors:
- Gigon Bae (https://github.com/gigony)
Approvers:
- https://github.com/jakirkham
URL: #234
) Closes #199 Corresponds to: scikit-image/scikit-image#6207 scikit-image/scikit-image#6211 scikit-image/scikit-image#6214 Additionally, the affines contained within the `PiecewiseAffineTransform` will have parameters in CuPy arrays when the inputs to `estimate` are CuPy arrays. This is one to make it consistent with the other transform classes. @chrisroat, can you confirm if this fixes the issue for you? Authors: - Gregory Lee (https://github.com/grlee77) Approvers: - https://github.com/jakirkham URL: #208
Signed-off-by: Gigon Bae <gbae@nvidia.com> Authors: - Gigon Bae (https://github.com/gigony) Approvers: - https://github.com/jakirkham URL: #249
Fix a wrong value assignment for the loaded region image. Fixes #247 Signed-off-by: Gigon Bae <gbae@nvidia.com> Authors: - Gigon Bae (https://github.com/gigony) Approvers: - https://github.com/jakirkham URL: #248
closes #251 by avoiding imports from private CuPy code The new files here are just subsets of files present in CuPy that are not part of its public API. Only a few functions use functionality from this `_vendored` folder. The whole folder is mainly here in order to have a version of `cupyx.scipy.signal.fftconvolve` with a modified `choose_conv_mode`. We should eventually just update the convolution selection code in CuPy so that we can remove these files. I think `fftconvolve` itself was not present at all in CuPy 9.x, but even in the current development branch, the [convolution choice function is still restricted to 1D](https://github.com/cupy/cupy/blob/ec6d2c9a98440b19a133868576fb299972c21f6c/cupy/_math/misc.py#L23-L25) Authors: - Gregory Lee (https://github.com/grlee77) Approvers: - https://github.com/jakirkham URL: #252
) - Expose typestr property on CuImage object - Expose DLDataType and DLDataTypeCode under cucim.clara Without this patch, DLDataType and DLDataTypecode can be accessible with the below workaround. ```python >>> from cucim import CuImage >>> a = CuImage("notebooks/input/image.tif") >>> b = a.read_region((0,0), (10,10)) >>> import numpy as np >>> np.dtype(b.__array_interface__["typestr"]) # b would expose `__cuda_array_interface__` if memory is in GPU. dtype('uint8') ``` With this patch, we can convert data type to NumPy's dtype easily, and also can access cuCIM's DLDataType. ```python >>> from cucim import CuImage >>> a = CuImage("notebooks/input/image.tif") >>> b = a.read_region((0,0), (10,10)) >>> import numpy as np >>> b.typestr '|u1' >>> np.dtype(b.typestr) == np.uint8 True >>> from cucim.clara import DLDataType, DLDataTypeCode >>> b.dtype == DLDataType(DLDataTypeCode.DLUInt, 8, 1) True ``` Fixes #243 Authors: - Gigon Bae (https://github.com/gigony) Approvers: - https://github.com/jakirkham URL: #246
As per #225 Randomness updated to be applied to per image in the batch. Existing functionality of applying randomness on entire batch at once is unchanged. Authors: - https://github.com/shekhardw Approvers: - Gigon Bae (https://github.com/gigony) - https://github.com/jakirkham URL: #231
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
❄️ Code freeze for
branch-22.04and v22.04 releaseWhat does this mean?
Only critical/hotfix level issues should be merged into
branch-22.04until release (merging of this PR).What is the purpose of this PR?
branch-22.04intomainfor the release