repo_id stringlengths 21 96 | file_path stringlengths 31 155 | content stringlengths 1 92.9M | __index_level_0__ int64 0 0 |
|---|---|---|---|
rapidsai_public_repos/cucim/cpp/cmake | rapidsai_public_repos/cucim/cpp/cmake/deps/taskflow.cmake | #
# Copyright (c) 2021, NVIDIA CORPORATION.
# 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 t... | 0 |
rapidsai_public_repos/cucim/cpp/cmake | rapidsai_public_repos/cucim/cpp/cmake/deps/boost-header-only.cmake | #
# Copyright (c) 2021, NVIDIA CORPORATION.
# 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 t... | 0 |
rapidsai_public_repos/cucim/cpp/cmake | rapidsai_public_repos/cucim/cpp/cmake/deps/pybind11.cmake | #
# Copyright (c) 2020, NVIDIA CORPORATION.
# 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 t... | 0 |
rapidsai_public_repos/cucim/cpp/cmake | rapidsai_public_repos/cucim/cpp/cmake/deps/nvtx3.cmake | #
# Copyright (c) 2021, NVIDIA CORPORATION.
# 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 t... | 0 |
rapidsai_public_repos/cucim/cpp/cmake | rapidsai_public_repos/cucim/cpp/cmake/deps/libcuckoo.cmake | # Apache License, Version 2.0
# Copyright 2021 NVIDIA Corporation
#
# 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 app... | 0 |
rapidsai_public_repos/cucim/cpp/cmake | rapidsai_public_repos/cucim/cpp/cmake/deps/libcuckoo.patch | diff --git a/libcuckoo/cuckoohash_map.hh b/libcuckoo/cuckoohash_map.hh
index 88f1f43..a36c273 100644
--- a/libcuckoo/cuckoohash_map.hh
+++ b/libcuckoo/cuckoohash_map.hh
@@ -24,6 +24,10 @@
#include <utility>
#include <vector>
+// [cuCIM patch] Include boost interprocess vector/list.
+#include <boost/interprocess/cont... | 0 |
rapidsai_public_repos/cucim/cpp | rapidsai_public_repos/cucim/cpp/src/cuimage.cpp | /*
* Copyright (c) 2020-2022, NVIDIA CORPORATION.
*
* 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... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/util/file.cpp | /*
* Copyright (c) 2021, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/util/platform.cpp | /*
* Copyright (c) 2021, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/config/config.cpp | /*
* Copyright (c) 2021, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/cache/image_cache_manager.cpp | /*
* Copyright (c) 2021, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/cache/image_cache_shared_memory.h | /*
* Copyright (c) 2021, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/cache/image_cache_per_process.h | /*
* Copyright (c) 2021, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/cache/image_cache.cpp | /*
* Apache License, Version 2.0
* Copyright 2021 NVIDIA Corporation
*
* 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 re... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/cache/image_cache_per_process.cpp | /*
* Apache License, Version 2.0
* Copyright 2021 NVIDIA Corporation
*
* 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 re... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/cache/image_cache_config.cpp | /*
* Copyright (c) 2021, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/cache/cache_type.cpp | /*
* Copyright (c) 2021, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/cache/image_cache_empty.h | /*
* Copyright (c) 2021, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/cache/image_cache_empty.cpp | /*
* Apache License, Version 2.0
* Copyright 2021 NVIDIA Corporation
*
* 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 re... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/cache/image_cache_shared_memory.cpp | /*
* Apache License, Version 2.0
* Copyright 2021 NVIDIA Corporation
*
* 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 re... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/logger/timer.cpp | /*
* Copyright (c) 2020, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/logger/logger.cpp | /*
* Copyright (c) 2020, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/core/cucim_framework.h | /*
* Copyright (c) 2020-2021, NVIDIA CORPORATION.
*
* 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... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/core/plugin_manager.h | /*
* Copyright (c) 2020, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/core/cucim_framework.cpp | /*
* Copyright (c) 2020-2021, NVIDIA CORPORATION.
*
* 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... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/core/plugin_manager.cpp | /*
* Copyright (c) 2020, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/core/framework.cpp | /*
* Copyright (c) 2020-2021, NVIDIA CORPORATION.
*
* 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... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/core/version.inl | /*
* Copyright (c) 2020, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/core/cucim_plugin.h | /*
* Copyright (c) 2020, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/core/cucim_plugin.cpp | /*
* Copyright (c) 2020-2021, NVIDIA CORPORATION.
*
* 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... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/profiler/profiler.cpp | /*
* Apache License, Version 2.0
* Copyright 2021 NVIDIA Corporation
*
* 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 re... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/profiler/profiler_config.cpp | /*
* Copyright (c) 2021, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/filesystem/file_handle.cpp | /*
* Copyright (c) 2021-2022, NVIDIA CORPORATION.
*
* 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... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/filesystem/cufile_driver.cpp | /*
* Copyright (c) 2020-2022, NVIDIA CORPORATION.
*
* 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... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/concurrent/threadpool.cpp | /*
* Copyright (c) 2021, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/memory/memory_manager.cpp | /*
* Copyright (c) 2020-2021, NVIDIA CORPORATION.
*
* 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... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/loader/thread_batch_data_loader.cpp | /*
* Apache License, Version 2.0
* Copyright 2021-2023 NVIDIA Corporation
*
* 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
*
* Unle... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/loader/batch_data_processor.cpp | /*
* Apache License, Version 2.0
* Copyright 2021 NVIDIA Corporation
*
* 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 re... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/plugin/plugin_config.cpp | /*
* Copyright (c) 2021, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/plugin/image_format.cpp | /*
* Copyright (c) 2020-2021, NVIDIA CORPORATION.
*
* 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... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/codec/base64.cpp | /*
* Copyright (c) 2021, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/io/device_type.cpp | /*
* Copyright (c) 2021, NVIDIA CORPORATION.
*
* 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 ... | 0 |
rapidsai_public_repos/cucim/cpp/src | rapidsai_public_repos/cucim/cpp/src/io/device.cpp | /*
* Copyright (c) 2020-2021, NVIDIA CORPORATION.
*
* 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... | 0 |
rapidsai_public_repos/cucim/cpp/src/io | rapidsai_public_repos/cucim/cpp/src/io/format/image_format.cpp | /*
* Copyright (c) 2020-2021, NVIDIA CORPORATION.
*
* 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... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/notebooks/vesselness_example.ipynb | from time import time
import numpy as np
from skimage import data
from skimage import color
from skimage.filters import meijering, sato, frangi, hessian
import matplotlib.pyplot as plt
def identity(image, **kwargs):
"""Return the original image, ignoring any kwargs."""
return image
retina = data.retina()[2... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/notebooks/Working_with_Albumentation.ipynb | #!conda install -c conda-forge matplotlib albumentations
# or
#!pip install matplotlib albumentationsINPUT_PATH = 'input/image2.tif'from cucim import CuImage
img = CuImage(INPUT_PATH)try:
import matplotlib
except ImportError:
raise ImportError("This example requires 'matplotlib' library")from matplotlib impo... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/notebooks/Working_with_DALI.ipynb | #!conda install -c rapidsai -c conda-forge cucim cudatoolkit=11.0 matplotlib
#!pip install --extra-index-url https://developer.download.nvidia.com/compute/redist --upgrade nvidia-dali-cuda110
# or
#!pip install cucim scipy scikit-image cupy-cuda110 matplotlib
# Assume that CUDA Toolkit 11.0 is available on the systse... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/notebooks/gabor_example.ipynb | import time
import cupy as cp
import matplotlib.pyplot as plt
import numpy as np
from skimage import data
durations = {}
for use_gpu in (False, True):
if use_gpu:
from cupyx.scipy import ndimage as ndi
from cucim.skimage.util import img_as_float32
from cucim.skimage.filters import gabor_k... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/notebooks/Supporting_Aperio_SVS_Format.ipynb | DATA_PATH_LIST = []
import json
import wget
from pathlib import Path
data_url = "https://openslide.cs.cmu.edu/download/openslide-testdata"
if not Path("index.json").exists():
wget.download(f"{data_url}/index.json")
with open("index.json") as fp:
data_index = json.load(fp)
Path("Aperio").mkdir(parents=True, ... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/notebooks/Multi-thread_and_Multi-process_Tests.ipynb | #!conda install -c conda-forge openslide
# or
#!apt-get install --yes --fix-missing --no-install-recommends libopenslide0
#!pip install openslide-pythonfrom contextlib import ContextDecorator
from time import perf_counter
class Timer(ContextDecorator):
def __init__(self, message):
self.message = message
... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/notebooks/random_walker_example.ipynb | import time
import cupy as cp
import numpy as np
import matplotlib.pyplot as plt
durations = {}
for use_gpu in (False, True):
length = 1500
blob_size_fraction = 0.025
if use_gpu:
from cucim import skimage
from cucim.skimage.exposure import rescale_intensity
from cucim.skimage.segm... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/notebooks/Accessing_File_with_GDS.ipynb | #!conda install -c pytorch -c conda-forge pytorch==1.7.1 torchvision==0.8.2 torchaudio==0.7.2 cudatoolkit=11.0
# or
#!pip install cupy-cuda110
#!pip install torch==1.7.1+cu110 torchvision==0.8.2+cu110 torchaudio==0.7.2 -f https://download.pytorch.org/whl/torch_stable.htmlimport os
from cucim.clara.filesystem import C... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/notebooks/Basic_Usage.ipynb | #!conda install -c conda-forge pillow
# or
# !pip install pillow
# !pip install numpy scipy scikit-image cupy-cuda110 # for cucim dependency (assuming that CUDA 11.0 is used for CuPy)from cucim import CuImage
img = CuImage("input/image.tif")import json
print(img.is_loaded) # True if ima... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/notebooks/Using_Cache.ipynb | from cucim import CuImage
cache = CuImage.cache()
print(f' type: {cache.type}({int(cache.type)})')
print(f'memory_size: {cache.memory_size}/{cache.memory_capacity}')
print(f'free_memory: {cache.free_memory}')
print(f' size: {cache.size}/{cache.capacity}')
print(f' hit_count: {cache.hit_count}')
print(f' ... | 0 |
rapidsai_public_repos/cucim/notebooks | rapidsai_public_repos/cucim/notebooks/input/README.md |
# Test Dataset
TUPAC-TR-488.svs and TUPAC-TR-467.svs are breast cancer cases from the dataset
of Tumor Proliferation Assessment Challenge 2016 (TUPAC16 | MICCAI Grand Challenge) which are publicly
available through [The Cancer Genome Atlas (TCGA)](https://www.cancer.gov/about-nci/organization/ccg/research/structural-... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/docker/Dockerfile-cmake | #
# Copyright (c) 2020-2021, NVIDIA CORPORATION.
# 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 agr... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/docker/Dockerfile-claratrain | #
# Copyright (c) 2020, NVIDIA CORPORATION.
# 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 t... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/docker/requirements-jupyter.txt | openslide-python==1.1.2
tifffile>=2022.7.28
itk==5.1.2
dask[array,delayed,distributed]==2021.2.0
dask-cuda==0.17.0
zarr==2.6.1
fsspec==0.8.5
numpy==1.19.5
opencv-contrib-python==4.5.1.48
imagecodecs>=2021.6.8
cupy-cuda110==8.4.0
jupyterlab==3.0.7
dask_labextension==5.0.0
cmake>=3.18
--extra-index-url https://developer.... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/docker/Dockerfile-jupyter-gds-dev | #
# Copyright (c) 2020-2021, NVIDIA CORPORATION.
# 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 agr... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/docker/Dockerfile-jupyter-dev | #
# Copyright (c) 2020-2021, NVIDIA CORPORATION.
# 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 agr... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/docker/cufile.json | {
// NOTE : Application can override custom configuration via export CUFILE_ENV_PATH_JSON=<filepath>
// e.g : export CUFILE_ENV_PATH_JSON="/home/<xxx>/cufile.json"
"logging": {
// log directory, if not enabled will create log file under current working directory
... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/docker/Dockerfile-jupyter | #
# Copyright (c) 2020-2021, NVIDIA CORPORATION.
# 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 agr... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/docker/requirements-claratrain.txt | openslide-python==1.1.2
tifffile>=2022.7.28
itk==5.1.2
dask[array,delayed,distributed]==2021.2.0
dask-cuda==0.17.0
zarr==2.6.1
fsspec==0.8.5
numpy # 1.17.3 already exists in the image
opencv-contrib-python==4.5.1.48
imagecodecs>=2021.6.8
| 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/docker/requirements-jupyter-dev.txt | openslide-python==1.1.2
tifffile>=2022.7.28
itk==5.1.2
dask[array,delayed,distributed]==2021.2.0
dask-cuda==0.17.0
zarr==2.6.1
fsspec==0.8.5
numpy==1.19.5
opencv-contrib-python==4.5.1.48
imagecodecs>=2021.6.8
cupy-cuda110==8.4.0
jupyterlab==3.0.7
dask_labextension==5.0.0
cmake>=3.18
--extra-index-url https://developer.... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/docker/Dockerfile-jupyter-gds | #
# Copyright (c) 2020-2021, NVIDIA CORPORATION.
# 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 agr... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/.idea/misc.xml | <?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="CMakeWorkspace" PROJECT_DIR="$PROJECT_DIR$" />
<component name="JavaScriptSettings">
<option name="languageLevel" value="ES6" />
</component>
</project>
| 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/.idea/cucim.iml | <?xml version="1.0" encoding="UTF-8"?>
<module classpath="CMake" type="CPP_MODULE" version="4" />
| 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/.idea/vcs.xml | <?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="VcsDirectoryMappings">
<mapping directory="$PROJECT_DIR$" vcs="Git" />
</component>
</project>
| 0 |
rapidsai_public_repos/cucim/.idea | rapidsai_public_repos/cucim/.idea/codeStyles/codeStyleConfig.xml | <component name="ProjectCodeStyleConfiguration">
<state>
<option name="USE_PER_PROJECT_SETTINGS" value="true" />
</state>
</component>
| 0 |
rapidsai_public_repos/cucim/.idea | rapidsai_public_repos/cucim/.idea/codeStyles/Project.xml | <component name="ProjectCodeStyleConfiguration">
<code_scheme name="Project" version="173">
<clangFormatSettings>
<option name="ENABLED" value="true" />
</clangFormatSettings>
</code_scheme>
</component>
| 0 |
rapidsai_public_repos/cucim/.idea/fileTemplates | rapidsai_public_repos/cucim/.idea/fileTemplates/includes/NVIDIA_CMAKE_HEADER.cmake | #
# Copyright (c) $YEAR, NVIDIA CORPORATION.
# 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 ... | 0 |
rapidsai_public_repos/cucim/.idea/fileTemplates | rapidsai_public_repos/cucim/.idea/fileTemplates/includes/NVIDIA_C_HEADER.h | /*
* Copyright (c) $YEAR, NVIDIA CORPORATION.
*
* 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... | 0 |
rapidsai_public_repos/cucim/.idea/fileTemplates | rapidsai_public_repos/cucim/.idea/fileTemplates/internal/CMakeLists.txt.cmake | #parse("NVIDIA_CMAKE_HEADER.cmake")
| 0 |
rapidsai_public_repos/cucim/.idea/fileTemplates | rapidsai_public_repos/cucim/.idea/fileTemplates/internal/C Header File.h | #parse("NVIDIA_C_HEADER.h")
#[[#ifndef]]# ${INCLUDE_GUARD}
#[[#define]]# ${INCLUDE_GUARD}
#[[#endif]]# //${INCLUDE_GUARD}
| 0 |
rapidsai_public_repos/cucim/.idea/fileTemplates | rapidsai_public_repos/cucim/.idea/fileTemplates/internal/C++ Class.cc | #parse("NVIDIA_C_HEADER.h")
#[[#include]]# "${HEADER_FILENAME}"
| 0 |
rapidsai_public_repos/cucim/.idea/fileTemplates | rapidsai_public_repos/cucim/.idea/fileTemplates/internal/C Source File.c | #parse("NVIDIA_C_HEADER.h")
#if (${HEADER_FILENAME})
#[[#include]]# "${HEADER_FILENAME}"
#end
| 0 |
rapidsai_public_repos/cucim/.idea/fileTemplates | rapidsai_public_repos/cucim/.idea/fileTemplates/internal/C++ Class Header.h | #parse("NVIDIA_C_HEADER.h")
#[[#ifndef]]# ${INCLUDE_GUARD}
#[[#define]]# ${INCLUDE_GUARD}
${NAMESPACES_OPEN}
class ${NAME} {
};
${NAMESPACES_CLOSE}
#[[#endif]]# //${INCLUDE_GUARD}
| 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/docs/requirement.txt | nbsphinx
recommonmark
sphinx
pydata-sphinx-theme
numpydoc
ipython
| 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/docs/references.css | /* Fix references to not look like parameters */
dl.citation > dt.label {
display: unset !important;
float: left !important;
border: unset !important;
background: unset !important;
padding: unset !important;
margin: unset !important;
font-size: unset !important;
line-height: unset !important;
padding-... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/docs/README.md | # Building Documentation
A basic python environment with packages listed in `./requirement.txt` is
enough to build the docs.
## Get additional dependency
```bash
pip install -r requirement.txt
```
## Run makefile:
```bash
make html
```
Outputs to `build/html/index.html`
| 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/docs/make.bat | @ECHO OFF
pushd %~dp0
REM Command file for Sphinx documentation
if "%SPHINXBUILD%" == "" (
set SPHINXBUILD=sphinx-build
)
set SOURCEDIR=source
set BUILDDIR=build
set SPHINXPROJ=cuImage
if "%1" == "" goto help
%SPHINXBUILD% >NUL 2>NUL
if errorlevel 9009 (
echo.
echo.The 'sphinx-build' command was not found. Make... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/docs/Makefile | # Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
SPHINXPROJ = cuCIM
SOURCEDIR = source
BUILDDIR = build
# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURC... | 0 |
rapidsai_public_repos/cucim/docs | rapidsai_public_repos/cucim/docs/adr/README.md | # Architecture Decision Record
Documents in this folder follow the concept from [this blog - Why Write ADRs?](https://github.blog/2020-08-13-why-write-adrs/).
Please refer to https://github.com/joelparkerhenderson/architecture_decision_record for examples.
## ADR file name conventions
- The name starts with three-... | 0 |
rapidsai_public_repos/cucim/docs | rapidsai_public_repos/cucim/docs/adr/example.md | # 001 - Choose Programming languages
Note: this example is from https://github.com/joelparkerhenderson/architecture_decision_record/blob/master/examples/programming-languages.md#related-decisions
Contents:
* [Summary](#summary)
* [Issue](#issue)
* [Decision](#decision)
* [Status](#status)
* [Details](#details)... | 0 |
rapidsai_public_repos/cucim/docs | rapidsai_public_repos/cucim/docs/source/conf.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Copyright (c) 2018, NVIDIA CORPORATION.
#
# pygdf documentation build configuration file, created by
# sphinx-quickstart on Wed May 3 10:59:22 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible con... | 0 |
rapidsai_public_repos/cucim/docs | rapidsai_public_repos/cucim/docs/source/api.rst | ~~~~~~~~~~~~~~~~~~~~~~
cuCIM API Reference
~~~~~~~~~~~~~~~~~~~~~~
Clara Submodules
================
.. automodule:: cucim.clara
:members:
:undoc-members:
cache
-----
.. automodule:: cucim.clara.cache
:members:
:undoc-members:
filesystem
----------
.. automodule:: cucim.clara.filesystem
:member... | 0 |
rapidsai_public_repos/cucim/docs | rapidsai_public_repos/cucim/docs/source/index.rst |
Welcome to cuCIM's documentation!
====================================
cuCIM (Compute Unified Device Architecture Clara IMage) is an open-source, accelerated computer vision and image processing software library for multidimensional images used in biomedical, geospatial, material and life science, and remote sensing u... | 0 |
rapidsai_public_repos/cucim/docs/source | rapidsai_public_repos/cucim/docs/source/ext/doi_role.py | # From scikit-image:
# https://github.com/scikit-image/scikit-image/blob/16e0b87b8cb1abc4c78ebf6cd013dadc90810f39/doc/ext/doi_role.py
# -*- coding: utf-8 -*-
"""
doilinks
~~~~~~~~~~~~~~~~~~~
Extension to add links to DOIs. With this extension you can use e.g.
:doi:`10.1016/S0022-2836(05)80360-2` in your... | 0 |
rapidsai_public_repos/cucim/experiments | rapidsai_public_repos/cucim/experiments/Using_Cache/benchmark.py | #
# Copyright (c) 2021, NVIDIA CORPORATION.
# 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 t... | 0 |
rapidsai_public_repos/cucim/experiments | rapidsai_public_repos/cucim/experiments/Supporting_Aperio_SVS_Format/benchmark.py | #
# Copyright (c) 2021, NVIDIA CORPORATION.
# 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 t... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/ci/test_python.sh | #!/bin/bash
# Copyright (c) 2022-2023, NVIDIA CORPORATION.
# Common setup steps shared by Python test jobs
set -euo pipefail
. /opt/conda/etc/profile.d/conda.sh
rapids-logger "Generate Python testing dependencies"
rapids-dependency-file-generator \
--output conda \
--file_key test_python \
--matrix "cuda=${RA... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/ci/build_python.sh | #!/bin/bash
# Copyright (c) 2022, NVIDIA CORPORATION.
set -euo pipefail
source rapids-env-update
export CMAKE_GENERATOR=Ninja
rapids-print-env
package_name="cucim"
package_dir="python/cucim"
package_src_dir="${package_dir}/src/${package_name}"
version=$(rapids-generate-version)
commit=$(git rev-parse HEAD)
echo... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/ci/build_wheel.sh | #!/bin/bash
# Copyright (c) 2023, NVIDIA CORPORATION.
set -euo pipefail
package_name="cucim"
package_dir="python/cucim"
package_src_dir="${package_dir}/src/${package_name}"
CMAKE_BUILD_TYPE="release"
source rapids-configure-sccache
source rapids-date-string
version=$(rapids-generate-version)
commit=$(git rev-parse... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/ci/check_style.sh | #!/bin/bash
# Copyright (c) 2020-2022, NVIDIA CORPORATION.
set -euo pipefail
rapids-logger "Create checks conda environment"
. /opt/conda/etc/profile.d/conda.sh
rapids-dependency-file-generator \
--output conda \
--file_key checks \
--matrix "cuda=${RAPIDS_CUDA_VERSION%.*};arch=$(arch);py=${RAPIDS_PY_VERSION}"... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/ci/test_wheel.sh | #!/bin/bash
# Copyright (c) 2023, NVIDIA CORPORATION.
set -eou pipefail
RAPIDS_PY_CUDA_SUFFIX="$(rapids-wheel-ctk-name-gen ${RAPIDS_CUDA_VERSION})"
RAPIDS_PY_WHEEL_NAME="cucim_${RAPIDS_PY_CUDA_SUFFIX}" rapids-download-wheels-from-s3 ./dist
# echo to expand wildcard before adding `[extra]` requires for pip
python -m ... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/ci/wheel_smoke_test.py | import cupy as cp
import cucim
import cucim.skimage
if __name__ == "__main__":
# verify that all top-level modules are available
assert cucim.is_available("clara")
assert cucim.is_available("core")
assert cucim.is_available("skimage")
# generate a synthetic image and apply a filter
img = cuc... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/ci/build_cpp.sh | #!/bin/bash
# Copyright (c) 2022, NVIDIA CORPORATION.
set -euo pipefail
source rapids-env-update
export CMAKE_GENERATOR=Ninja
rapids-print-env
version=$(rapids-generate-version)
rapids-logger "Begin cpp build"
RAPIDS_PACKAGE_VERSION=${version} rapids-conda-retry mambabuild conda/recipes/libcucim
rapids-upload-c... | 0 |
rapidsai_public_repos/cucim | rapidsai_public_repos/cucim/ci/build_docs.sh | #!/bin/bash
set -euo pipefail
rapids-logger "Create test conda environment"
. /opt/conda/etc/profile.d/conda.sh
rapids-dependency-file-generator \
--output conda \
--file_key docs \
--matrix "cuda=${RAPIDS_CUDA_VERSION%.*};arch=$(arch);py=${RAPIDS_PY_VERSION}" | tee env.yaml
rapids-mamba-retry env creat... | 0 |
rapidsai_public_repos/cucim/ci | rapidsai_public_repos/cucim/ci/release/update-version.sh | #!/bin/bash
#########################
# cuCIM Version Updater #
#########################
## Usage
# bash update-version.sh <new_version>
# Format is YY.MM.PP - no leading 'v' or trailing 'a'
NEXT_FULL_TAG=$1
# Get current version
CURRENT_TAG=$(git tag --merged HEAD | grep -xE '^v.*' | sort --version-sort | tail -n... | 0 |
rapidsai_public_repos/cucim/examples | rapidsai_public_repos/cucim/examples/python/distance_transform_edt_demo.py | import math
import cupy as cp
import numpy as np
try:
import colorcet
import matplotlib.pyplot as plt
except ImportError as e:
print("This demo requires the matplotlib and colorcet packages.")
raise (e)
from skimage import data
from cucim.core.operations.morphology import distance_transform_edt
from... | 0 |
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