Add Jupyter notebook for SVS Support (#147)

- Update `notebooks/Welcome.ipynb`
- Add `notebooks/Supporting_Aperio_SVS_Format.ipynb` to show loading Aperio SVS images

Authors:
  - Gigon Bae (https://github.com/gigony)

Approvers:
  - https://github.com/jakirkham

URL: #147

experiments/Supporting_Aperio_SVS_Format/benchmark.py

@@ -0,0 +1,232 @@
+#
+# 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 to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import concurrent.futures
+from contextlib import ContextDecorator
+from datetime import datetime
+from itertools import repeat
+from time import perf_counter
+
+import numpy as np
+from cucim import CuImage
+from cucim.clara.filesystem import discard_page_cache
+from openslide import OpenSlide
+
+
+class Timer(ContextDecorator):
+    def __init__(self, message):
+        self.message = message
+        self.end = None
+
+    def elapsed_time(self):
+        self.end = perf_counter()
+        return self.end - self.start
+
+    def __enter__(self):
+        self.start = perf_counter()
+        return self
+
+    def __exit__(self, exc_type, exc, exc_tb):
+        if not self.end:
+            self.elapsed_time()
+        print("{} : {}".format(self.message, self.end - self.start))
+
+
+def load_tile_openslide(slide, start_loc, patch_size):
+    _ = slide.read_region(start_loc, 0, [patch_size, patch_size])
+
+
+def load_tile_openslide_chunk(inp_file, start_loc_list, patch_size):
+    with OpenSlide(inp_file) as slide:
+        for start_loc in start_loc_list:
+            region = slide.read_region(start_loc, 0, [patch_size, patch_size])
+
+
+def load_tile_cucim(slide, start_loc, patch_size):
+    _ = slide.read_region(start_loc, [patch_size, patch_size], 0)
+
+
+def load_tile_cucim_chunk(inp_file, start_loc_list, patch_size):
+    try:
+        slide = CuImage(inp_file)
+        for start_loc in start_loc_list:
+            region = slide.read_region(start_loc, [patch_size, patch_size], 0)
+    except Exception as e:
+        print(e)
+
+
+def load_tile_openslide_chunk_mp(inp_file, start_loc_list, patch_size):
+    with OpenSlide(inp_file) as slide:
+        for start_loc in start_loc_list:
+            region = slide.read_region(start_loc, 0, [patch_size, patch_size])
+
+
+def load_tile_cucim_chunk_mp(inp_file, start_loc_list, patch_size):
+    slide = CuImage(inp_file)
+    for start_loc in start_loc_list:
+        region = slide.read_region(start_loc, [patch_size, patch_size], 0)
+
+
+def experiment_thread(cache_strategy, input_file, num_threads, start_location, patch_size):
+    import psutil
+    print("  ", psutil.virtual_memory())
+    for num_workers in (1, 3, 6, 9, 12):  # range(1, num_threads + 1):
+        openslide_time = 1
+        cucim_time = 1
+        rasterio_time = 1
+
+        #discard_page_cache(input_file)
+        with OpenSlide(input_file) as slide:
+            width, height = slide.dimensions
+
+            start_loc_data = [(sx, sy)
+                              for sy in range(start_location, height, patch_size)
+                              for sx in range(start_location, width, patch_size)]
+            chunk_size = len(start_loc_data) // num_workers
+            start_loc_list_iter = [start_loc_data[i:i+chunk_size]
+                                   for i in range(0, len(start_loc_data), chunk_size)]
+            with Timer("  Thread elapsed time (OpenSlide)") as timer:
+                with concurrent.futures.ThreadPoolExecutor(
+                    max_workers=num_workers
+                ) as executor:
+                    executor.map(
+                        load_tile_openslide_chunk,
+                        repeat(input_file),
+                        start_loc_list_iter,
+                        repeat(patch_size)
+                    )
+                openslide_time = timer.elapsed_time()
+        print("  ", psutil.virtual_memory())
+
+        cache_size = psutil.virtual_memory().available // 1024 // 1024 // 20
+        cache = CuImage.cache(
+            cache_strategy, memory_capacity=cache_size, record_stat=True)
+        cucim_time = 0
+        #discard_page_cache(input_file)
+        slide = CuImage(input_file)
+        start_loc_data = [(sx, sy)
+                          for sy in range(start_location, height, patch_size)
+                          for sx in range(start_location, width, patch_size)]
+        chunk_size = len(start_loc_data) // num_workers
+        start_loc_list_iter = [start_loc_data[i:i+chunk_size]
+                               for i in range(0, len(start_loc_data), chunk_size)]
+        with Timer("  Thread elapsed time (cuCIM)") as timer:
+            with concurrent.futures.ThreadPoolExecutor(
+                max_workers=num_workers
+            ) as executor:
+                executor.map(
+                    load_tile_cucim_chunk,
+                    repeat(input_file),
+                    start_loc_list_iter,
+                    repeat(patch_size)
+                )
+            cucim_time = timer.elapsed_time()
+        print(f"  hit: {cache.hit_count}   miss: {cache.miss_count}")
+        print("  ", psutil.virtual_memory())
+
+        output_text = f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S')},thread,{cache_strategy},{input_file},{start_location},{patch_size},{num_workers},{openslide_time},{cucim_time},{rasterio_time},{openslide_time / cucim_time},{rasterio_time / cucim_time},{cache_size},{cache.hit_count},{cache.miss_count}\n"
+        with open("experiment.txt", "a+") as f:
+            f.write(output_text)
+        print(output_text)
+
+
+def experiment_process(cache_strategy, input_file, num_processes, start_location, patch_size):
+    import psutil
+    print("  ", psutil.virtual_memory())
+    for num_workers in (1, 3, 6, 9, 12):  # range(1, num_processes + 1):
+        openslide_time = 1
+        cucim_time = 1
+        rasterio_time = 1
+
+        #discard_page_cache(input_file)
+        with OpenSlide(input_file) as slide:
+            width, height = slide.dimensions
+
+            start_loc_data = [(sx, sy)
+                              for sy in range(start_location, height, patch_size)
+                              for sx in range(start_location, width, patch_size)]
+            chunk_size = len(start_loc_data) // num_workers
+            start_loc_list_iter = [start_loc_data[i:i+chunk_size]
+                                   for i in range(0, len(start_loc_data), chunk_size)]
+
+            with Timer("  Process elapsed time (OpenSlide)") as timer:
+                with concurrent.futures.ProcessPoolExecutor(
+                    max_workers=num_workers
+                ) as executor:
+                    executor.map(
+                        load_tile_openslide_chunk_mp,
+                        repeat(input_file),
+                        start_loc_list_iter,
+                        repeat(patch_size)
+                    )
+                openslide_time = timer.elapsed_time()
+        print("  ", psutil.virtual_memory())
+
+        cache_size = psutil.virtual_memory().available // 1024 // 1024 // 20
+        if cache_strategy == "shared_memory":
+            cache_size = cache_size * num_workers
+        cache = CuImage.cache(
+            cache_strategy, memory_capacity=cache_size, record_stat=True)
+        cucim_time = 0
+        #discard_page_cache(input_file)
+        slide = CuImage(input_file)
+        start_loc_data = [(sx, sy)
+                          for sy in range(start_location, height, patch_size)
+                          for sx in range(start_location, width, patch_size)]
+        chunk_size = len(start_loc_data) // num_workers
+        start_loc_list_iter = [start_loc_data[i:i+chunk_size]
+                               for i in range(0, len(start_loc_data), chunk_size)]
+
+        with Timer("  Process elapsed time (cuCIM)") as timer:
+            with concurrent.futures.ProcessPoolExecutor(
+                max_workers=num_workers
+            ) as executor:
+                executor.map(
+                    load_tile_cucim_chunk_mp,
+                    repeat(input_file),
+                    start_loc_list_iter,
+                    repeat(patch_size)
+                )
+            cucim_time = timer.elapsed_time()
+        print("  ", psutil.virtual_memory())
+
+        rasterio_time = 0
+        start_loc_data = [(sx, sy)
+                          for sy in range(start_location, height, patch_size)
+                          for sx in range(start_location, width, patch_size)]
+        chunk_size = len(start_loc_data) // num_workers
+        start_loc_list_iter = [start_loc_data[i:i+chunk_size]
+                               for i in range(0, len(start_loc_data), chunk_size)]
+
+        print("  ", psutil.virtual_memory())
+        output_text = f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S')},process,{cache_strategy},{input_file},{start_location},{patch_size},{num_workers},{openslide_time},{cucim_time},{rasterio_time},{openslide_time / cucim_time},{rasterio_time / cucim_time},{cache_size},{cache.hit_count},{cache.miss_count}\n"
+        with open("experiment.txt", "a+") as f:
+            f.write(output_text)
+        print(output_text)
+
+
+for i in range(10):
+    experiment_thread(
+        "per_process", "notebooks/input/TUPAC-TR-488.svs", 12, 120, 240)
+    experiment_thread(
+        "per_process", "notebooks/input/JP2K-33003-2.svs", 12, 128, 256)
+    experiment_thread(
+        "per_process", "notebooks/input/CMU-1-JP2K-33005.svs", 12, 120, 240)
+    experiment_process(
+        "per_process", "notebooks/input/TUPAC-TR-488.svs", 12, 120, 240)
+    experiment_process(
+        "per_process", "notebooks/input/JP2K-33003-2.svs", 12, 128, 256)
+    experiment_process(
+        "per_process", "notebooks/input/CMU-1-JP2K-33005.svs", 12, 120, 240)