Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add some examples. #21

Merged
merged 8 commits into from
Dec 19, 2024
Merged

Add some examples. #21

Show file tree
Hide file tree
Changes from 2 commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
47c5d0c
Add some examples.
aliddell Dec 4, 2024
a008027
Move Python tests to their own directories.
aliddell Dec 4, 2024
16e9b61
Merge remote-tracking branch 'upstream/main' into examples
aliddell Dec 17, 2024
6d877d8
Respond to PR comments
aliddell Dec 17, 2024
0a94681
Add multiscale examples.
aliddell Dec 17, 2024
c83afb6
Merge remote-tracking branch 'upstream/main' into examples
aliddell Dec 19, 2024
0510ba8
Include <string> in vectorized.file.writer.hh.
aliddell Dec 19, 2024
1ab2061
Merge remote-tracking branch 'upstream/main' into examples
aliddell Dec 19, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 7 additions & 0 deletions CMakeLists.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)

option(BUILD_PYTHON "Build Python bindings" OFF)
option(BUILD_EXAMPLES "Build examples" OFF)

if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
include(CTest)
Expand All @@ -39,4 +40,10 @@ else ()
message(STATUS "Skipping Python bindings")
endif ()

if (${BUILD_EXAMPLES})
add_subdirectory(examples)
else ()
message(STATUS "Skipping examples")
endif ()

include(CPack)
34 changes: 34 additions & 0 deletions examples/CMakeLists.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
set(project acquire-zarr)

set(examples
zarrv2-raw-filesystem
zarrv2-compressed-s3
zarrv3-compressed-filesystem
zarrv3-raw-s3
)

foreach (name ${examples})
set(tgt "${project}-${name}")
add_executable(${tgt} ${name}.c)
set_target_properties(${tgt} PROPERTIES
MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>"
)
target_include_directories(${tgt} PRIVATE
${PROJECT_SOURCE_DIR}/include
)
target_link_libraries(${tgt} PRIVATE
acquire-logger
acquire-zarr
nlohmann_json::nlohmann_json
miniocpp::miniocpp
)

add_test(NAME example-${tgt} COMMAND ${tgt})

set(test_labels "examples")
if (name MATCHES ".*s3.*")
list(APPEND test_labels "s3")
endif ()

set_tests_properties(example-${tgt} PROPERTIES LABELS "${test_labels}")
endforeach ()
78 changes: 78 additions & 0 deletions examples/python/zarrv2-compressed-s3.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,78 @@
# Zarr V2 with ZSTD compression to S3
import numpy as np
from acquire_zarr import (
StreamSettings, ZarrStream, Dimension, DimensionType, ZarrVersion,
DataType, Compressor, CompressionCodec, CompressionSettings, S3Settings
)


def main():
settings = StreamSettings()

# Configure S3
settings.s3 = S3Settings(
endpoint="http://localhost:9000",
bucket_name="mybucket",
access_key_id="myaccesskey",
secret_access_key="mysecretkey"
)

# Configure compression
settings.compression = CompressionSettings(
compressor=Compressor.BLOSC1,
codec=CompressionCodec.BLOSC_ZSTD,
level=1,
shuffle=1,
)

# Configure 4D array (t, c, y, x)
settings.dimensions.extend([
Dimension(
name="t",
kind=DimensionType.TIME,
array_size_px=0, # Unlimited
chunk_size_px=32,
shard_size_chunks=1,
),
Dimension(
name="c",
kind=DimensionType.CHANNEL,
array_size_px=3,
chunk_size_px=3,
shard_size_chunks=1,
),
Dimension(
name="y",
kind=DimensionType.SPACE,
array_size_px=48,
chunk_size_px=16,
shard_size_chunks=1,
),
Dimension(
name="x",
kind=DimensionType.SPACE,
array_size_px=64,
chunk_size_px=32,
shard_size_chunks=1,
),
])

settings.store_path = "output_v2_s3.zarr"
settings.version = ZarrVersion.V2
settings.data_type = DataType.INT32

# Create stream
stream = ZarrStream(settings)

# Create and write sample data
for i in range(10):
data = np.random.randint(
0, 65535,
(32, 3, 48, 64), # Shape matches chunk sizes
dtype=np.int32
)
stream.append(data)


if __name__ == "__main__":
main()
55 changes: 55 additions & 0 deletions examples/python/zarrv2-raw-filesystem.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,55 @@
# Basic Zarr V2 to filesystem
import numpy as np
from acquire_zarr import (
StreamSettings, ZarrStream, Dimension, DimensionType, ZarrVersion, DataType
)


def main():
# Configure stream settings
settings = StreamSettings()

# Configure dimensions (t, y, x)
settings.dimensions.extend([
Dimension(
name="t",
kind=DimensionType.TIME,
array_size_px=0, # Unlimited
chunk_size_px=32,
shard_size_chunks=1,
),
Dimension(
name="y",
kind=DimensionType.SPACE,
array_size_px=48,
chunk_size_px=16,
shard_size_chunks=1,
),
Dimension(
name="x",
kind=DimensionType.SPACE,
array_size_px=64,
chunk_size_px=32,
shard_size_chunks=1,
),
])

settings.store_path = "output_v2.zarr"
settings.version = ZarrVersion.V2
settings.data_type = DataType.INT32

# Create stream
stream = ZarrStream(settings)

# Create and write sample data
for i in range(10):
jeskesen marked this conversation as resolved.
Show resolved Hide resolved
data = np.random.randint(
0, 65535,
(32, 48, 64), # Shape matches chunk size for time dimension
dtype=np.int32
)
stream.append(data)


if __name__ == "__main__":
main()
76 changes: 76 additions & 0 deletions examples/python/zarrv3-compressed-filesystem.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,76 @@
# Zarr V3 with LZ4 compression to filesystem
import numpy as np
from acquire_zarr import (
StreamSettings, ZarrStream, Dimension, DimensionType, ZarrVersion,
DataType, Compressor, CompressionCodec, CompressionSettings
)


def main():
settings = StreamSettings()

# Configure compression
settings.compression = CompressionSettings(
compressor=Compressor.BLOSC1,
codec=CompressionCodec.BLOSC_LZ4,
level=1,
shuffle=1,
)

# Configure 5D array (t, c, z, y, x)
settings.dimensions.extend([
Dimension(
name="t",
kind=DimensionType.TIME,
array_size_px=10,
chunk_size_px=5,
shard_size_chunks=2,
),
Dimension(
name="c",
kind=DimensionType.CHANNEL,
array_size_px=8,
chunk_size_px=4,
shard_size_chunks=2,
),
Dimension(
name="z",
kind=DimensionType.SPACE,
array_size_px=6,
chunk_size_px=2,
shard_size_chunks=1,
),
Dimension(
name="y",
kind=DimensionType.SPACE,
array_size_px=48,
chunk_size_px=16,
shard_size_chunks=1,
),
Dimension(
name="x",
kind=DimensionType.SPACE,
array_size_px=64,
chunk_size_px=16,
shard_size_chunks=2,
),
])

settings.store_path = "output_v3_compressed.zarr"
settings.version = ZarrVersion.V3
settings.data_type = DataType.UINT16

# Create stream
stream = ZarrStream(settings)

# Create and write sample data
data = np.random.randint(
0, 65535,
(5, 4, 2, 48, 64), # Shape matches chunk sizes
dtype=np.uint16
)
stream.append(data)


if __name__ == "__main__":
main()
69 changes: 69 additions & 0 deletions examples/python/zarrv3-raw-s3.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,69 @@
# zarr_v3_s3_raw.py
import numpy as np
from acquire_zarr import (
StreamSettings, ZarrStream, Dimension, DimensionType, ZarrVersion,
DataType, S3Settings
)


def main():
settings = StreamSettings()

# Configure S3
settings.s3 = S3Settings(
endpoint="http://localhost:9000",
bucket_name="mybucket",
access_key_id="myaccesskey",
secret_access_key="mysecretkey"
)

# Configure 4D array (t, z, y, x)
settings.dimensions.extend([
Dimension(
name="t",
kind=DimensionType.TIME,
array_size_px=0, # Unlimited
chunk_size_px=5,
shard_size_chunks=2,
),
Dimension(
name="z",
kind=DimensionType.SPACE,
array_size_px=10,
chunk_size_px=2,
shard_size_chunks=1,
),
Dimension(
name="y",
kind=DimensionType.SPACE,
array_size_px=48,
chunk_size_px=16,
shard_size_chunks=1,
),
Dimension(
name="x",
kind=DimensionType.SPACE,
array_size_px=64,
chunk_size_px=16,
shard_size_chunks=2,
),
])

settings.store_path = "output_v3_s3.zarr"
settings.version = ZarrVersion.V3
settings.data_type = DataType.UINT16

# Create stream
stream = ZarrStream(settings)

# Create and write sample data
data = np.random.randint(
0, 65535,
(5, 2, 48, 64), # Shape matches chunk sizes
dtype=np.uint16
)
stream.append(data)


if __name__ == "__main__":
main()
Loading
Loading