Generate a multiscale, chunked, multi-dimensional spatial image data structure that can be serialized to OME-NGFF.
Project description
multiscale-spatial-image
Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.
Each scale is a scientific Python Xarray spatial-image Dataset, organized into nodes of an Xarray Datatree.
Installation
pip install multiscale_spatial_image
Usage
import numpy as np
from spatial_image import to_spatial_image
from multiscale_spatial_image import to_multiscale
import zarr
# Image pixels
array = np.random.randint(0, 256, size=(128,128), dtype=np.uint8)
image = to_spatial_image(array)
print(image)
An Xarray spatial-image DataArray. Spatial metadata can also be passed during construction.
<xarray.SpatialImage 'image' (y: 128, x: 128)>
array([[114, 47, 215, ..., 245, 14, 175],
[ 94, 186, 112, ..., 42, 96, 30],
[133, 170, 193, ..., 176, 47, 8],
...,
[202, 218, 237, ..., 19, 108, 135],
[ 99, 94, 207, ..., 233, 83, 112],
[157, 110, 186, ..., 142, 153, 42]], dtype=uint8)
Coordinates:
* y (y) float64 0.0 1.0 2.0 3.0 4.0 ... 123.0 124.0 125.0 126.0 127.0
* x (x) float64 0.0 1.0 2.0 3.0 4.0 ... 123.0 124.0 125.0 126.0 127.0
# Create multiscale pyramid, downscaling by a factor of 2, then 4
multiscale = to_multiscale(image, [2, 4])
print(multiscale)
A chunked Dask Array MultiscaleSpatialImage Xarray Datatree.
DataTree('multiscales', parent=None)
├── DataTree('scale0')
│ Dimensions: (y: 128, x: 128)
│ Coordinates:
│ * y (y) float64 0.0 1.0 2.0 3.0 4.0 ... 123.0 124.0 125.0 126.0 127.0
│ * x (x) float64 0.0 1.0 2.0 3.0 4.0 ... 123.0 124.0 125.0 126.0 127.0
│ Data variables:
│ image (y, x) uint8 dask.array<chunksize=(128, 128), meta=np.ndarray>
├── DataTree('scale1')
│ Dimensions: (y: 64, x: 64)
│ Coordinates:
│ * y (y) float64 0.5 2.5 4.5 6.5 8.5 ... 118.5 120.5 122.5 124.5 126.5
│ * x (x) float64 0.5 2.5 4.5 6.5 8.5 ... 118.5 120.5 122.5 124.5 126.5
│ Data variables:
│ image (y, x) uint8 dask.array<chunksize=(64, 64), meta=np.ndarray>
└── DataTree('scale2')
Dimensions: (y: 16, x: 16)
Coordinates:
* y (y) float64 3.5 11.5 19.5 27.5 35.5 ... 91.5 99.5 107.5 115.5 123.5
* x (x) float64 3.5 11.5 19.5 27.5 35.5 ... 91.5 99.5 107.5 115.5 123.5
Data variables:
image (y, x) uint8 dask.array<chunksize=(16, 16), meta=np.ndarray>
Store as an Open Microscopy Environment-Next Generation File Format (OME-NGFF) / netCDF Zarr store.
It is highly recommended to use dimension_separator='/'
in the construction of the Zarr stores.
store = zarr.storage.DirectoryStore('multiscale.zarr', dimension_separator='/')
multiscale.to_zarr(store)
Note: The API is under development, and it may change until 1.0.0 is released. We mean it :-).
Examples
- Hello MultiscaleSpatialImage World!
- Convert itk.Image
- Convert imageio ImageResource
- Convert pyimagej Dataset
Development
Contributions are welcome and appreciated.
To run the test suite:
git clone https://github.com/spatial-image/multiscale-spatial-image
cd multiscale-spatial-image
pip install -e ".[test]"
pytest
# Notebook tests
pytest --nbmake --nbmake-timeout=3000 examples/*ipynb
To add new or update testing data, such as a new baseline for this block:
dataset_name = "cthead1"
image = input_images[dataset_name]
baseline_name = "2_4/XARRAY_COARSEN"
multiscale = to_multiscale(image, [2, 4], method=Methods.XARRAY_COARSEN)
verify_against_baseline(test_data_dir, dataset_name, baseline_name, multiscale)
Add a store_new_image
call in your test block:
dataset_name = "cthead1"
image = input_images[dataset_name]
baseline_name = "2_4/XARRAY_COARSEN"
multiscale = to_multiscale(image, [2, 4], method=Methods.XARRAY_COARSEN)
store_new_image(web3_data, multiscale, dataset_name, baseline_name)
verify_against_baseline(web3_data, dataset_name, baseline_name, multiscale)
Run the tests to generate the output. Remove the store_new_image
call.
Then, create a tarball of the current testing data
cd test/data
tar cvf ../data.tar *
gzip -9 ../data.tar
python3 -c 'import pooch; print(pooch.file_hash("../data.tar.gz"))'
Update the test_data_sha256
variable in the test/test_multiscale_spatial_image.py file.
Upload the data to web3.storage.
nd update the test_data_ipfs_cid
Content Identifier (CID) variable, which is available in the web3.storage web page interface.
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