Feat smartspim zarr compression

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "aind-smartspim-data-transformation"
 description = "Generated from aind-library-template"
 license = {text = "MIT"}
-requires-python = ">=3.7"
+requires-python = ">=3.9"
 authors = [
     {name = "Allen Institute for Neural Dynamics"}
 ]
@@ -17,6 +17,17 @@ readme = "README.md"
 dynamic = ["version"]
 
 dependencies = [
+    'aind-data-transformation>=0.0.18',
+    'zarr==2.18.2',
+    'numcodecs==0.11.0',
+    'dask-image==2024.5.3',
+    'xarray_multiscale==1.1.0',
+    'bokeh==2.4.2',
+    'pims==0.6.1',
+    'dask[distributed]==2024.5.1',
+    'ome-zarr==0.8.2',
+    'imagecodecs[all]==2023.3.16',
+    'natsort==8.4.0',
 ]
 
 [project.optional-dependencies]

scripts/singularity_build.def

@@ -0,0 +1,25 @@
+Bootstrap: docker
+From: python:3.10-bullseye
+
+%setup
+    # Copy project directory into container
+    cp -R . ${SINGULARITY_ROOTFS}/aind-smartspim-data-transformation
+
+%post
+    # Installing dask mpi
+    wget https://www.mpich.org/static/downloads/3.2/mpich-3.2.tar.gz
+    tar xfz mpich-3.2.tar.gz
+    rm mpich-3.2.tar.gz
+    mkdir mpich-build
+    cd mpich-build
+    ../mpich-3.2/configure --disable-fortran 2>&1 | tee c.txt
+    make 2>&1 | tee m.txt
+    make install 2>&1 | tee mi.txt
+    cd ..
+
+    cd ${SINGULARITY_ROOTFS}/aind-smartspim-data-transformation
+    pip install . --no-cache-dir
+    rm -rf ${SINGULARITY_ROOTFS}/aind-smartspim-data-transformation
+
+    pip install mpi4py --no-cache-dir
+    pip install dask_mpi

src/aind_smartspim_data_transformation/__init__.py

@@ -1,2 +1,3 @@
 """Init package"""
-__version__ = "0.0.0"
+
+__version__ = "0.0.1"

src/aind_smartspim_data_transformation/dask_utils.py

@@ -0,0 +1,121 @@
+import logging
+import os
+import socket
+from enum import Enum
+from typing import Optional, Tuple
+
+import distributed
+import requests
+from distributed import Client, LocalCluster
+
+try:
+    from dask_mpi import initialize
+
+    DASK_MPI_INSTALLED = True
+except ImportError:
+    DASK_MPI_INSTALLED = False
+
+LOGGER = logging.getLogger(__name__)
+
+
+class Deployment(Enum):
+    LOCAL = "local"
+    SLURM = "slurm"
+
+
+def log_dashboard_address(
+    client: distributed.Client, login_node_address: str = "hpc-login"
+) -> None:
+    """
+    Logs the terminal command required to access the Dask dashboard
+
+    Args:
+        client: the Client instance
+        login_node_address: the address of the cluster login node
+    """
+    host = client.run_on_scheduler(socket.gethostname)
+    port = client.scheduler_info()["services"]["dashboard"]
+    user = os.getenv("USER")
+    LOGGER.info(
+        f"To access the dashboard, run the following in a terminal: ssh -L {port}:{host}:{port} {user}@"
+        f"{login_node_address} "
+    )
+
+
+def get_deployment() -> str:
+    if os.getenv("SLURM_JOBID") is None:
+        deployment = Deployment.LOCAL.value
+    else:
+        # we're running on the Allen HPC
+        deployment = Deployment.SLURM.value
+    return deployment
+
+
+def get_client(
+    deployment: str = Deployment.LOCAL.value,
+    worker_options: Optional[dict] = None,
+    n_workers: int = 1,
+    processes=True,
+) -> Tuple[distributed.Client, int]:
+    """
+    Create a distributed Client
+
+    Args:
+        deployment: the type of deployment. Either "local" or "slurm"
+        worker_options: a dictionary of options to pass to the worker class
+        n_workers: the number of workers (only applies to "local" deployment)
+
+    Returns:
+        the distributed Client and number of workers
+    """
+    if deployment == Deployment.SLURM.value:
+        if not DASK_MPI_INSTALLED:
+            raise ImportError(
+                "dask-mpi must be installed to use the SLURM deployment"
+            )
+        if worker_options is None:
+            worker_options = {}
+        slurm_job_id = os.getenv("SLURM_JOBID")
+        if slurm_job_id is None:
+            raise Exception(
+                "SLURM_JOBID environment variable is not set. Are you running under SLURM?"
+            )
+        initialize(
+            nthreads=int(os.getenv("SLURM_CPUS_PER_TASK", 1)),
+            local_directory=f"/scratch/fast/{slurm_job_id}",
+            worker_class="distributed.nanny.Nanny",
+            worker_options=worker_options,
+        )
+        client = Client()
+        log_dashboard_address(client)
+        n_workers = int(os.getenv("SLURM_NTASKS"))
+    elif deployment == Deployment.LOCAL.value:
+        client = Client(
+            LocalCluster(
+                n_workers=n_workers, processes=processes, threads_per_worker=1
+            )
+        )
+    else:
+        raise NotImplementedError
+    return client, n_workers
+
+
+def cancel_slurm_job(
+    job_id: str, api_url: str, headers: dict
+) -> requests.Response:
+    """
+    Attempt to release resources and cancel the job
+
+    Args:
+        job_id: the SLURM job ID
+        api_url: the URL of the SLURM REST API. E.g., "http://myhost:80/api/slurm/v0.0.36"
+
+    Raises:
+        HTTPError: if the request to cancel the job fails
+    """
+    # Attempt to release resources and cancel the job
+    # Workaround for https://github.com/dask/dask-mpi/issues/87
+    endpoint = f"{api_url}/job/{job_id}"
+    response = requests.delete(endpoint, headers=headers)
+
+    return response

src/aind_smartspim_data_transformation/io/__init__.py

@@ -0,0 +1,7 @@
+"""
+Input and output operations
+"""
+
+# flake8: noqa: F403
+from ._io import *
+from .utils import *