Add LSM modules

.dockerignore

@@ -0,0 +1,53 @@
+# Git
+.git
+.gitignore
+.github
+
+# Python
+__pycache__
+*.py[cod]
+*$py.class
+*.so
+.Python
+*.egg-info
+dist
+build
+.venv
+venv
+env
+ENV
+
+# Testing
+.pytest_cache
+.coverage
+htmlcov
+.tox
+.mypy_cache
+.ruff_cache
+
+# Documentation
+site
+docs/requirements.txt
+
+# IDE
+.vscode
+.idea
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Project specific
+scripts/*.ipynb
+scripts/*.nii
+scripts/*.tiff
+scripts/*.jpeg
+scripts/*.yaml
+tests/data
+
+# Poetry
+poetry.lock.bak
+

.github/workflows/ci.yml

@@ -37,4 +37,4 @@ jobs:
         run: poetry install --with dev --extras all
       - name: Run the automated tests
         run: poetry run pytest -v
-        working-directory: ./tests
+        working-directory: tests

.github/workflows/docker-build.yml

@@ -0,0 +1,66 @@
+name: Build and Push Docker Image
+
+on:
+  push:
+    branches:
+      - main
+      - master
+    tags:
+      - 'v*'
+  pull_request:
+    branches:
+      - main
+      - master
+  workflow_dispatch:
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to Container Registry
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=semver,pattern={{major}}
+            type=sha,prefix={{branch}}-,enable=${{ github.event_name != 'pull_request' }}
+            type=sha,enable=${{ github.event_name == 'pull_request' }}
+            type=raw,value=latest,enable={{is_default_branch}}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+

Dockerfile

@@ -0,0 +1,62 @@
+# ----------------------------------------------------------------------------
+# STAGE 1: Builder
+# Used to install Poetry, compile dependencies, and create the virtual environment.
+# ----------------------------------------------------------------------------
+FROM python:3.11-slim AS builder
+
+# Set working directory
+WORKDIR /app
+
+# Install build dependencies (GCC, etc.)
+# We need these to compile packages, but we don't want them in the final image.
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install Poetry
+RUN pip install poetry==1.8.4
+
+# Configure Poetry to create the venv inside the project folder
+# This makes it easy to copy the whole folder to the next stage
+ENV POETRY_NO_INTERACTION=1 \
+    POETRY_VIRTUALENVS_IN_PROJECT=1 \
+    POETRY_VIRTUALENVS_CREATE=1 \
+    POETRY_CACHE_DIR=/tmp/poetry_cache
+
+# Copy dependency definition files first (for caching)
+COPY pyproject.toml poetry.lock ./
+RUN poetry lock
+# Install dependencies (only the libraries)
+RUN poetry install --no-root --no-dev --extras all && rm -rf $POETRY_CACHE_DIR
+
+# Copy the rest of the application code
+COPY . .
+RUN poetry lock
+# Install the application itself
+#RUN poetry install --no-dev --extras all
+RUN poetry build -f wheel
+RUN ./.venv/bin/pip install dist/*.whl
+# ----------------------------------------------------------------------------
+# STAGE 2: Runtime
+# A fresh, empty image that only contains the Python runtime and our copied venv.
+# ----------------------------------------------------------------------------
+FROM python:3.11-slim AS runtime
+
+WORKDIR /app
+
+# Create a non-root user for security (Best Practice)
+RUN useradd -m -r appuser && chown appuser /app
+USER appuser
+
+# Copy the virtual environment from the builder stage
+# We assume the path structure is identical (/app/.venv)
+COPY --from=builder --chown=appuser:appuser /app/.venv /app/.venv
+
+# Update PATH environment variable
+# This allows us to type 'linc-convert' instead of '/app/.venv/bin/linc-convert'
+ENV PATH="/app/.venv/bin:$PATH"
+LABEL org.opencontainers.image.source=https://github.com/lincbrain/linc-convert
+# Set the entrypoint
+ENTRYPOINT ["linc-convert"]
+# Default command
+CMD ["--help"]

linc_convert/modalities/lsm/__init__.py

@@ -3,8 +3,24 @@
 try:
     import tifffile as _  # noqa: F401
 
-    __all__ = ["cli", "mosaic", "multi_slice", "spool"]
+    __all__ = [
+        "cli",
+        "mosaic",
+        "multi_slice",
+        "spool",
+        "single_volume",
+        "strip",
+        "stitch_strips"
+    ]
 
-    from . import cli, mosaic, multi_slice, spool
+    from . import (
+        cli,
+        mosaic,
+        multi_slice,
+        single_volume,
+        spool,
+        stitch_strips,
+        strip,
+    )
 except ImportError:
     pass

linc_convert/modalities/lsm/mosaic.py

@@ -4,6 +4,7 @@
 Example input files can be found at
 https://lincbrain.org/dandiset/000004/0.240319.1924/files?location=derivatives%2F
 """
+
 import logging
 
 # stdlib

linc_convert/modalities/lsm/multi_slice.py

@@ -4,6 +4,7 @@
 Example input files can be found at
 https://lincbrain.org/dandiset/000010/draft/files?location=sourcedata%2Fderivatives
 """
+
 import logging
 
 # stdlib
@@ -45,7 +46,7 @@ def convert(
 ) -> None:
     """
     Convert a collection of tiff files generated by the LSM pipeline into a Zarr.
-    
+
     Parameters
     ----------
     inp

linc_convert/modalities/lsm/single_volume.py

@@ -0,0 +1,94 @@
+"""Converts TIFF to OME-Zarr or NIfTI-Zarr."""
+
+import logging
+import os
+
+import cyclopts
+import dask.array as da
+import dask_image.imread
+import numpy as np
+
+from linc_convert.modalities.lsm.cli import lsm
+from linc_convert.utils.io.zarr import from_config
+from linc_convert.utils.nifti_header import build_nifti_header
+from linc_convert.utils.unit import to_ome_unit
+from linc_convert.utils.zarr_config import (
+    GeneralConfig,
+    NiftiConfig,
+    ZarrConfig,
+    autoconfig,
+)
+
+logger = logging.getLogger(__name__)
+single_volume = cyclopts.App(name="single_volume", help_format="markdown")
+lsm.command(single_volume)
+
+
+@single_volume.default
+@autoconfig
+def convert(
+    inp: str,
+    *,
+    voxel_size: list[float] = (1, 1, 1),
+    general_config: GeneralConfig = None,
+    zarr_config: ZarrConfig = None,
+    nii_config: NiftiConfig = None,
+) -> None:
+    """
+    Tiff to OME-Zarr.
+
+    Convert tiff files
+    into a pyramidal OME-ZARR (or NIfTI-Zarr) hierarchy.
+
+    Parameters
+    ----------
+    inp
+        Path to the input tiff file
+    voxel_size
+        Voxel size along the X, Y and Z dimensions, in microns.
+    general_config
+        General configuration
+    zarr_config
+        Zarr related configuration
+    nii_config
+        NIfTI header related configuration
+    """
+    general_config.set_default_name(os.path.splitext(inp)[0])
+
+    inp_data = dask_image.imread.imread(inp)
+
+    # Prepare Zarr group
+    zgroup = from_config(general_config.out, zarr_config)
+
+    if not hasattr(inp_data, "dtype"):
+        raise Exception("Input is not a numpy array. This is unexpected.")
+
+    dataset = zgroup.create_array(
+        "0",
+        shape=inp_data.shape,
+        dtype=np.dtype(inp_data.dtype),
+        zarr_config=zarr_config,
+    )
+
+    if dataset.shards:
+        inp_data = da.rechunk(inp_data, dataset.shards)
+    else:
+        inp_data = da.rechunk(inp_data, dataset.chunks)
+
+    da.store(inp_data, dataset)
+    voxel_size = list(map(float, reversed(voxel_size)))
+    # Generate Zarr pyramid and metadata
+    zgroup.generate_pyramid(mode="mean", no_pyramid_axis=zarr_config.no_pyramid_axis)
+    logger.info("Write OME-Zarr multiscale metadata")
+    zgroup.write_ome_metadata(axes=["z", "y", "x"], space_unit=to_ome_unit("um"))
+
+    if nii_config.nii:
+        header = build_nifti_header(
+            zgroup=zgroup,
+            voxel_size_zyx=tuple(voxel_size),
+            unit="micrometer",
+            nii_config=nii_config,
+        )
+        zgroup.write_nifti_header(header)
+
+    logger.info("Conversion complete.")

linc_convert/modalities/lsm/spool.py

@@ -5,6 +5,7 @@
 https://lincbrain.org/dandiset/000010/draft/files?location=sourcedata%2Frawdata
 %2Fmicr%2Fsample18_run10__y10_z01_HR&page=1
 """
+
 import logging
 
 # stdlib
@@ -233,4 +234,3 @@ def convert(
         omz.write_nifti_header(header)
 
     logger.info("Conversion complete.")
-