feat(starrynight: modules): add sbs preprocess cli

Author: leoank

starrynight/src/starrynight/cli/main.py

@@ -7,6 +7,7 @@
 from starrynight.cli.illum import illum
 from starrynight.cli.index import index
 from starrynight.cli.inv import inventory
+from starrynight.cli.preprocess import preprocess
 from starrynight.cli.presegcheck import presegcheck
 from starrynight.cli.segcheck import segcheck
 
@@ -24,3 +25,4 @@ def main() -> None:
 main.add_command(presegcheck)
 main.add_command(segcheck)
 main.add_command(align)
+main.add_command(preprocess)

starrynight/src/starrynight/cli/preprocess.py

@@ -0,0 +1,92 @@
+"""Preprocess module cli wrapper."""
+
+import click
+from cloudpathlib import AnyPath
+
+from starrynight.algorithms.preprocess import (
+    gen_preprocess_cppipe_by_batch_plate,
+    gen_preprocess_load_data_by_batch_plate,
+)
+
+
+@click.command(name="loaddata")
+@click.option("-i", "--index", required=True)
+@click.option("-o", "--out", required=True)
+@click.option("-c", "--corr_images", required=True)
+@click.option("-a", "--align_images", required=True)
+@click.option("-n", "--nuclei", required=True)
+@click.option("-m", "--path_mask", default=None)
+def gen_preprocess_load_data(
+    index: str,
+    out: str,
+    corr_images: str,
+    align_images: str,
+    nuclei: str,
+    path_mask: str | None,
+) -> None:
+    """Generate preprocess loaddata file.
+
+    Parameters
+    ----------
+    index : str | None
+        Index path. Can be local or a cloud path.
+    out : str
+        Output dir. Can be local or a cloud path.
+    corr_images : str
+        Corrected images dir. Can be local or a cloud path.
+    align_images : str
+        Aligned images dir. Can be local or a cloud path.
+    nuclei : str
+        Channel to use for nuceli segmentation
+    path_mask : str | Mask
+        Path prefix mask to use. Can be local or a cloud path.
+
+    """
+    gen_preprocess_load_data_by_batch_plate(
+        AnyPath(index),
+        AnyPath(out),
+        path_mask,
+        nuclei,
+        AnyPath(corr_images),
+        AnyPath(align_images),
+    )
+
+
+@click.command(name="cppipe")
+@click.option("-l", "--loaddata", required=True)
+@click.option("-o", "--out", required=True)
+@click.option("-w", "--workspace", required=True)
+@click.option("-b", "--barcode", required=True)
+@click.option("-n", "--nuclei", required=True)
+def gen_preprocess_cppipe(
+    loaddata: str, out: str, workspace: str, barcode: str, nuclei: str
+) -> None:
+    """Generate preprocess cppipe file.
+
+    Parameters
+    ----------
+    loaddata : str
+        Loaddata dir path. Can be local or a cloud path.
+    out : str
+        Path to output directory. Can be local or a cloud path.
+    workspace : str
+        Path to workspace directory. Can be local or a cloud path.
+    barcode : str
+        Path to barcode csv. Can be local or a cloud path.
+    nuclei : str
+        Channel to use for nuceli segmentation
+
+    """
+    gen_preprocess_cppipe_by_batch_plate(
+        AnyPath(loaddata), AnyPath(out), AnyPath(workspace), AnyPath(barcode), nuclei
+    )
+
+
+@click.group()
+def preprocess() -> None:
+    """Preprocess commands."""
+    pass
+
+
+preprocess.add_command(gen_preprocess_load_data)
+preprocess.add_command(gen_preprocess_cppipe)