From 9bd60d4552d6fdae165e65c25994798f6840bfb7 Mon Sep 17 00:00:00 2001
From: Kaidong Chai <dev@kchai.me>
Date: Wed, 13 Nov 2024 11:28:49 -0500
Subject: [PATCH] Move PSOCT conversion script into modalities

---
 linc_convert/modalities/psoct/__init__.py     |  5 ++
 linc_convert/modalities/psoct/cli.py          |  9 +++
 .../modalities/psoct/placeholder.py           | 32 +++-----
 .../utils.py => linc_convert/utils/unit.py    | 76 -------------------
 4 files changed, 25 insertions(+), 97 deletions(-)
 create mode 100644 linc_convert/modalities/psoct/__init__.py
 create mode 100644 linc_convert/modalities/psoct/cli.py
 rename scripts/oct_mat_to_zarr.py => linc_convert/modalities/psoct/placeholder.py (96%)
 rename scripts/utils.py => linc_convert/utils/unit.py (71%)

diff --git a/linc_convert/modalities/psoct/__init__.py b/linc_convert/modalities/psoct/__init__.py
new file mode 100644
index 00000000..a6d9d6f2
--- /dev/null
+++ b/linc_convert/modalities/psoct/__init__.py
@@ -0,0 +1,5 @@
+"""Dark Field microscopy converters."""
+
+__all__ = ["cli", "multi_slice", "single_slice"]
+
+from . import cli, multi_slice, single_slice
diff --git a/linc_convert/modalities/psoct/cli.py b/linc_convert/modalities/psoct/cli.py
new file mode 100644
index 00000000..12d4c065
--- /dev/null
+++ b/linc_convert/modalities/psoct/cli.py
@@ -0,0 +1,9 @@
+"""Entry-points for Dark Field microscopy converter."""
+
+from cyclopts import App
+
+from linc_convert.cli import main
+
+help = "Converters for PS-OCT .mat files"
+psoct = App(name="psoct", help=help)
+main.command(psoct)
diff --git a/scripts/oct_mat_to_zarr.py b/linc_convert/modalities/psoct/placeholder.py
similarity index 96%
rename from scripts/oct_mat_to_zarr.py
rename to linc_convert/modalities/psoct/placeholder.py
index a2ff53e5..964b4e9f 100644
--- a/scripts/oct_mat_to_zarr.py
+++ b/linc_convert/modalities/psoct/placeholder.py
@@ -1,17 +1,8 @@
 """
-(OCT) Matlab to OME-ZARR
-========================
-
-This script converts Matlab files generated by the MGH in-house OCT pipeline
-into a pyramidal OME-ZARR hierarchy.
-
-dependencies:
-    numpy
-    scipy
-    zarr
-    nibabel
-    cyclopts
+Converts Matlab files generated by the MGH in-house OCT pipeline
+into a OME-ZARR pyramid.
 """
+
 import ast
 import json
 import math
@@ -30,12 +21,14 @@
 import zarr
 from scipy.io import loadmat
 
-from utils import (
-    ceildiv, make_compressor, convert_unit, to_ome_unit, to_nifti_unit,
-    orientation_to_affine, center_affine
-)
+from linc_convert.modalities.psoct.cli import psoct
+from linc_convert.utils.orientation import orientation_to_affine, center_affine
+from linc_convert.utils.math import ceildiv
+from linc_convert.utils.zarr import make_compressor
+from linc_convert.utils.unit import (convert_unit, to_ome_unit, to_nifti_unit)
 
-app = cyclopts.App(help_format="markdown")
+placeholder = cyclopts.App(name="placeholder", help_format="markdown")
+psoct.command(placeholder)
 
 
 def automap(func):
@@ -53,7 +46,7 @@ def wrapper(inp, out=None, **kwargs):
     return wrapper
 
 
-@app.default
+@placeholder.default
 @automap
 def convert(
         inp: List[str],
@@ -435,6 +428,3 @@ def parse_value_unit(string, n=None):
 
     return meta
 
-
-if __name__ == "__main__":
-    app()
diff --git a/scripts/utils.py b/linc_convert/utils/unit.py
similarity index 71%
rename from scripts/utils.py
rename to linc_convert/utils/unit.py
index 88d6ff55..fc276957 100644
--- a/scripts/utils.py
+++ b/linc_convert/utils/unit.py
@@ -1,78 +1,3 @@
-import math
-import numcodecs
-import numpy as np
-
-
-def orientation_ensure_3d(orientation):
-    """
-    Parameters
-    ----------
-    orientation : str
-        Either one of {'coronal', 'axial', 'sagittal'}, or a two- or
-        three-letter permutation of {('R', 'L'), ('A', 'P'), ('S', 'I')}
-
-    Returns
-    -------
-    orientation : str
-        A three-letter permutation of {('R', 'L'), ('A', 'P'), ('S', 'I')}
-    """
-    orientation = {
-        'coronal': 'LI',
-        'axial': 'LP',
-        'sagittal': 'PI',
-    }.get(orientation.lower(), orientation).upper()
-    if len(orientation) == 2:
-        if 'L' not in orientation and 'R' not in orientation:
-            orientation += 'R'
-        if 'P' not in orientation and 'A' not in orientation:
-            orientation += 'A'
-        if 'I' not in orientation and 'S' not in orientation:
-            orientation += 'S'
-    return orientation
-
-
-def orientation_to_affine(orientation, vxw=1, vxh=1, vxd=1):
-    orientation = orientation_ensure_3d(orientation)
-    affine = np.zeros([4, 4])
-    vx = np.asarray([vxw, vxh, vxd])
-    for i in range(3):
-        letter = orientation[i]
-        sign = -1 if letter in 'LPI' else 1
-        letter = {'L': 'R', 'P': 'A', 'I': 'S'}.get(letter, letter)
-        index = list('RAS').index(letter)
-        affine[index, i] = sign * vx[i]
-    return affine
-
-
-def center_affine(affine, shape):
-    if len(shape) == 2:
-        shape = [*shape, 1]
-    shape = np.asarray(shape)
-    affine[:3, -1] = -0.5 * affine[:3, :3] @ (shape - 1)
-    return affine
-
-
-def ceildiv(x, y):
-    return int(math.ceil(x / y))
-
-
-def floordiv(x, y):
-    return int(math.floor(x / y))
-
-
-def make_compressor(name, **prm):
-    if not isinstance(name, str):
-        return name
-    name = name.lower()
-    if name == 'blosc':
-        Compressor = numcodecs.Blosc
-    elif name == 'zlib':
-        Compressor = numcodecs.Zlib
-    else:
-        raise ValueError('Unknown compressor', name)
-    return Compressor(**prm)
-
-
 ome_valid_units = {
     'space': [
         'angstrom',
@@ -178,7 +103,6 @@ def make_compressor(name, **prm):
     for short, long in si_prefix_short2long.items()
 }
 
-
 si_prefix_exponent = {
     'Q': 30,
     'R': 27,