Refactor NGFF module and migrate to Pydantic v2 (#233)

* unify comment format * fix typing and docstring * create ngff sub-package and refactor display util file * refactor ngff meta file * refactor ngff * export transformation model * fix type hint * bump ome-zarr target in docstring * migrate to pydantic v2 * isort * fix validators * remove union type * fix dependency * update docstring * typing improvements * Update iohub/ngff/models.py Co-authored-by: Jordão Bragantini <[email protected]> * fix style * update module docstring to specify their content --------- Co-authored-by: Jordão Bragantini <[email protected]>
czbiohub-sf · Jul 31, 2024 · ee502b2 · ee502b2
1 parent 6edd790
commit ee502b2
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Showing 12 changed files with 290 additions and 268 deletions.
diff --git a/iohub/convert.py b/iohub/convert.py
@@ -10,7 +10,8 @@
 from tqdm.contrib.logging import logging_redirect_tqdm
 
 from iohub._version import version as iohub_version
-from iohub.ngff import Position, TransformationMeta, open_ome_zarr
+from iohub.ngff.models import TransformationMeta
+from iohub.ngff.nodes import Position, open_ome_zarr
 from iohub.reader import MMStack, NDTiffDataset, read_images
 
 __all__ = ["TIFFConverter"]

diff --git a/iohub/ngff/__init__.py b/iohub/ngff/__init__.py
@@ -0,0 +1,4 @@
+from iohub.ngff.models import TransformationMeta
+from iohub.ngff.nodes import Plate, Position, open_ome_zarr
+
+__all__ = ["open_ome_zarr", "Plate", "Position", "TransformationMeta"]
diff --git a/iohub/display_utils.py → iohub/ngff/display.py b/iohub/display_utils.py → iohub/ngff/display.py
@@ -1,9 +1,9 @@
-""" Utility functions for displaying data """
+"""OME-Zarr display settings (OMERO metadata)"""
 
 import numpy as np
 from PIL.ImageColor import colormap
 
-from iohub.ngff_meta import ChannelMeta, WindowDict
+from iohub.ngff.models import ChannelMeta, WindowDict
 
 """ Dictionary with key works and most popular fluorescent probes """
 CHANNEL_COLORS = {
@@ -25,8 +25,10 @@
     # emission around 440 - 460 nmm
     "blue": ["Blue", "DAPI", "BFP", "Hoechst"],
     "red": ["Red"],
-    "yellow": ["Yellow", "Cy3"],  # Emission around 540-570 nm
-    "orange": ["Orange", "Cy5", "Y5"],  # emission around 650-680 nm
+    # Emission around 540-570 nm
+    "yellow": ["Yellow", "Cy3"],
+    # emission around 650-680 nm
+    "orange": ["Orange", "Cy5", "Y5"],
 }
 
 
@@ -49,12 +51,12 @@ def color_to_hex(color: str) -> str:
 
 def channel_display_settings(
     chan_name: str,
-    clim: tuple[float, float, float, float] = None,
+    clim: tuple[float, float, float, float] | None = None,
     first_chan: bool = False,
 ):
-    """This will create a dictionary used for OME-zarr metadata.
-    Allows custom contrast limits and channel.
-    names for display. Defaults everything to grayscale.
+    """This will create a dictionary used for OME-Zarr metadata.
+    Allows custom contrast limits and channel names for display.
+    Defaults everything to grayscale.
 
     Parameters
     ----------
@@ -85,7 +87,7 @@ def channel_display_settings(
         "S3": (-1.0, 1.0, -10.0, -10.0),
         "Other": (0, U16_FMAX, 0.0, U16_FMAX),
     }
-    if not clim:
+    if clim is None:
         if chan_name in channel_settings.keys():
             clim = channel_settings[chan_name]
         else: