Merge branch 'threshold_for_v1' into 'main'

Threshold for v1

See merge request !157

docs/doc/visualization/viz.md

@@ -24,6 +24,7 @@ The `qim3d` library aims to provide easy ways to explore and get insights from v
             - colormaps
             - fade_mask
             - line_profile
+            - threshold
             
 ::: qim3d.viz.colormaps
     options:

qim3d/io/__init__.py

 # from ._sync import Sync # this will be added back after future development
-from ._convert import convert
-from ._downloader import Downloader
 from ._loading import load, load_mesh
-from ._ome_zarr import export_ome_zarr, import_ome_zarr
+from ._downloader import Downloader
 from ._saving import save, save_mesh
+from ._convert import convert
+from ._ome_zarr import export_ome_zarr, import_ome_zarr

qim3d/io/_convert.py

@@ -7,9 +7,10 @@ import numpy as np
 import tifffile as tiff
 import zarr
 import zarr.core
+import qim3d
+
 from tqdm import tqdm
 
-from qim3d.io import save
 from qim3d.utils._misc import stringify_path
 
 
@@ -121,7 +122,7 @@ class Convert:
 
         """
         z = zarr.open(zarr_path)
-        save(tif_path, z)
+        qim3d.io.save(tif_path, z)
 
     def convert_nifti_to_zarr(self, nifti_path: str, zarr_path: str) -> zarr.core.Array:
         """
@@ -173,7 +174,7 @@ class Convert:
 
         """
         z = zarr.open(zarr_path)
-        save(nifti_path, z, compression=compression)
+        qim3d.io.save(nifti_path, z, compression=compression)
 
 
 def convert(

qim3d/viz/__init__.py

@@ -4,12 +4,11 @@ from ._data_exploration import (
     chunks,
     fade_mask,
     histogram,
+    line_profile,
     slicer,
     slicer_orthogonal,
     slices_grid,
-    chunks,
-    histogram,
-    line_profile
+    threshold,
 )
 from ._detection import circles
 from ._k3d import mesh, volumetric