From f7b98459fac8e26d352f69696a5c0754e9191a23 Mon Sep 17 00:00:00 2001
From: Karol Gotkowski <karol.gotkowski@dkfz-heidelberg.de>
Date: Wed, 10 Jul 2024 17:41:00 +0200
Subject: [PATCH] feat: Added blosc2 read & write support

---
 pyproject.toml                |  2 +-
 src/napari_blosc2/_reader.py  | 11 ++++-------
 src/napari_blosc2/_writer.py  |  3 ++-
 src/napari_blosc2/napari.yaml |  4 ++--
 4 files changed, 9 insertions(+), 11 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 03f3ca6..5aa1915 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,7 +25,7 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "numpy",
+    "blosc2",
 ]
 
 [project.optional-dependencies]
diff --git a/src/napari_blosc2/_reader.py b/src/napari_blosc2/_reader.py
index 8d93ff9..fdb727d 100644
--- a/src/napari_blosc2/_reader.py
+++ b/src/napari_blosc2/_reader.py
@@ -5,6 +5,7 @@
 implement multiple readers or even other plugin contributions. see:
 https://napari.org/stable/plugins/guides.html?#readers
 """
+import blosc2
 import numpy as np
 
 
@@ -29,7 +30,7 @@ def napari_get_reader(path):
         path = path[0]
 
     # if we know we cannot read the file, we immediately return None.
-    if not path.endswith(".npy"):
+    if not path.endswith(".b2nd"):
         return None
 
     # otherwise we return the *function* that can read ``path``.
@@ -58,12 +59,8 @@ def reader_function(path):
         layer. Both "meta", and "layer_type" are optional. napari will
         default to layer_type=="image" if not provided
     """
-    # handle both a string and a list of strings
-    paths = [path] if isinstance(path, str) else path
-    # load all files into array
-    arrays = [np.load(_path) for _path in paths]
-    # stack arrays into single array
-    data = np.squeeze(np.stack(arrays))
+    data = blosc2.open(urlpath=path, mode='r', mmap_mode='r')
+    data = data[...]
 
     # optional kwargs for the corresponding viewer.add_* method
     add_kwargs = {}
diff --git a/src/napari_blosc2/_writer.py b/src/napari_blosc2/_writer.py
index e67fcc9..94b53e3 100644
--- a/src/napari_blosc2/_writer.py
+++ b/src/napari_blosc2/_writer.py
@@ -9,6 +9,7 @@
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, Any, List, Sequence, Tuple, Union
+import blosc2
 
 if TYPE_CHECKING:
     DataType = Union[Any, Sequence[Any]]
@@ -33,7 +34,7 @@ def write_single_image(path: str, data: Any, meta: dict) -> List[str]:
     [path] : A list containing the string path to the saved file.
     """
 
-    # implement your writer logic here ...
+    blosc2.asarray(array=data, urlpath=path, meta=meta)
 
     # return path to any file(s) that were successfully written
     return [path]
diff --git a/src/napari_blosc2/napari.yaml b/src/napari_blosc2/napari.yaml
index 45f5467..c339e55 100644
--- a/src/napari_blosc2/napari.yaml
+++ b/src/napari_blosc2/napari.yaml
@@ -18,11 +18,11 @@ contributions:
   readers:
     - command: napari-blosc2.get_reader
       accepts_directories: false
-      filename_patterns: ['*.npy']
+      filename_patterns: ['*.b2nd']
   writers:
     - command: napari-blosc2.write_multiple
       layer_types: ['image*','labels*']
       filename_extensions: []
     - command: napari-blosc2.write_single_image
       layer_types: ['image']
-      filename_extensions: ['.npy']
+      filename_extensions: ['.b2nd']