Implement seedee lib for serialisation

setup.py

@@ -17,7 +17,7 @@ VERSION = '0.0.4'
 # What packages are required for this module to be executed?
 REQUIRED = [
     'attrs', 'numpy', 'asapo_consumer', 'asapo_producer', 'scikit-image',
-    'h5py', 'hdf5plugin'
+    'h5py', 'hdf5plugin', 'seedee'
 ]
 
 # What packages are optional?

src/AsapoWorker/data_handler.py

@@ -2,11 +2,15 @@ import io
 import numpy as np
 import hdf5plugin
 import h5py
+import seedee
 import zlib
 from skimage.io import imread
 
 
+
 def get_image(data, metadata):
+    if "_data_type" in metadata["meta"]:
+        return seedee.deserialize(data, metadata["meta"]["_data_type"])
     if metadata["name"] == 'liveimage':
         image = zlib.decompress(data)
         if metadata['meta']['frame_depth'] == 24:
@@ -41,6 +45,12 @@ def get_image(data, metadata):
     return image
 
 
+def serialize_image(array, compression=None):
+    if not compression:
+        compression = seedee.COMPRESSION_BITSHUFFLE
+    return seedee.serialize(images, compression)
+
+
 def serialize_ndarray(array):
     """
     Serialize ndarray into compressed h5 in-memory file
@@ -74,3 +84,4 @@ def get_filename_parts(metadata):
     base, sep, index_and_ext = name.rpartition("-")
     index, ext = index_and_ext.split(".")
     return base, int(index), ext
+

[Tim Schoof]

I would name this _data_format. _data_type sounds more like float vs integer or array vs curve to me.

[Mikhail Karnevskiy]

Done.

[Tim Schoof]

seedee can serialize any ndarray, not just images. I would make a breaking change to serialize_ndarray.

[Mikhail Karnevskiy]

Done.

[Tim Schoof]

You could directly use seedee.COMPRESSION_BITSHUFFLE as the default argument. Checking for None is only necessary for mutable default arguments.

[Mikhail Karnevskiy]

Done.