From a96611b177bbd2bba52300e8a5b5a5d3f8d62309 Mon Sep 17 00:00:00 2001
From: Felipe <fima@dtu.dk>
Date: Wed, 25 Sep 2024 12:11:18 +0200
Subject: [PATCH] Saving zarr now does not use dask
---
qim3d/io/saving.py | 31 +++++++++++++++++++++++--------
1 file changed, 23 insertions(+), 8 deletions(-)
diff --git a/qim3d/io/saving.py b/qim3d/io/saving.py
index 42f8e29f..dda53eb5 100644
--- a/qim3d/io/saving.py
+++ b/qim3d/io/saving.py
@@ -77,6 +77,7 @@ class DataSaver:
self.compression = kwargs.get("compression", False)
self.basename = kwargs.get("basename", None)
self.sliced_dim = kwargs.get("sliced_dim", 0)
+ self.chunk_shape = kwargs.get("chunk_shape", "auto")
def save_tiff(self, path, data):
"""Save data to a TIFF file to the given path.
@@ -258,7 +259,7 @@ class DataSaver:
ds.save_as(path)
def save_to_zarr(self, path, data):
- """ Saves a Dask array to a Zarr array on disk.
+ """Saves a Dask array to a Zarr array on disk.
Args:
path (str): The path to the Zarr array on disk.
@@ -267,12 +268,18 @@ class DataSaver:
Returns:
zarr.core.Array: The Zarr array saved on disk.
"""
- assert isinstance(data, da.Array), 'data must be a dask array'
- # forces compute when saving to zarr
- da.to_zarr(data, path, compute=True, overwrite=self.replace, compressor=zarr.Blosc(cname='zstd', clevel=3, shuffle=2))
-
-
+ # Old version that is using dask
+
+ # assert isinstance(data, da.Array), 'data must be a dask array'
+
+ # # forces compute when saving to zarr
+ # da.to_zarr(data, path, compute=True, overwrite=self.replace, compressor=zarr.Blosc(cname='zstd', clevel=3, shuffle=2))
+ zarr_array = zarr.open(
+ path, mode="w", shape=data.shape, chunks=self.chunk_shape, dtype=data.dtype
+ )
+ zarr_array[:] = data
+
def save_PIL(self, path, data):
"""Save data to a PIL file to the given path.
@@ -378,7 +385,7 @@ class DataSaver:
return self.save_dicom(path, data)
elif path.endswith((".zarr")):
return self.save_to_zarr(path, data)
- elif path.endswith((".jpeg",".jpg", ".png")):
+ elif path.endswith((".jpeg", ".jpg", ".png")):
return self.save_PIL(path, data)
else:
raise ValueError("Unsupported file format")
@@ -396,7 +403,14 @@ class DataSaver:
def save(
- path, data, replace=False, compression=False, basename=None, sliced_dim=0, **kwargs
+ path,
+ data,
+ replace=False,
+ compression=False,
+ basename=None,
+ sliced_dim=0,
+ chunk_shape="auto",
+ **kwargs,
):
"""Save data to a specified file path.
@@ -427,5 +441,6 @@ def save(
compression=compression,
basename=basename,
sliced_dim=sliced_dim,
+ chunk_shape=chunk_shape,
**kwargs,
).save(path, data)
--
GitLab