From 85f3dfaabfa3b43c0cb6845fbdcc4fc68f6d4309 Mon Sep 17 00:00:00 2001
From: Christian Kento Rasmussen <christian.kento@gmail.com>
Date: Thu, 30 May 2024 14:35:21 +0200
Subject: [PATCH] added progress bar to tif to zar convert
---
qim3d/io/convert.py | 11 ++++++++++-
1 file changed, 10 insertions(+), 1 deletion(-)
diff --git a/qim3d/io/convert.py b/qim3d/io/convert.py
index e08629d8..24c41e8c 100644
--- a/qim3d/io/convert.py
+++ b/qim3d/io/convert.py
@@ -1,6 +1,9 @@
+from itertools import product
+
import numpy as np
import tifffile as tiff
import zarr
+from tqdm import tqdm
def convert_tif_to_zarr(tif_path, zarr_path, chunks=(64, 64, 64)):
@@ -16,7 +19,13 @@ def convert_tif_to_zarr(tif_path, zarr_path, chunks=(64, 64, 64)):
"""
vol = tiff.memmap(tif_path)
z = zarr.open(zarr_path, mode='w', shape=vol.shape, chunks=chunks, dtype=vol.dtype)
- z[:] = vol[:]
+ chunk_shape = tuple((s + c - 1) // c for s, c in zip(z.shape, z.chunks))
+ for chunk_indices in tqdm(product(*[range(n) for n in chunk_shape]), total=np.prod(chunk_shape)):
+ slices = tuple(slice(c * i, min(c * (i + 1), s))
+ for s, c, i in zip(z.shape, z.chunks, chunk_indices))
+ temp_data = vol[slices]
+ # The assignment takes 99% of the cpu-time
+ z.blocks[chunk_indices] = temp_data
return z
--
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