From 39d362a80b9945a93c969c95db54437fc1d1cfd2 Mon Sep 17 00:00:00 2001
From: Christian Kento Rasmussen <christian.kento@gmail.com>
Date: Mon, 13 Jan 2025 13:26:58 +0100
Subject: [PATCH] Add basename and contains arguments to convert function for
TIFF stack processing
---
qim3d/cli/__init__.py | 20 +++++++++++++++++++-
qim3d/io/_convert.py | 29 ++++++++++++++++++++++++-----
2 files changed, 43 insertions(+), 6 deletions(-)
diff --git a/qim3d/cli/__init__.py b/qim3d/cli/__init__.py
index cec79d57..1bf9a658 100644
--- a/qim3d/cli/__init__.py
+++ b/qim3d/cli/__init__.py
@@ -124,6 +124,20 @@ def main():
default=(64, 64, 64),
help="Chunk size for the zarr file. Defaults to (64, 64, 64).",
)
+ convert_parser.add_argument(
+ "--basename",
+ type=str,
+ metavar="basename",
+ default="tiff_stack",
+ help="The base name for the saving of a tiff stack.",
+ )
+ convert_parser.add_argument(
+ "--contains",
+ type=str,
+ metavar="contains",
+ default=None,
+ help="Specify common part of file names for tiff stack.",
+ )
args = parser.parse_args()
if args.subcommand == "gui":
@@ -193,7 +207,11 @@ def main():
elif args.subcommand == "convert":
- qim3d.io.convert(args.input_path, args.output_path, chunk_shape=args.chunks)
+ qim3d.io.convert(args.input_path,
+ args.output_path,
+ chunk_shape=args.chunks,
+ basename=args.basename,
+ contains=args.contains)
elif args.subcommand is None:
print(QIM_TITLE)
diff --git a/qim3d/io/_convert.py b/qim3d/io/_convert.py
index b7124a52..c02776bf 100644
--- a/qim3d/io/_convert.py
+++ b/qim3d/io/_convert.py
@@ -21,6 +21,8 @@ class Convert:
chunk_shape (tuple, optional): chunk size for the zarr file. Defaults to (64, 64, 64).
"""
self.chunk_shape = kwargs.get("chunk_shape", (64, 64, 64))
+ self.base_name = kwargs.get("basename", "tiff_stack")
+ self.contains = kwargs.get("contains", None)
def convert(self, input_path: str, output_path: str):
def get_file_extension(file_path):
@@ -115,7 +117,7 @@ class Convert:
z = zarr.open(zarr_path)
save(tif_path, z)
- def convert_zarr_to_tiff_stack(self, zarr_path, tiff_stack_path):
+ def convert_zarr_to_tiff_stack(self, zarr_path: str, tiff_stack_path: str):
"""Convert a zarr file to a tiff stack
Args:
@@ -128,7 +130,7 @@ class Convert:
z = zarr.open(zarr_path)
save(tiff_stack_path, z, basename=self.base_name)
- def convert_tiff_stack_to_zarr(self, tiff_stack_path, zarr_path):
+ def convert_tiff_stack_to_zarr(self, tiff_stack_path: str, zarr_path: str):
"""Convert a tiff stack to a zarr file
Args:
@@ -140,7 +142,23 @@ class Convert:
"""
# ! tiff stack memmap is stored as slices on disk and not as a single file, making assignments to blocks slow.
vol = load(tiff_stack_path, virtual_stack=True, contains=self.contains)
- return self._save_zarr(zarr_path, vol)
+ z = zarr.open(
+ zarr_path, mode="w", shape=vol.shape, chunks=self.chunk_shape, dtype=vol.dtype
+ )
+ chunk_shape = tuple((s + c - 1) // c for s, c in zip(z.shape, z.chunks))
+ # ! Fastest way is z[:] = vol[:], but does not have a progress bar
+ 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
def convert_nifti_to_zarr(self, nifti_path: str, zarr_path: str) -> zarr.core.Array:
"""Convert a nifti file to a zarr file
@@ -185,13 +203,14 @@ class Convert:
save(nifti_path, z, compression=compression)
-def convert(input_path: str, output_path: str, chunk_shape: tuple = (64, 64, 64)) -> None:
+def convert(input_path: str, output_path: str, chunk_shape: tuple = (64, 64, 64), basename: str = 'tiff_stack', contains: str = None) -> None:
"""Convert a file to another format without loading the entire file into memory
Args:
input_path (str): path to the input file
output_path (str): path to the output file
chunk_shape (tuple, optional): chunk size for the zarr file. Defaults to (64, 64, 64).
+ basename (str, optional): base name for the saving of a tiff stack. Defaults to 'tiff_stack'.
"""
- converter = Convert(chunk_shape=chunk_shape)
+ converter = Convert(chunk_shape=chunk_shape, basename=basename, contains=contains)
converter.convert(input_path, output_path)
--
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