From 2fd4fae77a9e9592dc9329313fde37f4288ab1a4 Mon Sep 17 00:00:00 2001
From: s204159 <s204159@student.dtu.dk>
Date: Fri, 28 Jun 2024 11:27:18 +0200
Subject: [PATCH] Conv zarr nifti
---
qim3d/io/convert.py | 97 ++++++++++++++++++++++++++++++++++++---------
qim3d/utils/cli.py | 3 ++
2 files changed, 81 insertions(+), 19 deletions(-)
diff --git a/qim3d/io/convert.py b/qim3d/io/convert.py
index b2ab1e49..f2af9e6b 100644
--- a/qim3d/io/convert.py
+++ b/qim3d/io/convert.py
@@ -2,36 +2,44 @@ import difflib
import os
from itertools import product
+import nibabel as nib
import numpy as np
import tifffile as tiff
import zarr
from tqdm import tqdm
from qim3d.utils.internal_tools import stringify_path
+from qim3d.io.saving import save
class Convert:
-
- def __init__(self,**kwargs):
- """ Utility class to convert files to other formats without loading the entire file into memory
+ def __init__(self, **kwargs):
+ """Utility class to convert files to other formats without loading the entire file into memory
Args:
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))
-
def convert(self, input_path, output_path):
+ def get_file_extension(file_path):
+ root, ext = os.path.splitext(file_path)
+ if ext in ['.gz', '.bz2', '.xz']: # handle common compressed extensions
+ root, ext2 = os.path.splitext(root)
+ ext = ext2 + ext
+ return ext
# Stringify path in case it is not already a string
input_path = stringify_path(input_path)
- input_ext = os.path.splitext(input_path)[1]
- output_ext = os.path.splitext(output_path)[1]
+ input_ext = get_file_extension(input_path)
+ output_ext = get_file_extension(output_path)
output_path = stringify_path(output_path)
- if os.path.isfile(input_path):
+ if os.path.isfile(input_path):
match input_ext, output_ext:
- case (".tif", ".zarr") | (".tiff", ".zarr"):
- return self.convert_tif_to_zarr(input_path, output_path, chunks=self.chunk_shape)
+ case (".tif", ".zarr") | (".tiff", ".zarr"):
+ return self.convert_tif_to_zarr(input_path, output_path)
+ case (".nii", ".zarr") | (".nii.gz", ".zarr"):
+ return self.convert_nifti_to_zarr(input_path, output_path)
case _:
raise ValueError("Unsupported file format")
# Load a directory
@@ -39,6 +47,10 @@ class Convert:
match input_ext, output_ext:
case (".zarr", ".tif") | (".zarr", ".tiff"):
return self.convert_zarr_to_tif(input_path, output_path)
+ case (".zarr", ".nii"):
+ return self.convert_zarr_to_nifti(input_path, output_path)
+ case (".zarr", ".nii.gz"):
+ return self.convert_zarr_to_nifti(input_path, output_path, compression=True)
case _:
raise ValueError("Unsupported file format")
# Fail
@@ -55,8 +67,8 @@ class Convert:
else:
raise ValueError("Invalid path")
- def convert_tif_to_zarr(self, tif_path, zarr_path, chunks=(64, 64, 64)):
- """ Convert a tiff file to a zarr file
+ def convert_tif_to_zarr(self, tif_path, zarr_path):
+ """Convert a tiff file to a zarr file
Args:
tif_path (str): path to the tiff file
@@ -67,12 +79,18 @@ class Convert:
zarr.core.Array: zarr array containing the data from the tiff file
"""
vol = tiff.memmap(tif_path)
- z = zarr.open(zarr_path, mode='w', shape=vol.shape, chunks=chunks, dtype=vol.dtype)
+ 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))
+ 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
@@ -80,7 +98,7 @@ class Convert:
return z
def convert_zarr_to_tif(self, zarr_path, tif_path):
- """ Convert a zarr file to a tiff file
+ """Convert a zarr file to a tiff file
Args:
zarr_path (str): path to the zarr file
@@ -90,17 +108,58 @@ class Convert:
None
"""
z = zarr.open(zarr_path)
- tiff.imwrite(tif_path, z)
+ save(tif_path, z)
+ def convert_nifti_to_zarr(self, nifti_path, zarr_path):
+ """Convert a nifti file to a zarr file
+
+ Args:
+ nifti_path (str): path to the nifti file
+ zarr_path (str): path to the zarr file
+
+ Returns:
+ zarr.core.Array: zarr array containing the data from the nifti file
+ """
+ vol = nib.load(nifti_path).dataobj
+ 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_zarr_to_nifti(self, zarr_path, nifti_path, compression=False):
+ """Convert a zarr file to a nifti file
+
+ Args:
+ zarr_path (str): path to the zarr file
+ nifti_path (str): path to the nifti file
+
+ Returns:
+ None
+ """
+ z = zarr.open(zarr_path)
+ save(nifti_path, z, compression=compression)
+
def convert(input_path: str, output_path: str, chunk_shape: tuple = (64, 64, 64)):
- """ Convert a file to another format without loading the entire file into memory
+ """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).
"""
-
converter = Convert(chunk_shape=chunk_shape)
converter.convert(input_path, output_path)
diff --git a/qim3d/utils/cli.py b/qim3d/utils/cli.py
index ac8708c4..750997de 100644
--- a/qim3d/utils/cli.py
+++ b/qim3d/utils/cli.py
@@ -189,6 +189,9 @@ def main():
parser.print_help()
print("\n")
+ elif args.subcommand == 'convert':
+ qim3d.io.convert(args.input_path, args.output_path)
+
if __name__ == "__main__":
main()
--
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