From 13958fda3e53f5c7b8547bb237071ad1225919b6 Mon Sep 17 00:00:00 2001
From: Christian Kento Rasmussen <christian.kento@gmail.com>
Date: Wed, 24 Jan 2024 16:15:05 +0100
Subject: [PATCH] added support to save nifti file
---
qim3d/io/save.py | 33 ++++++++++++++++++++++++++++++++-
1 file changed, 32 insertions(+), 1 deletion(-)
diff --git a/qim3d/io/save.py b/qim3d/io/save.py
index 73cea5c5..24e53bda 100644
--- a/qim3d/io/save.py
+++ b/qim3d/io/save.py
@@ -1,8 +1,11 @@
"""Provides functionality for saving data to various file formats."""
import os
-import tifffile
+
+import nibabel as nib
import numpy as np
+import tifffile
+
from qim3d.io.logger import log
from qim3d.utils.internal_tools import sizeof, stringify_path
@@ -90,6 +93,32 @@ class DataSaver:
log.info(f"Total of {no_slices} files saved following the pattern '{pattern_string}'")
+ def save_nifti(self, path, data):
+ """ Save data to a NIfTI file to the given path.
+
+ Args:
+ path (str): The path to save file to
+ data (numpy.ndarray): The data to be saved
+ """
+ # Create header
+ header = nib.Nifti1Header()
+ header.set_data_dtype(data.dtype)
+
+ # Create NIfTI image object
+ img = nib.Nifti1Image(data, np.eye(4), header)
+
+ # nib does automatically compress if filetype ends with .gz
+ if self.compression and not path.endswith(".gz"):
+ path += ".gz"
+ log.warning("File extension '.gz' is added since compression is enabled.")
+
+ if not self.compression and path.endswith(".gz"):
+ path = path[:-3]
+ log.warning("File extension '.gz' is ignored since compression is disabled.")
+
+ # Save image
+ nib.save(img, path)
+
def save(self, path, data):
"""Save data to the given path.
@@ -154,6 +183,8 @@ class DataSaver:
if path.endswith((".tif", ".tiff")):
return self.save_tiff(path, data)
+ elif path.endswith((".nii","nii.gz")):
+ return self.save_nifti(path, data)
else:
raise ValueError("Unsupported file format")
# If there is no file extension in the path
--
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