diff --git a/qim3d/io/load.py b/qim3d/io/load.py
index 33a7c6b13512a1c8b08418d6f9514c874d9e9350..7a5ebe881b6d2267f638309ba6f780f870ecc796 100644
--- a/qim3d/io/load.py
+++ b/qim3d/io/load.py
@@ -378,10 +378,14 @@ class DataLoader:
match dt:
case 'float':
dt = np.float32
+ case 'float32':
+ dt = np.float32
case 'uint8':
dt = np.uint8
case 'unsigned integer':
dt = np.uint16
+ case 'uint16':
+ dt = np.uint16
case _:
raise ValueError(f"Unsupported data type: {dt}")
diff --git a/qim3d/io/save.py b/qim3d/io/save.py
index 73cea5c5115f6893a537cd4e98ed66828bde29df..8f4d70129f64b76e15f731cb95bc404a204eb8e8 100644
--- a/qim3d/io/save.py
+++ b/qim3d/io/save.py
@@ -1,8 +1,13 @@
"""Provides functionality for saving data to various file formats."""
import os
-import tifffile
+
+import h5py
+import nibabel as nib
import numpy as np
+import PIL
+import tifffile
+
from qim3d.io.logger import log
from qim3d.utils.internal_tools import sizeof, stringify_path
@@ -90,6 +95,89 @@ 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_vol(self, path, data):
+ """ Save data to a VOL file to the given path.
+
+ Args:
+ path (str): The path to save file to
+ data (numpy.ndarray): The data to be saved
+ """
+ # No support for compression yet
+ if self.compression:
+ raise NotImplementedError("Saving compressed .vol files is not yet supported")
+
+ # Create custom .vgi metadata file
+ metadata = ""
+ metadata += "{volume1}\n" # .vgi organization
+ metadata += "[file1]\n" # .vgi organization
+ metadata += "Size = {} {} {}\n".format(data.shape[1], data.shape[2], data.shape[0]) # Swap axes to match .vol format
+ metadata += "Datatype = {}\n".format(str(data.dtype)) # Get datatype as string
+ metadata += "Name = {}.vol\n".format(path.rsplit('/', 1)[-1][:-4]) # Get filename without extension
+
+ # Save metadata
+ with open(path[:-4] + ".vgi", "w") as f:
+ f.write(metadata)
+
+ # Save data using numpy in binary format
+ data.tofile(path[:-4] + ".vol")
+
+ def save_h5(self, path, data):
+ """ Save data to a HDF5 file to the given path.
+
+ Args:
+ path (str): The path to save file to
+ data (numpy.ndarray): The data to be saved
+ """
+
+ with h5py.File(path, "w") as f:
+ f.create_dataset("dataset", data=data, compression="gzip" if self.compression else None)
+
+ def save_PIL(self, path, data):
+ """ Save data to a PIL file to the given path.
+
+ Args:
+ path (str): The path to save file to
+ data (numpy.ndarray): The data to be saved
+ """
+ # No support for compression yet
+ if self.compression and path.endswith(".png"):
+ raise NotImplementedError("png does not support compression")
+ elif not self.compression and path.endswith((".jpeg",".jpg")):
+ raise NotImplementedError("jpeg does not support no compression")
+
+ # Convert to PIL image
+ img = PIL.Image.fromarray(data)
+
+ # Save image
+ img.save(path)
+
+
def save(self, path, data):
"""Save data to the given path.
@@ -154,6 +242,16 @@ 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)
+ elif path.endswith(("TXRM","XRM","TXM")):
+ raise NotImplementedError("Saving TXRM files is not yet supported")
+ elif path.endswith((".h5")):
+ return self.save_h5(path, data)
+ elif path.endswith((".vol",".vgi")):
+ return self.save_vol(path, data)
+ elif path.endswith((".jpeg",".jpg", ".png")):
+ return self.save_PIL(path, data)
else:
raise ValueError("Unsupported file format")
# If there is no file extension in the path
diff --git a/qim3d/tests/io/test_save.py b/qim3d/tests/io/test_save.py
index fa5c2d22c47d19aa101bf5cee33fa884c4b1b132..ad61587213c36a52e569f88726a7fddef3257ebb 100644
--- a/qim3d/tests/io/test_save.py
+++ b/qim3d/tests/io/test_save.py
@@ -1,10 +1,13 @@
-import qim3d
+import hashlib
+import os
+import re
import tempfile
+
import numpy as np
-import os
-import hashlib
import pytest
-import re
+
+import qim3d
+
def test_image_exist():
# Create random test image
@@ -221,6 +224,143 @@ def test_tiff_stack_slicing_dim():
qim3d.io.save(path2save,test_image,basename='test',sliced_dim=dim)
assert len(os.listdir(path2save))==test_image.shape[dim]
+def test_tiff_save_load():
+ # Create random test image
+ original_image = qim3d.examples.blobs_256x256
+
+ # Create temporary directory
+ with tempfile.TemporaryDirectory() as temp_dir:
+ image_path = os.path.join(temp_dir,"test_image.tif")
+
+ # Save to temporary directory
+ qim3d.io.save(image_path,original_image)
+
+ # Load from temporary directory
+ saved_image = qim3d.io.load(image_path)
+
+ # Get hashes
+ original_hash = calculate_image_hash(original_image)
+ saved_hash = calculate_image_hash(saved_image)
+
+ # Assert that original image is identical to saved_image
+ assert original_hash == saved_hash
+
+def test_vol_save_load():
+ # Create random test image
+ original_image = qim3d.examples.blobs_256x256x256
+
+ # Create temporary directory
+ with tempfile.TemporaryDirectory() as temp_dir:
+ image_path = os.path.join(temp_dir,"test_image.vol")
+
+ # Save to temporary directory
+ qim3d.io.save(image_path,original_image)
+
+ # Load from temporary directory
+ saved_image = qim3d.io.load(image_path)
+
+ # Get hashes
+ original_hash = calculate_image_hash(original_image)
+ saved_hash = calculate_image_hash(saved_image)
+
+ # Assert that original image is identical to saved_image
+ assert original_hash == saved_hash
+
+def test_pil_save_load():
+ # Create random test image
+ original_image = qim3d.examples.blobs_256x256
+
+ # Create temporary directory
+ with tempfile.TemporaryDirectory() as temp_dir:
+ image_path_png = os.path.join(temp_dir,"test_image.png")
+ image_path_jpg = os.path.join(temp_dir,"test_image.jpg")
+
+ # Save to temporary directory
+ qim3d.io.save(image_path_png,original_image)
+ qim3d.io.save(image_path_jpg,original_image, compression=True)
+
+ # Load from temporary directory
+ saved_image_png = qim3d.io.load(image_path_png)
+ saved_image_jpg = qim3d.io.load(image_path_jpg)
+
+ # Get hashes
+ original_hash = calculate_image_hash(original_image)
+ saved_png_hash = calculate_image_hash(saved_image_png)
+
+ # Assert that original image is identical to saved_image
+ assert original_hash == saved_png_hash
+
+ # jpg is lossy so the hashes will not match, checks that the image is the same size and similar values
+ assert original_image.shape == saved_image_jpg.shape
+
+def test_nifti_save_load():
+ # Create random test image
+ original_image = qim3d.examples.blobs_256x256
+
+ # Create temporary directory
+ with tempfile.TemporaryDirectory() as temp_dir:
+ image_path = os.path.join(temp_dir,"test_image.nii")
+ image_path_compressed = os.path.join(temp_dir,"test_image_compressed.nii.gz")
+
+ # Save to temporary directory
+ qim3d.io.save(image_path,original_image)
+ qim3d.io.save(image_path_compressed,original_image, compression=True)
+
+ # Load from temporary directory
+ saved_image = qim3d.io.load(image_path)
+ saved_image_compressed = qim3d.io.load(image_path_compressed)
+
+ # Get hashes
+ original_hash = calculate_image_hash(original_image)
+ saved_hash = calculate_image_hash(saved_image)
+ saved_compressed_hash = calculate_image_hash(saved_image_compressed)
+
+ # Assert that original image is identical to saved_image
+ assert original_hash == saved_hash
+ assert original_hash == saved_compressed_hash
+
+ # Compute file sizes
+ file_size = os.path.getsize(image_path)
+ compressed_file_size = os.path.getsize(image_path_compressed)
+
+ # Assert that compressed file size is smaller than non-compressed file size
+ assert compressed_file_size < file_size
+
+
+def test_h5_save_load():
+ # Create random test image
+ original_image = qim3d.examples.blobs_256x256x256
+
+ # Create temporary directory
+ with tempfile.TemporaryDirectory() as temp_dir:
+ image_path = os.path.join(temp_dir,"test_image.h5")
+ image_path_compressed = os.path.join(temp_dir,"test_image_compressed.nii.gz")
+
+ # Save to temporary directory
+ qim3d.io.save(image_path,original_image)
+ qim3d.io.save(image_path_compressed,original_image, compression=True)
+
+ # Load from temporary directory
+ saved_image = qim3d.io.load(image_path)
+ saved_image_compressed = qim3d.io.load(image_path_compressed)
+
+ # Get hashes
+ original_hash = calculate_image_hash(original_image)
+ saved_hash = calculate_image_hash(saved_image)
+ saved_compressed_hash = calculate_image_hash(saved_image_compressed)
+
+ # Assert that original image is identical to saved_image
+ # Assert that original image is identical to saved_image
+ assert original_hash == saved_hash
+ assert original_hash == saved_compressed_hash
+
+ # Compute file sizes
+ file_size = os.path.getsize(image_path)
+ compressed_file_size = os.path.getsize(image_path_compressed)
+
+ # Assert that compressed file size is smaller than non-compressed file size
+ assert compressed_file_size < file_size
+
def calculate_image_hash(image):
image_bytes = image.tobytes()
hash_object = hashlib.md5(image_bytes)