Conv zarr tiff folders

Created convert function between zarr and tiff stack

https://www.notion.so/qim-dtu/Convert-Zarr-to-tiff-folder-05d32e0b4ce549d4b69dc4fe7885a41d?pvs=4

qim3d/io/convert.py

@@ -9,6 +9,7 @@ import zarr
 from tqdm import tqdm
 
 from qim3d.utils.internal_tools import stringify_path
+from qim3d.io.saving import save
 
 
 class Convert:
@@ -21,17 +22,23 @@ class Convert:
         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):
             match input_ext, output_ext:
                 case (".tif", ".zarr") | (".tiff", ".zarr"):
                     return self.convert_tif_to_zarr(input_path, output_path)
-                case (".nii", ".zarr"):
+                case (".nii", ".zarr") | (".nii.gz", ".zarr"):
                     return self.convert_nifti_to_zarr(input_path, output_path)
                 case _:
                     raise ValueError("Unsupported file format")
@@ -41,7 +48,9 @@ class Convert:
                 case (".zarr", ".tif") | (".zarr", ".tiff"):
                     return self.convert_zarr_to_tif(input_path, output_path)
                 case (".zarr", ".nii"):
-                    return self.convert_zarr_to_tif(input_path, output_path)
+                    return self.convert_zarr_to_nifti(input_path, output_path)
+                case (".zarr", ".nii.gz"):
+                    return self.convert_zarr_to_nifti(input_path, output_path, compress=True)
                 case _:
                     raise ValueError("Unsupported file format")
         # Fail
@@ -71,7 +80,7 @@ class Convert:
         """
         vol = tiff.memmap(tif_path)
         z = zarr.open(
-            zarr_path, mode="w", shape=vol.shape, chunks=self.chunks, dtype=vol.dtype
+            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
@@ -99,7 +108,7 @@ 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
@@ -113,7 +122,7 @@ class Convert:
         """
         vol = nib.load(nifti_path).dataobj
         z = zarr.open(
-            zarr_path, mode="w", shape=vol.shape, chunks=self.chunks, dtype=vol.dtype
+            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
@@ -130,7 +139,7 @@ class Convert:
 
         return z
 
-    def convert_zarr_to_nifti(self, zarr_path, nifti_path):
+    def convert_zarr_to_nifti(self, zarr_path, nifti_path, compress=False):
         """Convert a zarr file to a nifti file
 
         Args:
@@ -141,7 +150,8 @@ class Convert:
             None
         """
         z = zarr.open(zarr_path)
-        nib.save(nib.Nifti1Image(z, np.eye(4)), nifti_path)
+        save(nifti_path, z, compress=compress)
+        
 
 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
@@ -151,6 +161,5 @@ def convert(input_path: str, output_path: str, chunk_shape: tuple = (64, 64, 64)
         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)