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

+import difflib
+import os
 from itertools import product
 
 import numpy as np
@@ -5,56 +7,113 @@ import tifffile as tiff
 import zarr
 from tqdm import tqdm
 
+from qim3d.utils.internal_tools import stringify_path
 
-def convert_tif_to_zarr(tif_path, zarr_path, chunks=(64, 64, 64)):
-    """ Convert a tiff file to a zarr file
 
-    Args:
-        tif_path (str): path to the tiff file
-        zarr_path (str): path to the zarr file
-        chunks (tuple, optional): chunk size for the zarr file. Defaults to (64, 64, 64).
+class Convert:
 
-    Returns:
-        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)
-    chunk_shape = tuple((s + c - 1) // c for s, c in zip(z.shape, z.chunks))
-    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
+    def __init__(self,**kwargs):
+        """ Utility class to convert files to other formats without loading the entire file into memory
 
-    return z
+        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_npy_to_zarr(npy_path, zarr_path, shape, dtype=np.float32, chunks=(64, 64, 64)):
-    """ Convert a numpy file to a zarr file
+    def convert(self, input_path, output_path):
+        # Stringify path in case it is not already a string
+        input_path = stringify_path(input_path)
 
-    Args:
-        npy_path (str): path to the numpy file
-        zarr_path (str): path to the zarr file
-        chunks (tuple, optional): chunk size for the zarr file. Defaults to (64, 64, 64).
+        if os.path.isfile(input_path) and os.path.isfile(output_path):
+            match input_path, output_path:
+                case (".tif", ".zarr"):
+                    return self.convert_tif_to_zarr(input_path, output_path)
+                case (".npy", ".zarr"):
+                    return self.convert_npy_to_zarr(input_path, output_path, shape=(64, 64, 64))
+                case (".zarr", ".tif"):
+                    return self.convert_zarr_to_tif(input_path, output_path)
+                case _:
+                    raise ValueError("Unsupported file format")
+        # Load a directory
+        elif os.path.isdir(input_path):
+            raise ValueError("Unsupported file format")
+        # Fail
+        else:
+            # Find the closest matching path to warn the user
+            parent_dir = os.path.dirname(input_path) or "."
+            parent_files = os.listdir(parent_dir) if os.path.isdir(parent_dir) else ""
+            valid_paths = [os.path.join(parent_dir, file) for file in parent_files]
+            similar_paths = difflib.get_close_matches(input_path, valid_paths)
+            if similar_paths:
+                suggestion = similar_paths[0]  # Get the closest match
+                message = f"Invalid path. Did you mean '{suggestion}'?"
+                raise ValueError(repr(message))
+            else:
+                raise ValueError("Invalid path")
 
-    Returns:
-        zarr.core.Array: zarr array containing the data from the numpy file
-    """
-    vol = np.memmap(npy_path, dtype=dtype, mode='r', shape=shape)
-    z = zarr.open(zarr_path, mode='w', shape=vol.shape, chunks=chunks, dtype=vol.dtype)
-    z[:] = vol[:]
+    def convert_tif_to_zarr(self, tif_path, zarr_path, chunks=(64, 64, 64)):
+        """ Convert a tiff file to a zarr file
 
-    return z
+        Args:
+            tif_path (str): path to the tiff file
+            zarr_path (str): path to the zarr file
+            chunks (tuple, optional): chunk size for the zarr file. Defaults to (64, 64, 64).
 
-def convert_zarr_to_tif(zarr_path, tif_path):
-    """ Convert a zarr file to a tiff file
+        Returns:
+            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)
+        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
 
-    Args:
-        zarr_path (str): path to the zarr file
-        tif_path (str): path to the tiff file
+        return z
+
+    def convert_npy_to_zarr(self, npy_path, zarr_path, shape, dtype=np.float32, chunks=(64, 64, 64)):
+        """ Convert a numpy file to a zarr file
+
+        Args:
+            npy_path (str): path to the numpy file
+            zarr_path (str): path to the zarr file
+            chunks (tuple, optional): chunk size for the zarr file. Defaults to (64, 64, 64).
+
+        Returns:
+            zarr.core.Array: zarr array containing the data from the numpy file
+        """
+        vol = np.memmap(npy_path, dtype=dtype, mode='r', shape=shape)
+        z = zarr.open(zarr_path, mode='w', shape=vol.shape, chunks=chunks, dtype=vol.dtype)
+        z[:] = vol[:]
 
-    returns:
-        None
+        return z
+
+    def convert_zarr_to_tif(self, zarr_path, tif_path):
+        """ Convert a zarr file to a tiff file
+
+        Args:
+            zarr_path (str): path to the zarr file
+            tif_path (str): path to the tiff file
+
+        returns:
+            None
+        """
+        z = zarr.open(zarr_path)
+        tiff.imwrite(tif_path, z)
+
+
+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
+
+    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).
     """
-    z = zarr.open(zarr_path)
-    tiff.imwrite(tif_path, z)
\ No newline at end of file
+
+    converter = Convert(chunk_shape=chunk_shape)
+    converter.convert(input_path, output_path)