Began work on convert tool

qim3d/io/convert.py

+import numpy as np
+import tifffile as tiff
+import zarr
+
+
+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).
+
+    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)
+    z[:] = vol[:]
+
+    return z
+
+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
+
+    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[:]
+
+    return z
+
+def convert_zarr_to_tif(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)
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