From 5828cda743a086e22dace2825f75bccd9c9c398b Mon Sep 17 00:00:00 2001
From: Christian Kento Rasmussen <christian.kento@gmail.com>
Date: Mon, 10 Jun 2024 13:13:22 +0200
Subject: [PATCH] finalized convert function for zarr to tiff
---
qim3d/io/__init__.py | 1 +
qim3d/io/convert.py | 26 +++++---------------------
2 files changed, 6 insertions(+), 21 deletions(-)
diff --git a/qim3d/io/__init__.py b/qim3d/io/__init__.py
index f97cb7d4..7efd57b8 100644
--- a/qim3d/io/__init__.py
+++ b/qim3d/io/__init__.py
@@ -2,4 +2,5 @@ from .loading import DataLoader, load, ImgExamples
from .downloader import Downloader
from .saving import DataSaver, save
from .sync import Sync
+from .convert import convert
from . import logger
\ No newline at end of file
diff --git a/qim3d/io/convert.py b/qim3d/io/convert.py
index dd29d7e2..aa803d8b 100644
--- a/qim3d/io/convert.py
+++ b/qim3d/io/convert.py
@@ -23,13 +23,14 @@ class Convert:
def convert(self, input_path, output_path):
# Stringify path in case it is not already a string
input_path = stringify_path(input_path)
+ output_path = stringify_path(output_path)
- if os.path.isfile(input_path) and os.path.isfile(output_path):
- match input_path, output_path:
+ if os.path.isfile(input_path):
+ input_ext = os.path.splitext(input_path)[1]
+ output_ext = os.path.splitext(output_path)[1]
+ match input_ext, output_ext:
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 _:
@@ -75,23 +76,6 @@ class Convert:
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[:]
-
- return z
-
def convert_zarr_to_tif(self, zarr_path, tif_path):
""" Convert a zarr file to a tiff file
--
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