coPylot IO

copylot/io/dataset.py

@@ -0,0 +1,49 @@
+import tensorstore as ts
+
+
+class Dataset:
+    def __init__(
+            self,
+            path,
+            nb_slices: int = 16,
+            nb_view: int = 1,
+            nb_frames: int = 1,
+            y_len: int = 2048,
+            x_len: int = 2048,
+    ):
+        self.ds = ts.open(
+            {
+                "driver": "zarr",
+                'kvstore': {
+                    'driver': 'file',
+                    'path': path,
+                },
+                "key_encoding": ".",
+                "metadata": {
+                    "shape": [nb_slices, nb_view, nb_frames, y_len, x_len],
+                    "chunks": [128, 1, 128, 128, 128],
+                    "dtype": "<i2",
+                    "order": "C",
+                    "compressor": {
+                        "id": "blosc",
+                        "shuffle": -1,
+                        "clevel": 5,
+                        "cname": "lz4",
+                    },
+                },
+                'create': True,
+                'delete_existing': True,
+            }
+        ).result()
+
+    @property
+    def shape(self):
+        return self.ds.shape
+
+    # TODO: dtype, channel, etc..
+
+    def sync_write(self):
+        raise NotImplementedError
+
+    def async_write(self):
+        raise NotImplementedError

copylot/io/path.py

@@ -0,0 +1,42 @@
+import tempfile
+from os import makedirs
+from os.path import exists
+
+
+def get_home_folder():
+    """
+    Method that returns home folder in the current runtime.
+
+    Returns
+    -------
+    str
+
+    """
+    from pathlib import Path
+
+    home_folder = f"{Path.home()}"
+    return home_folder
+
+
+def get_temp_folder():
+    """
+    Method that creates a new temp folder and returns
+    the path to the created temp folder.
+
+    Returns
+    -------
+    str
+
+    """
+    temp_folder = None
+
+    try:
+        temp_folder = tempfile.gettempdir()
+        if exists(temp_folder):
+            raise FileExistsError
+        else:
+            makedirs(temp_folder)
+    except Exception:
+        pass
+
+    return temp_folder

copylot/io/test/test_path.py

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+from os import access, W_OK
+from os.path import exists
+
+from copylot.util import get_temp_folder, get_home_folder
+
+
+def test_home_folder():
+    home_folder = get_home_folder()
+    print(home_folder)
+    assert exists(home_folder)
+    assert access(home_folder, W_OK)
+
+
+def test_temp_folder():
+    temp_folder = get_temp_folder()
+    print(temp_folder)
+    assert exists(temp_folder)
+    assert access(temp_folder, W_OK)