From 13ed9a597236eb15d7412fcea8c7780ed4b1cc60 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Fri, 6 Jan 2023 18:49:57 +0000
Subject: [PATCH] refactor(dataset): create dispatch function
---
src/aliby/io/dataset.py | 34 +++++++++++++++++++++++++++++-----
1 file changed, 29 insertions(+), 5 deletions(-)
diff --git a/src/aliby/io/dataset.py b/src/aliby/io/dataset.py
index 62366d0f..a07dce0e 100644
--- a/src/aliby/io/dataset.py
+++ b/src/aliby/io/dataset.py
@@ -20,6 +20,30 @@ from aliby.io.image import ImageLocalOME
from aliby.io.omero import BridgeOmero
+def dispatch_dataset(expt_id: int or str, **kwargs):
+ """
+ Choose a subtype of dataset based on the identifier.
+
+ Input:
+ --------
+ expt_id: int or string serving as dataset identifier.
+
+ Returns:
+ --------
+ Callable Dataset instance, either network-dependent or local.
+ """
+ if isinstance(expt_id, int): # Is an experiment online
+ return Dataset(x, **kwargs["general"].get("server_info"))
+ elif isinstance(expt_id, str): # Files or Dir
+ expt_path = Path(expt_id)
+ if expt_path.is_dir():
+ return DatasetLocalDir(expt_path)
+ else:
+ return DatasetLocalOME(expt_path)
+ else:
+ raise Warning("Invalid expt_id")
+
+
class DatasetLocalABC(ABC):
"""
Abstract Base class to fetch local files, either OME-XML or raw images.
@@ -74,7 +98,7 @@ class DatasetLocalABC(ABC):
@abstractmethod
def get_images(self):
- # Return location of images and their unique names
+ # Return a dictionary with the name of images and their unique identifiers
pass
@@ -95,15 +119,15 @@ class DatasetLocalDir(DatasetLocalABC):
)
def get_images(self):
- return [
- folder
+ return {
+ folder.name: folder
for folder in self.path.glob("*/")
if any(
path
- for suffix in self._valid_meta_suffixes
+ for suffix in self._valid_suffixes
for path in folder.glob(f"*.{suffix}")
)
- ]
+ }
class DatasetLocalOME(DatasetLocalABC):
--
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