From 1b2197555ff6e842423796254f9bf845402f1a57 Mon Sep 17 00:00:00 2001
From: Arin Wongprommoon <arin.wongprommoon@ed.ac.uk>
Date: Thu, 12 Jan 2023 16:13:54 +0000
Subject: [PATCH] [WIP] feat(aliby): base image class lazy-loads dummy image
WHY IS THIS CHANGE NEEDED?:
- need function that creates the expected output from dummy image file,
as an interface for other classes' get_data_lazy() methods
HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- create abstract method that loads the dummy image file and returns
2d dask array
- define function to get examples directory, following logfile_parser.legacy
WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?:
- only able to handle one TIF file (i.e. 1 z-section)
EVIDENCE THAT COMMIT WORKS:
- created a test class that extends BaseLocalImage and has a
get_data_lazy() function that extends the base class's function; it is
able to load the dummy image into a dask array
REFERENCES:
- issue #53
---
src/aliby/io/image.py | 23 ++++++++++++++++++++++-
1 file changed, 22 insertions(+), 1 deletion(-)
diff --git a/src/aliby/io/image.py b/src/aliby/io/image.py
index 3ff5e3d1..a2b1e6e1 100644
--- a/src/aliby/io/image.py
+++ b/src/aliby/io/image.py
@@ -1,8 +1,9 @@
#!/usr/bin/env python3
import typing as t
-from abc import ABC, abstractproperty
+from abc import ABC, abstractmethod, abstractproperty
from datetime import datetime
+from importlib_resources import files
from pathlib import Path, PosixPath
import dask.array as da
@@ -13,6 +14,11 @@ from tifffile import TiffFile
from agora.io.metadata import dir_to_meta
+def get_examples_dir():
+ """Get examples directory which stores dummy image for tiler"""
+ return files("aliby").parent.parent / "examples" / "tiler"
+
+
def get_image_class(source: t.Union[str, int, t.Dict[str, str], PosixPath]):
"""
Wrapper to pick the appropiate Image class depending on the source of data.
@@ -68,6 +74,21 @@ class BaseLocalImage(ABC):
)
return self._rechunked_img
+ @abstractmethod
+ def get_data_lazy(self) -> da.Array:
+ """Return 5D dask array. For lazy-loading multidimensional tiff files. Dummy image."""
+ examples_dir = get_examples_dir()
+ # TODO: Make this robust to having multiple TIFF images, one for each z-section,
+ # all falling under the same "pypipeline_unit_test_00_000001_Brightfield_*.tif"
+ # naming scheme. The aim is to create a multidimensional dask array that stores
+ # the z-stacks.
+ img_filename = "pypipeline_unit_test_00_000001_Brightfield_003.tif"
+ img_path = examples_dir / img_filename
+ # img has two dimensions: x, y
+ # This line assumes that the image being imported is of shape (1, *, *).
+ img = imread(str(img_path))[0]
+ return img
+
@abstractproperty
def name(self):
pass
--
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