From 00a747eb121e0d307eb576d05952ef89cd45448b Mon Sep 17 00:00:00 2001
From: Arin Wongprommoon <arin.wongprommoon@ed.ac.uk>
Date: Tue, 17 Jan 2023 11:06:33 +0000
Subject: [PATCH] fix!(aliby): dimensions in tiler consistent with image
WHY IS THIS CHANGE NEEDED?:
- tiler dimensions are ctzyx, but image dimensions are tczyx by default.
this leads to incorrect storage of shapes
HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- re-arrange the dimensions in the shape property to match image
- justifying this for the purpose of getting ImageDummy to play well
with Tiler
WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?:
- this exposes technical debt: there are places in which the order of
dimensions are hard-coded and later assumed like this, and leads to
indexing dimensions by index rather than by name. in addition, the
assumed order of dimensions is inconsistent throughout tiler. this is
a recipe for confusion. worth a refactor soon.
---
src/aliby/tile/tiler.py | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/src/aliby/tile/tiler.py b/src/aliby/tile/tiler.py
index f1db705c..9de61621 100644
--- a/src/aliby/tile/tiler.py
+++ b/src/aliby/tile/tiler.py
@@ -358,7 +358,12 @@ class Tiler(StepABC):
no of pixels in y direction
no of pixels in z direction
"""
- c, t, z, y, x = self.image.shape
+ # FIXME: TECHNICAL DEBT -- hard-coding dimension order.
+ # This is valid for dummy tiler and conforms to the default order
+ # in Image instances. However, there is no guarantee that it will
+ # work with the other tiler instances.
+ # c, t, z, y, x = self.image.shape
+ t, c, z, y, x = self.image.shape
return (c, t, x, y, z)
@property
--
GitLab