From 1a762d7ed853eef1698ad2951e586cd226650bfc Mon Sep 17 00:00:00 2001
From: Arin Wongprommoon <arin.wongprommoon@ed.ac.uk>
Date: Tue, 17 Jan 2023 11:38:20 +0000
Subject: [PATCH] fix!(aliby): incorporate ref_z in creating dummy image object
WHY IS THIS CHANGE NEEDED?:
- using dev_testimage.py in skeletons: when dummy tiler is created and
tiler.initialise_traps() is invoked, segment_traps() (still) raises 'No valid
'tiling regions found'
HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- in tiler.initialise_traps(), initial_image was defined based on
self.ref_channel and self.ref_z; however, if ref_z was not 0, then
initial_image would be a zero array.
- this was because ImageDummy.pad_array() put the input image at the 0
position and pads with zeros regardless of the value of ref_z.
- so i wanted the output of ImageDummy.get_data_lazy() to be defined in
such a way that the (ref_z)th slice in the z-direction is the input
image.
- therefore, i added a new argument to Image.Dummy.pad_array() so
that ref_z can be used to achieve the above.
WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?:
- tech debt: no (easy) way to deal with ref_channel because it's a
string. workaround is to keep the ref_channel the first channel
in the dummy tiler, and assume that throughout.
EVIDENCE THAT COMMIT WORKS:
- modified test_image.py works
- skeletons: dummy tiler can be defined and dummy_tiler._run_tp(0) runs
without errors
---
src/aliby/io/image.py | 27 ++++++++++++++++++++++-----
src/aliby/tile/tiler.py | 3 ++-
tests/aliby/pipeline/test_image.py | 12 ++++++++----
3 files changed, 32 insertions(+), 10 deletions(-)
diff --git a/src/aliby/io/image.py b/src/aliby/io/image.py
index 0bd41880..da563f3e 100644
--- a/src/aliby/io/image.py
+++ b/src/aliby/io/image.py
@@ -138,7 +138,12 @@ class ImageDummy(BaseLocalImage):
# Goal: make Tiler happy.
@staticmethod
- def pad_array(image_array: da.Array, dim: int, n_empty_slices: int):
+ def pad_array(
+ image_array: da.Array,
+ dim: int,
+ n_empty_slices: int,
+ image_position: int = 0,
+ ):
"""Extends a dimension in a dask array and pads with zeros
Extends a dimension in a dask array that has existing content, then pads
@@ -153,19 +158,29 @@ class ImageDummy(BaseLocalImage):
n_empty_slices : int
Number of empty slices to extend the dask array by, in the specified
dimension/axis.
+ image_position : int
+ Position within the new dimension to place the input arary, default 0
+ (the beginning).
Examples
--------
```
- extended_array = pad_array(my_da_array, dim = 2, n_empty_slices = 4)
+ extended_array = pad_array(
+ my_da_array, dim = 2, n_empty_slices = 4, image_position = 1)
```
Extends a dask array called `my_da_array` in the 3rd dimension
- (dimensions start from 0) by 4 slices, filled with zeros.
+ (dimensions start from 0) by 4 slices, filled with zeros. And puts the
+ original content in slice 1 of the 3rd dimension
"""
# Concats zero arrays with same dimensions as image_array, and puts
# image_array as first element in list of arrays to be concatenated
+ zeros_array = da.zeros_like(image_array)
return da.concatenate(
- [image_array, *([da.zeros_like(image_array)] * n_empty_slices)],
+ [
+ *([zeros_array] * image_position),
+ image_array,
+ *([zeros_array] * (n_empty_slices - image_position)),
+ ],
axis=dim,
)
@@ -192,7 +207,9 @@ class ImageDummy(BaseLocalImage):
img, dim=0, n_empty_slices=199
) # 200 timepoints total
img = self.pad_array(img, dim=1, n_empty_slices=2) # 3 channels
- img = self.pad_array(img, dim=2, n_empty_slices=4) # 5 z-stacks
+ img = self.pad_array(
+ img, dim=2, n_empty_slices=4, image_position=self.ref_z
+ ) # 5 z-stacks
return img
def name(self):
diff --git a/src/aliby/tile/tiler.py b/src/aliby/tile/tiler.py
index 9de61621..93ae8cc4 100644
--- a/src/aliby/tile/tiler.py
+++ b/src/aliby/tile/tiler.py
@@ -258,6 +258,7 @@ class Tiler(StepABC):
"""
imgdmy_obj = ImageDummy(parameters)
dummy_image = imgdmy_obj.get_data_lazy()
+ # FIXME: TECHNICAL DEBT: hard-coding dimension orders
dummy_omero_metadata = {
"size_x": dummy_image.shape[3],
"size_y": dummy_image.shape[4],
@@ -265,8 +266,8 @@ class Tiler(StepABC):
"size_c": dummy_image.shape[1],
"size_t": dummy_image.shape[0],
"channels": [
- *(["nil"] * (dummy_image.shape[1] - 1)),
parameters["ref_channel"],
+ *(["nil"] * (dummy_image.shape[1] - 1)),
],
"name": " ",
}
diff --git a/tests/aliby/pipeline/test_image.py b/tests/aliby/pipeline/test_image.py
index d8343a5d..3a211400 100644
--- a/tests/aliby/pipeline/test_image.py
+++ b/tests/aliby/pipeline/test_image.py
@@ -17,23 +17,27 @@ sample_da = da.reshape(
@pytest.mark.parametrize("sample_da", [sample_da])
@pytest.mark.parametrize("dim", [2])
@pytest.mark.parametrize("n_empty_slices", [4])
-def test_pad_array(sample_da, dim, n_empty_slices):
+@pytest.mark.parametrize("image_position", [1])
+def test_pad_array(sample_da, dim, n_empty_slices, image_position):
"""Test ImageDummy.pad_array() method"""
# create object
imgdmy = ImageDummy(tiler_parameters)
# pads array
padded_da = imgdmy.pad_array(
- sample_da, dim=dim, n_empty_slices=n_empty_slices
+ sample_da,
+ dim=dim,
+ n_empty_slices=n_empty_slices,
+ image_position=image_position,
)
# select which dimension to index the multidimensional array
- indices = {dim: 0}
+ indices = {dim: image_position}
ix = [
indices.get(dim, slice(None))
for dim in range(padded_da.compute().ndim)
]
- # Checks that original image array is there and is at the first index
+ # Checks that original image array is there and is at the correct index
assert np.array_equal(padded_da.compute()[ix], sample_da.compute()[0])
# Checks that the additional axis is extended correctly
assert padded_da.compute().shape[dim] == n_empty_slices + 1
--
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