Hi, apologies for the late answer, I had time to look at this again today.
transformations after cropping
Also my previous answer was ambiguous (didnât read your code carefully enough, apologies). Here is the explanation for what you got in your plots.
After the cropping these are the transformations present in the data:
Precisely:
- the image and the labels object before cropping had an identity, now they have a translation that takes into account for the new position of the pixel (0, 0).
- the shapes before cropping had a scale, now after cropping they have the same scale and no translation is needed (the cropping operation didnât change the origin).
translating by 500
Now, to translate everything by (500, 500) units you have two options, to replace the existing transformation, to append a new transformation to the already existing one.
replacing the transformation
Now, set_transformation() follows the first option, so the new transformation for images should be equal to (15000 + 500, 70000 + 500), as you are doing. This works, in this case, for images, but wonât for shapes. Note also that in general this approach itâs not guaranteed to work for images: for instance with Visium data images have a scale, so replacing the transformation will displace the old image alignment.
appending the transformation
The approach I recommend is to append a new transformation. Here is a function to do this:
def _postpone_transformation(
sdata: SpatialData,
from_coordinate_system: str,
to_coordinate_system: str,
transformation: BaseTransformation
):
for element in sdata._gen_spatial_element_values():
d = get_transformation(element, get_all=True)
assert isinstance(d, dict)
t = d[from_coordinate_system]
sequence = Sequence([t, transformation])
set_transformation(element, sequence, to_coordinate_system)
We could introduce a new public API to perform this opertation.
code
Here is the adjusted code (please notice that you have to replace the dataset path and change x0, y1, as I was using a different dataset).
##
# https://discourse.scverse.org/t/spatialdata-wrong-shapes-translation/2276/6
import spatialdata as sd
import spatialdata_plot
import matplotlib.pyplot as plt
# Load spatial data
f = "/Users/macbook/embl/projects/basel/spatialdata-sandbox/xenium_rep1_io/data.zarr"
sdata = sd.read_zarr(f)
##
sd.get_extent(sdata)
##
# Crop spatial data. I selected a tile of size (2000, 2000)
x0 = 15000
y0 = 20000
x1 = x0 + 2000
y1 = y0 + 2000
crop_sample_3 = lambda x: sd.bounding_box_query(
x,
min_coordinate=[x0, y0],
max_coordinate=[x1, y1],
axes=("x", "y"),
target_coordinate_system="global",
)
sdata_sample3 = crop_sample_3(sdata)
##
# plot image with shapes and labels
sdata_sample3.pl.render_images().pl.render_shapes().pl.render_labels().pl.show(title="Image with shapes and labels")
plt.show()
##
from spatialdata.transformations import (
Translation,
set_transformation,
BaseTransformation,
Sequence,
get_transformation,
)
def _postpone_transformation(
sdata: sd.SpatialData, from_coordinate_system: str, to_coordinate_system: str, transformation: BaseTransformation
):
for element in sdata._gen_spatial_element_values():
d = get_transformation(element, get_all=True)
assert isinstance(d, dict)
print(d)
t = d[from_coordinate_system]
sequence = Sequence([t, transformation])
set_transformation(element, sequence, to_coordinate_system)
##
# Define small transformation of 500 pixels
translation = Translation([500, 500], axes=("x", "y"))
_postpone_transformation(sdata_sample3, "global", "global", translation)
# Plot translated image with shapes and labels
sdata_sample3.pl.render_images().pl.render_shapes().pl.render_labels().pl.show(
title="Image translated with shapes and labels"
)
plt.show()
# Plot translated image and labels, with shapes
sdata_sample3.pl.render_images().pl.render_shapes().pl.render_labels().pl.show(
title="Image & labels translated with shapes"
)
plt.show()
# Plot translated image, labels and shapes. This is the weird plot as shown above
sdata_sample3.pl.render_images().pl.render_shapes().pl.render_labels().pl.show(
title="Image & labels & shapes translated"
)
plt.show()
final note
A final note, in the above I talked about units (of the coordinate system 'global') and not pixels (even if in this case pixels and units coincide for the image and labels because no scale is present); in general our APIs require to specify a target coordinate system and deal with coordinates in terms of units in that coordinate system.
