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add axis labels to display() #1682

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merged 4 commits into from
Dec 3, 2019
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add axis labels to display() #1682

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499a369
add axis labels to display()
kevinyamauchi Dec 2, 2019
e37817b
update display() docstring
kevinyamauchi Dec 2, 2019
ff27195
get axis order from starfish.core.imagestack.dataorder
kevinyamauchi Dec 2, 2019
7aba7a7
rais error when AXES_DATA is missing an entry
Dec 3, 2019
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12 changes: 10 additions & 2 deletions starfish/core/_display.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
Viewer = None


NAPARI_VERSION = "0.2.0" # when changing this, update docs in display
NAPARI_VERSION = "0.2.6" # when changing this, update docs in display
INTERACTIVE = not hasattr(__main__, "__file__")


Expand Down Expand Up @@ -226,7 +226,15 @@ def display(
from qtpy.QtWidgets import QApplication
app = QApplication.instance() or QApplication([])

viewer = Viewer()
viewer = Viewer(
axis_labels=[
Axes.ROUND.value,
Axes.CH.value,
Axes.ZPLANE.value,
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I would grab these three from starfish/core/imagestack/dataorder.py

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Will do!

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@ttung , it looks like AXES_DATA contains names and orders for round, channel, and z, but not x and y. Should I just assume (y, 3) and (x, 4)? Or is the axis ordering for y and x stored elsewhere?

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@kevinyamauchi kevinyamauchi Dec 2, 2019 •
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(you can rotate views in napari, so the y and x axis names may get displayed)

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Unfortunately, Y and X are not stored anywhere. It has always been assumed Y then X.

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Sounds good!

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@ttung, I changed it such that the axis order comes from starfish.core.imagestack.dataorder.

Axes.Y.value,
Axes.X.value
]
)
new_viewer = True
elif isinstance(viewer, Viewer):
new_viewer = False
Expand Down