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Fix Travis build #1

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Merged
merged 11 commits into from
Feb 25, 2020
Merged

Fix Travis build #1

merged 11 commits into from
Feb 25, 2020

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imagejan
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@imagejan imagejan commented Feb 25, 2020

This PR tries to fix the Travis build issues on imagej#56. In the xarray branch, I rebased mpinkert/master onto imagej/travis-conda.

See imagej#64 for details about the changes.

ctrueden and others added 11 commits January 9, 2020 11:33
We now go into a little more detail about why this can be nice.
Thanks to Tatsuaki Kobayashi for the guide! :-D

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Update the brew command for macos
There are incompatible changes in imglyb 0.4.0 (e.g. Accesses class moved from imglib2-imglyb to imglib2-unsafe)
On the Travis CI linux environment, JAVA_HOME was pointing to an openjdk11 installation. We want to work with the JDK of the current conda environment, so let's unset JAVA_HOME here.
This new convention supports bi-directional conversion between xarrays and datasets, under the assumption that an xarray is an image.

Currently, this does flip the axes order for C-style (default) indexed xarrays, as Java uses F-style indexing.  This behavior conforms to the current status for regular numpy arrays.

Right now the conversion also assumes that the axes are linear, such that the axes can be defined with just an origin and a scale (aX + b).

Any non-numeric axes labels are currently lost (e.g., if you have coords of [R, G, B] they become [0, 1, 2] upon conversion)
@mpinkert mpinkert merged commit 32f6551 into mpinkert:master Feb 25, 2020
@imagejan imagejan deleted the xarray branch February 25, 2020 14:32
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4 participants