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Update to scijava 34.1.0 and use Location API #7

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Update to scijava 34.1.0 and use Location API #7

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ecmagnuson
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@ecmagnuson ecmagnuson commented Apr 6, 2023 •
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closes #5

This updates the tutorials to use the scijava location api.

Some things to note:

  1. I made a class FakeTutorialImages to use the builder for getting fake image locations. There is a method sampleIndexedImage where I'm not certain if that is the best name for the method, but it is used in T2bTypedComponents.java to see if the Color table isn't null.
  2. In T1OpeningOMEXML the class runs exactly the same, but for some reason there is an error when running. This is a log error at the top and doesn't kill the program
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.

When it calls T1dSavingImagePlanes.main(); this error gets thrown at creating a new SCIFIO instance, which I am not certain on currently.

@ecmagnuson ecmagnuson requested a review from hinerm April 6, 2023 21:16
@ecmagnuson ecmagnuson force-pushed the scijava-location-api branch from 1579978 to a3cedb5 Compare April 7, 2023 21:46
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hinerm commented Jun 19, 2023

2. In T1OpeningOMEXML the class runs exactly the same, but for some reason there is an error when running. This is a log error at the top and doesn't kill the program

try adding:

     <dependency>
      <groupId>ch.qos.reload4j</groupId>
      <artifactId>reload4j</artifactId>
    </dependency>

as a dependency and see if this warning goes away. It's probably because we (appropriately) stopped shipping a logging implementation (and the whole log4j security vulnerability thing).

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Update scifio-tutorials to new Location API
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@ecmagnuson @hinerm