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Erwin Frise frederikfly Fabric Genomics Oakland, CA https://fabricgenomics.com

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Python DSL for setting up business intelligence rules that can be configured without code

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Plugin development for StarCluster

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Wayne Rasband

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2021.01.24 (1.53h54; Calibration bars)

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Wayne Rasband

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2021.01.24 (1.53h53; Selection brush tool)

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PR opened imglib/imglib2

numElements returns zero for empty Intervals

Changes the implementation of Intervals.numElements so that it returns zero "empty" Intervals Where an Interval is "empty" if its max(d) < min(d) for any d

If we agree, then this definition should be documented.

see #300

+25 -6

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issue commentimglib/imglib2

Empty Intervals - numElements and intersection

Indeed, that was a typo - but the issue persists when A and B are defined correctly. (I edited) Sorry for confusion

bogovicj

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issue commentimglib/imglib2

Empty Intervals - numElements and intersection

I think the misconception here is that you call the constructor of B with a min that is larger than max in (at least) one dimension.

The following (Groovy) script works as expected for me:

import net.imglib2.FinalInterval
import net.imglib2.util.Intervals

// make an interval
FinalInterval A = new FinalInterval( 
		new long[]{ 0, 0, 0 },
		new long[]{ 5, 5, 5 });

// make B such that A intersect B is empty
FinalInterval B = new FinalInterval( 
		new long[]{ 6, 0, 0 }, 
		new long[] { 10, 5, 5 });

// compute the intersection
FinalInterval AandB = Intervals.intersect( A, B );
println( AandB );

// how many elements in the intersection
println( Intervals.numElements( AandB ));
bogovicj

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issue commentimglib/imglib2

Empty Intervals - numElements and intersection

"anything with zero or fewer elements is empty"

This does not work with the current intersection implementation because:

FinalInterval A = new FinalInterval( 
		new long[]{ 0, 0, 0 },
		new long[]{ 5, 5, 5 });

// make B such that A intersect B is empty
FinalInterval B = new FinalInterval( 
		new long[]{ 10, 0, 10 }, 
		new long[] { 5, 5, 5 });

// compute the intersection
FinalInterval AandB = Intervals.intersect( A, B );
System.out.println( Intervals.numElements( AandB ));

returns 96

i.e., the number of elements of the intersection of two non-intersecting intervals currently can return a positive number.

bogovicj

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issue openedimglib/imglib2

mpty Intervals

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Mark Hiner

commit sha 2b9ca3eb4d35856206913def6c1bd5de5e1e245c

Bump to next development cycle Signed-off-by: Mark Hiner <hinerm@gmail.com>

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created tagimagej/ij1-patcher

tagij1-patcher-1.2.1

Extension points for ImageJ 1.x via runtime patching to support (limited) headless operation and ImageJ2's legacy layer

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pull request commentimagej/ij1-patcher

Adapt to code changes in ij version 1.53d

@imagejan I rescued your patch: https://github.com/imagej/ij1-patcher/commit/0f3c057c9ff1bf9730e179d22a07607a538a41b9

imagejan

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Jan Eglinger

commit sha 0f3c057c9ff1bf9730e179d22a07607a538a41b9

Adapt to code changes introduced in 1.53d - moved MacAdapter to package ij.plugin

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pull request commentimagej/ij1-patcher

Adapt to code changes in ij version 1.53d

except for the MacAdapter => ij.plugin.MacAdapter-related changes in LegacyExtensions and LegacyInjector.

😭 😭 you're right, I'm so sorry!

imagejan

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pull request commentimagej/ij1-patcher

Adapt to code changes in ij version 1.53d

@hinerm wrote:

I replicated it in 54c3af1

except for the MacAdapter => ij.plugin.MacAdapter-related changes in LegacyExtensions and LegacyInjector.

imagejan

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pull request commentimagej/ij1-patcher

Adapt to code changes in ij version 1.53d

@imagejan crud I'm sorry I didn't see this. I replicated it in https://github.com/imagej/ij1-patcher/commit/54c3af15afb16986c7937088a8b753ceba45327f

imagejan

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pull request commentmastodon-sc/mastodon

ADD: ability to adjust graph model, not only reset it.

As suggested by Tobias elsewhere, another option would be to allow for controlling the listeners. Like have something like:

model.listeners().pause(); // pseudo code hein
try
{
    // Add, remove, do plenty of things in bulk
}
finally
{
    model.listeners().resume(); // fire listeners if a change happen.
}

What would you favor?

xulman

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pull request commentmastodon-sc/mastodon

ADD: ability to adjust graph model, not only reset it.

Hi, I've revamped this piece. It's been rebased to the latest master.

I could use such "official" way to pause listeners when updating graph, the original code was always clearing the graph. V.

xulman

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created tagimglib/imglib2-roi

tagimglib2-roi-0.11.0

Regions of interest (ROIs) and labelings for ImgLib2

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Mark Hiner

commit sha f1e5daae75cab827790293b0bd9c9859f160d7c8

Bump to next development cycle Signed-off-by: Mark Hiner <hinerm@gmail.com>

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Mark Hiner

commit sha 39e16ef051e1ed776059fb4728b6cf5f8bc237cd

Bye bye 2020!

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Mark Hiner

commit sha 4e80eb5511d4b51eef932b0563a27ab49dbb9631

Increase minor version 96f454cb5f6f506825b69d24149dc997ea5e4c31 adds new API

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Mark Hiner

commit sha e7f6f0cc8561d00736b665aa686ef6d199b58abd

Bump pom-scijava to 30.0.0 RealIntervals now validate their own dimensions, so we do not have to add a layer of checking on top.

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issue commenttrakem2/TrakEM2

Update pom-scijava to 30.0.0

Yes! see #25 (07d67a9?diff=split&w=1). The PR may be a bit outdated, but it does exactly that.

@tferr oh perfect. I opened https://github.com/trakem2/TrakEM2/pull/28 which includes your changes and updates the pom as well, now that we have something to pin to.

hinerm

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pull request commenttrakem2/TrakEM2

Pom scijava 30.0.0

@acardona @axtimwalde

This PR includes and can replace https://github.com/trakem2/TrakEM2/pull/25

Can you merge this and cut a new minor release? Then I can make a new pom-scijava and get everything into Fiji.

hinerm

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PR opened trakem2/TrakEM2

Pom scijava 30.0.0

Closes #27

+16 -18

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issue closedfiji/fiji

How can I save 16 bit images sequence to amira ascii format

How can I save 16 bit images sequence to amira ascii format. Works when images are 8 bits.

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gitlabspy

issue commenttrakem2/TrakEM2

Update pom-scijava to 30.0.0

Yes! see #25 (https://github.com/trakem2/TrakEM2/pull/25/commits/07d67a947fd7c23d2b608c4b46b55f50338482cf?diff=split&w=1). The PR may be a bit outdated, but it does exactly that.

hinerm

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Mark Hiner

commit sha c6647c9fdd04a548cab7cd60846a8d7bf3fa620f

Bump to pom-scijava 30.0.0 This is not strictly necessary, but pom-scijava 12.0.0 + pom-scijava-base 2.0.0 do not have a version property for net.imagej:ij, instead using the older imagej1.version, which can make attempts at overriding the version unexpected.

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