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axtimwalde/mpicbg 44

Fiji module for image transformation and related algorithms

acardona/Fiji-TrakEM2-scripts 4

Fiji ImageJ scripts

acardona/xmms2-clj 3

xmms2 clojure GUI front end

scijava/script-editor 3

Script Editor and Interpreter for SciJava script languages

acardona/incanter 1

Clojure-based, R-like statistical computing and graphics environment for the JVM

acardona/nxnk 1

A networkx-like wrapper for the NetworKit library

acardona/scripts 1

A collection of scripts related to neural circuit analysis and image processing for python, Fiji, TrakEM2, CATMAID, and others.

acardona/FourierConvolutionCUDALib 0

Implementation of 3d non-separable convolution using CUDA & FFT Convolution

created tagimglib/imglib2-roi

tagimglib2-roi-0.11.0

Regions of interest (ROIs) and labelings for ImgLib2

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Mark Hiner

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Mark Hiner

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Mark Hiner

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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 The PR may be a bit outdated, but it does exactly that.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 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 The PR may be a bit outdated, but it does exactly that.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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issue commenttrakem2/TrakEM2

Update pom-scijava to 30.0.0

@tferr can you suggest an alternative? Or can we re-introduce that method?

I am assuming the individual X-Y-Z methods can be looped over from 0..result.size()?

hinerm

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issue commenttrakem2/TrakEM2

Update pom-scijava to 30.0.0

https://github.com/trakem2/TrakEM2/blob/94e44580ebecafe036aeb96fa3150b7e4fa6f7af/src/main/java/ini/trakem2/display/Polyline.java#L716

This can be replaced by result.size().

https://github.com/trakem2/TrakEM2/blob/94e44580ebecafe036aeb96fa3150b7e4fa6f7af/src/main/java/ini/trakem2/display/Polyline.java#L717

That one is more difficult. The getXYZUnscaled() method was removed here:

https://github.com/morphonets/SNT/commit/8f74838884911f4276b09764372d277378872ba4#diff-9d18d39571ccc3273052cc8eb8a38f88b03cb2ef6edccde1f06956dab28288ae

@tferr can you suggest an alternative? Or can we re-introduce that method?

hinerm

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issue commenttrakem2/TrakEM2

Update pom-scijava to 30.0.0

Polyline is part of TrakEM2.

argh. Of course, thank you. Polyline itself needs its imports updated to the new packages:

import sc.fiji.snt.Path;
import sc.fiji.snt.SearchInterface;
import sc.fiji.snt.SearchProgressCallback;
import sc.fiji.snt.TracerThread;

And these lines need to be updated for changed API/field visibility.

hinerm

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issue commenttrakem2/TrakEM2

Update pom-scijava to 30.0.0

@hinerm wrote:

the ini.trakem2.display.Polyline class is no longer present in SNT.

Polyline is part of TrakEM2.

hinerm

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issue commenttrakem2/TrakEM2

Update pom-scijava to 30.0.0

@axtimwalde @acardona can one of you make this change? I do not have commit rights and am not sure how Polyline usage should be updated.

hinerm

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issue openedtrakem2/TrakEM2

Update pom-scijava to 30.0.0

As of pom-scijava 30.0.0, [the Simple_Neurite_Tracer] dependency](https://github.com/trakem2/TrakEM2/blob/94e44580ebecafe036aeb96fa3150b7e4fa6f7af/pom.xml#L218-L226) can now be updated to org.morphonets:SNT.

Some migration is necessary as TrakEM2 as the ini.trakem2.display.Polyline class is no longer present in SNT.

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Tom Kazimiers

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Export mgmt. command: include tags on connectors in export Previously, only the links to those tags where exported and not the tags themselves, leading to a consistency error during import (if tags where included). This is fixed now.

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Tom Kazimiers

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Doc: slightly improve wording in training section The referred to fly nomenclature is now the 'standard fly brain nomenclature', rather than the 'virtual fly brain nomenclature'. This is the intended meaning and avoids confusion with VFB. Thanks to Marta Costa for this suggestion!

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created tagimglib/imglib2-unsafe

tagimglib2-unsafe-0.4.0

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Mark Hiner

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

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Mark Hiner

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Good bye 2020!

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Mark Hiner

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Update to pom-scijava 29.2.1 Includes imglib2 minor bump, requiring pow added to numeric types.

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Stephan Saalfeld

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change to pom-scijava parent

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Stephan Saalfeld

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add two simplified relabel methods to UnionFind without masks and id generators, also impement them as default methods instead of static methods

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Stephan Saalfeld

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add connected components for affinity maps

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Stephan Saalfeld

commit sha 352fa0ef3326e595229aea742f58cfe025d46b2f

fix unionfind relabel bug (never 'clean up')

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Stephan Saalfeld

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connected component analysis update labelId

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Stephan Saalfeld

commit sha 8d7577905b781b097dd5fae2ccff993df3645aea

Merge branch 'master' into affinity-connected-components # Conflicts: # pom.xml

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Stephan Saalfeld

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build on jdk >8

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Stephan Saalfeld

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Merge pull request #90 from imglib/affinity-connected-components * add connected components for affinity maps * bump to pom-scijava-29.2.1 * enable building on jdk >8 * bugfixes

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Tom Kazimiers

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Export mgmt. command: don't let connectors ref. not-exorted tags If there are constraints set on which tags to export, they need to be respected by the connector-tag-link export.

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Stephan Saalfeld

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use pom-scijava as parent

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Matthias Arzt

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Smoothen the edge of the truncated Gaussian kernel in Gauss3

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Matthias Arzt

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Fix FastGauss There was an error, in one of the equations for calculating a determinant.

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Matthias Arzt

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Refactor FastGaussCalculator

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Matthias Arzt

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Improve performace of FastGaussCalculator

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Curtis Rueden

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Bump to next development cycle Signed-off-by: Curtis Rueden <ctrueden@wisc.edu>

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Curtis Rueden

commit sha 1096528b09ed05333a798c6a1fdb7168576395ab

POM: update parent to pom-scijava 29.0.0 This updates the following components: * imglib2-realtransform: 2.2.1 -> 3.0.0 * imglib2-roi: 0.9.0 -> 0.10.2 * imglib2: 5.6.3 -> 5.9.2

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Albert Cardona

commit sha 1a233eb7a66e1c98c95ec2165a60d303c1cff441

ImgMath: an implementation in plain native double rather than RealType, side by side with the RealType one. It is at least twice as fast.

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Albert Cardona

commit sha 46d8051545f93659c66909a468600f655bd1dedc

ImgMath Util: no need for LinkedList, List suffices as argument type.

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Albert Cardona

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ImgMath: Compute implements methods for trivially storing result into ArrayImg or into Img of the same kind as one of the input images, with the additional ability to define a Type for computing.

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Albert Cardona

commit sha 4834861ab156d28203d5a178d5e5ad98121357b2

ImgMath: Compute.asRandomAccessibleInterval, i.e. view of the computation without actually running anything. So, instead of copying the result into an image, merely return it as a recipe for generating the result at any one sample, with random access. Works great because computations are pixel-wise.

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Albert Cardona

commit sha c56b2d5812710983813985e7dd399aea3f0f0c96

ImgMath: Compute implements parallel processing methods based on LoopBuilder and the asRandomAccessibleInterval view of the computations.

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Albert Cardona

commit sha 1b1059549d2202745a61a9a3bd4e240d04651f10

ImgMath: static methods for computing into an image that gets created anew to contain the result of the pixel-wise computations.

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Albert Cardona

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ImgMath: static methods equal, notEqual, greaterThan and lessThan which are more readable than EQ, NEQ, GT and LT (which are otherwise the exact same thing).

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Curtis Rueden

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POM: pin imglib2 version to 5.10.0 We want to call the new pow(...) method on a RealType.

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Albert Cardona

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ImgMath: add pow as an operation, following the addition of the Pow interface to NumericType.

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Albert Cardona

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ImgMath: added documentation to parallel execution methods.

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Albert Cardona

commit sha cc919c6b5a4b6e5d0eed9e09ef1ac2b00a9d5bf4

ImgMath: new math operations Log and Exp. Not based on NumericType math as it lacks these functions. Uses RealType.setReal and RealType.getRealDouble(), which is the standard approach as used by e.g. net.imglib2.util.Util.genericRealTypeConverter.

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Curtis Rueden

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Merge pull request #87 from imglib/io-package ImgMath updates

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Albert Cardona

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ImgMath: IFunction interface is cleaner, with abstract class ViewableFunction being the first place where the view methods are declared and defined.

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Tom Kazimiers

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Export mgmt. command: use better default types It's more consistent and makes mypy happy.

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Tom Kazimiers

commit sha 3ed39491914d09cc53e6b086238b80a4d08ee19e

Export mgmt. command: fix export of connector tags So far all tag links for a projevt in the connector_class_instance table have been exported, if tags shoul be part of the export in the first place. This is a problem, because first this potentiaally adds a lot of extra data to the export and, more importantly, second it results in inconsistent exports: Connectors are referenced by the exported tag links, without the connector being present. This is fixed now.

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Tom Kazimiers

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Provide a dev version

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