Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Tried to install and use this with imageJ v 1.50h, but it complains it cannot find it #43

Open
zimonth opened this issue Sep 7, 2017 · 1 comment
Open

Tried to install and use this with imageJ v 1.50h, but it complains it cannot find it #43

zimonth opened this issue Sep 7, 2017 · 1 comment

Comments

@zimonth
Copy link

zimonth commented Sep 7, 2017

I have Trainable_Segmentation-Trainable_Segmentation-3.2.12.jar in /usr/share/imagej/plugins, where also other installed plugins (jars) are and are working, ie. "Volume Viewer" and "3d Viewer"

It shows in the ImageJ menu: Plugins > Segmentation > Trainable Wega Segmentation

But when tried to use it:
"Plugin or class not found: "trainableSegmentation.Weka_Segmentation" (java.lang.ClassNotFoundException: trainableSegmentation.Weka_Segmentation)

The content of the jar is:

$ unzip -v /usr/share/imagej/plugins/Trainable_Segmentation-Trainable_Segmentation-3.2.12.jar 

Archive:  /usr/share/imagej/plugins/Trainable_Segmentation-Trainable_Segmentation-3.2.12.jar
2e61e42e06e80f537c40e9dde2231cc669f219a3
 Length   Method    Size  Cmpr    Date    Time   CRC-32   Name
--------  ------  ------- ---- ---------- ----- --------  ----
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/
      70  Defl:N       67   4% 05-25-2017 21:28 e8b9ec07  Trainable_Segmentation-Trainable_Segmentation-3.2.12/.gitignore
     582  Defl:N      438  25% 05-25-2017 21:28 b14a217a  Trainable_Segmentation-Trainable_Segmentation-3.2.12/.travis.yml
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/.travis/
     233  Defl:N      178  24% 05-25-2017 21:28 0cdad390  Trainable_Segmentation-Trainable_Segmentation-3.2.12/.travis/build.sh
     162  Defl:N      142  12% 05-25-2017 21:28 a97cfd57  Trainable_Segmentation-Trainable_Segmentation-3.2.12/.travis/notify.sh
     323  Defl:N      128  60% 05-25-2017 21:28 00bd632e  Trainable_Segmentation-Trainable_Segmentation-3.2.12/.travis/settings.xml
    2588  Defl:N     1255  52% 05-25-2017 21:28 13752b1f  Trainable_Segmentation-Trainable_Segmentation-3.2.12/README.md
    6202  Defl:N     1596  74% 05-25-2017 21:28 4ce3adf4  Trainable_Segmentation-Trainable_Segmentation-3.2.12/pom.xml
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/ai/
     587  Defl:N      263  55% 05-25-2017 21:28 3f6dd6b9  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/ai/AttributeClassPair.java
   14430  Defl:N     4433  69% 05-25-2017 21:28 61a977a1  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/ai/BalancedRandomForest.java
    9138  Defl:N     2622  71% 05-25-2017 21:28 747d31e0  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/ai/BalancedRandomTree.java
    5941  Defl:N     2217  63% 05-25-2017 21:28 8f16ac01  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/ai/GiniFunction.java
    5371  Defl:N     1825  66% 05-25-2017 21:28 fea62256  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/ai/InformationGainFunction.java
     525  Defl:N      270  49% 05-25-2017 21:28 ef703b89  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/ai/SplitFunction.java
    1691  Defl:N      864  49% 05-25-2017 21:28 7e57d786  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/ai/Splitter.java
    1549  Defl:N      718  54% 05-25-2017 21:28 18c7c12d  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/ai/VotesCollector.java
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/hr/
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/hr/irb/
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/hr/irb/fastRandomForest/
   10328  Defl:N     3651  65% 05-25-2017 21:28 786ddbf1  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/hr/irb/fastRandomForest/Benchmark.java
   10242  Defl:N     3218  69% 05-25-2017 21:28 bc70baae  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/hr/irb/fastRandomForest/DataCache.java
    2179  Defl:N      769  65% 05-25-2017 21:28 aa85d602  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/hr/irb/fastRandomForest/FRFAttributeEval.java
   19931  Defl:N     5173  74% 05-25-2017 21:28 f67c3102  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/hr/irb/fastRandomForest/FastRandomForest.java
   51962  Defl:N    11946  77% 05-25-2017 21:28 f7f508d9  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/hr/irb/fastRandomForest/FastRandomTree.java
   21839  Defl:N     6029  72% 05-25-2017 21:28 2a103d48  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/hr/irb/fastRandomForest/FastRfBagging.java
    7212  Defl:N     2478  66% 05-25-2017 21:28 02a0a24e  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/hr/irb/fastRandomForest/FastRfUtils.java
    4548  Defl:N     1715  62% 05-25-2017 21:28 16ea1d53  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/hr/irb/fastRandomForest/SplitCriteria.java
    3092  Defl:N     1289  58% 05-25-2017 21:28 5b81526c  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/hr/irb/fastRandomForest/VotesCollector.java
    3073  Defl:N     1334  57% 05-25-2017 21:28 6293b343  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/hr/irb/fastRandomForest/VotesCollectorDataCache.java
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/
  101846  Defl:N    16842  84% 05-25-2017 21:28 0a4f92c7  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/FeatureStack.java
   32645  Defl:N     6140  81% 05-25-2017 21:28 9607c31e  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/FeatureStack3D.java
   13196  Defl:N     3270  75% 05-25-2017 21:28 b8b2adf2  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/FeatureStackArray.java
    2473  Defl:N     1069  57% 05-25-2017 21:28 fbc59c08  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/ImageOverlay.java
    3795  Defl:N      890  77% 05-25-2017 21:28 5f72b166  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/ImageScience.java
     961  Defl:N      462  52% 05-25-2017 21:28 181dd8f7  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/ReusableDenseInstance.java
    3514  Defl:N     1402  60% 05-25-2017 21:28 5d39a24f  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/RoiListOverlay.java
   70089  Defl:N    15855  77% 05-25-2017 21:28 d20080a0  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/Trainable_Segmentation.java
  200542  Defl:N    30650  85% 05-25-2017 21:28 432f6f0f  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/WekaSegmentation.java
   99354  Defl:N    21820  78% 05-25-2017 21:28 ef126f67  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/Weka_Segmentation.java
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/filters/
    3623  Defl:N     1347  63% 05-25-2017 21:28 53d27481  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/filters/Entropy_Filter.java
   14912  Defl:N     4233  72% 05-25-2017 21:28 ddb01451  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/filters/Kuwahara.java
   10063  Defl:N     3164  69% 05-25-2017 21:28 9ddbd2cb  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/filters/Lipschitz_.java
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/metrics/
    9816  Defl:N     3032  69% 05-25-2017 21:28 82c4961b  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/metrics/AdjustedRandError.java
    3058  Defl:N     1065  65% 05-25-2017 21:28 ae7887eb  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/metrics/ClassificationStatistics.java
    1674  Defl:N      710  58% 05-25-2017 21:28 ecbb223b  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/metrics/ClusteredWarpingMismatches.java
    1666  Defl:N      567  66% 05-25-2017 21:28 17a06896  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/metrics/InformationStatistics.java
    2677  Defl:N     1141  57% 05-25-2017 21:28 36a85588  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/metrics/Metrics.java
   21479  Defl:N     4124  81% 05-25-2017 21:28 a61eb85d  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/metrics/PixelError.java
   73710  Defl:N     9946  87% 05-25-2017 21:28 e86bc3a7  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/metrics/RandError.java
   50087  Defl:N     6135  88% 05-25-2017 21:28 b7b27011  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/metrics/VariationOfInformation.java
   93543  Defl:N    15957  83% 05-25-2017 21:28 b1ed1990  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/metrics/WarpingError.java
    1177  Defl:N      649  45% 05-25-2017 21:28 5cc2107e  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/metrics/WarpingResults.java
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/utils/
     336  Defl:N      163  52% 05-25-2017 21:28 9ae59e93  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/utils/Cursor2D.java
     300  Defl:N      165  45% 05-25-2017 21:28 b40eeb0c  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/utils/Neighborhood2D.java
     560  Defl:N      263  53% 05-25-2017 21:28 6af1d0b2  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/utils/Neighborhood2DC4.java
     740  Defl:N      276  63% 05-25-2017 21:28 81609816  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/utils/Neighborhood2DC8.java
    2074  Defl:N      968  53% 05-25-2017 21:28 7fab5458  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/utils/PixelRecord.java
    3231  Defl:N     1354  58% 05-25-2017 21:28 0fa529d1  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/utils/PrincipalComponentAnalysis.java
   22604  Defl:N     5584  75% 05-25-2017 21:28 44cdca90  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/utils/Utils.java
   11753  Defl:N     3345  72% 05-25-2017 21:28 84c6156e  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/java/trainableSegmentation/utils/WatershedTransform2D.java
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/resources/
   17977  Defl:N     6857  62% 05-25-2017 21:28 804021c7  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/resources/LICENSE-FastRandomForest.txt
    4064  Defl:N     1620  60% 05-25-2017 21:28 793bc837  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/resources/README-FastRandomForest.txt
     573  Defl:N      201  65% 05-25-2017 21:28 79858fae  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/resources/plugins.config
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/resources/trainableSegmentation/
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/resources/trainableSegmentation/images/
    7588  Stored     7588   0% 05-25-2017 21:28 5c213ad3  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/main/resources/trainableSegmentation/images/weka.png
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/test/
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/test/java/
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/test/java/trainableSegmentation/
    5454  Defl:N     1750  68% 05-25-2017 21:28 11269b09  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/test/java/trainableSegmentation/BasicTest.java
     460  Defl:N      292  37% 05-25-2017 21:28 35087393  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/test/java/trainableSegmentation/TestGUI.java
       0  Stored        0   0% 05-25-2017 21:28 00000000  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/test/resources/
    5083  Defl:N     4939   3% 05-25-2017 21:28 3a64d10d  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/test/resources/bridge-expected.png
  156889  Stored   156889   0% 05-25-2017 21:28 6f20fb4c  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/test/resources/bridge.png
  943445  Defl:N   838479  11% 05-25-2017 21:28 09212d05  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/test/resources/nuclei-features.tif
    3388  Defl:N     2824  17% 05-25-2017 21:28 09a7eb2b  Trainable_Segmentation-Trainable_Segmentation-3.2.12/src/test/resources/nuclei.tif
--------          -------  ---                            -------
 2186217          1238645  43%                            86 files
@iarganda
Copy link
Collaborator

iarganda commented Sep 8, 2017

Hello @zimonth,
The Trainable Segmentation has many dependencies, namely:

jars/ij.jar,
jars/fiji-lib.jar,
plugins/Anisotropic_Diffusion_2D.jar,
jars/VIB-lib.jar,
jars/commons-math3.jar,
jars/weka-dev.jar,
jars/imglib2-algorithm.jar,
jars/imglib2-algorithm-gpl.jar,
jars/imglib2-ij.jar,
jars/imglib2.jar,
plugins/Stitching_.jar

The recommended way to have everything correctly installed is to use Fiji instead of plain ImageJ.

I hope this helps!

PS: the latest release of project is 3.2.15. You have it here. But again, it is just simpler to use Fiji and get the automatic updates of all plugins and dependencies.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@iarganda @zimonth