Closed thanneken closed 5 years ago
The Null pointers are because of
[INFO] What is transmissive source ...Ambrosiana_C73inf_116_TX500CN_041.tif
Since you use short names, there is an elipses instead of the the directory path. A crucial line of code was removed in a previous commit
transmissiveSource = transmissiveSource.replace("...", transmissive_gamma_dir.toString()+File.separator); //in case of shortName
which ensures even in the case of wanting short names that this variable stores the actual Path.
Still getting a null pointer exception in Extended Spectrum. Here is the log:
[INFO] shotFileNames: false
[INFO] Set a fixed brightness value. It is 1.0
[INFO] List of transmissive sources
[INFO] [/home/thanneken/Downloads/Ambrosiana_C73inf_115/Captures-Transmissive-Gamma/Ambrosiana_C73inf_115_TX500CN_041.tif, /home/thanneken/Downloads/Ambrosiana_C73inf_115/Captures-Transmissive-Gamma/Ambrosiana_C73inf_115_TX580YL_040.tif, /home/thanneken/Downloads/Ambrosiana_C73inf_115/Captures-Transmissive-Gamma/Ambrosiana_C73inf_115_TX735IR_042.tif, /home/thanneken/Downloads/Ambrosiana_C73inf_115/Captures-Transmissive-Gamma/Ambrosiana_C73inf_115_TX940IR_039.tif]
[INFO] Gathered 56 raking image selections.
[INFO] [false, true, false, false, false, false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, true, false, false, false, true, false]
[INFO] We should have red, green and blue narrow bands
[INFO] [Ambrosiana_C73inf_115_MB630RD_009_F.tif, Ambrosiana_C73inf_115_MB655DR_010_F.tif, Ambrosiana_C73inf_115_MB735IR_012_F.tif, Ambrosiana_C73inf_115_MB850IR_013_F.tif, Ambrosiana_C73inf_115_MB940IR_014_F.tif]
[INFO] [Ambrosiana_C73inf_115_MB505CN_004_F.tif, Ambrosiana_C73inf_115_MB530GN_005_F.tif, Ambrosiana_C73inf_115_MB560LI_006_F.tif, Ambrosiana_C73inf_115_MB590AM_007_F.tif, Ambrosiana_C73inf_115_MB615RO_008_F.tif]
[INFO] [Ambrosiana_C73inf_115_MB365UV_011_F.tif, Ambrosiana_C73inf_115_MB420VI_001_F.tif, Ambrosiana_C73inf_115_MB450RB_002_F.tif, Ambrosiana_C73inf_115_MB470LB_003_F.tif]
Sep 27, 2018 5:36:39 PM com.slu.imagej.SpectralRTI_Toolkit run
SEVERE: null
java.lang.NullPointerException
at com.slu.imagej.SpectralRTI_Toolkit.theMacro_tested(SpectralRTI_Toolkit.java:1685)
at com.slu.imagej.SpectralRTI_Toolkit.run(SpectralRTI_Toolkit.java:2445)
at org.scijava.command.CommandModule.run(CommandModule.java:199)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
[WARNING] Finished processing the run().
Similar result with and without short filenames. Is 'shotFileNames' a deliberate shortening of short?
Also noticed that the log says the brightness multiplier was set to 1. I had set it to normalize based on a user-selected a region of interest. Actually maybe that is right for the RTI processing, and the ROI normalization is for a later/different step, the raking processing.
With PCA:
[INFO] List of transmissive sources
[INFO] [/home/thanneken/Downloads/Ambrosiana_C73inf_115/Captures-Transmissive-Gamma/Ambrosiana_C73inf_115_TX500CN_041.tif, /home/thanneken/Downloads/Ambrosiana_C73inf_115/Captures-Transmissive-Gamma/Ambrosiana_C73inf_115_TX580YL_040.tif, /home/thanneken/Downloads/Ambrosiana_C73inf_115/Captures-Transmissive-Gamma/Ambrosiana_C73inf_115_TX735IR_042.tif, /home/thanneken/Downloads/Ambrosiana_C73inf_115/Captures-Transmissive-Gamma/Ambrosiana_C73inf_115_TX940IR_039.tif]
[INFO] Gathered 56 raking image selections.
[INFO] [false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false]
[INFO] Got PCA method: Generate and manually select two
Sep 27, 2018 5:45:12 PM com.slu.imagej.SpectralRTI_Toolkit run
SEVERE: null
java.lang.NullPointerException
at com.slu.imagej.SpectralRTI_Toolkit.theMacro_tested(SpectralRTI_Toolkit.java:1931)
at com.slu.imagej.SpectralRTI_Toolkit.run(SpectralRTI_Toolkit.java:2445)
at org.scijava.command.CommandModule.run(CommandModule.java:199)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
[WARNING] Finished processing the run().
Windows 7 ImageJ 1.52h All version of included plugins in the GitHub code page - notOK branch, most importantly Stack_Manipulation-2.0.1 ImageJ Java version 1.8.0_172 (64 bit)
Testing these today, I was not able to replicate these NullPointerExceptions. Hopefully this round of big fixes hit what was causing the problem.
I just go through a complete run of the typical processing set on linux... no errors.
I'm not sure what is meant above about the plugins and the notOK branch. I was using the latest jar from the master branch.
Plugin Version: 0.0.9 ImageJ 1.52g, 2.0.0-rc-68 What was the specific component that changed? Operating systems tested: Windows10, Linux Prefs file: Appropriate file separators added/verified before starting (see separate issue)
(It didn't like this prefs file, asked to locate fitter and deferred batch, wrote back the prefs file with forward slashes on Windows)
Tested Task Set 1: Accurate Color RTI, WebRTI, raking Result 1:
Tested Task Set 2: PCA Pseudo RTI, WebRTI, raking Result 2:
Tested Task Set 3: Custom RTI, WebRTI, raking Result 3: pop up message: "There are no windows open"