get_polygons_from_binary_mask issue #47
Description
Hi @carlosuc3m,
When running SAMJ from the GUI using the preset prompts mode (ROIs - rectangular selections) it stops prematurely before processing all ROIs (after ~50 ROIs).
When running run("SAMJ Annotator", "model=[SAM2 Large] export=true"); , also using rectangular selections in ROI manager. It also stops prematurely.
I get the error below:
(Fiji Is Just) ImageJ 2.16.0/1.54p; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 308MB of 48873MB (<1%)
java.lang.RuntimeException: Traceback (most recent call last):
File "E:\Fiji.app\appose_x86_64\envs\sam2\Lib\site-packages\appose\python_worker.py", line 123, in execute_script
exec(compile(block, "<string>", mode="exec"))
File "<string>", line 81, in <module>
File "<string>", line 138, in get_polygons_from_binary_mask
ValueError: attempt to get argmax of an empty sequence
at ai.nets.samj.models.AbstractSamJ.processAndRetrieveContours(AbstractSamJ.java:423)
at ai.nets.samj.models.AbstractSamJ.processBatchOfPrompts(AbstractSamJ.java:540)
at ai.nets.samj.communication.model.SAMModel.processBatchOfPrompts(SAMModel.java:195)
at ai.nets.samj.ij.SAMJ_Annotator.macroRunSAMJ(SAMJ_Annotator.java:411)
at ai.nets.samj.ij.SAMJ_Annotator.runMacro(SAMJ_Annotator.java:378)
at ai.nets.samj.ij.SAMJ_Annotator.run(SAMJ_Annotator.java:186)
at ij.IJ.runUserPlugIn(IJ.java:244)
at ij.IJ.runPlugIn(IJ.java:210)
at ij.Executer.runCommand(Executer.java:152)
at ij.Executer.run(Executer.java:70)
at ij.IJ.run(IJ.java:326)
at ij.IJ.run(IJ.java:337)
at ij.macro.Functions.doRun(Functions.java:703)
at ij.macro.Functions.doFunction(Functions.java:99)
at ij.macro.Interpreter.doStatement(Interpreter.java:280)
at ij.macro.Interpreter.doStatements(Interpreter.java:266)
at ij.macro.Interpreter.run(Interpreter.java:162)
at ij.macro.Interpreter.run(Interpreter.java:92)
at ij.macro.Interpreter.run(Interpreter.java:106)
at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:164)
at ij.IJ.runMacro(IJ.java:165)
at ij.IJ.runMacro(IJ.java:154)
at net.imagej.legacy.IJ1Helper$2.call(IJ1Helper.java:1185)
at net.imagej.legacy.IJ1Helper$2.call(IJ1Helper.java:1181)
at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:1132)
at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:1181)
at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:145)
at org.scijava.script.ScriptModule.run(ScriptModule.java:173)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:125)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Is there a limit ROI count in preset-prompts mode?
Thanks!