Crash when pressing Run for selected after having selected a cell with the rectangle tool

[bpavie]

QuPath:
Version: 0.6.0
Java version:
21.0.7

Windows 11

Server installation:

conda create -n samapi -y python=3.10
conda activate samapi 
pip install "torch>=2.3.1,<2.4" torchvision --index-url https://download.pytorch.org/whl/cu118
python -m pip install git+https://github.com/ksugar/samapi.git

Start server:

(samapi) C:\Users\u0094799>uvicorn samapi.main:app --workers 2
INFO:     Uvicorn running on http://127.0.0.1:8000 (Press CTRL+C to quit)
INFO:     Started parent process [7100]
C:\GBW_MyPrograms\mambaforge\envs\samapi\lib\site-packages\mobile_sam\modeling\tiny_vit_sam.py:656: UserWarning: Overwriting tiny_vit_5m_224 in registry with mobile_sam.modeling.tiny_vit_sam.tiny_vit_5m_224. This is because the name being registered conflicts with an existing name. Please check if this is not expected.
  return register_model(fn_wrapper)
C:\GBW_MyPrograms\mambaforge\envs\samapi\lib\site-packages\mobile_sam\modeling\tiny_vit_sam.py:656: UserWarning: Overwriting tiny_vit_11m_224 in registry with mobile_sam.modeling.tiny_vit_sam.tiny_vit_11m_224. This is because the name being registered conflicts with an existing name. Please check if this is not expected.
  return register_model(fn_wrapper)
C:\GBW_MyPrograms\mambaforge\envs\samapi\lib\site-packages\mobile_sam\modeling\tiny_vit_sam.py:656: UserWarning: Overwriting tiny_vit_21m_224 in registry with mobile_sam.modeling.tiny_vit_sam.tiny_vit_21m_224. This is because the name being registered conflicts with an existing name. Please check if this is not expected.
  return register_model(fn_wrapper)
C:\GBW_MyPrograms\mambaforge\envs\samapi\lib\site-packages\mobile_sam\modeling\tiny_vit_sam.py:656: UserWarning: Overwriting tiny_vit_21m_384 in registry with mobile_sam.modeling.tiny_vit_sam.tiny_vit_21m_384. This is because the name being registered conflicts with an existing name. Please check if this is not expected.
  return register_model(fn_wrapper)
C:\GBW_MyPrograms\mambaforge\envs\samapi\lib\site-packages\mobile_sam\modeling\tiny_vit_sam.py:656: UserWarning: Overwriting tiny_vit_21m_512 in registry with mobile_sam.modeling.tiny_vit_sam.tiny_vit_21m_512. This is because the name being registered conflicts with an existing name. Please check if this is not expected.
  return register_model(fn_wrapper)
C:\GBW_MyPrograms\mambaforge\envs\samapi\lib\site-packages\mobile_sam\modeling\tiny_vit_sam.py:656: UserWarning: Overwriting tiny_vit_5m_224 in registry with mobile_sam.modeling.tiny_vit_sam.tiny_vit_5m_224. This is because the name being registered conflicts with an existing name. Please check if this is not expected.
  return register_model(fn_wrapper)
C:\GBW_MyPrograms\mambaforge\envs\samapi\lib\site-packages\mobile_sam\modeling\tiny_vit_sam.py:656: UserWarning: Overwriting tiny_vit_11m_224 in registry with mobile_sam.modeling.tiny_vit_sam.tiny_vit_11m_224. This is because the name being registered conflicts with an existing name. Please check if this is not expected.
  return register_model(fn_wrapper)
C:\GBW_MyPrograms\mambaforge\envs\samapi\lib\site-packages\mobile_sam\modeling\tiny_vit_sam.py:656: UserWarning: Overwriting tiny_vit_21m_224 in registry with mobile_sam.modeling.tiny_vit_sam.tiny_vit_21m_224. This is because the name being registered conflicts with an existing name. Please check if this is not expected.
  return register_model(fn_wrapper)
C:\GBW_MyPrograms\mambaforge\envs\samapi\lib\site-packages\mobile_sam\modeling\tiny_vit_sam.py:656: UserWarning: Overwriting tiny_vit_21m_384 in registry with mobile_sam.modeling.tiny_vit_sam.tiny_vit_21m_384. This is because the name being registered conflicts with an existing name. Please check if this is not expected.
  return register_model(fn_wrapper)
C:\GBW_MyPrograms\mambaforge\envs\samapi\lib\site-packages\mobile_sam\modeling\tiny_vit_sam.py:656: UserWarning: Overwriting tiny_vit_21m_512 in registry with mobile_sam.modeling.tiny_vit_sam.tiny_vit_21m_512. This is because the name being registered conflicts with an existing name. Please check if this is not expected.
  return register_model(fn_wrapper)
C:\GBW_MyPrograms\mambaforge\envs\samapi\lib\site-packages\sam2\modeling\sam\transformer.py:23: UserWarning: Flash Attention is disabled as it requires a GPU with Ampere (8.0) CUDA capability.
  OLD_GPU, USE_FLASH_ATTN, MATH_KERNEL_ON = get_sdpa_settings()
C:\GBW_MyPrograms\mambaforge\envs\samapi\lib\site-packages\sam2\modeling\sam\transformer.py:23: UserWarning: Flash Attention is disabled as it requires a GPU with Ampere (8.0) CUDA capability.
  OLD_GPU, USE_FLASH_ATTN, MATH_KERNEL_ON = get_sdpa_settings()
INFO:     Started server process [27488]
INFO:     Waiting for application startup.
INFO:     Application startup complete.
INFO:     Started server process [25592]
INFO:     Waiting for application startup.
INFO:     Application startup complete.

When I start the plugin in QuPath after having started the server, which point to the address http://127.0.0.1:8000, I get the following warning:

even if the address is the one given when I start the server.

Then, when I use the rectangle tool draw one and press Run for selected, it crash:

Cannot invoke "org.elephant.sam.entities.SAMWeights.getUrl()" because the return value of "javafx.beans.property.ObjectProperty.get()" is null
java.lang.NullPointerException: Cannot invoke "org.elephant.sam.entities.SAMWeights.getUrl()" because the return value of "javafx.beans.property.ObjectProperty.get()" is null
	at org.elephant.sam.commands.SAMMainCommand.submitDetectionTask(SAMMainCommand.java:1217)
	at org.elephant.sam.commands.SAMMainCommand.runPrompt2D(SAMMainCommand.java:593)
	at org.elephant.sam.commands.SAMMainCommand.runPrompt(SAMMainCommand.java:605)
	at org.elephant.sam.ui.SAMPromptPane.lambda$addButtons$13(SAMPromptPane.java:444)
	at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
	at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:232)
	at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:189)
	at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
	at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
	at javafx.event.Event.fireEvent(Event.java:199)
	at javafx.scene.Node.fireEvent(Node.java:8963)
	at javafx.scene.control.Button.fire(Button.java:203)
	at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:207)
	at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274)
	at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247)
	at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
	at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:232)
	at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:189)
	at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
	at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
	at javafx.event.Event.fireEvent(Event.java:199)
	at javafx.scene.Scene$MouseHandler.process(Scene.java:3987)
	at javafx.scene.Scene.processMouseEvent(Scene.java:1893)
	at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2711)
	at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:411)
	at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:301)
	at java.base/java.security.AccessController.doPrivileged(Unknown Source)
	at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:450)
	at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:430)
	at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:449)
	at com.sun.glass.ui.View.handleMouseEvent(View.java:560)
	at com.sun.glass.ui.View.notifyMouse(View.java:946)
	at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
	at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:184)
	at java.base/java.lang.Thread.run(Unknown Source)

[carlosuc3m]

I am having the same problem, it seems that the api is expecting weigths but it receives samweigths.
It is a conflict in versions, if you install qupath-sam-extension 0.6.0 and have the api version 0.6.1 installed it will work fine.
@bpavie

[bpavie]

Thanks @carlosuc3m , but i still struggle to make it work.

I installed version v0.6.0 of the qupath-extension-sam plugin and use it on QuPath 0.6.0.

The samapi version installed is 0.6.1

I started the server :

conda activate samapi
uvicorn samapi.main:app --workers 2
INFO:     Uvicorn running on http://127.0.0.1:8000 (Press CTRL+C to quit)

I set the server path in the plugin to http://127.0.0.1:8000/sam

But I still get the same error.

In the log of the sampi server, I can see:

INFO:     127.0.0.1:62040 - "GET /samweights/?type=sam2_l HTTP/1.1" 404 Not Found

when I start the plugin in QuPath via Extension>SAM

Not sure what to do exactly... ;-(

[carlosuc3m]

make sure there is no other qupath extension installed. It is what worked for me.
In your browser paste http://127.0.0.1:8000/sam/weights and you will see some info.
However, http://127.0.0.1:8000/sam/samweights does not exist, which is what the code is looking for.

Just in case, i have not developed QuPath SAM, nor I am familiar with the codebase but I had the same issue and that is what fixed it for me.

@ksugar is the great developer behind this