Split view figure big images #412

will-moore · 2022-10-05T10:14:17Z

Fixes #391

To test:

Select 1 or more images, including a Big image
Run Split_View_Figure script
Big Image won't be included in the UI and a warning is shown:

snoopycrimecop · 2022-10-07T00:43:07Z

Conflicting PR. Removed from build OMERO-python-superbuild-push#1211. See the console output for more details.
Possible conflicts:

PR Right panel performance fixes #17 will-moore 'Right panel performance fixes'
- omeroweb/webclient/views.py
PR Query string ids #225 will-moore 'Query string ids'
- omeroweb/webclient/views.py
PR Handle chgrp dry-run LogicalChannel[ID] to show images #399 will-moore 'Handle chgrp dry-run LogicalChannel[ID] to show images'
- omeroweb/webclient/views.py
PR Allow multiple file-annotations to be uploaded #410 will-moore 'Allow multiple file-annotations to be uploaded'
- omeroweb/webclient/views.py

--conflicts

jburel · 2023-01-10T13:48:24Z

@will-moore This PR could also be considered but first other PRs will need to be excluded due to the conflict so it can be tested

snoopycrimecop · 2023-01-11T00:34:31Z

Conflicting PR. Removed from build OMERO-python-superbuild-push#114. See the console output for more details.
Possible conflicts:

PR Right panel performance fixes #17 will-moore 'Right panel performance fixes'
- omeroweb/webclient/views.py
PR Query string ids #225 will-moore 'Query string ids'
- omeroweb/webclient/views.py
Upstream changes
- omeroweb/webclient/views.py

~~--conflicts~~ Conflict resolved in build OMERO-python-superbuild-push#1318. See the console output for more details.

jburel · 2023-01-16T10:02:15Z

Select a big image only
The image is correctly not added to the UI
Warning message is displayed
I can still click on the button to create a figure. This should be disabled

Error in the info

WARNING:omero.gateway:ApiUsageException on <class 'omero.gateway.OmeroGatewaySafeCallWrapper'> to <0f04e147-e94c-4fd9-aafd-b93befe2eb70omero.api.RenderingEngine> renderCompressed((object #0 (::omero::romio::PlaneDef)
{
    slice = 0
    x = 0
    y = 0
    z = 0
    t = 0
    region = <nil>
    stride = 0
},), {})
Traceback (most recent call last):
  File "/home/omero/workspace/OMERO-server/.venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 4863, in __call__
    return self.f(*args, **kwargs)
  File "/home/omero/workspace/OMERO-server/.venv3/lib64/python3.6/site-packages/omero_api_RenderingEngine_ice.py", line 913, in renderCompressed
    return _M_omero.api.RenderingEngine._op_renderCompressed.invoke(self, ((_def, ), _ctx))
omero.ApiUsageException: exception ::omero::ApiUsageException
{
    serverStackTrace = ome.conditions.ApiUsageException: 78656Ã—106560 plane too large, cannot exceed 2^31 pixels
	at omeis.providers.re.RGBIntBuffer.<init>(RGBIntBuffer.java:63)
	at omeis.providers.re.RenderingStrategy.getIntBuffer(RenderingStrategy.java:186)
	at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:291)
	at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:558)
	at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:512)
	at ome.services.RenderingBean.renderCompressed(RenderingBean.java:542)
	at sun.reflect.GeneratedMethodAccessor2181.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
	at com.sun.proxy.$Proxy122.renderCompressed(Unknown Source)
	at sun.reflect.GeneratedMethodAccessor2181.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
	at com.sun.proxy.$Proxy122.renderCompressed(Unknown Source)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172)
	at ome.services.throttling.Callback.run(Callback.java:56)
	at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
	at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140)
	at ome.services.blitz.impl.RenderingEngineI.renderCompressed_async(RenderingEngineI.java:354)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at omero.cmd.CallContext.invoke(CallContext.java:85)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
	at com.sun.proxy.$Proxy124.renderCompressed_async(Unknown Source)
	at omero.api._RenderingEngineTie.renderCompressed_async(_RenderingEngineTie.java:298)
	at omero.api._RenderingEngineDisp.___renderCompressed(_RenderingEngineDisp.java:1028)
	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:2418)
	at IceInternal.Incoming.invoke(Incoming.java:221)
	at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
	at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
	at Ice.ConnectionI.message(ConnectionI.java:1056)
	at IceInternal.ThreadPool.run(ThreadPool.java:395)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
	at java.lang.Thread.run(Thread.java:748)

    serverExceptionClass = ome.conditions.ApiUsageException
    message = 78656Ã—106560 plane too large, cannot exceed 2^31 pixels
}
Traceback (most recent call last):
  File "./script", line 803, in <module>
    run_script()
  File "./script", line 791, in run_script
    [file_annotation, message] = split_view_figure(conn, script_params)
  File "./script", line 634, in split_view_figure
    height, image_labels, algorithm, stepping, scalebar, overlay_colour)
  File "./script", line 385, in make_split_view_figure
    algorithm, stepping, scalebar, overlay_colour)
  File "./script", line 209, in get_split_view
    overlay = re.renderCompressed(plane_def)
  File "/home/omero/workspace/OMERO-server/.venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 4866, in __call__
    return self.handle_exception(e, *args, **kwargs)
  File "/home/omero/workspace/OMERO-server/.venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 4863, in __call__
    return self.f(*args, **kwargs)
  File "/home/omero/workspace/OMERO-server/.venv3/lib64/python3.6/site-packages/omero_api_RenderingEngine_ice.py", line 913, in renderCompressed
    return _M_omero.api.RenderingEngine._op_renderCompressed.invoke(self, ((_def, ), _ctx))
omero.ApiUsageException: exception ::omero::ApiUsageException
{
    serverStackTrace = ome.conditions.ApiUsageException: 78656Ã—106560 plane too large, cannot exceed 2^31 pixels
	at omeis.providers.re.RGBIntBuffer.<init>(RGBIntBuffer.java:63)
	at omeis.providers.re.RenderingStrategy.getIntBuffer(RenderingStrategy.java:186)
	at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:291)
	at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:558)
	at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:512)
	at ome.services.RenderingBean.renderCompressed(RenderingBean.java:542)
	at sun.reflect.GeneratedMethodAccessor2181.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
	at com.sun.proxy.$Proxy122.renderCompressed(Unknown Source)
	at sun.reflect.GeneratedMethodAccessor2181.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
	at com.sun.proxy.$Proxy122.renderCompressed(Unknown Source)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172)
	at ome.services.throttling.Callback.run(Callback.java:56)
	at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
	at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140)
	at ome.services.blitz.impl.RenderingEngineI.renderCompressed_async(RenderingEngineI.java:354)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at omero.cmd.CallContext.invoke(CallContext.java:85)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
	at com.sun.proxy.$Proxy124.renderCompressed_async(Unknown Source)
	at omero.api._RenderingEngineTie.renderCompressed_async(_RenderingEngineTie.java:298)
	at omero.api._RenderingEngineDisp.___renderCompressed(_RenderingEngineDisp.java:1028)
	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:2418)
	at IceInternal.Incoming.invoke(Incoming.java:221)
	at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
	at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
	at Ice.ConnectionI.message(ConnectionI.java:1056)
	at IceInternal.ThreadPool.run(ThreadPool.java:395)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
	at java.lang.Thread.run(Thread.java:748)

    serverExceptionClass = ome.conditions.ApiUsageException
    message = 78656Ã—106560 plane too large, cannot exceed 2^31 pixels
}

will-moore · 2023-01-17T09:35:10Z

@jburel That last commit should disable the Submit if there are no images

jburel · 2023-01-17T09:50:17Z

The Submit button is now disabled.
There is still a problem:

Select 2 images, one is a big image
Only one in the UI: expected
Error message in info

{
slice = 0
x = 0
y = 0
z = 0
t = 0
region =
stride = 0
},), {})
Traceback (most recent call last):
File "/home/omero/workspace/OMERO-server/.venv3/lib64/python3.6/site-packages/omero/gateway/init.py", line 4863, in call
return self.f(*args, **kwargs)
File "/home/omero/workspace/OMERO-server/.venv3/lib64/python3.6/site-packages/omero_api_RenderingEngine_ice.py", line 913, in renderCompressed
return _M_omero.api.RenderingEngine._op_renderCompressed.invoke(self, ((_def, ), _ctx))
omero.ApiUsageException: exception ::omero::ApiUsageException
{
serverStackTrace = ome.conditions.ApiUsageException: 62425Ã—60101 plane too large, cannot exceed 2^31 pixels
at omeis.providers.re.RGBIntBuffer.(RGBIntBuffer.java:63)
at omeis.providers.re.RenderingStrategy.getIntBuffer(RenderingStrategy.java:186)
at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:291)
at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:558)
at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:512)
at ome.services.RenderingBean.renderCompressed(RenderingBean.java:542)
at sun.reflect.GeneratedMethodAccessor2173.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)

indicates that the big image is still pass to the server.

Since this PR still requires some work, we should not hold back on the dependencies upgrade work and include this PR in a later version and release asap

jburel · 2023-01-17T11:18:44Z

This time:

Selected 2 images (not big). Both images are in the UI. The figure is created with the 2 images and attached to the first one
Selected 2 images: one big. Only the "small" image is in the UI. The figure is created with 1 image and attached to the image
Select one big image only:

 File "/home/omero/workspace/OMERO-web/.venv3/lib64/python3.6/site-packages/django/core/handlers/exception.py", line 47, in inner
    response = get_response(request)

  File "/home/omero/workspace/OMERO-web/.venv3/lib64/python3.6/site-packages/django/core/handlers/base.py", line 181, in _get_response
    response = wrapped_callback(request, *callback_args, **callback_kwargs)

  File "/home/omero/workspace/OMERO-web/.venv3/lib64/python3.6/site-packages/omeroweb/decorators.py", line 544, in wrapped
    retval = f(request, *args, **kwargs)

  File "/home/omero/workspace/OMERO-web/.venv3/lib64/python3.6/site-packages/omeroweb/decorators.py", line 603, in wrapper
    context = f(request, *args, **kwargs)

  File "/home/omero/workspace/OMERO-web/.venv3/lib64/python3.6/site-packages/omeroweb/webclient/views.py", line 4271, in figure_script
    image = validImages[imageIds[0]]

IndexError: list index out of range

<WSGIRequest: GET '/web/webclient/figure_script/SplitView/?Image=105665'>

jburel · 2023-02-14T21:24:52Z

I have removed exclude label. This will be included in the build

will-moore · 2023-02-17T14:13:00Z

Since the Split-View Figure is broken now (see #443 (comment)) and might be removed, this PR is on-hold till that is resolved

will-moore · 2023-02-24T13:03:54Z

The issues with #443 (comment) are now resolved, so this is ready for another test.

will-moore · 2023-03-07T06:47:20Z

Saw from demo today - coming from Split-View figure...

Internal Server Error: /webclient/render_image/249148/

ApiUsageException at /webclient/render_image/249148/
exception ::omero::ApiUsageException
{
    serverStackTrace = ome.conditions.ApiUsageException: 81672×37589 plane too large, cannot exceed 2^31 pixels

will-moore · 2023-03-09T16:11:23Z

Ready for a "final" test... I'll list in standup...

pwalczysko · 2023-03-10T11:02:12Z

Tested all the workflows mentioned above by @jburel - lgtm

will-moore added 2 commits October 5, 2022 11:11

Warning and remove Big images from Split_View_Figure

5e5cf32

Also add big image warning to MakeMovie script UI

b11d5df

Move new lines to avoid merge conflict

4b55425

will-moore force-pushed the split_view_figure_big_images branch from 8179663 to 4b55425 Compare January 13, 2023 06:50

Disable Split View Figure submit if no images

bfc9a1f

Really remove Big Images from split view figure script

ae638d8

Fix error if no valid images

15f0354

pwalczysko approved these changes Mar 10, 2023

View reviewed changes

knabar added this to the 5.19.0 milestone Mar 10, 2023

knabar merged commit 3f6061a into ome:master Mar 15, 2023

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Split view figure big images #412

Split view figure big images #412

will-moore commented Oct 5, 2022

snoopycrimecop commented Oct 7, 2022

jburel commented Jan 10, 2023

snoopycrimecop commented Jan 11, 2023 •

edited

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edited

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will-moore commented Jan 17, 2023

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will-moore commented Feb 24, 2023

will-moore commented Mar 7, 2023

will-moore commented Mar 9, 2023

pwalczysko commented Mar 10, 2023

Split view figure big images #412

Split view figure big images #412

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will-moore commented Oct 5, 2022

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will-moore commented Feb 24, 2023

will-moore commented Mar 7, 2023

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