setChannelWindow ArrayIndexOutOfBoundsException uint16 czi

[will-moore]

Not sure if this is the right repo for this issue?

Initially reported automatically from demo server and reproduced locally with the czi from https://forum.image.sc/t/zoom-from-overview-to-detailed-scan-for-imported-czi-files/85002/7
Both are uint16 images.

If you set the start channel slider > 4096 then you get the exception below.

I haven't managed to reproduce this on any other uint16 images

Traceback (most recent call last):
  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/django/core/handlers/exception.py", line 47, in inner
    response = get_response(request)
  File "/opt/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 "/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/decorators.py", line 538, in wrapped
    retval = f(request, *args, **kwargs)
  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/webgateway/views.py", line 1127, in render_image
    pi = _get_prepared_image(request, iid, server_id=server_id, conn=conn)
  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/webgateway/views.py", line 964, in _get_prepared_image
    if not img.setActiveChannels(requestedChannels, windows, colors, invert_flags):
  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 7953, in wrapped
    return f(self, *args, **kwargs)
  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 8872, in setActiveChannels
    invertMaps, reverseMaps, False)
  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 7953, in wrapped
    return f(self, *args, **kwargs)
  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 8851, in set_active_channels
    self._conn.SERVICE_OPTS)
  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 4859, in __call__
    return self.handle_exception(e, *args, **kwargs)
  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/webclient/webclient_gateway.py", line 2123, in handle_exception
    super(OmeroWebSafeCallWrapper, self).handle_exception(e, *args, **kwargs)
  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 4856, in __call__
    return self.f(*args, **kwargs)
  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero_api_RenderingEngine_ice.py", line 1748, in setChannelWindow
    return _M_omero.api.RenderingEngine._op_setChannelWindow.invoke(self, ((w, start, end), _ctx))

Exception Type: InternalException at /webclient/render_image/302784/0/0/
Exception Value: exception ::omero::InternalException
{
    serverStackTrace = ome.conditions.InternalException:  Wrapped Exception: (java.lang.ArrayIndexOutOfBoundsException):
null

    serverExceptionClass = ome.conditions.InternalException
    message =  Wrapped Exception: (java.lang.ArrayIndexOutOfBoundsException):
null
}

[sbesson]

Sounds like either an incorrect request is being passed or there is a mismatch between the pixel type populated in the metadata and the real data type. What is the version of OMERO.server (and ultimately Bio-Formats) in the deployment where this sample file was imported? And which series / image name does ID 302784 correspond to?

[will-moore]

This is reproducible on current demo server:
https://demo.openmicroscopy.org/webgateway/render_image/302781/0/0/?c=1|4100:4468$FF0000,2|416:4462$00FF00,3|409:4414$0000FF

and merge-ci:
https://merge-ci.openmicroscopy.org/web/webclient/render_image/24121/0/0/?c=1|4100:4660$FF0000,2|211:3805$00FF00,3|239:3537$0000FF

So it's latest OMERO.server and Bio-Formats.

[sbesson]

This issue can be reproduced by using any file where the significant bits is lower than the total number of bits implied by the pixel type. A common real-world scenario like the CZI file linked above would be a 12-bit camera saved the data as uint16.

The exception can minimally be reproduced using a synthetic image generated with Bio-Formats with a number of valid bytes lower than the total number of bits in the pixel type e.g. test&pixelType=uint16&bitsPerPixel=12.fake, importing it into OMERO and then selecting a rendering range outside [0, 4096[ in that case.

The relevant place in the renderer code making use of this metadata is

omero-renderer/src/main/java/omeis/providers/re/metadata/StatsFactory.java

Lines 238 to 251 in a239fb6

	// Use significant bits if they are available for integral pixel types.
	Integer significantBits = metadata.getSignificantBits();
	if (significantBits == null) {
	significantBits = type.getBitSize();
	}
	significantBits = Math.min(significantBits, type.getBitSize());
	if (FormatTools.isSigned(bfPixelsType)) {
	minmax[0] = -Math.pow(2, significantBits - 1);
	minmax[1] = Math.pow(2, significantBits - 1) - 1;
	} else {
	minmax[0] = 0;
	minmax[1] = Math.pow(2, significantBits) - 1;
	}
	return minmax;

but I haven't established whether this is a bug at the renderer level which should be able to set channel windows outside the dynamic range set by the significant bits or whether the client is expected to be aware of this limitation. In the latter case, an InternalException caused by an ArrayIndexOutOfBoundsException still does not feel like the greatest and there is probably a better way to communicate to the caller that the selected range is not relevant

[will-moore]

Do OMERO clients need to know about bitsPerPixel or even have a way to access it?
As a client, if I set the rendering start value greater than the brightest pixel then I would expect to render a black image, regardless of what the bitsPerPixel value is (I shouldn't need to care about it).
To teach all the clients about it seems like a lot of work for no real gain.

[sbesson]

To expand on the above, the error in this case comes from

omero-renderer/src/main/java/omeis/providers/re/quantum/Quantization_8_16_bit.java

Lines 243 to 245 in a239fb6

	for (; x < dStart; ++x) {
	LUT[x - lutMin] = (byte) cdStart;
	}

as shown in the server-side stack trace

java.lang.ArrayIndexOutOfBoundsException: Index 4096 out of bounds for length 4096
	at omeis.providers.re.quantum.Quantization_8_16_bit.buildLUT(Quantization_8_16_bit.java:244)
	at omeis.providers.re.quantum.Quantization_8_16_bit.onWindowChange(Quantization_8_16_bit.java:280)
	at omeis.providers.re.quantum.QuantumStrategy.setWindow(QuantumStrategy.java:296)
	at omeis.providers.re.Renderer.setChannelWindow(Renderer.java:795)
	at ome.services.RenderingBean.setChannelWindow(RenderingBean.java:1519)
	at jdk.internal.reflect.GeneratedMethodAccessor1883.invoke(Unknown Source)