mickp
commented
4 years ago Cockpit should trigger whatever cameras are active even if a light source is not active, but the exposure time will not be defined. For calibration, the Clarity uses its own internal light source. You should activate the "ambient" light source in cockpit to control exposure time.
Those messages from the BSI on startup are normal - they're warning you that certain parameters are unsupported, either by the device or by our python wrapper. On Tue, 18 Feb 2020, 09:02 Nick Hall, notifications@github.com wrote:
We recently swapped out the Andor Zyla we previously had on the Clarity for a Photometrics Prime BSI. The machine is running this branch of microscope, NickHallONBI/mirao_stuff https://github.com/NickHallONBI/microscope/tree/mirao_stuff, which has the microscope stuff for the Mirao52e DM as well as the latest commits from MicronOxford/microscope/master.
When starting up the deviceserver with the Clarity with the BSI as the slaved camera there are some errors in the log:
2020-02-18 16:41:37,340:Clarity (microscope.cameras.pvcam):WARNING:PID 12380: Skipping unsupported parameter PARAM_SMART_STREAM_EXP_PARAMS. 2020-02-18 16:41:37,341:Clarity (microscope.cameras.pvcam):WARNING:PID 12380: Skipping unsupported parameter PARAM_SMART_STREAM_DLY_PARAMS. 2020-02-18 16:41:37,346:Clarity (microscope.cameras.pvcam):WARNING:PID 12380: Skipping parameter PARAM_FRAME_BUFFER_SIZE: not supported in python.
On starting Cockpit, if you take a calibration image with no light source defined, the BSI behaves normally, the data is fetched and the calibration routine is run. However, if you define a light source (in our case, "ambient" with 100ms exposure time) you get this error:
2020-02-18 16:42:03,534:Clarity (microscope.cameras.pvcam):DEBUG:PID 12380: Fetched frame from circular buffer. 2020-02-18 16:42:04,264:Clarity (microscope.devices):ERROR:PID 12380: in _dispatch_loop: Traceback (most recent call last): File "c:\microscope\microscope\devices.py", line 540, in _dispatch_loop self._send_data(client, self._process_data(data), timestamp) File "c:\microscope\microscope\devices.py", line 706, in _process_data return super()._process_data(data) File "c:\microscope\microscope\devices.py", line 507, in _process_data return functools.reduce(lambda x, f: f(x), self.pipeline, data) File "c:\microscope\microscope\devices.py", line 507, in return functools.reduce(lambda x, f: f(x), self.pipeline, data) File "c:\microscope\microscope\filterwheels\aurox.py", line 164, in _c_process_data self._processor = ClarityProcessor(data) File "C:\clarity_processor\clarity_process.py", line 122, in init (dmidr, pos6r, diff6r) = self._find_penrose(posr) File "C:\clarity_processor\clarity_process.py", line 89, in _find_penrose dmid = np.sort(sep.ravel())[int(3.5 * n)] IndexError: index 0 is out of bounds for axis 0 with size 0
It's also worth noting that no new data is fetched and displayed in the cockpit camera viewer either. If you then turn off the light source (and now once again have no light source defined) and try and take a calibration image, you get the same error as above except the last line is changed to:
IndexError: index 3 is out of bounds for axis 0 with size 1
The "raw" and "difference" modes work fine with and without a light source being defined.
It would appear that either the Clarity and/or the BSI are not being triggered in "calibration" mode when an light source is (or has been previously) defined.
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iandobbie
NickHallPhysics
We recently swapped out the Andor Zyla we previously had on the Clarity for a Photometrics Prime BSI. The machine is running this branch of microscope, NickHallONBI/mirao_stuff, which has the microscope stuff for the Mirao52e DM as well as the latest commits from MicronOxford/microscope/master.
When starting up the deviceserver with the Clarity with the BSI as the slaved camera there are some errors in the log:
On starting Cockpit, if you take a calibration image with no light source defined, the BSI behaves normally, the data is fetched and the calibration routine is run. However, if you define a light source (in our case, "ambient" with 100ms exposure time) you get this error:
It's also worth noting that no new data is fetched and displayed in the cockpit camera viewer either. If you then turn off the light source (and now once again have no light source defined) and try and take a calibration image, you get the same error as above except the last line is changed to:
The "raw" and "difference" modes work fine with and without a light source being defined.
It would appear that either the Clarity and/or the BSI are not being triggered in "calibration" mode when an light source is (or has been previously) defined.