Image disappears when focusing
Bug report
Summary
Image disappears when focusing
Configuration
I'm using:
Camera: Raspberry Pi 2 model B, camera v2
Motor controller: none
Steps to reproduce
Peek_2020-06-11_12-12 The problem is in images with many details (my guess) when you try to fine-tune the focus. Shaking does not affect the disappearance of the image, only an attempt to focus accurately or the location of the slide in the field of view of a focused microscope. On less detailed slides this was not the case. Defocus or removing a slide from the field of view solves the problem of image loss. The exception at the end of the log appeared only once, before that, with similar problems, the exception did not raise ...
Relevant logs and/or screenshots
[2020-06-11 11:33:45,410] [DummyThread-34] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:33:45,425] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:33:45,551] [DummyThread-36] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:33:45,586] [DummyThread-36] [INFO] Got Action response quickly
[2020-06-11 11:33:45,617] [DummyThread-36] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:33:45,714] [DummyThread-36] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:33:45,785] [DummyThread-36] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:33:45,864] [DummyThread-36] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:33:45,944] [DummyThread-36] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:33:46,124] [DummyThread-33] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:33:46,151] [DummyThread-33] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:33:46,234] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:33:46,256] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:33:46,318] [DummyThread-35] [INFO] Got Action response quickly
[2020-06-11 11:33:46,331] [DummyThread-37] [INFO] Got Action response quickly
[2020-06-11 11:33:46,380] [DummyThread-36] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:33:46,476] [DummyThread-37] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:34:44,483] [DummyThread-37] [INFO] Got Action response quickly
[2020-06-11 11:35:06,445] [DummyThread-36] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:06,473] [DummyThread-34] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:35:06,709] [DummyThread-37] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:35:06,733] [DummyThread-37] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:35:06,767] [DummyThread-37] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:06,904] [DummyThread-31] [INFO] Got Action response quickly
[2020-06-11 11:35:06,938] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:06,970] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:07,002] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:07,035] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:07,046] [DummyThread-35] [INFO] Got Action response quickly
[2020-06-11 11:35:07,066] [DummyThread-34] [INFO] Got Action response quickly
[2020-06-11 11:35:07,089] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:35:07,182] [DummyThread-38] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:07,273] [DummyThread-37] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:07,380] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:07,474] [DummyThread-38] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:19,678] [DummyThread-31] [INFO] Got Action response quickly
[2020-06-11 11:35:21,035] [DummyThread-34] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:21,069] [DummyThread-38] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:35:21,102] [DummyThread-38] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:21,156] [DummyThread-37] [INFO] Got Action response quickly
[2020-06-11 11:35:21,183] [DummyThread-34] [INFO] Got Action response quickly
[2020-06-11 11:35:21,253] [DummyThread-35] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:35:21,276] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:35:21,309] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:21,338] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:21,433] [DummyThread-38] [INFO] Got Action response quickly
[2020-06-11 11:35:21,533] [DummyThread-34] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:21,631] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:21,666] [DummyThread-39] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:21,746] [DummyThread-38] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:21,832] [DummyThread-37] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:21,913] [DummyThread-39] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:21,935] [DummyThread-39] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:35:30,271] [DummyThread-39] [INFO] Got Action response quickly
[2020-06-11 11:35:38,563] [DummyThread-35] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:38,585] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:35:38,620] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:38,694] [DummyThread-34] [INFO] Got Action response quickly
[2020-06-11 11:35:38,721] [DummyThread-35] [INFO] Got Action response quickly
[2020-06-11 11:35:38,763] [DummyThread-35] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:38,791] [DummyThread-35] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:38,800] [DummyThread-31] [INFO] Got Action response quickly
[2020-06-11 11:35:38,819] [DummyThread-39] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:35:38,842] [DummyThread-34] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:35:39,033] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:39,060] [DummyThread-35] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:39,134] [DummyThread-34] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:39,164] [DummyThread-31] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:39,243] [DummyThread-40] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:39,321] [DummyThread-35] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:35:39,432] [DummyThread-35] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:35:54,152] [DummyThread-35] [INFO] Got Action response quickly
[2020-06-11 11:36:56,632] [DummyThread-34] [INFO] Got Action response quickly
[2020-06-11 11:36:56,652] [DummyThread-41] [INFO] Got Action response quickly
[2020-06-11 11:36:56,665] [DummyThread-35] [INFO] Got Action response quickly
[2020-06-11 11:57:19,209] [DummyThread-42] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:57:19,244] [DummyThread-43] [INFO] Got Action response quickly
[2020-06-11 11:57:19,261] [DummyThread-43] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:57:19,302] [DummyThread-42] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:57:19,345] [DummyThread-42] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:57:19,373] [DummyThread-42] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:57:19,404] [DummyThread-42] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:57:19,437] [DummyThread-42] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:57:19,539] [DummyThread-44] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:57:19,642] [DummyThread-45] [INFO] Got Action response quickly
[2020-06-11 11:57:19,675] [DummyThread-45] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:57:19,703] [DummyThread-45] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:57:19,728] [DummyThread-45] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:57:19,742] [DummyThread-46] [INFO] Got Action response quickly
[2020-06-11 11:57:19,846] [DummyThread-42] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 11:57:52,309] [DummyThread-43] [INFO] Got Action response quickly
[2020-06-11 11:59:29,307] [DummyThread-42] [INFO] Got Action response quickly
[2020-06-11 11:59:46,460] [DummyThread-49] [INFO] Got Action response quickly
[2020-06-11 11:59:54,924] [DummyThread-50] [INFO] Stopping stream in pause_stream context manager
[2020-06-11 11:59:54,941] [DummyThread-50] [INFO] Stopped MJPEG stream on port 1. Switching to [3280, 2464].
[2020-06-11 11:59:55,544] [DummyThread-50] [INFO] Restarting stream in pause_stream context manager
[2020-06-11 11:59:55,708] [DummyThread-50] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:59:55,715] [DummyThread-50] [INFO] Saving /var/openflexure/settings/microscope_settings.json...
[2020-06-11 11:59:55,725] [DummyThread-49] [INFO] Got Action response quickly
[2020-06-11 12:00:12,186] [DummyThread-49] [INFO] Got Action response quickly
[2020-06-11 12:00:13,488] [DummyThread-49] [INFO] Got Action response quickly
[2020-06-11 12:00:13,571] [DummyThread-52] [INFO] Got Action response quickly
[2020-06-11 12:00:13,589] [DummyThread-53] [INFO] Got Action response quickly
[2020-06-11 12:00:14,897] [DummyThread-54] [INFO] Starting microscope recalibration...
[2020-06-11 12:00:14,900] [DummyThread-54] [INFO] Stopping stream in pause_stream context manager
[2020-06-11 12:00:14,912] [DummyThread-54] [INFO] Stopped MJPEG stream on port 1. Switching to [3280, 2464].
[2020-06-11 12:00:15,233] [DummyThread-54] [INFO] Allowing the camera to auto-expose
[2020-06-11 12:00:18,242] [DummyThread-54] [INFO] done
[2020-06-11 12:00:18,245] [DummyThread-54] [INFO] Freezing the camera settings...
[2020-06-11 12:00:18,249] [DummyThread-54] [INFO] Shutter speed = 577
[2020-06-11 12:00:18,253] [DummyThread-54] [INFO] Auto exposure disabled
[2020-06-11 12:00:18,259] [DummyThread-54] [INFO] Auto white balance disabled, gains are (Fraction(71, 64), Fraction(667, 256))
[2020-06-11 12:00:18,263] [DummyThread-54] [INFO] Analogue gain: 307/256, Digital gain: 1
[2020-06-11 12:00:30,191] [DummyThread-54] [INFO] Generating a lens shading table at 39x52
[2020-06-11 12:00:30,214] [DummyThread-54] [INFO] Channel shape: 1232x1640, shading table shape: 1248x1664, after padding (1248, 1664)
[2020-06-11 12:00:30,244] [DummyThread-54] [INFO] Channel shape: 1232x1640, shading table shape: 1248x1664, after padding (1248, 1664)
[2020-06-11 12:00:30,273] [DummyThread-54] [INFO] Channel shape: 1232x1640, shading table shape: 1248x1664, after padding (1248, 1664)
[2020-06-11 12:00:30,302] [DummyThread-54] [INFO] Channel shape: 1232x1640, shading table shape: 1248x1664, after padding (1248, 1664)
[2020-06-11 12:00:40,755] [DummyThread-54] [INFO] Restarting stream in pause_stream context manager
[2020-06-11 12:00:40,918] [DummyThread-54] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:00:40,926] [DummyThread-54] [INFO] Saving /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:00:55,243] [DummyThread-52] [INFO] Got Action response quickly
[2020-06-11 12:01:47,322] [DummyThread-52] [INFO] Got Action response quickly
[2020-06-11 12:01:54,785] [DummyThread-55] [INFO] Got Action response quickly
[2020-06-11 12:02:42,614] [DummyThread-55] [INFO] Got Action response quickly
[2020-06-11 12:03:33,570] [DummyThread-55] [INFO] Got Action response quickly
[2020-06-11 12:04:03,044] [DummyThread-55] [INFO] Got Action response quickly
[2020-06-11 12:04:07,672] [DummyThread-59] [INFO] Got Action response quickly
[2020-06-11 12:04:15,054] [DummyThread-60] [INFO] Got Action response quickly
[2020-06-11 12:04:23,568] [DummyThread-60] [INFO] Got Action response quickly
[2020-06-11 12:07:49,378] [DummyThread-67] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 12:07:49,593] [DummyThread-70] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:07:49,619] [DummyThread-70] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:07:49,821] [DummyThread-68] [INFO] Got Action response quickly
[2020-06-11 12:07:49,860] [DummyThread-71] [INFO] Got Action response quickly
[2020-06-11 12:07:49,909] [DummyThread-72] [INFO] Got Action response quickly
[2020-06-11 12:07:50,063] [DummyThread-69] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 12:07:50,136] [DummyThread-67] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:07:50,303] [DummyThread-70] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:07:50,458] [DummyThread-67] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:07:50,527] [DummyThread-72] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:07:50,569] [DummyThread-71] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:07:50,602] [DummyThread-71] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:07:50,623] [DummyThread-71] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 12:07:50,754] [DummyThread-72] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:07:55,294] [DummyThread-69] [INFO] Got Action response quickly
[2020-06-11 12:08:04,724] [DummyThread-71] [INFO] Got Action response quickly
[2020-06-11 12:08:41,194] [DummyThread-68] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 12:08:41,242] [DummyThread-73] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:08:41,294] [DummyThread-74] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:08:41,382] [DummyThread-68] [INFO] Got Action response quickly
[2020-06-11 12:08:41,399] [DummyThread-68] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 12:08:41,421] [DummyThread-73] [INFO] Got Action response quickly
[2020-06-11 12:08:41,452] [DummyThread-73] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:08:41,479] [DummyThread-73] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:08:41,489] [DummyThread-74] [INFO] Got Action response quickly
[2020-06-11 12:08:41,515] [DummyThread-70] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 12:08:41,560] [DummyThread-70] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:08:41,793] [DummyThread-74] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:08:41,824] [DummyThread-73] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:08:41,912] [DummyThread-74] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:08:41,994] [DummyThread-75] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:08:42,078] [DummyThread-73] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:08:42,194] [DummyThread-73] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 12:08:44,757] [DummyThread-73] [INFO] Got Action response quickly
[2020-06-11 12:08:48,164] [DummyThread-73] [INFO] Got Action response quickly
[2020-06-11 12:08:48,240] [DummyThread-76] [INFO] Got Action response quickly
[2020-06-11 12:08:48,255] [DummyThread-74] [INFO] Got Action response quickly
[2020-06-11 12:08:49,846] [DummyThread-73] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:08:49,876] [DummyThread-76] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 12:08:50,305] [DummyThread-77] [INFO] Unregistering zeroconf services
[2020-06-11 12:08:50,439] [DummyThread-74] [INFO] Got Action response quickly
[2020-06-11 12:08:50,865] [DummyThread-77] [INFO] Shutting down WSGI server
[2020-06-11 12:08:50,878] [DummyThread-77] [INFO] Done
[2020-06-11 12:08:51,403] [MainThread] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:08:51,408] [MainThread] [INFO] Saving /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:08:51,915] [MainThread] [INFO] Closing <openflexure_microscope.microscope.Microscope object at 0x7415c8d0>
[2020-06-11 12:08:51,918] [MainThread] [INFO] Closing <openflexure_microscope.camera.pi.PiCameraStreamer object at 0x73ce0e90>
[2020-06-11 12:08:51,941] [DummyThread-78] [INFO] Stopped MJPEG stream on port 1. Switching to [3280, 2464].
[2020-06-11 12:08:52,284] [MainThread] [INFO] Closed <openflexure_microscope.camera.pi.PiCameraStreamer object at 0x73ce0e90>
[2020-06-11 12:08:52,315] [MainThread] [INFO] Closing <openflexure_microscope.captures.capture_manager.CaptureManager object at 0x73ce0270>
[2020-06-11 12:08:52,318] [MainThread] [INFO] Closed <openflexure_microscope.microscope.Microscope object at 0x7415c8d0>
[2020-06-11 12:08:52,326] [DummyThread-74] [INFO] Waiting for frames
[2020-06-11 12:09:13,694] [MainThread] [INFO] Running with data path /var/openflexure
[2020-06-11 12:09:13,698] [MainThread] [INFO] Creating app
[2020-06-11 12:09:16,080] [MainThread] [WARNING] ThingAction decorator is deprecated and will be removed in LabThings 1.0.Please use the ActionView class instead.
[2020-06-11 12:09:16,095] [MainThread] [WARNING] ThingAction decorator is deprecated and will be removed in LabThings 1.0.Please use the ActionView class instead.
[2020-06-11 12:09:16,103] [MainThread] [WARNING] ThingAction decorator is deprecated and will be removed in LabThings 1.0.Please use the ActionView class instead.
[2020-06-11 12:09:16,113] [MainThread] [WARNING] ThingAction decorator is deprecated and will be removed in LabThings 1.0.Please use the ActionView class instead.
[2020-06-11 12:09:16,121] [MainThread] [WARNING] ThingAction decorator is deprecated and will be removed in LabThings 1.0.Please use the ActionView class instead.
[2020-06-11 12:09:16,129] [MainThread] [WARNING] ThingProperty decorator is deprecated and will be removed in LabThings 1.0.Please use the PropertyView class instead.
[2020-06-11 12:09:17,807] [MainThread] [INFO] Starting OpenFlexure Microscope Server...
[2020-06-11 12:11:52,284] [DummyThread-3] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 12:11:52,397] [DummyThread-4] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 12:11:52,434] [DummyThread-4] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:11:52,525] [DummyThread-4] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:11:52,608] [DummyThread-4] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:11:52,683] [DummyThread-4] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:11:52,756] [DummyThread-4] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:11:52,784] [DummyThread-3] [INFO] Got Action response quickly
[2020-06-11 12:11:52,802] [DummyThread-3] [INFO] Loading /var/openflexure/settings/microscope_configuration.json...
[2020-06-11 12:11:52,957] [DummyThread-5] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:11:52,985] [DummyThread-5] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:11:53,015] [DummyThread-5] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:11:53,044] [DummyThread-5] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:11:53,088] [DummyThread-6] [INFO] Got Action response quickly
[2020-06-11 12:11:53,110] [DummyThread-7] [INFO] Got Action response quickly
[2020-06-11 12:12:10,994] [DummyThread-6] [INFO] Got Action response quickly
[2020-06-11 12:12:26,289] [DummyThread-3] [INFO] Got Action response quickly
[2020-06-11 12:12:36,615] [DummyThread-3] [INFO] Got Action response quickly
[2020-06-11 12:12:56,455] [DummyThread-10] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:12:56,462] [DummyThread-10] [ERROR] The microscope has not yet been calibrated.
[2020-06-11 12:12:56,486] [DummyThread-10] [ERROR] Traceback (most recent call last):
File "/var/openflexure/application/openflexure-microscope-server/.venv/src/camera-stage-mapping/camera_stage_mapping/ofm_extension.py", line 133, in image_to_stage_displacement_matrix
settings = self.get_settings()
File "/var/openflexure/application/openflexure-microscope-server/.venv/src/camera-stage-mapping/camera_stage_mapping/ofm_extension.py", line 79, in get_settings
return get_by_path(self.microscope.read_settings(), keys)
File "/var/openflexure/application/openflexure-microscope-server/.venv/lib/python3.7/site-packages/labthings/core/utilities.py", line 119, in get_by_path
return reduce(operator.getitem, items, root)
KeyError: 'org.openflexure.camera_stage_mapping'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/var/openflexure/application/openflexure-microscope-server/.venv/lib/python3.7/site-packages/labthings/core/tasks/thread.py", line 104, in wrapped
self._return_value = f(*args, **kwargs)
File "/var/openflexure/application/openflexure-microscope-server/.venv/lib/python3.7/site-packages/flask/ctx.py", line 158, in wrapper
return f(*args, **kwargs)
File "/var/openflexure/application/openflexure-microscope-server/.venv/lib/python3.7/site-packages/webargs/core.py", line 366, in wrapper
return func(*args, **kwargs)
File "/var/openflexure/application/openflexure-microscope-server/.venv/src/camera-stage-mapping/camera_stage_mapping/ofm_extension.py", line 227, in post
np.array([args.get("x"), args.get("y")])
File "/var/openflexure/application/openflexure-microscope-server/.venv/src/camera-stage-mapping/camera_stage_mapping/ofm_extension.py", line 141, in move_in_image_coordinates
relative_move = np.dot(p, self.image_to_stage_displacement_matrix)
File "/var/openflexure/application/openflexure-microscope-server/.venv/src/camera-stage-mapping/camera_stage_mapping/ofm_extension.py", line 136, in image_to_stage_displacement_matrix
raise ValueError("The microscope has not yet been calibrated.")
ValueError: The microscope has not yet been calibrated.
[2020-06-11 12:12:56,546] [DummyThread-11] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:12:56,554] [DummyThread-11] [ERROR] The microscope has not yet been calibrated.
[2020-06-11 12:12:56,560] [DummyThread-11] [ERROR] Traceback (most recent call last):
File "/var/openflexure/application/openflexure-microscope-server/.venv/src/camera-stage-mapping/camera_stage_mapping/ofm_extension.py", line 133, in image_to_stage_displacement_matrix
settings = self.get_settings()
File "/var/openflexure/application/openflexure-microscope-server/.venv/src/camera-stage-mapping/camera_stage_mapping/ofm_extension.py", line 79, in get_settings
return get_by_path(self.microscope.read_settings(), keys)
File "/var/openflexure/application/openflexure-microscope-server/.venv/lib/python3.7/site-packages/labthings/core/utilities.py", line 119, in get_by_path
return reduce(operator.getitem, items, root)
KeyError: 'org.openflexure.camera_stage_mapping'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/var/openflexure/application/openflexure-microscope-server/.venv/lib/python3.7/site-packages/labthings/core/tasks/thread.py", line 104, in wrapped
self._return_value = f(*args, **kwargs)
File "/var/openflexure/application/openflexure-microscope-server/.venv/lib/python3.7/site-packages/flask/ctx.py", line 158, in wrapper
return f(*args, **kwargs)
File "/var/openflexure/application/openflexure-microscope-server/.venv/lib/python3.7/site-packages/webargs/core.py", line 366, in wrapper
return func(*args, **kwargs)
File "/var/openflexure/application/openflexure-microscope-server/.venv/src/camera-stage-mapping/camera_stage_mapping/ofm_extension.py", line 227, in post
np.array([args.get("x"), args.get("y")])
File "/var/openflexure/application/openflexure-microscope-server/.venv/src/camera-stage-mapping/camera_stage_mapping/ofm_extension.py", line 141, in move_in_image_coordinates
relative_move = np.dot(p, self.image_to_stage_displacement_matrix)
File "/var/openflexure/application/openflexure-microscope-server/.venv/src/camera-stage-mapping/camera_stage_mapping/ofm_extension.py", line 136, in image_to_stage_displacement_matrix
raise ValueError("The microscope has not yet been calibrated.")
ValueError: The microscope has not yet been calibrated.
[2020-06-11 12:12:56,598] [DummyThread-12] [INFO] Loading /var/openflexure/settings/microscope_settings.json...
[2020-06-11 12:12:56,606] [DummyThread-12] [ERROR] The microscope has not yet been calibrated.
[2020-06-11 12:12:56,612] [DummyThread-12] [ERROR] Traceback (most recent call last):
File "/var/openflexure/application/openflexure-microscope-server/.venv/src/camera-stage-mapping/camera_stage_mapping/ofm_extension.py", line 133, in image_to_stage_displacement_matrix
settings = self.get_settings()
File "/var/openflexure/application/openflexure-microscope-server/.venv/src/camera-stage-mapping/camera_stage_mapping/ofm_extension.py", line 79, in get_settings
return get_by_path(self.microscope.read_settings(), keys)
File "/var/openflexure/application/openflexure-microscope-server/.venv/lib/python3.7/site-packages/labthings/core/utilities.py", line 119, in get_by_path
return reduce(operator.getitem, items, root)
KeyError: 'org.openflexure.camera_stage_mapping'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/var/openflexure/application/openflexure-microscope-server/.venv/lib/python3.7/site-packages/labthings/core/tasks/thread.py", line 104, in wrapped
self._return_value = f(*args, **kwargs)
File "/var/openflexure/application/openflexure-microscope-server/.venv/lib/python3.7/site-packages/flask/ctx.py", line 158, in wrapper
return f(*args, **kwargs)
File "/var/openflexure/application/openflexure-microscope-server/.venv/lib/python3.7/site-packages/webargs/core.py", line 366, in wrapper
return func(*args, **kwargs)
File "/var/openflexure/application/openflexure-microscope-server/.venv/src/camera-stage-mapping/camera_stage_mapping/ofm_extension.py", line 227, in post
np.array([args.get("x"), args.get("y")])
File "/var/openflexure/application/openflexure-microscope-server/.venv/src/camera-stage-mapping/camera_stage_mapping/ofm_extension.py", line 141, in move_in_image_coordinates
relative_move = np.dot(p, self.image_to_stage_displacement_matrix)
File "/var/openflexure/application/openflexure-microscope-server/.venv/src/camera-stage-mapping/camera_stage_mapping/ofm_extension.py", line 136, in image_to_stage_displacement_matrix
raise ValueError("The microscope has not yet been calibrated.")
ValueError: The microscope has not yet been calibrated.
[2020-06-11 12:13:04,289] [DummyThread-14] [INFO] Got Action response quickly
[2020-06-11 12:13:48,526] [DummyThread-9] [INFO] Got Action response quicklyAdditional details
htop - from raspberry pi same result .AppImage or browser access
/cc @jtc42
Edited by Julian Stirling