jonasoh / spiro Goto Github PK

Live view crashes upon exit. Related to waveform80/picamera#47. See if we can find a workaround.

Suggestion for an automated alignment script

• find the tiny dick (it is bolted to the cube now, so we can estimate approx. how many steps it is away from the initial position)

• make estimated number of steps

• Match reference points or text on the cube (scale bar should be always in the pic?) to the existing reference grid

• If doesn't match make more steps or step back (is it possible to estimate what direction and is preferential?)

• Re-match, if ok-> write the total n of steps made from tiny dick to the initial position into spiro.py

spiro --reset-password command prints out "resetting web ui password", but even after restarting web ui, it still requests the password for log in.

Please change Line 116 to: hw.LEDControl(True)

The wiringPi library which is used for GPIO has long been deprecated. It's a bad idea to rely on it in the long run. Look into options for replacing with something like gpiozero.

Sync initial position in the live view and spiro.py

Rename the repo and change references in the code.

Not an issue, but some questions about functionality and customization. Please let me know if this is not the place for these questions.

• Is it possible to have the stage static (not rotating)?
• Is it possible to have the LED on at all times (even during day settings)?

If possible, please let me know how to do it. Thank you!

Abhishesh

Hello There,

I've built the SPIRO at the Laboratory of Nematology at Wageningen University & Research. Our interest is to image the Nematode infection site which requires a high definition image of the plant root. For this purpose I tried to install the raspberry pi v3 camera module but it turned out to be not compatible with the SPIRO script.

I received the following lines of error code:
File "/usr/local/lib/python3.7/dist-packages/spiro/spiro.py", line 143, in main
cam = initCam()
File "/usr/local/lib/python3.7/dist-packages/spiro/spiro.py", line 42, in initCam
cam = PiCamera()
File "/usr/local/lib/python3.7/dist-packages/picamera/camera.py", line 433, in init
self._init_preview()
File "/usr/local/lib/python3.7/dist-packages/picamera/camera.py", line 513, in _init_preview
self, self._camera.outputs[self.CAMERA_PREVIEW_PORT])
File "/usr/local/lib/python3.7/dist-packages/picamera/renderers.py", line 558, in init
self.renderer.inputs[0].connect(source).enable()
File "/usr/local/lib/python3.7/dist-packages/picamera/mmalobj.py", line 2212, in enable
prefix="Failed to enable connection")
File "/usr/local/lib/python3.7/dist-packages/picamera/exc.py", line 184, in mmal_check
raise PiCameraMMALError(status, prefix)

-- Logs begin at Thu 2023-01-26 10:35:00 CET, end at Thu 2023-01-26 10:35:22 CET. --

Jan 26 10:35:05 raspberrypi systemd[529]: Started SPIRO control software.
Jan 26 10:35:08 raspberrypi spiro[558]: mmal: mmal_vc_port_enable: failed to enable port vc.null_sink:in:0(OPQV): ENOSPC
Jan 26 10:35:08 raspberrypi spiro[558]: mmal: mmal_port_enable: failed to enable connected port (vc.null_sink:in:0(OPQV))0x2500020 (ENOSPC)
Jan 26 10:35:08 raspberrypi spiro[558]: mmal: mmal_connection_enable: output port couldn't be enabled. This is the raspberry pi error log

I updated the picamera library and legacy OS but still returned the same error. Do you have any idea what causes this and is there a workaround to make the raspberry pi camera module v3 work?

Kind regards,

Wannes Tacken
Msc student Wageningen University & Research
Laboratory of Nematology

convert links into buttons and place them according to the direction they indicate

If possible, it would be great to have controls (e.g. window to type in the value in msec -> set/ reset to default) for --day-shutter and --night-shutter values. The values set in Live View should be then taken up by spiro.py

If SPIRO fails to find its start position after a set amount of time, it should time out and log an error.

A regression has caused white balance to not be set correctly, even though test pictures generated with the -t command-line option turn out fine.

The LED remains on while running experiment under day conditions if the experiment was started right after adjusting the night image settings

Track how long it takes to capture the images so that we can have more reliable delays between images, and proper lengths of experiments.

The live view sometimes hangs, with the only option for resuming operation being rebooting the machine. Sometimes, power cycling is needed as the machine also locks during reboot. This issue is likely related to camera access, but we haven't been able to narrow down the issue.

If you experience this problem, please add to this issue with any information that you think might help identify the issue (e.g., what seemed to trigger the hang, what network connection you were on, what browser you were using, what version of spiro, and so on).

On spiro --install, Python reports an import error cannot import 'escape' from 'jinja2'. This is a known issue for Flask projects, as the latest version of jinja2 deprecated escape. Upgrading to the latest version of Flask fixes this, so I suggest bumping the Flask version number in the package.

Preferably, installing spiro can be done using a one-liner.

(Lines 19- 27) The pinout in the current scheme is:

'sensor': 23, # positional sensor
'LED': 25, # pin for turning on/off led
'PWMa': 17, # first pwm pin
'PWMb': 16, # second pwm pin
'coilpin_M11': 27, # ain2
'coilpin_M12': 22, # ain1
'coilpin_M21': 6, # bin1
'coilpin_M22': 26, # bin2
'stdby': 5, # stby

Please introduce in the line 73: cam.rotation=90

spasibo!

A.

Hi guys - thanks a lot for sharing the resources. I am able to connect to SPIRO through WiFi network, but when I try to run the experiment I get the "Error: Write failed", and no images are being saved on my Raspberry Pi computer. I checked i2cdetect -y 1 and none of the ports are engaged. Any advice on how to proceed would be highly appreciated!

This has to be done when spiro.py is just started, before taking any images

• calculate total space needed for the experiment:
  number of images calculated from the current flags: (-l 2460)/-d
  a single jpeg is just below 4 Mb

• pull info about available space on SD. Mark suggests using shutil.disk_usage

• print a message to user " total disk space required: xx, total disk space available: yy. Proceed y/n"

Zoom/pan is buggy. Make sure its behavior is acceptable for the release.

Settings such as calibration steps and focus distance should be saved and ideally configured through the web UI.

• Add crude and fine focus adjustment tools for the shitty camera.

• Make focusing values writable into spiro.py

• Make sure the focusing values are taken up at each image acquisition event

Add a check box for the reference grid

Hi guys

Kudos to you for making such a machine, and thanks for sharing the resources.
I have assembled everything and have installed the Raspberry Pi (Legacy) as well as SPIRO according to the instructions. But after I access the SPIRO hotspot through WiFi and set the new password, I get an error:

Internal Server Error
The server encountered an internal error and was unable to complete your request. Either the server is overloaded or there is an error in the application.

Please let me know how to solve this issue. Keep up the good work!

Abhishesh

Allow writing the number of steps assessed in live view into spiro.py

In hwcontrol.py please introduce the following changes:

Line 13: gpio.setup(self.pins['sensor'], gpio.IN, pull_up_down=gpio.PUD_DOWN)

Line 27: while not gpio.input(self.pins['sensor']):

New pictures of the hardware. Maybe short demo video? Also a new picture/video showing off the image quality.