Commit graph

92 commits

Author SHA1 Message Date
Richard Bowman
5279dffe6a Dummy stage class 2024-08-09 01:12:16 +01:00
Richard Bowman
3f92ed8266 Add a stub OpenCV-based camera
This allows the server to run on a laptop, to some extent. I've not tested if this will make the whole
web app work properly.

As StreamingPiCamera2 is hardcoded in various places, this certainly doesn't make cameras totally
interchangeable - but it is a step towards that.
2024-08-09 00:52:31 +01:00
Joe Knapper
4ea3b5b623 Increase minimum fraction coverage - makes stitching much more reliable 2024-05-30 11:42:25 +00:00
jaknapper
f08840f0e8 Zip a stitched image with the scan name in the filename 2024-03-05 13:38:24 +00:00
jaknapper
43cf7e837a Produce tiff as property 2024-02-21 14:42:52 +00:00
jaknapper
169df15fd1 More restricted range 2024-02-21 14:04:07 +00:00
Joe Knapper
6031280a19 Merge branch 'changes-into-saturation-fix' into verify-focus 2024-02-20 14:17:25 +00:00
Joe Knapper
eafeaca3ff Readd zip name 2024-02-20 12:22:06 +00:00
Joe Knapper
2c8660e01f Capture metadata before image to ensure consistency 2024-02-20 12:11:04 +00:00
jaknapper
e6eb4d419d Live logging (requires unbuffered program output from stitching) 2024-02-20 10:51:32 +00:00
Richard Bowman
41f03958c6 Save images with saturated pixels
If any pixels in the manually processed raw image end up
saturated (>255), this causes an error. I've now manually
clamped the values between 0 and 255 to fix this.

It would probably be a good idea to warn when this happens,
as it does mean we're losing data.
2024-02-15 17:34:29 +00:00
Richard Bowman
82e2a250fc Include colour correction matrix and gamma in saved images
I've replicated more of the camera pipeline in the images
saved during scans - in particular, I've added the colour
correction matrix (increases saturation) and the contrast
agorithm (implements gamma correction).

This slows down saving to ~0.5-2 seconds, but that's still less time than it takes to move.
2024-02-15 16:38:15 +00:00
jaknapper
aed5a22983 Autofocus verify based on sharpness range, removed repetitive logging 2024-02-15 11:02:44 +00:00
Richard Bowman
a16c54d2db Update raw image processing in scan
This matches recent commits in labthings-picamera2
2024-02-14 18:03:13 +00:00
Joe Knapper
f1c315783c Test the success of refocusing 2024-02-13 15:24:42 +00:00
Joe Knapper
f2d85cb891 sleep before capturing 2024-02-09 19:06:58 +00:00
Joe Knapper
61d7712c27 tiff as an option 2024-02-09 19:05:20 +00:00
Richard Bowman
a61ffbf75a WIP: use code from labthings-picamera2 for EXIF writing
I've now switched to using piexif to write the EXIF tag, which
is slower - but still does not seem to work in openflexure-
stitching.
2024-02-05 17:14:56 +00:00
Richard Bowman
bc8db396bf Acquire raw images rather than processed ones
I've swapped `capture_jpeg` for `capture_array`. This will acquire a raw image and process it manually. Currently I've included LST correction, colour balance, but **not** the colour unmixing matrix. In the future we could add this to implement proper correction for saturation.

Currently EXIF data does not seem to be working properly.
2024-02-01 21:55:15 +00:00
Richard Bowman
24a1d9d020 WIP: try just waiting 0.5s rather than using an Event 2024-02-01 17:37:44 +00:00
Richard Bowman
4a18ef729a Parallelise capture of images and the next move 2024-02-01 17:36:05 +00:00
Richard Bowman
6e4e79f2d2 Factor out moving to the next scan point into a method 2024-02-01 16:49:18 +00:00
jaknapper
db51cd8067 Make overlap value consistent 2024-02-01 15:31:14 +00:00
jaknapper
e6e809cea4 Zip files as we scan, saving the regenerated ones to the end
Removed maximum scan size of 750 images

Save json of scan inputs and use it for future stitching (ensures consistent parameters)

Moved looping autofocus to autofocus thing from recentering thing

Rewrote looping autofocus to skip unneeded moves, as if peak is out of range, no need to nicely focus
2024-01-30 18:46:34 +00:00
jaknapper
a0b98a1adc Fixed autofocus to not combine logs 2024-01-29 19:56:24 +00:00
Joe Knapper
528406137f Start autofocus from base of range for speed 2024-01-29 18:10:11 +00:00
Joe Knapper
53eb51e964 Improved default scan values 2024-01-23 15:22:30 +00:00
Richard Bowman
b35db02f34 Improved error handling and zip download
I've swapped out various `logging.exception` calls for
`logging.error` with `exc_info` set to the exception.
My reading of the docs is that the two shoulld be equivalent,
but the former fails with an error related to
message formatting, as if there was an extra (or missing) '%'.

I've changed the format of the downloaded zip file, so that it
now puts the stitched images at the top level (if they exist).

I've also modified the time of the last stitched image so it
returns None if it doesn't exist - this avoids HTTP errors in
the client.
2024-01-17 13:14:43 +00:00
Richard Bowman
65ae6c1f76 Removed a couple of print statements 2024-01-17 12:25:17 +00:00
Richard Bowman
f627d6e2f2 Always generate the preview stitch
The preview stitch is useful even if stitch-as-you-go is not
desired. I've enabled it all the time, not just when the box
is ticked.
2024-01-17 11:59:30 +00:00
Richard Bowman
36a7ec3d2e Expose hostname in settings manager
I've added a `hostname` property to the settings manager.
2024-01-17 11:53:08 +00:00
Richard Bowman
9ac0a11ce1 Add a property to enable/disable auto-stitching 2024-01-15 21:35:27 +00:00
Richard Bowman
b9f7e6f1e3 Make it possible to manually save all settings to disk
There's now an action that will save all settings to disk.
This copies code from `labthings_fastapi.thing_server` so
may want to be deduplicated in the fullness of time.
2024-01-15 21:17:43 +00:00
Richard Bowman
e7a3003c47 Add a closing ` to the logging statement
This was mistakenly not added to the previous commit.
2024-01-15 20:42:54 +00:00
Richard Bowman
dca2d1fabb Improve scan naming logic and type hints
Removed an unnecessary `Optional` and removed the `scan_` prefix from scans that have a non-empty name.

I also added a closing ` to a logging statement.
2024-01-15 20:27:35 +00:00
Joe Knapper
e483c3ddfb custom scan name from gui 2024-01-15 17:40:17 +00:00
Joe Knapper
c2f1b591b1 Fix to CSM scaling for Fiji config as images are now captured at double width 2024-01-13 14:29:34 +00:00
Joe Knapper
d1908eb29a Run stitching thing with appropriate overlap setting 2024-01-13 13:38:39 +00:00
jaknapper
c4e02d9087 Maximum lateral range and minimum autofocus range 2024-01-11 20:38:47 +00:00
Richard Bowman
e611840aca Save microscope id as a string
UUIDs don't serialise to JSON, so I'm now saving it as a plain
string and reconstructing a UUID object when it's returned.

Returning a UUID seems clearer than returning a string.
2024-01-11 19:53:08 +00:00
Richard Bowman
a279831c41 Reordered cleanup operations for robustness
I now define the variables needed in the finally: block at
the very start, so I can test if they are None.

I've reordered the final move so it can happen as we are awaiting the background processes. I've added exception handling so this won't cause problems with the lock.
2024-01-11 16:39:06 +00:00
Richard Bowman
074b9c67f8 Serialise microscope ID to string
UUID objects don't serialise with `json.dumps` and thus cause
errors when we try to embed `thing_state` into images.
2024-01-11 15:58:42 +00:00
Richard Bowman
f51d6ced71 Add hostname and microscope ID to metadata
It's often helpful to tell if images came from the same
microscope - this metadata should answer that question.
2024-01-11 14:48:08 +00:00
Richard Bowman
924cce649a Autofocus tweaks for smart scan
We've removed the initial double-autofocus (we just do a
single looping autofocus at the start), and now only do 3 retries rather than 5 if the focus is rejected.
2024-01-11 14:15:54 +00:00
Richard Bowman
a965d04047 Move raw images folder inside images folder
This ensures images.zip contains everything - a neater solution
for this is TBD.
2024-01-11 13:56:24 +00:00
Richard Bowman
f4c4206a53 Return an empty scans list if the folder is missing 2024-01-11 13:40:47 +00:00
Richard Bowman
ba86c37292 Swap background detection from argument to property
For consistency, I've made background detection a property.
2024-01-11 03:21:50 +00:00
Richard Bowman
717cf7657c Combine stitcher and smart scan Things
I'm now running stitching in subprocesses during the scan.
This seems to be working well - I'm using multiple CPU
cores and getting images out. However, the only way to
avoid circular dependencies was to combine the Things.

I'm still getting not-infrequent memory allocation errors from the camera, which may or may not be related.
2024-01-11 01:49:24 +00:00
Richard Bowman
b5fbcc85b5 Succeed immediately if the stitched image is up to date
To save some CPU cycles, we will return immediately if the
images don't look newer than the stitch. NB this does mean
that the stitched image will be repeatedly transferred, as its
URL will change each time it's re-requested.

Alternatively, we could fail with an error, which may be more efficient, at the expense of being uglier.
2024-01-10 23:17:16 +00:00
Richard Bowman
00a4b38a83 Prevent scans from filling the SD card 2024-01-10 21:07:25 +00:00