rahix/openflexure-microscope-server
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665 commits

Author SHA1 Message Date
Wei Ouyang
d2d0dc4518 Add comment 2021-05-14 11:41:22 +02:00
Wei Ouyang
f129244c26 Fix _rvalue key error 2021-05-14 11:36:48 +02:00
Wei Ouyang
508d9d9acf Support imagej.js stack, upgrade core; 2021-05-14 11:11:06 +02:00
Richard
7585e24744 Swap windows for tabs 
Each ImJoy window now gets its own top-level tab.
This involved some fairly significant refactoring of the ImJoy
component, but I think it's cleaner now.
I've moved imjoy-related stuff into a store "module" to keep it clean.
 2021-05-13 17:10:36 +01:00
Richard
0e16835e1b Streamlined code and added multi-JPEG 
It's now possible to open a folder of JPEGs
in ImageJ at once; they appear as separate, named images.
 2021-05-12 17:15:17 +01:00
Richard
a1fce44a4d kludge to fix the color of text in drop-down 
something strange is happening with CSS precedence that makes the
elements of the dropdown go white-on-white.
I have added a specific color:black to fix this.
 2021-05-11 22:01:11 +01:00
Richard
b0f26f1b1e Transfers of stacks and using ndarrays 2021-05-11 21:43:33 +01:00
Wei Ouyang
c9cd6fc3bf Bump core version and fix service interface 2021-04-27 19:17:17 +00:00
Richard
6b8d34761c Merge remote-tracking branch 'origin/master' into imjoy-support 
Merge in changes from master,

This matters because we need to get the fixes to Python
package management and the stage API for absolute moves.
 2021-04-27 12:25:12 +01:00
Richard
297908fbc8 Stage move API now works 
The test plugin seems to have problems
calling setPosition more than once.
We don't understand this...

Co-authored-by: Kaspar Emanuel <kaspar@monostable.co.uk>
 2021-04-27 12:23:37 +01:00
Richard
757ee216cf Merge branch 'imjoy-support' of gitlab.com:rwb27/openflexure-microscope-server into imjoy-support 2021-04-27 11:31:20 +01:00
Richard Bowman
a2ba95c1d3 Minor linting improvements 
I have now disabled W1203 globally, see comment in
pyproject.toml
 2021-04-27 11:17:11 +01:00
Richard Bowman
90f5a755b1 Handle absolute moves correctly 
I've changed the default values in MoveStageAPI
so that it correctly handles absolute moves with missing axes.
I've also simplified it so it isn't using axes_to_array as that
resulted in a confusing code path.
 2021-04-27 10:55:51 +01:00
Richard Bowman
e86e4d983a Merge branch 'abandon-poetry' into 'master' 
Move away from poetry

Closes #218

See merge request openflexure/openflexure-microscope-server!124
 2021-04-21 10:57:28 +00:00
Wei Ouyang
ab2523e231 Use official version of default_base_frame.html 2021-04-07 10:05:27 +00:00
Wei Ouyang
2a8536c386 Allow insecure url in imjoy plugins 2021-04-07 09:49:09 +00:00
Richard Bowman
1cea75be70 Formatting fixes 2021-03-31 09:40:31 +01:00
Richard Bowman
e73ee8875c Fixed type annotations in autofocus and mock stage 
I don't know why these didn't fail before - possibly because of
incomplete type information from old numpy...
I removed a few annotations because they were failing (e.g.
np.sum can return a scalar or an array), but I don't think
this should be a problem - the function inputs and return values
are still typed.
 2021-03-30 17:51:00 +01:00
Richard Bowman
cd5e32b843 Removed deprecated np.float 
numpy 1.20 deprecates np.float, which was only ever an alias for
``float``.  I've replaced all occurrences of np.float with float, as
recommended.  There should be no change in functionality.
 2021-03-30 17:40:19 +01:00
Kaspar Emanuel
97bbbdee84 Merge branch 'ihi_scan' into 'master' 
IHI scan style raster

See merge request openflexure/openflexure-microscope-server!113
 2021-03-30 12:29:32 +00:00
Richard Bowman
af7ef08f63 Move away from poetry 
More or less everything is now done by setup.py
Pipfile simply installs the module in editable mode, which
recursively resolves dependencies as defined in setup.py.
 2021-03-26 21:11:22 +00:00
Richard
9d81a80bbb Fixed infinite loop in pollUntilComplete 2021-03-24 13:25:54 +00:00
Richard
024f2566f0 Working stage positioning 
NB there is a server bug that means absolute moves fail -
this should be fixed in a separate branch.
 2021-03-24 13:23:20 +00:00
Richard Bowman
cd30872d62 Split out action polling to separate function. 2021-03-09 21:56:06 +00:00
Richard Bowman
2b0b548307 Removed some TODOs because we did them! 2021-03-09 12:16:36 +00:00
Richard Bowman
0165f0a798 Populated snapImage and getImage 
Co-authored-by: Kaspar Emanuel <kaspar@monostable.co.uk>
 2021-03-09 12:12:28 +00:00
Richard Bowman
621b99eb9b Switch tab when opening with ImJoy 2021-02-23 12:27:58 +00:00
Richard Bowman
9b52865f95 Added an implementation of snapImage() to API 
Co-authored-by: Kaspar Emanuel <kaspar@monostable.co.uk>
 2021-02-23 12:08:20 +00:00
oeway
1c8ebfce32 Add todo note 2021-02-14 22:45:18 +01:00
oeway
52c40791a9 Support Engine 2021-02-14 22:40:37 +01:00
oeway
6436034ccb Fix time 2021-02-14 22:21:01 +01:00
oeway
f80500fbb5 Improve showStatus/Message/Progress 2021-02-14 22:20:00 +01:00
oeway
e460c0faff Add template for microscope api and script editor 2021-02-14 21:17:15 +01:00
oeway
3b002d59a5 Add ImageJ.JS and Kaibu to the plugin menu 2021-02-14 20:04:59 +01:00
oeway
a692b90ede Load ITK VTK viewer 2021-02-14 18:16:50 +01:00
oeway
61c49e520f Support ImageJ.JS 2021-02-14 17:40:39 +01:00
Richard Bowman
cfa5297a23 Added an "open in kaibu" link 2021-02-09 12:45:48 +00:00
Richard Bowman
0a0687cdd6 Added imjoy support 
We now have an imjoy tab and the ability to load plugins
 2021-02-09 11:46:29 +00:00
Richard Bowman
2b3c0a9bac Make the origin override persistent 
The dev tools pane now remembers the last address you entered in
"override origin" to save a few clicks  when doing local Vue development
 2021-02-09 09:46:52 +00:00
Richard Bowman
afbb71607d Fix placement of tour messages for icons 
The tour pop-ups were getting stuck in the tab icon container.
Explicitly specifying that they could overflow said container,
and setting them to show to the right, seems to have fixed this issue.
 2021-02-06 15:32:27 +00:00
Joe Knapper
3d47591cc9 Explicitly state IHI scan style as raster rather than server default 2021-02-03 12:18:57 +00:00
Joel Collins
5232b36644 Test cobertura mypy coverage report 2021-01-08 10:05:31 +00:00
Joel Collins
f877c4f745 Added Spiral scan to standard options 2021-01-05 14:30:49 +00:00
Joel Collins
18956bf230 Update README.md 2020-12-09 16:04:23 +00:00
Joel Collins
d2488c566a Added more Advanced bitrate controls 2020-12-08 17:57:42 +00:00
Joel Collins
42e0dfd39c Replaced MJPEG quality setting with MJPEG bitrate 2020-12-07 17:05:56 +00:00
Joel Collins
c75a7c5401 Lockfile update 2020-12-07 11:13:35 +00:00
Joel Collins
9d04842c56 Handle missing this.$refs.textboxKey ref 2020-12-07 11:12:07 +00:00
Joel Collins
599c31534d globalUpdateCaptures after scan 2020-12-07 10:37:04 +00:00
Joel Collins
58b2967f53 Fixed autofocus 'PiCameraStreamer' object has no attribute 'annotate_text' error 2020-12-07 10:12:30 +00:00