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Author SHA1 Message Date
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
Richard Bowman
782ff05477 Merge branch 'oeway-imjoy-support-patch-33834' into 'imjoy-support' 
Bump core version and fix service interface

See merge request rwb27/openflexure-microscope-server!3
 2021-05-05 09:12:09 +00:00
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
6d62532d6a Merge branch 'fix-absolute-move' into 'master' 
Fix absolute moves

See merge request openflexure/openflexure-microscope-server!126
 2021-04-27 10:30:19 +00:00
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
2eade9ed30 Handle None in axes_to_array 
None values should be treated the same as missing ones -
previously it would just crash.
 2021-04-27 10:52:52 +01:00
Richard Bowman
f44d76d9dd Merge branch 'oeway-imjoy-support-patch-13914' into 'imjoy-support' 
Allow insecure url in ImJoy plugins

See merge request rwb27/openflexure-microscope-server!2
 2021-04-22 20:28:18 +00:00
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
Richard Bowman
5d5990f738 Described config files better in reame 2021-04-21 11:40:45 +01:00
Richard Bowman
1b5b576664 Improved comments 2021-04-21 11:28:30 +01:00
Richard Bowman
85df85c6e8 reworked readme to improve clarity and style 2021-04-21 11:12:54 +01:00
Richard Bowman
4629fa67c6 Consistent single backtick code 2021-04-21 10:35:09 +01:00
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
9783dfaeff Updated readme and version-bump for clarity 2021-03-31 10:21:45 +01:00
Richard Bowman
1cea75be70 Formatting fixes 2021-03-31 09:40:31 +01:00
Richard Bowman
300d6878bb Upgraded black to match master 2021-03-31 09:35:13 +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
17b19d7dfd fix poe 
poe was assuming we were using poetry - I have
configured it not to use poetry now. This required
using a newer version.
 2021-03-29 16:59:40 +01:00
Richard Bowman
53876ee70d Use pipenv to manage setup.py dependencies 2021-03-29 16:59:00 +01:00
Richard Bowman
3ca469cca6 Install dev dependencies 
We now install with --dev to make sure development dependencies
are included.  I've also removed "poetry run"
from the "poe" commands, as we are
already in an active virtual environment, so
it's unnecessary (and also broken).

Finally, I added a tarball of the vue app to
the output distribution.
 2021-03-29 14:57:18 +01:00
Richard Bowman
faa08f3aef Switch CI to use poetry 2021-03-29 11:26:38 +01:00
Richard Bowman
4c70562687 Updated readme with new install instructions 2021-03-26 21:13:16 +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
Richard Bowman
e6bfc9342b Merge branch 'support-imagej' into 'imjoy-support' 
Support open in ImageJ.JS plugin

See merge request rwb27/openflexure-microscope-server!1
 2021-02-15 13:49:59 +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