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Tiling Wizard#139

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AdvancedImagingUTSW merged 1 commit into
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tiling_wizard
Jul 7, 2022
Merged

Tiling Wizard#139
AdvancedImagingUTSW merged 1 commit into
developfrom
tiling_wizard

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@codeCollision4 codeCollision4 commented Jul 6, 2022

This pull request contains:

  • Tiling Wizard popup with widgets
  • Tilling Wizard controller
  • Connection between Channel Tab Controller -> Tiling Wizard Controller -> Tiling Wizard Popup
  • There is now a launch button on the main GUI next to the enable multi settings check button

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codecov Bot commented Jul 6, 2022

Codecov Report

Merging #139 (2c3701a) into develop (72b8288) will decrease coverage by 0.03%.
The diff coverage is 0.00%.

@@             Coverage Diff             @@
##           develop     #139      +/-   ##
===========================================
- Coverage    16.37%   16.34%   -0.04%     
===========================================
  Files           97       98       +1     
  Lines         8981     9002      +21     
===========================================
  Hits          1471     1471              
- Misses        7510     7531      +21
Flag Coverage Δ
unittests 16.34% <0.00%> (-0.04%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
...troller/sub_controllers/channels_tab_controller.py 0.00% <0.00%> (ø)
...roller/sub_controllers/tiling_wizard_controller.py 0.00% <0.00%> (ø)

Continue to review full report at Codecov.

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@AdvancedImagingUTSW AdvancedImagingUTSW merged commit b09aee5 into develop Jul 7, 2022
codeCollision4 added a commit that referenced this pull request Jul 12, 2022
@codeCollision4
Squashed commit of the following:
758383b 
commit 00570e3
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Tue Jul 12 09:59:48 2022 -0500

    Slight spacing tweak

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 03bd589
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Tue Jul 12 09:36:11 2022 -0500

    Remove mousewheel for now due to conflicts with camera_view_controller

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 3559657
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Tue Jul 12 09:29:22 2022 -0500

    Tweaks

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 637d591
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Tue Jul 12 09:14:38 2022 -0500

    Make @Rapuris wsad code work

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit b8c8e02
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Mon Jul 11 16:31:55 2022 -0500

    Chaos averted

commit 1d2a9a3
Merge: 9a3ced2 83cba7c
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Mon Jul 11 15:35:53 2022 -0500

    Resolving conflicts from Chaos

commit 9a3ced2
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Mon Jul 11 15:22:57 2022 -0500

    Redoing PR#142 Laser Settings

commit 83cba7c
Merge: 8cf7520 7c260f7
Author: Rapuris <91913098+Rapuris@users.noreply.github.com>
Date:   Mon Jul 11 16:13:27 2022 -0400

    Merge branch 'develop' of https://github.com/AdvancedImagingUTSW/ASLM into develop

commit 7c260f7
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Mon Jul 11 13:58:22 2022 -0500

    Revert "Chaos"

    This reverts commit ca317bb.

commit dccb021
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Mon Jul 11 13:52:27 2022 -0500

    Fixing stage control

commit 48b8c0a
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Mon Jul 11 13:46:32 2022 -0500

    Fixing acquire bar

commit ca317bb
Author: Rapuris <91913098+Rapuris@users.noreply.github.com>
Date:   Mon Jul 11 14:15:54 2022 -0400

    Chaos

    * working on redesigning stage control

    * added wasd + mousewheel

    * Prototype New Stage Movement GUI

    * Update aslm_controller.py

    * change mousewheel to f

    * fixing mousewheel

    * finished separating

    * removing for base branch

    Finished adding all changes (#142)

    Greyed out timepoints settings (#135)

    * working on redesigning stage control

    * added wasd + mousewheel

    * Prototype New Stage Movement GUI

    * Update aslm_controller.py

    * change mousewheel to f

    * fixing mousewheel

    * finished separating

    * get rid of mousewheel stuff

    create base branch to add other gui features/styling

    * grayed out timepoint settings

    * merge with develop

    Greyed out stack acq settings (#136)

    * working on redesigning stage control

    * added wasd + mousewheel

    * Prototype New Stage Movement GUI

    * Update aslm_controller.py

    * change mousewheel to f

    * fixing mousewheel

    * finished separating

    * get rid of mousewheel stuff

    create base branch to add other gui features/styling

    * greyed out stack acq settings

    * Updating xy

    Revert "Greyed out stack acq settings (#136)"

    This reverts commit 31d6422.

    Revert "Revert "Greyed out stack acq settings (#136)""

    This reverts commit fec4bfc.

    Fix

    Update acquire_bar_controller.py

    Update acquire_bar_controller.py

    Revert "WASD/Mousewheel (#134)"

    This reverts commit b8ac2e6.

    Revert "Finished adding all changes (#142)"

    This reverts commit 8cf7520.

    Update acquire_bar_controller.py

    Fix

    Update acquire_bar_controller.py

    Revert "Fix"

    This reverts commit d4ac45d.

    Co-Authored-By: Dax Collison <collisod@gmail.com>
    Co-Authored-By: Dax Collison <79557266+codeCollision4@users.noreply.github.com>

commit 8cf7520
Author: Rapuris <91913098+Rapuris@users.noreply.github.com>
Date:   Mon Jul 11 14:19:09 2022 -0400

    Finished adding all changes (#142)

commit b8ac2e6
Author: Rapuris <91913098+Rapuris@users.noreply.github.com>
Date:   Mon Jul 11 14:15:54 2022 -0400

    WASD/Mousewheel (#134)

    * working on redesigning stage control

    * added wasd + mousewheel

    * Prototype New Stage Movement GUI

    #107 finished the prototype of a new GUI that should work in minimized or maximized screen

    * Update aslm_controller.py

    * change mousewheel to f

    * fixing mousewheel

    * finished separating

    * removing for base branch

    Co-authored-by: Dax Collison <collisod@gmail.com>

commit 6c5147b
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Mon Jul 11 09:55:18 2022 -0500

    KCube updates

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 4bd42bd
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Mon Jul 11 08:36:06 2022 -0500

    Fixes for new display

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 4a4c04b
Author: Zach Marin <zacsimile@users.noreply.github.com>
Date:   Mon Jul 11 07:26:51 2022 -0500

    Cleanup, MoveJog and TLI_DeviceInfo (#141)

commit 031c922
Author: Microscopy Innovation Lab <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Sun Jul 10 13:35:45 2022 -0500

    The start of more view functionality

    Beginning to implement having MIPs displayed instead of live images, and a slider wheel to go through the individual frames as they are acquired.

commit 31ed0cb
Author: Microscopy Innovation Lab <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Sun Jul 10 06:24:49 2022 -0500

    Cleanup

    Getting a custody error.  I saw this yesterday on the Linux machine too.

    stage thread exception happened! Two different threads tried to use the same ObjectInSubprocess at the same time! This is bad. Look at the docstring of concurrency_tools.py to see an example of how to use a _Custody object to avoid this problem. Traceback (most recent call last):
      File "/Users/S155475/Desktop/GitHub/ASLM/src/aslm/controller/thread_pool.py", line 146, in func
        target(*args, **kwargs)
      File "/Users/S155475/Desktop/GitHub/ASLM/src/aslm/controller/aslm_controller.py", line 754, in move_stage
        success = self.model.move_stage(pos_dict)
      File "/Users/S155475/Desktop/GitHub/ASLM/src/aslm/model/concurrency/concurrency_tools.py", line 373, in __getattr__
        with self._.parent_pipe_lock:
      File "/Users/S155475/Desktop/GitHub/ASLM/src/aslm/model/concurrency/concurrency_tools.py", line 538, in __enter__
        raise RuntimeError(
    RuntimeError: Two different threads tried to use the same ObjectInSubprocess at the same time! This is bad. Look at the docstring of concurrency_tools.py to see an example of how to use a _Custody object to avoid this problem.

commit f6511e1
Merge: cb37ff4 5fc9b9b
Author: Microscopy Innovation Lab <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Sun Jul 10 06:16:17 2022 -0500

    Merge branch 'develop' of https://github.com/AdvancedImagingUTSW/ASLM into develop

commit cb37ff4
Author: Microscopy Innovation Lab <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Sun Jul 10 06:16:14 2022 -0500

    Progress bar and more.

    Not sure why this didn't push on Friday.  I've had some weird issues with my laptop. I did this on Friday, and it makes the progress bar more intelligent.  Also been slowly adding more image metrics.

commit 5fc9b9b
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Sat Jul 9 12:24:16 2022 -0500

    Cleanup

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 861486f
Author: AdvancedImagingUTSW <kevin.dean@utsouthwestern.edu>
Date:   Sat Jul 9 09:39:42 2022 -0500

    digital zoom and menu items on camera display.  Need to wire up the move stage command and account for the fact that it is relative to a 512x512 widget and not the image necessarily

commit 710b41d
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 19:23:44 2022 -0500

    Better control of the focus stage

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 4084b9b
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Fri Jul 8 17:54:27 2022 -0500

    Fixing Total Tiles #58

    This finishes base setup of tiling wizard

commit a2c7ef1
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 17:48:11 2022 -0500

    Slight more synthetic hardware avoidance for stages_r

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 733aa2f
Merge: 14d4add f21428b
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 17:46:06 2022 -0500

    Merge branch 'develop' of https://github.com/AdvancedImagingUTSW/ASLM into develop

commit 14d4add
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 17:46:00 2022 -0500

    Don't load stages_r if synthetic

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit f21428b
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Fri Jul 8 17:30:13 2022 -0500

    Tiling Wizard base setup done #58

    Tiles now update when FOV, overlay and distance are changed. Step size mimics stack acq settings. Total tiles now update when other axis tile amounts change.

commit 7b8db0a
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 16:55:00 2022 -0500

    Update using correct dictionary

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 771b26f
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 15:12:22 2022 -0500

    Stage reporting updates

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 6d2bbdd
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 14:05:52 2022 -0500

    Stage fixes

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 576cb1c
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 13:18:26 2022 -0500

    Typo fix

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit d92e9cb
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 13:16:35 2022 -0500

    Stage refactor and KCube Inertial Stage

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 277a181
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 11:58:43 2022 -0500

    Slight cleanup

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 758447f
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 11:54:56 2022 -0500

    Add API for high-res focusing piezo

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit dabe714
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 19:03:33 2022 -0500

    Offsets between channels

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit bbbc130
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Thu Jul 7 18:46:12 2022 -0500

    Tiling Wizard #58

    Most things done need to calculate num of tiles. And discuss negative direction tiling

commit 8e3464e
Author: Microscopy Innovation Lab <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 16:09:36 2022 -0500

    Changes to size...

    For the future.  It is coming.  We shall add stuff to the right size.

commit 8bd21ea
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 14:57:09 2022 -0500

    Progress bar tweaks

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 04322a8
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 14:52:18 2022 -0500

    Updated z-min

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 0942bf6
Author: Microscopy Innovation Lab <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 14:43:23 2022 -0500

    Negligible oranization.

    Also added a first pass API for an ASI stage.

commit d9a52b0
Author: Zach Marin <zacsimile@users.noreply.github.com>
Date:   Thu Jul 7 14:42:01 2022 -0500

    Lazy tiff loader for prototyping (#138)

    * Lazy tiff loader for prototyping

    * Forgotten imports

    * Space

    * Whoops

    * Whoops2

    * Convert to xyz slicing

    * Squeeze them

    * Comments

commit b09aee5
Merge: b938d31 2c3701a
Author: Dean Lab @ UTSW <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 13:14:48 2022 -0500

    Merge pull request #139 from AdvancedImagingUTSW/tiling_wizard

    Tiling Wizard

commit b938d31
Author: Microscopy Innovation Lab <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 13:12:07 2022 -0500

    Progress Bar.

    #128 - Complete.  Can continue to add functionality to it as additional modes are added.

commit ad6f6e7
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 11:32:57 2022 -0500

    Safer xz bounds

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 36f2f78
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 10:34:11 2022 -0500

    Turn off lasers when acquisition finishes

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 0ce6dce
Author: Microscopy Innovation Lab <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 05:59:31 2022 -0500

    Status bar

    #128 Status bar now semi-functional.  Top one runs continuously anytime we are acquiring data.  Bottom one is supposed to increment and report on our progress during a z-stack.  We can consider changing this to be a bit higher level.  Top one can go continuously in the continuous mode, for example, as an indeterminate progressbar.  In the z-stack mode, the top one could be come determinate, as the bottom one is now.  And then for time lapse, or multi position imaging, the bottom one could report on how long everything could take.  Total experiment duration.   Couldn't sleep, so knocked some of this out.  Now we just need to dial it in as we want it.

commit 75f3746
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Wed Jul 6 18:02:55 2022 -0500

    Fix resolution offset

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 75ab8f6
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Wed Jul 6 17:42:49 2022 -0500

    More stage refactoring

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 19fa67e
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Wed Jul 6 17:14:57 2022 -0500

    Stage updates

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>
zacsimile pushed a commit that referenced this pull request Jul 13, 2022
@codeCollision4
Tiling wizard now populates multi position table (#145)
e1cd765 
* Squashed commit of the following:

commit 00570e3
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Tue Jul 12 09:59:48 2022 -0500

    Slight spacing tweak

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 03bd589
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Tue Jul 12 09:36:11 2022 -0500

    Remove mousewheel for now due to conflicts with camera_view_controller

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 3559657
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Tue Jul 12 09:29:22 2022 -0500

    Tweaks

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 637d591
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Tue Jul 12 09:14:38 2022 -0500

    Make @Rapuris wsad code work

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit b8c8e02
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Mon Jul 11 16:31:55 2022 -0500

    Chaos averted

commit 1d2a9a3
Merge: 9a3ced2 83cba7c
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Mon Jul 11 15:35:53 2022 -0500

    Resolving conflicts from Chaos

commit 9a3ced2
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Mon Jul 11 15:22:57 2022 -0500

    Redoing PR#142 Laser Settings

commit 83cba7c
Merge: 8cf7520 7c260f7
Author: Rapuris <91913098+Rapuris@users.noreply.github.com>
Date:   Mon Jul 11 16:13:27 2022 -0400

    Merge branch 'develop' of https://github.com/AdvancedImagingUTSW/ASLM into develop

commit 7c260f7
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Mon Jul 11 13:58:22 2022 -0500

    Revert "Chaos"

    This reverts commit ca317bb.

commit dccb021
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Mon Jul 11 13:52:27 2022 -0500

    Fixing stage control

commit 48b8c0a
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Mon Jul 11 13:46:32 2022 -0500

    Fixing acquire bar

commit ca317bb
Author: Rapuris <91913098+Rapuris@users.noreply.github.com>
Date:   Mon Jul 11 14:15:54 2022 -0400

    Chaos

    * working on redesigning stage control

    * added wasd + mousewheel

    * Prototype New Stage Movement GUI

    * Update aslm_controller.py

    * change mousewheel to f

    * fixing mousewheel

    * finished separating

    * removing for base branch

    Finished adding all changes (#142)

    Greyed out timepoints settings (#135)

    * working on redesigning stage control

    * added wasd + mousewheel

    * Prototype New Stage Movement GUI

    * Update aslm_controller.py

    * change mousewheel to f

    * fixing mousewheel

    * finished separating

    * get rid of mousewheel stuff

    create base branch to add other gui features/styling

    * grayed out timepoint settings

    * merge with develop

    Greyed out stack acq settings (#136)

    * working on redesigning stage control

    * added wasd + mousewheel

    * Prototype New Stage Movement GUI

    * Update aslm_controller.py

    * change mousewheel to f

    * fixing mousewheel

    * finished separating

    * get rid of mousewheel stuff

    create base branch to add other gui features/styling

    * greyed out stack acq settings

    * Updating xy

    Revert "Greyed out stack acq settings (#136)"

    This reverts commit 31d6422.

    Revert "Revert "Greyed out stack acq settings (#136)""

    This reverts commit fec4bfc.

    Fix

    Update acquire_bar_controller.py

    Update acquire_bar_controller.py

    Revert "WASD/Mousewheel (#134)"

    This reverts commit b8ac2e6.

    Revert "Finished adding all changes (#142)"

    This reverts commit 8cf7520.

    Update acquire_bar_controller.py

    Fix

    Update acquire_bar_controller.py

    Revert "Fix"

    This reverts commit d4ac45d.

    Co-Authored-By: Dax Collison <collisod@gmail.com>
    Co-Authored-By: Dax Collison <79557266+codeCollision4@users.noreply.github.com>

commit 8cf7520
Author: Rapuris <91913098+Rapuris@users.noreply.github.com>
Date:   Mon Jul 11 14:19:09 2022 -0400

    Finished adding all changes (#142)

commit b8ac2e6
Author: Rapuris <91913098+Rapuris@users.noreply.github.com>
Date:   Mon Jul 11 14:15:54 2022 -0400

    WASD/Mousewheel (#134)

    * working on redesigning stage control

    * added wasd + mousewheel

    * Prototype New Stage Movement GUI

    #107 finished the prototype of a new GUI that should work in minimized or maximized screen

    * Update aslm_controller.py

    * change mousewheel to f

    * fixing mousewheel

    * finished separating

    * removing for base branch

    Co-authored-by: Dax Collison <collisod@gmail.com>

commit 6c5147b
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Mon Jul 11 09:55:18 2022 -0500

    KCube updates

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 4bd42bd
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Mon Jul 11 08:36:06 2022 -0500

    Fixes for new display

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 4a4c04b
Author: Zach Marin <zacsimile@users.noreply.github.com>
Date:   Mon Jul 11 07:26:51 2022 -0500

    Cleanup, MoveJog and TLI_DeviceInfo (#141)

commit 031c922
Author: Microscopy Innovation Lab <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Sun Jul 10 13:35:45 2022 -0500

    The start of more view functionality

    Beginning to implement having MIPs displayed instead of live images, and a slider wheel to go through the individual frames as they are acquired.

commit 31ed0cb
Author: Microscopy Innovation Lab <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Sun Jul 10 06:24:49 2022 -0500

    Cleanup

    Getting a custody error.  I saw this yesterday on the Linux machine too.

    stage thread exception happened! Two different threads tried to use the same ObjectInSubprocess at the same time! This is bad. Look at the docstring of concurrency_tools.py to see an example of how to use a _Custody object to avoid this problem. Traceback (most recent call last):
      File "/Users/S155475/Desktop/GitHub/ASLM/src/aslm/controller/thread_pool.py", line 146, in func
        target(*args, **kwargs)
      File "/Users/S155475/Desktop/GitHub/ASLM/src/aslm/controller/aslm_controller.py", line 754, in move_stage
        success = self.model.move_stage(pos_dict)
      File "/Users/S155475/Desktop/GitHub/ASLM/src/aslm/model/concurrency/concurrency_tools.py", line 373, in __getattr__
        with self._.parent_pipe_lock:
      File "/Users/S155475/Desktop/GitHub/ASLM/src/aslm/model/concurrency/concurrency_tools.py", line 538, in __enter__
        raise RuntimeError(
    RuntimeError: Two different threads tried to use the same ObjectInSubprocess at the same time! This is bad. Look at the docstring of concurrency_tools.py to see an example of how to use a _Custody object to avoid this problem.

commit f6511e1
Merge: cb37ff4 5fc9b9b
Author: Microscopy Innovation Lab <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Sun Jul 10 06:16:17 2022 -0500

    Merge branch 'develop' of https://github.com/AdvancedImagingUTSW/ASLM into develop

commit cb37ff4
Author: Microscopy Innovation Lab <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Sun Jul 10 06:16:14 2022 -0500

    Progress bar and more.

    Not sure why this didn't push on Friday.  I've had some weird issues with my laptop. I did this on Friday, and it makes the progress bar more intelligent.  Also been slowly adding more image metrics.

commit 5fc9b9b
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Sat Jul 9 12:24:16 2022 -0500

    Cleanup

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 861486f
Author: AdvancedImagingUTSW <kevin.dean@utsouthwestern.edu>
Date:   Sat Jul 9 09:39:42 2022 -0500

    digital zoom and menu items on camera display.  Need to wire up the move stage command and account for the fact that it is relative to a 512x512 widget and not the image necessarily

commit 710b41d
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 19:23:44 2022 -0500

    Better control of the focus stage

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 4084b9b
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Fri Jul 8 17:54:27 2022 -0500

    Fixing Total Tiles #58

    This finishes base setup of tiling wizard

commit a2c7ef1
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 17:48:11 2022 -0500

    Slight more synthetic hardware avoidance for stages_r

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 733aa2f
Merge: 14d4add f21428b
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 17:46:06 2022 -0500

    Merge branch 'develop' of https://github.com/AdvancedImagingUTSW/ASLM into develop

commit 14d4add
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 17:46:00 2022 -0500

    Don't load stages_r if synthetic

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit f21428b
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Fri Jul 8 17:30:13 2022 -0500

    Tiling Wizard base setup done #58

    Tiles now update when FOV, overlay and distance are changed. Step size mimics stack acq settings. Total tiles now update when other axis tile amounts change.

commit 7b8db0a
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 16:55:00 2022 -0500

    Update using correct dictionary

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 771b26f
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 15:12:22 2022 -0500

    Stage reporting updates

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 6d2bbdd
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 14:05:52 2022 -0500

    Stage fixes

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 576cb1c
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 13:18:26 2022 -0500

    Typo fix

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit d92e9cb
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 13:16:35 2022 -0500

    Stage refactor and KCube Inertial Stage

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 277a181
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 11:58:43 2022 -0500

    Slight cleanup

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 758447f
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Fri Jul 8 11:54:56 2022 -0500

    Add API for high-res focusing piezo

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit dabe714
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 19:03:33 2022 -0500

    Offsets between channels

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit bbbc130
Author: Dax Collison <79557266+codeCollision4@users.noreply.github.com>
Date:   Thu Jul 7 18:46:12 2022 -0500

    Tiling Wizard #58

    Most things done need to calculate num of tiles. And discuss negative direction tiling

commit 8e3464e
Author: Microscopy Innovation Lab <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 16:09:36 2022 -0500

    Changes to size...

    For the future.  It is coming.  We shall add stuff to the right size.

commit 8bd21ea
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 14:57:09 2022 -0500

    Progress bar tweaks

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 04322a8
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 14:52:18 2022 -0500

    Updated z-min

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 0942bf6
Author: Microscopy Innovation Lab <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 14:43:23 2022 -0500

    Negligible oranization.

    Also added a first pass API for an ASI stage.

commit d9a52b0
Author: Zach Marin <zacsimile@users.noreply.github.com>
Date:   Thu Jul 7 14:42:01 2022 -0500

    Lazy tiff loader for prototyping (#138)

    * Lazy tiff loader for prototyping

    * Forgotten imports

    * Space

    * Whoops

    * Whoops2

    * Convert to xyz slicing

    * Squeeze them

    * Comments

commit b09aee5
Merge: b938d31 2c3701a
Author: Dean Lab @ UTSW <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 13:14:48 2022 -0500

    Merge pull request #139 from AdvancedImagingUTSW/tiling_wizard

    Tiling Wizard

commit b938d31
Author: Microscopy Innovation Lab <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 13:12:07 2022 -0500

    Progress Bar.

    #128 - Complete.  Can continue to add functionality to it as additional modes are added.

commit ad6f6e7
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 11:32:57 2022 -0500

    Safer xz bounds

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 36f2f78
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 10:34:11 2022 -0500

    Turn off lasers when acquisition finishes

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 0ce6dce
Author: Microscopy Innovation Lab <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Thu Jul 7 05:59:31 2022 -0500

    Status bar

    #128 Status bar now semi-functional.  Top one runs continuously anytime we are acquiring data.  Bottom one is supposed to increment and report on our progress during a z-stack.  We can consider changing this to be a bit higher level.  Top one can go continuously in the continuous mode, for example, as an indeterminate progressbar.  In the z-stack mode, the top one could be come determinate, as the bottom one is now.  And then for time lapse, or multi position imaging, the bottom one could report on how long everything could take.  Total experiment duration.   Couldn't sleep, so knocked some of this out.  Now we just need to dial it in as we want it.

commit 75f3746
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Wed Jul 6 18:02:55 2022 -0500

    Fix resolution offset

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 75ab8f6
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Wed Jul 6 17:42:49 2022 -0500

    More stage refactoring

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

commit 19fa67e
Author: Kevin Dean <42547789+AdvancedImagingUTSW@users.noreply.github.com>
Date:   Wed Jul 6 17:14:57 2022 -0500

    Stage updates

    Co-Authored-By: Zach Marin <zacsimile@users.noreply.github.com>

* Tiling Wizard now populates Multiposition table

@zacsimile We need your help with iterating thru the table during a zstack in line 880 of aslm_model

* Undo weird behavior
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@codeCollision4 @AdvancedImagingUTSW