Lazy tiff loader for prototyping#138
Merged
Merged
Conversation
codeCollision4
approved these changes
Jul 7, 2022
codeCollision4
added a commit
that referenced
this pull request
Jul 12, 2022
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
* 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
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
I made this for use on BioHPC, but it's generally a decent way of loading up a set of TIFF images we write to a folder without destroying our memory in the process. Still very much a rough object, feel free to improve.