Develop (#192)

* Clear neural_widgets list on loadTrial

* Create pose plugin for SLEAP (#1)

* Create pose plugin for SLEAP

* Tested thoroughly on both analysis files containing edges and not containing edges

* May experience slow down on large files due to for-loops used in loading -> to be dealt with later

* Lint

* First revision SLEAP pose plugin (#2)

* Add arguments to local function for clarity

* Development checkpoint #1

* Development checkpoint #2: pose display can work

* Refactor VideoScene into abstract base class

* Development checkpoint #4: refactor out timeSource

* Development checkpoint #5: bug fixes

* Development checkpoint #6: attempt to fix crash
Plus some cleanup

* Development checkpoint #7: fix time update loop

* Development checkpoint #8
Try again to fix shutdown warning

* Try using pixmap-mode display for all but first native video file

* Variable naming in DLC plugin

* Bug fixes involving a little refactoring of seqIo and mp4Io

* specify start time for each data format

* Fix vertical scaling of neural view

* Fix bug in resizeEvent behavior

* fixed visibility of last trace in neural view

* fixed scaling when neural traces are less

* Fix bug to call rather than reference currentTime

* Pick earliest native player as time source

* adding a min_scale_h to limit horizontal scaling

* Switch to single list for all types of widget

* time changes based on native player if it exists

* update after code review

* Update framework for data export

* export data checkpoint #1: metadata

* Export pose data (MARS only for now)

* Implement tick marks on both neural and annotations widgets, and labels on annotation widget

* exporting data in NWB format

* changes done with JSON file support in MARS pose

* added pose file documentation

* added documentation for pose data support

* experimenting few things

* changes in yml file

* changes in UI and backend code

* behavior triggered average plugin feature added

* bug fix when there are two trials and one has NaNs

* launching BTA using plugin approach

* variable name changed

* included offset change in image array

* addition of comments

* neural plotting faster and reordering of traces

* switching from individual start time to trial start time with offset

* offset calculation not required in BTA plugin

* checking of newOrder array added

* typo error in Window title rectified

* replacing os.linesep with \n in behaviors saving

* small bugs fix

* deleted print statements

* changed the function of bin size box

* bug fix when there are no trials present

* Feature/event triggered average (#167)

* Switch to single list for all types of widget

* Update framework for data export

* export data checkpoint #1: metadata

* Export pose data (MARS only for now)

* exporting data in NWB format

* changes done with JSON file support in MARS pose

* added pose file documentation

* added documentation for pose data support

* experimenting few things

* changes in yml file

* changes in UI and backend code

* behavior triggered average plugin feature added

* bug fix when there are two trials and one has NaNs

* launching BTA using plugin approach

* variable name changed

* included offset change in image array

* addition of comments

* typo error in Window title rectified

* replacing os.linesep with \n in behaviors saving

* small bugs fix

* deleted print statements

* changed the function of bin size box

* bug fix when there are no trials present

---------

Co-authored-by: drumph <[email protected]>

* get rid of boolean arguments in new order function

* Enhancement/neural traces reordering (#170)

* adds support for re-ordering of neural traces, to be used by various analysis plugins

* changes for resolving merge conflict

* changes done to resolve merge conflict

* Bug/neural window scrolling (#173)

* Switch to single list for all types of widget

* Update framework for data export

* export data checkpoint #1: metadata

* Export pose data (MARS only for now)

* exporting data in NWB format

* changes done with JSON file support in MARS pose

* added pose file documentation

* added documentation for pose data support

* experimenting few things

* changes in yml file

* changes in UI and backend code

* behavior triggered average plugin feature added

* bug fix when there are two trials and one has NaNs

* launching BTA using plugin approach

* variable name changed

* included offset change in image array

* addition of comments

* neural plotting faster and reordering of traces

* switching from individual start time to trial start time with offset

* offset calculation not required in BTA plugin

* scrolling of neural window fixed (issue #156)

---------

Co-authored-by: drumph <[email protected]>

* Feature/kmeansclustering (#175)

* scrolling of neural window fixed (issue #156)

* added feature to do kMeans Clustering

---------

Co-authored-by: Ann Kennedy <[email protected]>

* Bug/increment trial num (#176)

* scrolling of neural window fixed (issue #156)

* added feature to do kMeans Clustering

* bug fix for trial number increment when editing trial

---------

Co-authored-by: Ann Kennedy <[email protected]>

* Enhancement/annotations support (#177)

* scrolling of neural window fixed (issue #156)

* added feature to do kMeans Clustering

* bug fix for trial number increment when editing trial

* added support for different annotations file format

---------

Co-authored-by: Ann Kennedy <[email protected]>

* Enhancement/deletebutton (#178)

* scrolling of neural window fixed (issue #156)

* added feature to do kMeans Clustering

* bug fix for trial number increment when editing trial

* added support for different annotations file format

* added delete buttons in add or edit trial window

---------

Co-authored-by: Ann Kennedy <[email protected]>

* Enhancement/jump to time or frame (#184)

* scrolling of neural window fixed (issue #156)

* added feature to do kMeans Clustering

* bug fix for trial number increment when editing trial

* added support for different annotations file format

* added delete buttons in add or edit trial window

* feature to jump to specific time or frame

---------

Co-authored-by: Ann Kennedy <[email protected]>

* Enhancement/warning no annot ch (#185)

* scrolling of neural window fixed (issue #156)

* added feature to do kMeans Clustering

* bug fix for trial number increment when editing trial

* added support for different annotations file format

* added delete buttons in add or edit trial window

* feature to jump to specific time or frame

* Warning when annotation is done without annot Ch

---------

Co-authored-by: Ann Kennedy <[email protected]>

* Bug/new environment file (#191)

* scrolling of neural window fixed (issue #156)

* added feature to do kMeans Clustering

* bug fix for trial number increment when editing trial

* added support for different annotations file format

* added delete buttons in add or edit trial window

* feature to jump to specific time or frame

* Warning when annotation is done without annot Ch

* added single environment file for all platforms

---------

Co-authored-by: Venus Sherathiya <[email protected]>

---------

Co-authored-by: drumph <[email protected]>
Co-authored-by: Liezl Maree <[email protected]>
Co-authored-by: Dave Rumph <[email protected]>
Co-authored-by: Venus Sherathiya <[email protected]>

bento.yml

@@ -0,0 +1,31 @@
+name: bento
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - cryptography
+  - gst-plugins-bad
+  - gst-plugins-good
+  - gst-plugins-base
+  - gstreamer
+  - h5py
+  - matplotlib-base
+  - pip
+  - progressbar
+  - pynwb
+  - pyside2
+  - python
+  - qtpy
+  - scikit-learn
+  - scikit-video
+  - sortedcontainers
+  - sqlalchemy
+  - vispy
+  - xlrd
+  - pip:
+    - colour-demosaicing
+    - colour-science
+    - ndx-pose
+    - opencv-python-headless
+    - pymatreader
+    - qimage2ndarray

documentation/installation.md

@@ -21,10 +21,9 @@ cd path_to_bento_folder
  - Ex : cd /Users/KennedyLab/all_codes/bento
 
 5. Execute the following command to install all the dependencies/packages required for Bento.<br>
-   - Note : filename in the command should be replaced by <b>bento_windows.yml</b> or <b>bento_mac.yml</b> or <b>bento_ubuntu.yml</b> (based on your OS) <br>
 
 ```
-conda env create -f filename
+conda env create -f bento.yml
 ```
 
 6. Execute the following two commands to open the Bento User Interface:

documentation/tutorial.md

@@ -89,10 +89,16 @@ Now that you have experimenters, animals, and cameras on record, you can start u
 3. Select a session in the **Select Session** table by clicking the corresponding row.
 4. Click on **Add New Trial...** button. **Add or Edit Trial dialog** will pop up.
 5. Add Stimulus in the **Stimulus** field.
-6. You can add **Video files**, **Annotation files** and **Neural Files** in the window. **Pose files** and **Audio files** are not yet supported.
+6. You can add **Video files**, **Pose files**, **Annotation files** and **Neural files** in the window. **Audio files** are not yet supported.
+- Note : **Pose files** can be added only if there is a video file present.
 7. Click **OK** button. You will see a trial added in the **Trial** table along with files you selected for the trial.
 8. You can add multiple trials under the same session. Repeat steps 1-7, every time you need to add a trial under a particular session.
 
+#### Adding a Pose file
+1. Click on a **Video file** and click on **Add Pose...** button
+2. Select the appropriate format for the file in the file selection window. Bento supports MARS, SLEAP and DeepLabCut files.
+3. You can add one pose file to each video file present in a trial.
+
 ![alt-text](_gifs/adding_trials.gif)