-
Notifications
You must be signed in to change notification settings - Fork 4
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
ENH: Update Pre-Processing UI to improve BVR workflow #141
base: main
Are you sure you want to change the base?
ENH: Update Pre-Processing UI to improve BVR workflow #141
Conversation
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
-voxel size should not be manually editable- but inherited from the volume node used to gen PV
-
as part of PV gen - assign the voxel size values
*create a subdirectory in Models folder 'AUT' so that the Models level h used in Segmentation generation remains unchanged -
remove 'virtual' radiograph subdirectory
@amymmorton In the last commit pushed to this branch, I moved a few of the UI widgets so that the pre-processing tab isn't so wide, made sure that the segmentation generation options are enabled/disabled based on which radio button is selected (automatic segmentation vs. seg from models), and also implemented the file selectors for the config generation group. |
'or enter:' label to 'AND enter:'
|
c83ec97
to
a5201c9
Compare
Remaining TODOs at this point:
Optional/Future PR:
|
1fefc3e
to
8af2265
Compare
"populate the "Voxel Size" according to the input volume node selected (should we let users have the ability to manually override it too?)" I say No. The only options are voxel size form volume node / volume.tfm (which must both be the same) |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
👍
ffe64d1
to
cadfda4
Compare
Cleaned up the commit history on this branch for ease of reviewing |
04eadf0
to
15940b2
Compare
* 'Volume Node' and 'Output Directory' at top of UI were swapped * 'Trial Name' moved to the config generation section as the '<blank>'.cfg field * The segmentation generation section was redesigned to better convey the two separate generation methods * The 'Adavnced Options' sections was renamed to 'Default Subdirectories', moved below the 'Segmentation Generation' section, and is now rendered as collapsed by default * The 'VRG Resolution' fields from 'Advanced Options' was moved to the config generation section * In the 'Generate Config' section, added file and path selectors to specify the camera calibration files, radiograph root directories, and volume files to be written to the generated config file. Also added 'Voxel Size' fields that are automatically populated based on the selected input volume node. * Elements in the .ui files were edited to be properly indexed and named Co-authored-by: Amy M Morton <[email protected]>
TODO: decide and implement correct pairing of radiograph subfolders with their camera calibration files
0f9c9e1
to
a594fac
Compare
Updated the config paths selection based on @amymmorton's draft. I ended up implementing a design that supports any number of corresponding camera file & radiograph subdir pairs (see updated screenshot in the PR summary). Feel free to review the update, particularly any UI text/labels and tooltips on the "add" buttons to see if we can better clarify their purpose and emphasize the importance of the order. |
d8045fd
to
dc97ba1
Compare
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
@jdholt04 any test updates from you from last week?...
I think the ui looks great. When testing I am unable to select files/subdirectories after populating the selection boxes. This could be an error on my part... I replaced AutoscoperM.py, IO.py and AutoscoperM.ui with the changed files. Are there any additional files that I need to replace? EDIT: Simply could not see boxes to select files in dark mode. Successfully generated config file. |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
I was able to successfully generate a config file using the changes made to the pre-processing module (tested in Slicer 5.6.2). Config file was generated and was able to be loaded into Autoscoper.
One change to the UI that would be helpful: In dark mode the boxes to select files to be added to the config file are not visible. Could changes be made to the UI to make it more intuitive for users in dark mode?
Changes include some reordering of the UI to better match the order of the config v1.1 file format. Co-authored-by: Amy M Morton <[email protected]>
dc97ba1
to
0b16371
Compare
Thanks for the feedback! I updated the checkbox background color so it stands out more in dark mode, following this fix in a similar issue in Slicer. |
Resolves #131, resolves #145.
These changes are aimed to improve the user workflow in the Pre-Processing module, specifically targeting the improvement of the Autoscoper configuration file generation. Further changes to improve error handling to make it more user-friendly are to be continued in a separate upcoming PR.
Changes in this PR include:
Remaining TODOs: