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There was an issue with producing grid images and there was a bug in displaying the plate heat-map in the QC.
These were fixed in this minor release.
Consider using next release as this one had issues
A large set of fixes have been made for this release dealing with a variety of bugs and smaller issues, but the most prominent feature is the Quality Control UI now included directly with Scan-o-matic.
There are a ton of new features out under the hood, but from the user perspective there are two nice new features:
The analysis tab now offset the ability to manually regrid a previous analysis in the rare case that the grid got misplaced. Simply start it by filling out the reference folder of the bad grid (typically
Manual selection of files included in a compile
You start out the compile instruction as usual, but now there's a check-box for manual selecting files included in the compile.
A note about using this version with scanning.
Though there shouldn't be any changes to the scanning mechanisms please not that this version has not yet been tested. So before you start a real project, ensure that it correctly scans one or three images and if you are having problems report this back to us. Else you could just use the previous release for scanning until this version has been verified for scanning.
You can now find server and app maintenance inside Scan-o-Matic. For most cases they should work in shutting down, rebooting and other stuff. It is a bit tricky to fully complete these actions in all scenarios, which is why they only attempt their actions, not guarantee them. You find the area from the status or settings pages.
Previously there were issues with mailing from behind routers, this should now be fixed. So write your emails when starting scanners and do update to v1.3.1 rather sooner than later.
The API is expanding and now features more robust handling of exit urls in requests as well as introducing a large section of new features. Generally you would start at using
/api/results/browse and navigate question responses from there. As the API is very much under development, expect things to change and documentation to be non-existent.
Due to extensive renaming it highly recommended to run an uninstall of previous Scan-o-Matic before installing this version.
Several of the advanced / non-gui introduced features have documentaion of their use on the wiki.
You can now uninstall previous installations with
python setup.py uninstall.
This will presently not remove the executable scripts or any installed menu-integration but remove the code libraries.
Made termination of project while the same scanner is actually scanning work safer.
Phenotypes now have different levels of trust (
Other). As a default, only trusted phenotypes are given to the user.
It is now possible to normalize all normalizable phenotypes (though there's no GUI for it).
There are several new types of phenotypes included that are under development or experimental or worse. They are not inteded to be used yet and several of them will most certainly evolve in the near future.
It is possible to perform curve inspection on the old QC GUI and save that state and thereafter in python load that state using the current release to normalize all phenotypes. When saving this state, backwards compatibility of the QC-work will be lost.
It is now possible to calculate alternative population size measures of a colony that has been tracked through analysis using the
Phenotyper object has easy interface for adding metadata. Added metadata is also stored with the state and automatically loaded after added when state is loaded again.
Plate positions can now ben marked as
BadData. When requesting phenotypes, this information is maintained, but usinged the
filled() method will replace any not
OK with NaN. If a phenotype calculation yields an infinite or NaN result, that position is automatically set as
Marking has a proper undo with stepwise undo.
CSV output outputs one file per plate.
The strain selector.
A quality control api has been introduced. It is stil under development but has most quality control interactions needed.
It is housed a
/api/results. Currently there's no automatic generation of specifications for the possible api calls.
- A one use purge import of modules imported to deal with matplotlib issues.
- Many files have changed names in order to follow standards better. If you have an old installation of Scan-o-Matic it might be worth removing it before upgrading. Note that this does not refer to your settings folder at
$HOME/.scan-o-matic. There's no reason to remove that on before updating.
- Many un-used functions have been removed
- Much code has been updated to comply with standards
- Using enums when possible.
- Gridding and analysis is threaded
- Plate index is now correctly reported in log files during analysis
- Matplotlib erroneously loaded unintended backend, issue fixed by stripping analysis of all references to matplotlib. As a consequence images are directly loaded by PIL/Pillow
If no admin had been set or the admin file had been deleted, there was no way to authenticate the admin privileges without manually creating a new pass phrase.
Admin pass phrase is now automatically generated by
app_config.Config if it is missing and if it can't be done a critical message is output.
util.project module that will house functionality relating to renaming stuff
The LAN power manager had an outdated field name for the name of the power manager server and was therefore not updated when initialized with app config settings.
Auto completion in all UI
Generalized and thus introduced auto-complete for all UI aspects to make it easier to navigate. This feature also locks the user inside the projects directory, which means the user needs to set the correct directory in settings tab.
Note that you will have to restart the UI for updates to settings-directory and such to take effect.
Removed a lot of irrelevant text and some outdated and unused code.