SlideR 🍔 issueshttps://git.fmrib.ox.ac.uk/seanf/slider/-/issues2021-06-22T23:03:26+01:00https://git.fmrib.ox.ac.uk/seanf/slider/-/issues/6Create usage example2021-06-22T23:03:26+01:00Sean FitzgibbonCreate usage examplehttps://git.fmrib.ox.ac.uk/seanf/slider/-/issues/7Create README2021-06-22T23:03:28+01:00Sean FitzgibbonCreate READMEInclude:
1. Acknowledgement to TIRL
2. Environment setup
3. Install instructions.Include:
1. Acknowledgement to TIRL
2. Environment setup
3. Install instructions.https://git.fmrib.ox.ac.uk/seanf/slider/-/issues/8Add license2021-06-22T23:03:30+01:00Sean FitzgibbonAdd licenseApache 2.0 licenseApache 2.0 licensehttps://git.fmrib.ox.ac.uk/seanf/slider/-/issues/2Add apply_xfm support2021-06-22T23:03:31+01:00Sean FitzgibbonAdd apply_xfm supportNeed to be able to apply xfm (either slide_reg nonlinear, or chart_reg affine) to an image.
1. Ideally the reference space can be higher resolution (or lower) than was original used in the registration.
2. Ideally this would be a sing...Need to be able to apply xfm (either slide_reg nonlinear, or chart_reg affine) to an image.
1. Ideally the reference space can be higher resolution (or lower) than was original used in the registration.
2. Ideally this would be a single command that understands either xfm type, and can have chart or image as input.https://git.fmrib.ox.ac.uk/seanf/slider/-/issues/1Add jp2k support to slide_reg2021-06-22T23:03:32+01:00Sean FitzgibbonAdd jp2k support to slide_reg1. ~~Include output support for transformed image~~
2. Must handle resolution and resolution_level1. ~~Include output support for transformed image~~
2. Must handle resolution and resolution_levelhttps://git.fmrib.ox.ac.uk/seanf/slider/-/issues/11change slide config from JSON to YAML2021-06-22T23:04:04+01:00Sean Fitzgibbonchange slide config from JSON to YAMLThis will allow comments within config file.
Also rename according to sub-program e.g. `slide.config` for `slider_app.py SLIDE`This will allow comments within config file.
Also rename according to sub-program e.g. `slide.config` for `slider_app.py SLIDE`https://git.fmrib.ox.ac.uk/seanf/slider/-/issues/14Add config for chart_reg that includes resolution_level2021-06-22T23:04:06+01:00Sean FitzgibbonAdd config for chart_reg that includes resolution_levelhttps://git.fmrib.ox.ac.uk/seanf/slider/-/issues/13Batch tool2021-06-23T13:52:57+01:00Sean FitzgibbonBatch toolTool to batch a bunch of files through SlideR.
Notes:
1. Should read a CSV of files (rows=single-job, cols=job-args)
2. Should be a sub-parser of `slider_app.py`
3. Needs to support CHART, SLIDE, and APPLYXFM
4. Add usage example to REA...Tool to batch a bunch of files through SlideR.
Notes:
1. Should read a CSV of files (rows=single-job, cols=job-args)
2. Should be a sub-parser of `slider_app.py`
3. Needs to support CHART, SLIDE, and APPLYXFM
4. Add usage example to README
Optional:
1. Could add parallel supporthttps://git.fmrib.ox.ac.uk/seanf/slider/-/issues/4Fix plots in chart_reg2021-06-23T17:38:45+01:00Sean FitzgibbonFix plots in chart_regAdd offscreen rendering and saving to file.Add offscreen rendering and saving to file.https://git.fmrib.ox.ac.uk/seanf/slider/-/issues/16Add resolution level option to APPLYXFM2021-06-23T20:50:21+01:00Sean FitzgibbonAdd resolution level option to APPLYXFMhttps://git.fmrib.ox.ac.uk/seanf/slider/-/issues/12Report registration performance.2021-07-05T09:55:04+01:00Sean FitzgibbonReport registration performance.This could occur at multiple levels.
1. `chart_reg` already produces diagnostic plots
2. `slide_reg` produces some diagnostic plots although some overlays are required
3. Report generator for single and multiple registrations is required.This could occur at multiple levels.
1. `chart_reg` already produces diagnostic plots
2. `slide_reg` produces some diagnostic plots although some overlays are required
3. Report generator for single and multiple registrations is required.https://git.fmrib.ox.ac.uk/seanf/slider/-/issues/5Add robust logging2021-06-16T22:54:53+01:00Sean FitzgibbonAdd robust logginghttps://git.fmrib.ox.ac.uk/seanf/slider/-/issues/3Simplify slide_reg2021-06-23T20:52:31+01:00Sean FitzgibbonSimplify slide_reg`slide_reg` was based on a TIRL script that was initially designed to be much more flexible than required here. As such, the code is more complex than necessary. It should be pruned/simplified to the task of 2D-to-2D slice registration...`slide_reg` was based on a TIRL script that was initially designed to be much more flexible than required here. As such, the code is more complex than necessary. It should be pruned/simplified to the task of 2D-to-2D slice registration as required here.https://git.fmrib.ox.ac.uk/seanf/slider/-/issues/10Support dark background in chart_reg2021-06-17T09:59:26+01:00Sean FitzgibbonSupport dark background in chart_reghttps://git.fmrib.ox.ac.uk/seanf/slider/-/issues/9implement more complete and robust neurolucida morphology reader2021-06-17T09:55:47+01:00Sean Fitzgibbonimplement more complete and robust neurolucida morphology readerhttps://git.fmrib.ox.ac.uk/seanf/slider/-/issues/15change from specifying rlevel to resolution2021-06-21T16:42:09+01:00Sean Fitzgibbonchange from specifying rlevel to resolution