Project Plan

1. Preliminary patches and updates. 2.5 months
   a) Become familiar with some parts of code.
   b) Check current process load on server and adjust parallelization.
   c) Automatically update table after making changes in review window.
   d) After selecting multiple datasets for an operation, show all errors in single window, and provide option to remove bad datasets from operation.
   e) Apply scale factor to all 72 images in batch.
   f) Fix resizing bugs after zoom.
   g) Do cropping in single step instead of 2 steps.

2. Integrate “add a top line” as an option in the Rootwork and RootworkPerspective steps. 1 week

3. Integrating with database. 2.5 months
   a) Become familiar with entire code.
   b) Evaluate, choose and install correct DB system.
   c) Design DB structure, with entities like "species", "experiment", "jar", "date", "run", "user", "config", etc.
   d) Create indexes to increase performance.
   e) Set up DB backups.

4. Integrating with database. 2.5 months
   a) Build data access layer in rsa-gia, make it easy to switch to another DB system in the future.
   b) Rewrite all file scan & parsing features in rsa-gia to use DB instead.
   c) Create UI windows to edit metadata in DB, like species, experiment, etc.
   d) Write script to do one-time scan of existing directory structure and import everything into DB.
   e) Write documentation on DB installation instructions.

5. Improvements to main window. 1 month
   a) Improve filtering options.
   b) Fix bugs in "Edit columns", e.g. missing RootworkPerspective columns and slow start.
   c) Show metadata about each experiment.
   d) Show better date & time information.

6. Improvements to review window and run selection windows. 1.5 months
   a) Show more useful information inside parentheses.
   b) Create better UI to make it faster to use.
   c) In run selection window, show all runs instead of only saved runs.
   d) In run selection window, allow multiple selection.
   e) Add filtering options.

7. Better gia_roots launch experience. 1 month
   a) Create new GUI window that takes gia_roots parameters and saves config file automatically.
   b) Run gia_roots with entered parameters, show thumbnails from inside rsa-gia, and allow revision of parameters.
   c) Make it optional to calculate descriptors.

8. Better Rootwork launch experience. 1 week
   a) Show results automatically in Meshlab.
   b) Any other minor improvements.

9. Integrating new algorithms. 3 weeks
   a) Refactor and comment code to make it easy to integrate new 3D reconstruction algorithms.
   b) Write documentation on how to do this in the future.

10. Improvements to QC. < 1 week
    a) Fix QC2 window thumbnail visibility problem.

11. Creating program package. 3 weeks
    a) Allow easy installation on new computers in lab, resulting in more parallelization.
    b) Allow easy installation in collaborators' labs.

12. Additional metadata editing windows. 3 weeks
    a) Add a filter/search window for finding seeds when editing seed metadata.
    b) Add batch import for seed metadata to database.
    c) Add a new window for adding/editing valid genotypes.

13. Unclear tasks.
    a) Fix QC3 bugs. ?
    b) Add stronger QC features. ?
    c) Investigate how to do 3D reconstruction before segmentation. ?
    d) Support different types of input images. ?
    e) Integrate a new reconstruction algorithm, with new UI for taking parameters.
    f) Integrate new version of gia_roots, with new UI for taking parameters.