Dvh-analytics

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* Organize modules in tools directory
* Generalize update_all_in_db functions in database_editor.py
* ensure all options read from custom options file if available
* Backup tab functionality in Admin view was incomplete since modularization of bokeh views
* Backup selection menus now update
* Backup preferences works again

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* Reorganize python files into directories:
* path updated with: import update_sys_path
* columns.py and custom_titles.py now have code wrapped in a class
* Multiple simultaneous sessions enabled again by wrapping all bokeh objects into classes
* Remove test files
* Catch keyboard interrupt in \_\_main\_\_.py for graceful shutdown
* Moved import_warning_log.txt to user's data directory
* All preferences stored in user folder now so that there's no need to run servers with sudo
* May need to copy files from <script-dir>/preferences into ~/Apps/dvh_analytics/preferences/
* Data directory defaults to ~/Apps/dvh_analytics/data but can still be customized
* All sql/preference backups stored in ~/Apps/dvh_analytics/data/backup now (can't customize)
* options.py now contains imports (os and paths.py)
* This broke load_options, code added to ignore ModuleType
* Automatically update uncategorized variations in ROI Manager after importing data, updating database, deleting data,
or reimporting database

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* Move csv creation to python for less javascript (download.js)
* Some bug catches if certain fields are too long to import into its SQL column
* ROI Name Manager in the Admin view displays a table of the currently saved ROI Map of the
currently selected physician

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* MAJOR restructuring with majority of main.py moved into bokeh_components directory
* Next release will begin working on better efficiency
* Residual chart added to Regression tab, will develop into Control Chart
* Begin making code more concise using classes and dictionaries
* Issue 42 - Regression drop-downs not updating properly when deleting/changing EP
* MLC Analyzer does not cause crash if DICOM plan file cannot be found

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* typo in keyword for parameter in dicom_to_sql (import_latest_plan_only changes to import_latest_only)
* Shapely speedups enabled, if available
* Shapely has calcs available in C, as opposed to C++
* centroid, dist_to_ptv_centroids, dth (distance to target histogram), spread_x, spread_y, spread_z, cross_section_max,
cross_section_median, columns added to DVHs
* These columns can be added by clicking Create Tables from Settings view, if running from source
* Running from Docker or pip install shouldn't need to do this manually
* dist_to_ptv_centroids and dth must be calculated from Admin view after proper ROI name mapping
* dth_string calculated with Calc PTV Dist in Admin view
* the string stored is csv representing a histogram with 0.1mm bins
* centroid, spread, and cross-sections also calculated at time of import
* calc in Admin view only required for data imported prior to 0.4.4 install
* Admin view now specifies Post-Import calculations via dropdown
* Added choice "Default Post-Import" to run through all calcs not done at time of DICOM import
* Endpoints for review DVH now calculated