todo.md

TODO next (remove as implemented and add under corresponding version in changes.md)

Database:

• Centre handle on user measurements maps incorrectly on a freshly loaded model that isn't in aligned position. Probably not taking into account model transform matrix.
• Add action to copy over subject data from other (loaded) image.

Version 7.0.0.20220131 (Prague)

• Local 3DF file indexing based on root location for 3DF storage
• When making symmetric face (and no landmarks), mirror points through plane
• Increase allowed length of user measurement name
• User measurements dialog to toggle visibility and update names
• When hovering over a user measurement, make it appear differently to the others

Version 7.1.0.20220210

• Volumetric measurement
• Asymmetry report improvements
• Average face generation from selected 3DFs
• Landmark selection / hiding / flagging
• Manual entry of facial measurements
• User surface area measurement
• Fix calliper handle snap range after switching views when in orthographic view
• Fix rotations from transform menu not sticking after changing view.

Version 8.0.0.20220501 (Babyface)

• Mahalanobis distance visualisation for facial cohorts
• Variation from cohort report
• Cohort mask averaging
• Improved coregistration

Unassigned

User measurements

• Allow mid path handle to be defined out of plane.
• Show angle at mid path handle as angles projected into standard planes.
• Add volumetric measurement.
• Copy user measurements to second loaded face or as a batch operation to a bunch in a directory.
• Make face transparent when hovering over handles (not just when moving them).
• If handle is over a landmark, show the landmark name too.
• Edit calliper handle size (fixed size vs scaled size)?
• Batch copying of user measurements to a bunch of other 3DF files based on AM correspondence.

Camera

• When updating field of view (preferences) maintain apparent camera distance.
• Upon view change, update the camera/model move interaction action.
• When holding ALT and making camera movements, lock movement to the axes.
• Interactive rotation about specific axes?

File I/O

• Generate average face from a user specified cohort (directory) - but check Harry's work.
• Search within cohorts (directory?)
  • For a particular HPO term or metric
  • Get the N most similar faces to the current from a cohort.
• After action, check model against initial state and set unsaved only if mismatch.
• When opening a registered file type by double clicking, open in existing Cliniface instance if found or a new instance if two models are already loaded.
• Add file menu to open an example from application directory.
• Add in Recent files menu.
• Add source and Z-scores for measurements in CSV file.
• On saving to a non-metadata format (ply etc), erase all metadata (since warning about it).
• Fix loading 3DFs with different stored masks
• Import from VRML format files.
• Allow addition of attachments to 3DF.
• Import metadata directly from a 3DF.
• Import/export from/to 3MF format (3D printing format).
• Extend 3DF file format to allow other kinds of models (hand, foot, jaw).
• Copy in action name for undo/redo states since action name may change.
• Record movie from viewer for mpeg export.

Visualisations / UI

• Fix crash when centre model on right click calliper handle.
• Mahalanobis distance visualisation.
• Change status text when toggling "texture" (surface) on with model with no texture.
• When loading file with measurements showing - ensure 0.99 opacity set.
• Show landmark labels for the selected measurement in measurement mode.
• Allow rotation by arbitrary amount (make interactive too).
• Coronal plane too far forward (though not used right now so fine to leave).
• Show scalar value in status bar and an arrow on legend as mouse moves over surface.
• Check if on high DPI display and resize graphical widgets (e.g. handles) accordingly.

Landmarks

• When moving landmarks, ensure bilateral landmarks remain on the correct face half.
• Show landmark labels for the left side of the face on the left side of the cursor.
• Customise which landmarks to use and flag reliability.
• Landmark labels need to account for individual visibility.
• Add info about where definitions of landmarks come from (Elements of Morphology).

Stats and standard measurements

• Allow for manual entry/adjustment of facial measurements.
• Add measurement information about source, use etc in Lua definitions.
• On graphs, if two subjects loaded, show selected (filled in circle) and other (circle).
• Centralise demographic mismatches and display everywhere (including report generation).
• Add fields for Weight, Height, Head Circumference, and free text medical history (conditions, treatment).
• Add MONDO disease codes.
• Display subject's calculated age.
• Include Japanese stats from Kate (email).
• In HPO dialog, make external link to HPO online a button.
• On press HPO browser button, raise as top window.
• Allow user to specify default syndrome(s).
• Flag detected phenotypic traits not associated with the selected syndrome(s).

Anthropometrics

• Check interpupillary
• Obtain Nasal Root Width
• Change Ptosis criteria to be below 2 standard deviations instead of 3 mm.
• Ear, long
• Ear, short
• Columella, broad
• Columella, high insertion
• Columella, low insertion
• Columella, low-hanging
• Ear, posterior angulation, increased
• Ear, low set
• Mouth, downturned corners of
• Mouth upturned corners of
• Chin, short
• Chin, tall
• Facial depth
• Prognathism
• Retrognathia
• Malar flattening/ malar prominence
• Midface prominence/ midface retrusion
• Hairline, low anterior/ hairline, high, anterior (need to sue texture and anatomical data for this)
• Philtrum depth
• Cornea diameter (if possible)
• Volume difference

AM co-registration

• Full head models don't work with the alignment algorithm.
• Resize the AM mask prior to fitting based on estimation of eye distance found.
• Use the 2D facial detection method to discover basic facial features (Python process).
• Use vertex normals to decide corresponding parts of the target and source surfaces to map.
• Fix holes using 3DMM after detection.
• Patient equivalent face generation

Mesh/Model Representation

• Add action to remove texture.
• Fix right symmetric face gap centreline gap.
• Add action to Centre Model on current focus.
• Rename Extract Facial Region to Extract Region if the radial selection tool is active.
• Check inconsistent triangle normals - returning twisted when it shouldn't? Not sure...
• Improve smoothing to remove spikes entirely (e.g. eyelashes).
• Fix hole filling to reorganise mesh.
• Add function to redistribute mesh vertices.
• Normal flip for specific polygons.
• Modify vertex positions by clicking and dragging.
• Localised smoothing/cropping tool.

Report generation

• Remove unused files to fix PDF generation issue (wrong pdflatex being referenced?).
• Exported 3D models in PDF should use much lower geometry meshes for reduced file size.
• Improve asymmetry report and ensure documentation present.
• Direct production of PDFs

Documentation

• Add info about the reference ranges to the documentation.
• Add info about generating the facial comparison report.
• In docs, links to anchor ids from other pages not working sometimes - BUG
• Check and change tooltips to be multiline (see Preferences).
• Log errors/issues and offer to email.
• Language Translations,Lyfe Languages

Build / Installation / Plugins / Updates

• Fix auto-update of FASD module analysis after changing measurements (e.g. in-plane PFL)
• Auto-restart after network update.
• Add option to delete .cliniface directory when uninstalling (Windows).
• Add "Add Plugin" button to plugins dialog.
• Allow plugin dialog to be resized.
• Remove diagnostic references from FASD plugin (see Eamon's email).
• Ensure dependent libraries of IDTFConverter are included (libpng12).

Miscellaneous

• Timeout for long running actions.