lavinrp/eyedevelopmentmodel

eyedevelopmentmodel's Issues

Add some unit tests for cell adhesion

Create a few tests with different types of cells surrounded by other types of cells.
Surround them with one or two layers.

This will be critical in debugging cell adhesion as we change it.

Saved Epithelium and Settings files are not forwards compatible

by using pickle to save our epithelium and simulation options we implicitly version lock things.
This can cause crashes or incorrect behavior if the saved epithelium or simulation options are somehow incompatible with the rest of the code.

Example: Cell is given a new property that is used in the collision handler. The cells form an old saved epithelium will not have this property and will explode in the collision handler.

Cell.target_size

cells should slowly grow or shrink to fit their target size.

This variable can be set by furrow events to cause cells to automatically change their size over time.

Logic error in collision handler

Cell collision handler moves each cell as soon as it interacts with another cell.
This means that after a cell is pushed by a different cell it will be in a different position when it interacts with the other cells around it.

This arbitrarily gives more weight to the first cell that a cell interacts with and can even entirely change the cells that are colliding.

When resolving collisions we should first gather all of the forces exerted on cells by all of their neighbors, then move the cells according to the sum of all of the forces.

Furrow Events can Still Miss Cells

Furrow events can still pass over cells without checking them. This most likely occurs b/c cells are pushed behind the furrow event in between its checks.
The furrow system also currently allows for furrow events to be run twice on the same groups of cells.

These problems cannot be in the full release of the program.

Find a way to fix this

These config files will work with release/4-20-2018 to reproduce the issue
Cells_Not_Killed.zip

update_epithelium_with_sim_options should be called from MainFrame

Call this function from MainFrame inside the simulation setter instead of inside the simulation controller.

Remove Try-Except in run_cell_death

This try - Except is a hack to get around the fact that cells that were killed will still be sent to the furrow for specialization.

These cells cant be removed from the epithelium and therefore cause an exception when they are killed a second time.

Find a way to be sure that these cells are not sent to the furrow a second time.

Add license

Add license to the project.

Dr. Buschbeck needs to approve license.

Cell Children get Half Area

At the moment when cells divide both resulting cells get half the radius of the original. This results in a total area that is much smaller than the area of the original cell.

Should we instead have each cell get a radius of sqrt((orig_radius**2) / 2) which would result in each child cell getting half the area of the parent?

Fix cell soup in center of late development epithelium

This is from a 10000 cell epithelium generated with default settings and run with default settings.
Everything seems fine until cells start to die.

R8 away from edge using bin strategy

Add the Second Mitotic Wave

Right now cells will grow from the beginning of the simulation and never stop.

Have the cells only grow in the mitotic wave.

Remove legacy display

Remove all code related to the legacy renderer.
Remove PyOpenGL from requirements.txt

It should be possible to replace epithelium_backend implementations with user specified types

Right now nothing is an interface and implementations of things like the cell factory and the cell collision handler are just hard coded. It should be possible and easy to replace our implementations of these things.

Look at implementing just about everything in terms of an ABC.

Construct all objects that can be replaced by the user somewhere in quick_change and ensure that the ones specified there are the ones used by the simulation.

Improve Selection Functions

Dont specialize a cell if it has already been specialized.
Make sure that they can specialize all of the cells.
* Currently we only select a certain number of neighbors for some of the selection functions regardless of how many cells we intend to recruit. That means that if we try to get over 100 r2 cells it doesn't actually specialize that many.

Fine tune specialized cells target radius

Sit down with Dr. Buschbeck and figure out the best target size that cells try to grow to. Maybe different cell types have different sizes? Stop growing after they're specialized? Could possibly be a user input

CellCollisionHandler breaks when cells are much bigger than average

When a cell is much bigger than the average cell CellCollisionHandler does not correctly handle its collision.
(if the cell is as big as two or more bins)

Temporary epithelium should be saved to users temp dir

We should use the system temp directory instead of a hardcoded temp directory relative to the path of the application.
Update the MainFrame.temporary_epithelium_location to use the system temp directory.

add default extension to sim and epith files

make .sim
and .epth

the default file types for simulation and epithelium saves respectively.

Epithelium neighboring_cells uses max cell size instead of average cell size

The epithelium is expected to be able to figure out how close together cells are and by forwarding its calls to the cell collision handler we're using max cell size instead of average cell size and reporting cells too far away as being neighbors.

Use __init__.py to simplify imports

http://mikegrouchy.com/blog/2012/05/be-pythonic-__init__py.html

lets get rid of the from package.file import File and replace it with from package import File

This can be done by importing the classes within the init.py for each module.

Crash on cell death

Sometimes cell death can cause a crash .

Error instead of warning when cant load simulation settings

Currently when an epithelium cant be loaded it shows a popup error. When a simulation setting cant be loaded it shows a popup warning.

This should be standardised to error.

Select R8 Cells away from edges of epithelium

Right now the first R8 cells that are selected are touching the edge of the epithelium.
Make it so that R8 cells are only selected if they are at least r8 distance away from the edge.

Start Epithelium in Center of Screen

It would be nice if the epithelium started centered on the screen instead of the bottom left.

Furrow position does not react to shifting epithelium

Consider an extreme situation where cell growth causes many of the right most cells to shift 100 average cell radii to the right within a single update of the furrow position. Everything that was pushed to the right of the furrow will be missed by the next pass.

This is a crazy edge case, that probably will never happen, but this may be happening in small ways throughout the simulation.

Consider revising the Furrow to accommodate for this (make the furrow move relative to the movement of the epithelium? ).

Register and Deregister Cells in Bulk

Every register and Deregister of a cell causes a the CellCollisionHandler to bin everything.
We can probably save some time if we just have to do that once per tick.

Update Default Parameters to Match Drosophila

The default parameters of the simulation should reflect Drosophila since that is what the simulation is based on.

From Dr. Buschbeck the paramaters should be:

Setting	Value
Min cell count	10000
Average cell size	8
cell size variance	0.1
Cell max size	15
Cell Growth rate	0.005
Furrow Velocity	20
simulation speed	100
r8 exclusion raidus	2
r8 target radius	20
min distance from edge	3
distance from furrow	0
r2,r5 selection count	2
r2,r5 target radius	20
max distance from R8	2
distance from furrow	100
r3, r4 selection count	2
r3, r4 target radius	20
max distance from R8	2
distance from furrow	150
r1, r6 selection count	2
r1, r6 target radius	25
max distance from R8	4
distance from furrow	200
border radius	1
target radius	20
distance from furrow	1000
death chance	30
distance from furrow	1200

Same/Load of Epithelium is Broken

Saving an epithelium does not put the epithelium where requested.
It is impossible to load an epithelium. "Error: Could not load epithelium!" error always occurs.

Backend logic is clearly working (b/c Save/Load is what actually goes on under the hood when pressing the "stop" button in the simulation tab).

Decompact 1000 Times on initial epithelium generation.

50 times is not sufficient for a large epithelium

Fix double selection of cells.

Sometimes one R8 cell will select other photoreceptor cells multiple times. Fix this.

requirements.txt

Add a requirements.txt file to simplify setup

CellCollisionHandler assumes that no cell has a negative position

Is this real?

CellCollisionHandler assumes that the positions of all cells are positive when determining how to partition the internal cell grid. This likely results in performance degradation and/or incorrect collision handling as cells expand/divide and push each other into negative positions.

Implement Relative Distance From Furrow

right now Furrow events all have absolute distances from the furrow. It would be a nice usability feature to allow for one furrow events distance from the furrow to be relative to another furrow events.

Add a combo box that determines if a distance from a furrow is relative or absolute. If it is relative allow the user to select which furrow event it is relative to (another combo box?).

Absolute distance from furrow would be unchanged, but relative distance would add/subtract/multiply/divide the furrow distance of the selected event to produce the absolute distance to the furrow of the new Event

Maximum Recruitment of Receptors

There appears to be a strange maximum number of receptors that can be recruited when trying to run configurations meant to create large units.

For some reason the maximum appears to be 256.
If 257 is input for any of these the entire field fills up with photoreceptors.

There should be no maximum.

Investigate Numba for improving performance

http://numba.pydata.org/numba-doc/latest/index.html#

Add Tests For Everything

There are currently almost no tests.
Ideally there should be a unit test for every functionality that we have and integration tests where the individual components interact.

We have been really lax on this so far, and that has created lots of opportunities for bugs and regressions.

Time to get some test coverage.
We should also add CI and require tests passing there before merging any PRs

Cell Max Size as input paramater for each cell type

in each cell selection function add a parameter to dictate what the max size of that cell type is

Support cells are being converted into photoreceptors

From Dr. Buschbeck's email:

if border cells are specified earlier than the photoreceptors, then the photoreceptors form from them (where they should stay what they are specified once that has been decided).

Split out cell grid from collision handler

Selecting R8 away from the edge can use the cell grid correctly, the cell collision handler uses the cell grid correctly

Add more validation types for FieldTypes

currently we only have IntigerFieldType this greatly limits the power of the dynamic GUI.

It is also not currently possible to add more validation rules to a FieldType. Modify field type to allow users to add validation restrictions without needing to create a new FieldType child class. Perhaps a function pointer?

Dynamic GUI System Rework

Right now the dynamic GUI system leaves a lot to be desired.
Adding inputs to the furrow event list requires three steps.

1. Create function that takes field_types, epithelium, cells
2. Create FurrowEvent from this function and specify the field types that the function will get
3. Add the new FurrowEvent to the furrow_event_list

There is a lot of room for error between 1 and 2.
It would be nice to take advantage of python's reflection capabilities.
Each furrow event could be a class. We could look at the properties of that class and autogenerate the fields and their widget types from that.

Cell adhesion

• It's ok if they also become more rigid

Update Documentation

The documentation is outdated and still references the initial senior design project.
Add full client-ready documentation

Border radius of 0 still produces border cells

When a border radius of 0 is input border cells are still created.
A radius of 0 should result in no border cells.

Fix Crashes

Fix crashes that occur when starting with cells of size 100.

This has to do with creating only enough bins to hold cells if they all have an average size.
This has to do with adding the default cell events.

Furrow Event ScrollBar does not work until window resize

For some reason the scrolled window for Furrow Events does not allow the user to scroll (regardless of how many inputs it contains) until the window is resized.

Migrate to QT

WxPython is causing lots of cross platform problems. QT seems like it may be a better choice.

Try to make the switch.

Make FieldTypes Have their own event handlers

It may be more readable and better maintainable if field types provide their own event handler functions rather than having a function in MainFrame that produces event handlers for each FieldType.

an attempt at this can be seen in bug/i81-FurrowEvents_dont_update_v2

OpenCL Collision

Moving collision logic to pyOpenCL would allow us to use CPU and GPU parallelism in our collision logic.

This would make things MUCH master. Lets look into this.

https://en.wikipedia.org/wiki/Barnes–Hut_simulation
Try:
determine number of bins
histogram to determine the number of cells in each bin
Put cells in each bin (prob use single array in shared memory)
PushPull Cells

We may want to add the option for this to be a n-body simulation. That way cells would tend towards clumping together.