Pass in Initial Glucose Concentration as a parameter for PatchProcessMetabolism #95
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* Added CLASS to population MiniBox in PottsSeries.java (similar to PatchSeries implementation). Added corresponding test to PottsSeriesTest.java * Deleted unused variable and formatted * reformatted again * deleted adjusted test * added updatepopulation_onePopulationWithClass_createsMap() test
…e() function (#12) * Broke setState into two functions so in future setStateModule can be implemented differently by different cell types * added divisions setter for use in future subclass make functions * added getCriticalRegionVolumes and Heights for use in future subclass cell constructors * changed parameter name to overcome HiddenFieldCheck error * added Javadoc comments on new getters and setters * changed parameter name in setStateModule to overcome hidden field error. Formatting fix. * added getter and setter tests. formatting fix * formatting fix * deleted getters/setters. Made necessary fields not public. Deleted associated tests * deleted unnecessary imports and formatting fix * made fields that already had getters public so no elements of PottsCell constructor need to be accessed via getters * typo fix * deleted unnecessary import and formatting fix
* Broke setState into two functions so in future setStateModule can be implemented differently by different cell types * added divisions setter for use in future subclass make functions * added getCriticalRegionVolumes and Heights for use in future subclass cell constructors * changed parameter name to overcome HiddenFieldCheck error * added Javadoc comments on new getters and setters * changed parameter name in setStateModule to overcome hidden field error. Formatting fix. * added getter and setter tests. formatting fix * formatting fix * deleted getters/setters. Made necessary fields not public. Deleted associated tests * deleted unnecessary imports and formatting fix * made fields that alread had getters public so no elements of PottsCell constructor need to be accessed via getters * typo fix * deleted unnecessary import and formatting fix * made PottsCell abstract class. Made default cell type PottsCellStem. Changed PottsCell tests to be PottsCellStem tests. Changed PottsCellContainer to default to making PottsCellStem cells * fixed merge issues * Moved assignment of potts cell class when none specified to PottsSeries. Deleted abstract make in PottsCell. Casted to PottsCell in PottsModule * updated parameters mock to return stem when parameters.get(CLASS) is called * Moved PottsCell make, state, and module tests into PottsCellStemTest. Made mock implementation of PottsCell for PottsCellTest * added content to PottsSeriesTest to make sure class is set to stem as default and to a given string if a given string is provided * Finished adjusting PottsSeriesTest to test for default cell class being set * formatting fixes * Addressing Jessica's comments * formattig fixes * removing code comments * added ability to assign one real state to PottsCellMock for testing purposes * formatting fix * added mocks for PottsModule getPhase return in PottsCellTest tests * formatting * Fix minor formatting and move remaining make test to PottsCellStem --------- Co-authored-by: jessicasyu <[email protected]>
… Split Method (#16) * added functionality so offset can be provided to split * formatting fixes * removed unnecessary import * removed unnecessary comment * formatting fixes: * adding in tabs * added ability to specify direction as well as offest in PottsLocation split * only call connect_voxels if splitpoint is not specified to split function in PottsLocation * formatting fixes * further formatting fix * adding ability to specify probability split returns voxelsA vs voxelsB * added tests * fixed broken test * formatting * renamed splitProbability * fixed accidental changing of cell offsetPercents field * deleting print statement I accidentally left in * Streamline method overloading and unit tests * Fix javadoc spacing * added split test using zx direction to test split functionality in z plane --------- Co-authored-by: jessicasyu <[email protected]>
* Renove size checkpoint for apoptosis * Remove apoptosis checkpoint tests
* Update patch series to parse percentage init * Update patch cell factory to initialize with counts or percents * Add calculation of total number of patches * Fix linting
* changed docstrung for getDirection to specify that it gets direction with shortest diameter through location * adding initial Plane, Point, Vector classes and associated tests * adding last file * adding Plane container and Plane factory to make planes from potts enums * wip many tests failing, fixing PottsLocationTest.java * corrected normal vectors in PottsPlaneFactory. Updated tests. Added tests. * moved all points and vectors to int3Ds, expanded direction enum, removed plane factory and container * small changes to PottsEnums test, formatting fixes * removed extra split function * Divide Distance to Plane by Normal Vector Magnitude (#52) * Signed distance to plane and tests for plane class * Signed distance to plane and tests * updated tests, renamed function --------- Co-authored-by: Danielle Vahdat <[email protected]> Co-authored-by: daniellevahdat <[email protected]> Co-authored-by: jannetty <[email protected]> * moved Plane to Potts, changed point type to Voxel, removed unused function * change plane to have point represented as voxel instead of int3d * changed signedDistance function to take voxel * updated test * changed enum back, formatting fixes * removing test.class * Update src/arcade/potts/env/location/PottsLocation.java Co-authored-by: Jessica S. Yu <[email protected]> * addressing Jess's comments. Normalizing plane normal vector. * formatting fixes * added a few white spaces * Update src/arcade/potts/env/location/PottsLocation.java Co-authored-by: Jessica S. Yu <[email protected]> * Update test/arcade/potts/env/location/PottsLocationTest.java Co-authored-by: Jessica S. Yu <[email protected]> --------- Co-authored-by: daniellevahdat <[email protected]> Co-authored-by: Danielle Vahdat <[email protected]> Co-authored-by: daniellevahdat <[email protected]> Co-authored-by: Jessica S. Yu <[email protected]>
* Add patch cell with randomly assigned states * Update cell container for random patch cells * Add tests for random patch cell * Update patch agents to increase divisions instead of decrease * Fix linting * Switch division counts back (to be implemented separately) * Fix divisions in random patch cell test
* Update source compatibility to 8 * Bump mockito versions * Update JDK versions in workflows * Fix illegal spy mocks in tests
* Bump to junit 5 * Update Test and Assertion import names * Update BeforeClass annotation to BeforeAll * Fix exception testing * Replace temp folders with injected temp dir * Enable junit 5 tests * Fix import orders
* Add formatter to build.gradle * Apply formatting * Add checks for XML files * Add whitespace around config for checker
* added tests for colors * changed functionality for below min values and below default values * added tests for alternate constructors * added test for nonlinear colormap specs * minor changes for linter * adjusted some functionality and changed references to getRGB * linter changes * Updated for JUnit 5 * cleaned up some tests * Adjusted test to reflect bin behavior
* added tests for ODE solvers and bisection * Adding tests for SOR and JUnit5 changes * linter changes * remove inner assignment * cleaned up tests * removed space * added tests to improve coverage by exposing default parameters * removed called from test headers
* improved coverage and added assertAlls * minor name updates
* added tests for graph core utilities * refactor Graph to pass tests * addressed linter issues * added static to subclass imports * updated some documentation * updated function changes * removed some duplicate returns * added upstream methods, changed to called by edges, updated test names * consilidated and grouped similar tests * updated some names * cleaned up some more tests * added some more tests for magic functions * completed test coverage and resolved cycle infinite loop * addressing linter issues once again * fixed typos * removed assert all strings * moved enums from patch to core for general graph purposes * cleaned up documentation and spotless * added missing param tag * added test and fixed bug
* added tests for Parameter class * added OOB exception for error handling * added docstrings to OOBException * spotless change * renamed OOB to OutOfBounds * spotless
* Update cell make interface for container * Update simulation interface to return factories * Update proliferation modules to call convert * Update tests
* Update cell make interface for container * Update simulation interface to return factories * Update proliferation modules to call convert * Update tests * Update patch cell constructors to use container * Update potts cell constructors to use container * Update tests for container constructors * Update gradle spotless targets * Fix formatting * reformatting tests that had merge conflicts with develop --------- Co-authored-by: Sophia K. Jannetty <[email protected]> Co-authored-by: jannetty <[email protected]>
* Update cell make interface for container * Update simulation interface to return factories * Update proliferation modules to call convert * Update tests * Update patch cell constructors to use container * Update potts cell constructors to use container * Update tests for container constructors * Update gradle spotless targets * Fix formatting * Update series to load links from setup file * Change link weights to doubles * Add population links to cell factories * Add population links to cell fields * Update cell agent tests for links * fix error from merge --------- Co-authored-by: Sophia K. Jannetty <[email protected]> Co-authored-by: jannetty <[email protected]>
* changed Plane constructor to take a Double3D instead of an Int3D * added Plane test that uses doubles in normalVector constructor
* Change parameters from minibox to dedicated parameters class * Add parameter and link getters to cell factory * Update parameters type in cell constructors * Update cell containers to create parameters * Add distribution interface and implementing classes * Update process calls to parameters * Update module calls to parameters * Update default parameters with distributions * Update potts module tests * Update implementing agent tests * Update potts cell tests * Update cell factory tests * Update distribution and distribution tests * Update distribution parsing in series * Replace cell factory calls to distributions with parameters * Fix tests * Update series parameter parsing * Update proliferation modules to call convert with parameters * Add tests for distributions * Update minibox tests for distributions * Add tests for parameters * Add series tests * Add expected values and update minibox get double for distributions * Add nextDouble and nextInt methods to distributions * Add getDistribution method to Parameters * Enforce that distribution type is uppercase * Round integers for normal distribution * Fix tests for rounded integers in normal distributions * Round integers for uniform distribution * Add Bernoulli distribution * Update series to parse distributions with one or more parameters * Make pop parameters private in parameters * Fix occasionally failing PottsCell tests * Merge branch 'develop' into feature/parameters-refactor
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Closes #93