Insert cells off center

[allison-li-1016]

Estimated time to review: M

Context: In an effort to insert multiple clusters for a population, I added new functionality that allows inserts to be off the center of the simulation FOV. Currently I describe the center with a direction and offset parameter.

For hex grids, the directions are N, S, NE, NW, SW, SE to describe the 6 neighbors of a hex location. For rect grids the directions are N, W, E, S to describe the 4 neighbors of each rect location.

Offset is the number of location units from the center (same unit as radius)

Summary of changes:
PatchActionInsert:

• Added parameter input read for offset
• Added parameter input read for direction
• Updated call to getCoordinates to describe the center
• Added parameter checking for direction (is it a valid direction)

Parameters

• Added default parameters for offset and direction

Enums

• Added enums for valid directions for hex and rect grid

PatchLocationFactory

• updated getCoordinates abstract method to now allow for offset and direction to describe centroid
• added clampOffset method to clamp insertion area if it is beyond the simulation FOV

PatchLocationFactoryHex

• added makeCenter method to calculate new center based on direction and offset
• updated getCoordinates method to now account for new center if it is not the default simulation center

PatchLocationFactoryRect

• added makeCenter method to calculate new center based on direction and offset
• updated getCoordinates method to now account for new center if it is not the default simulation center

Tests

• Added unit tests (specific to the new changes) for insert, PatchLocationFactory, PatchLocationFactoryHex, PatchLocationFactoryRect

Example usage:

<actions>
          <action id="INSERT_HIGH_DENSITY_TUMOR" class="insert">
             <action.parameter id="TIME_DELAY" value="5" />
             <action.parameter id="INSERT_NUMBER" value="1500" />
             <action.parameter id="INSERT_RADIUS" value="5" />
             <action.parameter id="INSERT_DIRECTION" value="SW" />
             <action.parameter id="INSERT_OFFSET" value="10" />
             <action.register id="cancer" />
         </action>

         <action id="INSERT_HIGH_DENSITY_TUMOR_2" class="insert">
             <action.parameter id="TIME_DELAY" value="10" />
             <action.parameter id="INSERT_NUMBER" value="1500" />
             <action.parameter id="INSERT_RADIUS" value="5" />
             <action.parameter id="INSERT_DIRECTION" value="NE" />
             <action.parameter id="INSERT_OFFSET" value="10" />
             <action.register id="cancer" />
         </action>
  </actions>

[kristaphommatha]

Everything looks great! I just had some documentation comments :)

[kristaphommatha]

You should update this javadoc to reflect all the changes! I think it should be specified somewhere too, whether in this javadoc or a later one, that the default for if the direction and/or offset is not specified by the user is CENTER and 0, respectively

[kristaphommatha]

Is there a reason this file is named PatchLocationFactoryHexOffsetTest.java and not just PatchLocationFactoryHexTest.java file? I'm just wondering because the rest of the test java files seem to be named exactly after the file that it's testing?