- 1 Coding Log Report for GSoc 2013
- 2 Test Results
- 3 17 June - 23 June
- 4 24 June - 30 June
- 5 1 July - 7 July
- 6 8 July - 14 July
- 7 15 July - 21 July
- 8 22 July - 28 July
- 9 29 July - 4 August
- 10 5 August - 11 August
- 11 12 August - 18 August
- 12 19 August - 25 August
- 13 Aug 26 - Sept 01
- 14 Sept 02 - Sept 08
- 15 Sept 09 - Sept 15
- 16 Sept 16 - Sept 22
- 17 Sept 23 - Sept 28
Coding Log Report for GSoc 2013
- Pulling unpushed object pulls matrix transformations up the tree.
- Pushing object after pull restores original matrix conditions.
17 June - 23 June
Coding Begins for GsoC working on codepatch to be uploaded to brlcad uploaded the sourcefile for new push routine which supports the -x option for xpush but still needs further testing and modifications.
18 june 2013 Added a new functionality to new push routine where the push would recognise the the xpush case even in a case where the -x option is ommitted or ignored.
Tested the new routine and extracted patch to be uploaded to sourceforge replacing the previous push file I uploaded.
To discuss with mentors whether there is an implementation of the Inverse of a 4x4 matrix in the brlcad source code.
Looking at the implementations of the Inverse of the matrix in BRL-CAD
24 June - 30 June
- Monday June 24
Looked at the definitions for the inverse of a 4x4 matrix as defined in /src/libbn/mat.c. However, i realised orthogonal matrices were not taken into consideration. So added functionality to determine inverse faster for othogonal matrices and to upload patch to sourceforge shortly.
Started creating structures for the pull routine that is ( pull_obj and p_solid) structures to hold objects to be pushed and solids currently being pushed on a CSG tree. Code to be added to sourceforge Shortly.
re-read the HACKING file to make sure i conformed with the coding standards for BRL-CAD.
- Tuesday June 25
Further tested the bn_mat_inverse routine(src/libbn/mat.c) and modified patch that was to be uploaded yesterday but failed due to poor network connection.
Looked at the libbn library especially mat.c which would be useful for implementing the pull.
Studied the vmath.h header and discovered the transform.c file which could be applied in creating the pull routine.
Uploaded the pull.c first patch and bn_mat_inverse patches due to failure in network for them to be uploaded yesterday. Inverse Matrix support for orthogonal matrices
Will need some clarification from mentors concerning my design strategy for the pull routine.( The necessary functions i would need to create or call from the source) in order to implement a complete pull routine.(Asked on mailing list.) still to continue work on push and xpush merger.
Saw the importance of magic numbers in taking note of visited nodes along the CSG tree. Also, thought of checking the matrix transformations for each node to determine if node has been visited but since magic IDs were used in the push then i could use both in pull when performing the inorder walk from the leaf(solid) nodes.
Moreover, for objects in database, dp->d_uses was used but not safe as defined push.
- Wednesday July 26
Earlier part of the day used for preparation for and wrote an Information System test before working.
Added the new pull routine to the setup.c(/src/mged/setup.c) interface and included the new command into the CMakeLists.txt file(/src/libged/CMakeLists.txt) in the brlcad source
These patches also included the removal of the xpush command to support the new push and xpush. Patches to be uploaded to sf.
Added new pull routine declaration(ged_pull(struct ged *,int, char *)) to the ged.h header so it can be accessed by other files. patches to be uploaded to sf.
Added new pull to tclcad_obj.c file(/src/libtclcad/) although with support of more than one arguments i'll first of all try to test with only one argument then see how far it goes;this is so that it's available in the internal database interface.
Added tentative ged_pull() function definition to the pull.c file to enable it to be accessed by files calling function.
However since ged_pull() routine does not compile code can't compile due to unused variables so will create some dummy operations just to see how blank routine works and get it started.
Well just realised that the orthogonal matrix consideration in the bn_mat_inverse routine in mat.c is causing the benchmark tests to fail. Gotta sit on it and fix the bug. Pull Patch
- Thursday 27 June
Travelled to Douala and spent the whole day trying to cash the prepaid GSoC deposit. However, tried working on a bug in the mat.c file(/src/libbn) where the inserted code patch for orthogonal matrix support is giving wrong answers during the benchmark test. Discovered a little error calling the bn_mat_mul2() routine and now code passes 3 benchmark tests and fails 3.Will perfect code and upload codepatch tomorrow on sf.
- Friday 28 June
Looking at the bn_mat_inv() routine and performing some tests to ensure all benchmark tests succeed.
Checked the orthogonal matrix support and code still fails 3 regression tests after testing and checking need some assistance for this. Started a detail analysis and study of the push command from the ged_push() routine. This is to enable me understand perfectly the implementation hacks of the push in order to implement a push correctly especially when it comes to dealing with the points and matrix transformations at the node and leaf levels on the CSG tree.
To check all reviews from code patches so as to start working on them tomorrow. Modified push Modified bn_mat_invThis patches passes some regression tests; but i don't understand why it still doesn't work perfect. Don't really see the problem here
1 July - 7 July
- Monday 1 July
Well did not code because of Preparations to attend the Google Student's Ambassador's Summit in Nairobi, Kenya for Africa. This summit goes on for the whole week. But will try to fix problems with my code patches while at the summit.
- Tuesday 2 July 2013
Boarded Kenyan Airways flight from Douala Int'l to the Jomo Kenyatta Int'l in Nairobi which took about 5 hours; then registered with the GSA team.
- Wednesday 3 July 2013
Attended the First day of Summit where we had talks with Google Engineers about being a good ambassador. Presentations were given by Mr. Obum Ekeke , Tayib Fall and others about opportunities at Google.
- Thursday 4 July 2013
Second Day of Summit focused on Google products like Adwords, Adsense and other products; also, Engr. Giacomo(Googler) gave a presentation on Webmaster tools and Google Search in general.
- Friday 5 July 2013
Third day of Summit where we focused on making greater impacts on our communities in Africa; with awards given to Star GSAs of the previous years. Shared ideas and experiences for the Moonshot idea competition organised as per country we emerged 3rd after South Africa and Kenya. Developed plans to execute our moonshot idea as we returned home after the summit
- Saturday 6 July
Preparing for return trip to Douala Int'l and went round Nairobi for shopping and other stuffs.
- Sunday 7 July
Returned from Nairobi to Douala and after meeting family travelled to Buea to prepare for coming week.
8 July - 14 July
- 8 July 2013
Wrote a report to be submitted to the Vice Chancellor concerning my experiences on Google Student Ambassador's summit and preparing for a Numerical Analysis Exam Took further look at source code(/src/push.c) to see how the matrix transformations are applied to the coordinate points of the node so as to determine a way of extracting the original matrix transformation or almost exact matrix transformation for source code.
Glad the Dean of the faculty of Science authorized the installation of Internet in the CS so we can have 24/7 Internet access
- Tuesday 9 July
Wrote my Numerical Analysis exams and to finish with exams tomorrow so i can focus on GSoC full time.
- Wednesday 10 July
Finished writing exams today and started preparing previous code patches(mat.c,push.c,pull.c) so that when the Internet access is available all files will be uploaded so as to get commit access.
- 11 July 2013
studied the brlcad primtive internals like(torus, spheroids, toruses (torii), spheres, ellipsoids, pyramids) so as to be able generate the original transformation matrix. Torus, struct rt_tor_internal Centerpoint, point_t v, is obviously the translation. The orientation and scale is defined by vect_t h, and radiuses by fast_t r_h and fast_t r_a. Because of symmetries, the original transformation matrix must have contained a translation of v, and a rotation that brings vect_t h to an axis
Spheres and ellipsoids, struct rt_ell_internal Centerpoint is at point_t v, which again is obviously the translation done.There are three vectors, point_t a, point_t b, and point_t c, that describe the spheroid axes. This means that I can construct the transformation matrix that transforms the unit sphere to this sphere directly.
for Truncated general cones, struct rt_tgc_internal Centerpoint is at vect_t v, with vect_t h describing the axis. The base of the cone is, I think, described by the vectors vect_t a and vect_t b, and the top of the cone by vectors vect_t c and vect_t d. This implies that aÂ·b=0 and cÂ·d=0, but they may not be perpendicular to h, since the base and top of a general cone may be cut along any direction. v is the translation, and h should be along an axis (probably z axis). This yields three vectors (h, f, g), that along with the translation vector v define the transformation matrix just like in the ellipsoid case.
Also, looked at data type for Pyramids: struct rt_arb8_internal This data type contains between four (tetrahedron) to eight vertices as point_t variables. Pyramids and tetrahedra have the apex vertex perpendicular and center to a face. This can be taken as the face vector. The second vector is one that bisects an edge (the longest edge?) of the face perpendicular to the apex. The third vector is their cross product, and is either towards a vertex (a tetrahedron) or halves another edge of the face perpendicular to the apex (a pyramid). These three vectors can be used to regenerate the initial transformation matrix, with e.g. the base on the XY plane, and the apex along the Z axis.
To look at wedges, Boxes, and convex polyhedra tomorrow.
- 12 July 2013
Prepared complete patches and uploaded to sf to replace the existing patches for new push routine(push.c), pull routines(pull.c) and bn_mat_inverse routine(mat.c) with orthogonal matrix support. Since there is no internet connection, I could not create these patches with the current svn checkout.
Continued study of implementation of push.c so as to see what happens to coordinate points of the node, to determine how some form of the original matrix transformation is stored so as to ease restore during the pull routine.
- 13 July 2013
Did no work because of a long meeting( in my capacity as Auditor of Computer Engineering students Association) of over 5 hours with the Dean of Faculty to draft modalities for new student union body and draft constitution and mission to govern association.
Will start implementing the pull leaf function as from Monday which will extract the matrix transformations from the primitives(solid) or leaf nodes.
15 July - 21 July
Monday 15 July
- Implemented the pull_leaf routine which build a linked list for object's tree which would be used in extracting matrix transformations in leaf_mat() routine I am to start working on tomorrow.
- continued with the implementation of the ged_pull by adding -d option to command to enable a debug of command as in push -d
Todo: To ask on mailing list how to generate a Magic ID since its needed for the pull.
Tuesday July 16 2013
- Further worked on the pull_leaf routine to make sure list is properly built and created loop to free up list if errors occured during the list build like pulling unpushed nodes.
- Started working on a loop to move through the nodes of the linked list making the necessary mat_t changes while moving upwards modifying the current matrix transformation as it encounters a new leaf when necessary calculating and storing the inverse matrices up the tree till it reaches the root. This will then be followed by writing these changes to the database.
TODO: Ask on mailing list how my current working model solves the method so as to make the necesary changes in approach and continue.
Wednesday July 17, 2013
- Finished writing loop that moves backwards on the newly built list of nodes on the tree, performing inverses as necesary,storing the changes on the node, writing to database and setting the matrix transformations for primitives(leaves) to identity as necessary.
- Wrote loop that frees up built list and returns result of object pull.
- started testing of pull command and to continue fixing bugs. Till command is ok before adding support to pull more than one object.
- Performed another benchmark test for the orthogonal matrix support for bn_mat_inverse() in mat.c
- Uploaded code patches for mat.c and combined push and xpush to sourceforge.
Todo: fix all problems with with currrent and past patches and upload to sf for mentor review.
Thursday July 18, 2013
- Started working on compile time errors of the pull.c by fixing some pointer casts and others.
Friday July 19, 2013
- Finished debugging compile errors and started testing routine.
- Tested for improper use of command(pull 'no object'), returned correct errors
- Tested for pulling a primitive.(returned correct error message).
- Tested for pulling an object which has not been previously pulled.(mged crashed due to segmentation fault) to start working on bug next week.
Will be taking tomorrow off since its my birthday and start working on bugs and patches next week.
22 July - 28 July
Monday July 22, 2013
- Added -x option to push.c to support new xpush command(recreated and tested new push command). Spent whole day debugging and still have not succeeded in removing bug causing the
loss of options to push command.
- Created new patch for pull command and patch applies cleanly but command still further development and debugging.
Tuesday July 23, 2013
- Installed Internet in the CS Lab so as to increase efficiency for BRL-CAD.
- Started downloading latest svn checkout for BRL-CAD source
- Set up account on bz.bzflag.bz server and Started downloading tutorials on how to use ssh and GNU Screen
- Upgrading my SL 6.2 distro so as to start further work on patches tomorrow.
Wednesday July 24, 2013
- Enabling pull routine to be able to pull a non leaf node; that is routine is able to pull geometric transformations from any node up to the root.(as @Sean adviced me on mailing list.)
- Found bug in code which returns error when pulling non-leaf node. Started fixing
- Prepared patch to stub pull routine unto brlcad using svn diff(Uploaded to sf Here
- Tests of pull routine shownhere
Thursday July 25, 2013
- Tested new algorithm for bn_mat_inverse() which used only Uses 100 multiplications and 61 additions or substractions.
- Tested new algorithm for bn_mat_determinant which requires only 34 multiplications and 20 additions or substractions, saving 6 multiplications
and 3 additions or substractions compared to the previous one. Integrated code into brlcad and tested. new passed all benchmark tests. Created patch and uploaded to sf
- Wrote Tests to compare runtime of old_determinant against new determinant routine which returned the following results below:
- Wrote Tests to compare Inverse of Old matrix inverse routine and new_matrix Inverse routine which returned the following results:
CPU: Pentium(R) Dual-Core CPU E5500 @ 2.80GHz Compiler used: gcc 4.4.6-3) Compiler command: gcc -W -Wall -O3 -fomit-frame-pointer Kernel: Linux localhost.localdomain 2.6.32-220.el6.i686 #1 SMP Sat Dec 10 17:47:51 EST 2011 i686 i686 i386 GNU/Linux
./determinant My implementation:
98 cycles minimum 112 cycles median
84 cycles minimum 84 cycles median
Results (relative differences of calculated determinants):
-3.836070396965505e-14 minimum 0 median 2.152181998793086e-13 maximum
./inverse Example: My implementation:
[ 0.803558 0.065957 -0.31977 0.174422 ]-1 [ 1.105838 -0.352959 0.306948 -0.191398 ] [ 0.178270 0.764400 -0.477912 0.560214 ] [ -0.546125 0.959763 0.471464 -0.743848 ] [ 0.567903 0.641359 0.602482 0.639353 ] = [ -0.461005 -0.688994 0.868583 -0.088937 ] [ 0.000000 0.000000 0 1.000000 ] [ 0.000000 0.000000 0 1.000000 ]
[ 0.803558 0.065957 -0.31977 0.174422 ]-1 [ 1.105838 -0.352959 0.306948 -0.191398 ] [ 0.178270 0.764400 -0.477912 0.560214 ] [ -0.546125 0.959763 0.471464 -0.743848 ] [ 0.567903 0.641359 0.602482 0.639353 ] = [ -0.461005 -0.688994 0.868583 -0.088937 ] [ 0.000000 0.000000 0 1.000000 ] [ 0.000000 0.000000 -0 1.000000 ]
462 cycles minimum 490 cycles median
434 cycles minimum 546 cycles median
Friday July 26, 2013
- Added -x option to push command. But command fails to read options in mged. Tried (Pd:x) and Pdx as arguments to bu_getopt() but command fails to read options. Continued testing and debugging.
- Changed the call of pushx(formerly ged_xpush to take as args gedp,dp so as to proceed to xpushing of object. Still testing routine.
- Debugged push command to support -x option, made patch and submitted on sourceforge. However command can push only an object at a time so further work needs to be done to added support for multiple objects.
- Some tests on command Here
TOD0: Add support for multiple objects then clean up xpush in BRL-CAD.
Saturday 27 July, 2013
- Added support to Push routine to push multiple objects. Created patch and modified patch uploaded to sourceforge.
- To clean up xpush routine from source code and make all new references to new push.
29 July - 4 August
Monday July 29, 2013
- Started studies on ssh, irssi, and GNU Screen, succeeded in uploading some of my code patches to bz.bzflag.bz.
- Downloaded code to bzflag and compiled code although there is a small in bug in current code repository.
- Started working on tests for some of the /src/libbn/mat.c routines using the modified test Sean gave me on bn_mat_inverse and bn_mat_determinant.
Tuesday July 30, 2013
- Started looking at the BRL-CAD Numerics library for tests and started wrote a unit test for the bn_poly_multiply() routine.
- Tested for very large and small values and answer was correct.
- Integrated test into BRL-CAD, created patch and submited code on sf.
- Filled the Mid-Term Evaluation form for participants.
To continue work on poly.c routines tomorrow.
Wednesday July 31, 2013
- Wrote the unit test for bn_poly_scale(), bn_poly_add(), bn_poly_sub(), bn_poly_synthetic_division() routines and uploaded code patches to source forge.
Will continue writing tests for the other poly.c tomorrow and finish by the end of the week.
Thursday Aug 1, 2013
- Wrote the unit test for bn_poly_quadratic_roots() routine and uploaded patch on sourceforge
- Spent day debugging test and doing some further extreme test.
Friday Aug 2, 2013
- Wrote and tested the unit tests for the bn_poly_cubic_roots and bn_poly_quartic_roots() routines. Created patches and uploaded to sourceforge.
- To modify patches include source of known test values( Use Octave or maxima) since mathportal.org doesn't give clear math solver.
- Modifying patches to match reference values from Octave.
Saturday Aug 3, 2013
- Spent whole day debugging all unit test patches making sure tests failed when expected and produced the right results and outputs.
- uploaded codes to sourceforge.
5 August - 11 August
Monday Aug 5, 2013
- Started working on the pull routine making sure non-leaf objects could be pulled.
started by building a linked list. and there is a bug lurking in there somewhere in. Spent whole day here; will continue work on it tomorrow after i finish moving the comments. starseeker talked about.
- will upload latest patch to sf which should apply cleanly
Tuesday Aug 6, 2013
- had to continue debugging pull.c but persistent problems with patches forced me to continue working on the libbn unit test patches I submitted on sourceforge.
- Currently fixing patches with Erik so they can apply cleanly.
Will be travelling home tomorrow and resume on Monday next week; So i'm to finish with these patches and get commit access so I could work freely on my project.
12 August - 18 August
Monday Aug 12 2013
- Finished correcting indentation errors on libbn unit tests for polynomial routines.
- Continued test of pull routine; since tree fails to build linked list and discoved that the problem actually lied in the fact that I was testing on invalid input so linked list was not built. Trying appropriate objects.
Tuesday Aug 13 2013
- Continued testing of pull routine on non leaf nodes like regions and combinations and this kept reporting a segmentation fault. To continue debugging
Wednesday Aug 14, 2013
- continued working on the pull or matrix transformations up one level but work halted due to lights out for the rest of day.
Thursday Aug 15, 2013
- Fixed patch on bn_poly_add() test and uploaded code to sourceforge, continued debugging bn_poly_synthetic_division() routine but error kept coming from bn_poly_synthetic routine itself as traced by gdb. Continue working on it.
- Resolved an issue with test but seg fault still lurks somewhere in code; been starting for over an hour and still getting nowhere. Will look at that tomorrow.
Friday Aug 16, 2013
- Fixed the bn_poly_synthetic_division() unit test and uploaded code to sourceforge.
- Started looking at the db_preorder_traverse() routine ( although its not clear what struct db_traverse is since i don't see definition in source code) and how I could use it in implementing pull routine.
- To ask about definition of db_traverse since i don't see in source code.
Saturday Aug 17, 2013
- Reworked the accepted patches and submitted patch on sourceforge.
- Fixed the bn_poly_quadratic_roots() routine and submitted code on sourceforge.
- Started working on plan to implement pull using the db_preorder_traverse() which will need some routines to work with combinations and extract matrix transoformations from primitives
ToDo: To start working on the leaf_mat() routine which extracts matrix transformation from primitive.
19 August - 25 August
Monday August 19, 2013
- Started reworking the pull_leaf routine to use db_functree instead of db_preorder_walk but may still use later to extract matrix transformation from primitives and continue walking up the tree. Still to ask on mailing which primitives to support first.
- Wrote the comb_enter_func() which restores the matrix transformations of a combination but is still dependent on pull_leaf() which is to deal with various primitives. To ask sean how to store changes on a combination matrix.
ToDo: Continue implementing pull_leaf() adding support to pull matrix transformation from torus then, spheres, ellipsoids and in that order. Still wondering why commit access is not coming!
Tuesday August 20, 2013
- Finished Writing the pull_comb() routine together with the pull_comb_mat() routines. Discussed with Sean about test driven development. Will start writing unit test for routines tomorrow
- Looked into BRL-CAD source on how to write pull_leaf() routines which will support various primitives in the pull process since they don't have matrix transformation as such. Still to look at pull_leaf to actually see how they dealt with primitives
Wednesday August 21, 2013
- Started looking at test provided by Sean to use of db_walk_tree so as to be able to create a similar for pull_comb using db_functree() but faced problems calling functions in BRL-CAD's libraries. So i'll continue working on test tomorrow
- Continued adding some functionalities to pull_leaf() routine.(still crude) will continue work on pull_leaf after testing pull_comb() perfectly
Thursday August 22, 2013
- Started and finished writing pull_comb() unit test. But there is actually a seg fault which prevents the cur_mat() pointer from being inverted. Probably NULL.
- Will continue debugging and finish testing pull_comb() tomorrow then move on to pull_leaf()
Friday August 23, 2013
- Finished debugging pull_comb() and tested routine. Works perfectly.
Any way to note changes made on combination. pulled matrix is stored on comb_leaf->tr_l.tl_mat.
- Created patch to stub empty pull routine into brlcad. then continue working on pull_leaf() routine tomorrow.
- Waiting for mentors to apply patch so i could create patch which adds pull_comb() routine into BRL-CAD.
Aug 26 - Sept 01
Monday 26 August 2013
- Started implementing the pull_leaf routine which extracts the 4x4 matrix transformations for a primitive. Succeeeded in implementing the pull_leaf for an ellipse, sphere, EPH, elliptical parabola, elliptical torus, extrude, hyperbola, and a particle.
- started testing function and will continue debugging tomorrow before continuing with the addition of the superellipse, metaball, arbitrary complex polyhedra, arb8, rhc, rpc, and pipe.
Tuesday 27 August 2013
- Finished debugging pull_leaf() but routine is incomplete since I don't currently support all primitives. Will follow Sean's instructions and start developing pull interface from tomorrow by adding synopsis, docs, full integration and test cases.
- Added support for truncated cones in pull_leaf() but a bug hangs in there. Will take a peek tomorrow or finish this night before going to sleep.
Wednesday August 28, 2013
- Started developing the interface by adding the stubbing the pull to archer interface.
- Added the pull routine to the tclscripts, libtclcad, and wrote the pull documentation in brlcad/doc/ directories.
Still to finish writing the regresssion tests before moving on to adding support for pulling primitives on BRL-CAD.
Thursday August 29, 2013
- Started and finished writing the regression tests for the pull command.
- Tested and compiled code but pull does not appear on the command line when regression tests are ran. Will ask on IRC for assistance here.
Todo: When done with developing the pull interface, I'll dive into writing the pull_leaf routine for all primitives.
Friday August 30, 2013
- Tested regression tests for pull and added manual pages and documentation for pull successfully such as in man pages, appropos library for pull
- To create patch and submit on sourceforge, also tried adding pull to archer but found a little problem. To discuss with mentor on how to proceed.
TodO: After approval of man pages, to continue adding support for all primitives into pull command. and fix bn_poly_sub() test patch.
Saturday August 31, 2013
- Finished testing regression tests and uploaded code to sourceforge
- Continued looking at the primitives such as arb8, arbn so as to continue working on primitives for pull.
Sept 02 - Sept 08
Monday Sept 02
- Started looking at the other primitives; left to complete the pull_leaf() routine. Saw many complications with many primitives. Will need the Assistance of Sean in extracting the matrix transformations from them.
Tuesday Sept 03
- Fixed bug in bn_poly_sub() unit test; uploaded code to sourceforge.
- Succeeded in pulling the following primitives(TGC, REC, PARTICLE, EPA, EHY, HYP, ETO, EXTRUDE). Still left with about 26 primitives to be pulled in order to complete the pull_leaf() routine.
Will need some directions on how to implement pull_leaf() since using switch case statements is not a good design choice.
Thursday05 - Sunday 08
- Took a break so as to recover from malaria.
Sept 09 - Sept 15
Monday 09 October
- Started looking at AABB bbox routines in BRL-CAD. Still to develop simple algorithm that automatically processes the translation from bbox return vectors to determine original translation.
- Read some online wiki pages on AABB bounding box of objects.
ToDO: To start writing routine and unit test tomorrow
Tuesday 10 October
- Started and finished writing tranlate routine which extracts and sets the translation component from the bounding box minimum and maximum points from the bounding box routine.
- To integrate general bounding box calculating function for every primitive.
Wednesday 10 October
- Started testing pull_leaf routine using the rt_functab bbox routine and successfully pulled some translations assuming object's centrepoint was translated from the origin(0,0,0). But still waiting on Sean for some clarifications on the math.
- To look at confirmation from sean and perfect the pull_leaf routine, completing the pull routine and running through valgrind.