Editing User:Cprecup/GSoC2012 progress

=Coding period=
===''Week 13''===
====17/08/2012====
* Introduced a '''graph''' command and its '''show''' subcommand.

* Tried to get rid of an ''"invalid command name "graph" while executing "graph show""'' error but didn't find a solution - this appears when I run my procedure in Archer. When running this procedure in MGED, no such error appears and the graph is generated correctly.

====16/08/2012====
* Enabled error message in MGED for the '''graph''' command in case the Adaptagrams library isn't available.

* Started reorganizing the '''graph''' command in subcommands.

====15/08/2012====
* Added a basic brlman documentation for the '''graph''' command.

====14/08/2012====
* Grouped top-level commands under a single '''graph''' command. Came up with an approach on how to tackle the following problem:  there would exist a C implemented "graph" command and also a Tcl procedure named "graph" and when ran in MGED the C one is ran instead of the Tcl one. Waiting for a response before committing the changes.

====13/08/2012====
* Fixed a bug that appeared when launching Archer due to the '''graph_objects_positions''' command.

* Started work on integrating the '''graph''' command in Archer. Encountered some problems due to the fact that there isn't a corresponding ''ged_graph'' C routine that can be used. The procedure is simply defined in Tcl.

===''Week 12''===
====12/08/2012====
* Cleaned up the layout source code that was about to be committed.

* Replaced the connection lines that existed between two nodes with polylines and added arrows at the end of each connection line.

====11/08/2012====
* Finished creating the routines that provide a decent layout for the graph.

* Added vertices between the nodes.

:Here is how the graph for the ''share/db/axis.g'' database looks like now:
:[[Image:Graph_editor_v2.png]]

:Commit will be made as soon as the source code is cleaned up.

====10/08/2012====
* Continued working on the layout part.

====09/08/2012====
* Started research and work for solving the layout issue of a graph.

====08/08/2012====
* Added the '''decorate_object(struct _ged_dag_data *, char *, int)''' routine in ''src/libged/dag.cpp''. This creates a new entry into a hash table for each newly detected object and sets the entry's value depending on the type of object: ''primitive'', ''combination'', or ''something else''.

* Used these types to differently colour the rectangles in the graph editor.

* Introduced a text widget with the name of the object within each rectangle.

:Here is the window that the '''graph''' command launches for the ''share/db/axis.g'' database:

:[[Image:Graph_editor_v1.png]]

====06/08/2012====
* Looked for a method to store object's colour and name related information within an Adaptagrams graph structure.
:This is needed for implementing the decorative routines for each type of object. Couldn't find a method. Worked on an alternative method to store this information.

===''Week 11''===
====05/08/2012====
* Updated the '''ged_graph_objects_positions''' routine; it now passes the objects and positions within the graph to the Tcl field.

* Used this command in the ''src/tclscripts/graph/GraphEditor.tcl''. The objects are now drawn at the specified positions using a Tk Canvas widget inside a window.

====04/08/2012====
* The '''ged_graph_objects_positions''' can now be used as a command within the Tcl field to retrieve objects' positions within the graph.

* Made sure that the commands '''graph_structure''', and '''graph_objects_positions''' always exist so that the user is informed that he/she invoked a valid command, although the Adaptagrams library is not available.


====01/08/2012====
* Again tried to figure out the logic between the data processed in the ''C'' implementation of a command and the data received in the ''tcl'' file when running this command.

* Finally got the idea after having a talk with '''starseeker'''.

====30/07/2012====
* Looked for a pattern to follow in the implementation of ''C'' commands that are to be used in the Tcl land. Found the files that need to be modified according to the existence of a new command.

* It's not clear to me how the data used in a ''tcl'' file where a command is ran is passed on to this ''tcl'' file.

===''Week 10''===
====29/07/2012====
Developed a first version of a routine (''ged_graph_objects_positions'') that returns the positions for each object from the database. This is supposed to be used by a GUI component that draws the objects using Tk Canvas inside a window.

====28/07/2012====
* Had trouble with a ''make distcheck'' error.
* Ran tests for the two commands that were implemented: "graph_structure" and "graph".
:The name of "graph_structure" might be adjusted. Subcommands need to be added. So far, there is a view command but what it actually does is traverse the database and define its corresponding graph. The steps for this need to be split in smaller routines that would eventually be called as subcommands.

====27/07/2012====
* Managed to pop up the window in MGED by simply running the "graph" command.

====24/07/2012====
* Worked on popping up a new window when running the ''graph'' command. With starseeker's help I found out that one of my script wasn't "loaded". Eventually I tackled this. However, the window still doesn't pop up when running the command; it shows up only when running ''<tcl_script_name> .window1''.

===''Week 9''===
====22/07/2012====
* Created the command "'''graph'''". For now, it can be ran in MGED like this: "'''graph view'''" and it calls a routine in src/libged/dag.cpp: ''ged_graph()''.

* Worked on creating a new window when running this command.

There is no commit because the code might need some restructuring.

====19/07/2012====
* Implemented the '''put_me_in_a_bucket''' routine that figures out the type of an object, adds its name to a vector and defines a corresponding shape in the graph.

====18/07/2012====
*Replaced the 3 hash tables (solids, regions, and groups) with 3 vectors of names (primitives, combimations, and non_geometries).

====16-17/07/2012====
* Discussed about modifications for the current src/libged/dag.cpp file: use a single hash table that stores the names and IDs of all the objects and lists of names for each type of an object: primitive, combination, non-geometry.

* Worked on the above modification. So far:
**created a new master hash table called "objects" with the names and IDs of all the objects;
**worked on switching from the hash tables to simple lists of names for each type of an object.

===''Week 8''===
====13/07/2012====
* Summarized the progress made so far

* Updated the future milestones for this project

* Currently figuring out a plan for a user-visible feature in Archer/MGED, i.e., a command that would open a window displaying the graph corresponding to the displayed geometry.
 
====11/07/2012====
* Allocated space for each ''value'' of an entry of a hash table outside the hash table. In the ''value'' field of an entry I've just copied the pointer to this memory space.

* Implemented a method that frees the space allocated for these values.

====10/07/2012====
* Removed entries from the ''solids'' hash table whenever an object is discovered to be a ''region'' or a ''group''. Switched to working with pointers for ''bu_hash_tbl'' structures. Freed memory for each allocation.

====09/07/2012====
* Made some small modifications on the ''src/libged/dag.cpp'' related to memory allocation.

* Tried to deallocate memory for a certain entry in a hash table but didn't find a proper solution to this. In the ''hash.c'' I've only found the function '''bu_hash_tbl_free(struct bu_hash_tbl *hsh_tbl)''' which is not what I need because I don't want to deallocate the memory for the whole table but, instead, just for one entry. Need to find out how it's supposed to be done.

===''Week 7''===
====07/07/2012====
* Introduced id's for each object in the database and finished memorizing the data.

* Taking into account what hash table it belongs to, each object has now a corresponding shape and (if needed) links to the nodes of its 'subtree' in the graph.

* Duplication is now avoided because each shape of the router has a corresponding id.
:Here's the graphical output for the ''share/brlcad/7.22.1/db/axis.g'' (that was put in a .svg file, for now): [[Image:Graph_link_nodes_no_duplications.png]]

:Compared to the one mentioned on ''01/07/2012'', one can observe that the number of nodes has been reduced to a single one in case of duplications. The links between the nodes are overlapping for now. This needs to be taken care of.

====06/07/2012====
* Continued working on the code that is meant to memorize data related to each object in a database into the three below mentioned hash tables.

====05/07/2012====
* Replaced the '''bu_ptbl''' structures with '''bu_hash_tbl''' for the three kinds of tables: ''regions'', ''groups'' and ''solids''.

* Implemented code for adding '''bu_hash_entry'''s into the hash tables. Encountered some problems on this part as well as where I have to establish the size of each ''lists'' field in a hash table.

====03/07/2012====
* Found a way to eliminate node duplications depending on their names - use the '''struct bu_hash_tbl'''.

====02/07/2012====
* Fixed the representation of solid objects: instead of dashed line they are represented by rectangles now.

* Introduced a temporary method for positioning the nodes into the graph.

* Cleaned up the code and committed the changes.

===''Week 6''===
====01/07/2012====
* Managed to link each COMB node with the nodes of its subtree.
:Here's the graphical output (that was put in a .svg file, for now): [[Image:Graph_link_nodes.png]]

:One can observe that for some nodes there are branches that link to other nodes. As a helper, [http://pastebin.mozilla.org/1687225 here] is the listed output of what the algorithm is doing in the background.

:The order in which they were outputted is the one in which the directory was traversed. The alignment is due to a linear function that I used for the coordinates of the rectangles that represent each node. This needs to be modified as well as the duplicated nodes and the representation of solids (here, they appear as a single dash line instead of a rectangle).

====30/06/2012====
* Looked for an example that would give me hints on how to find and traverse a subtree of a combination in order to create actual links between the nodes. Decided that ''src/conv/g-dot.c'' is a good starting point.

* Worked on the implementation of a method called ''dag_comb'' that is meant to create links between the COMB node and the ones from its subtree. Didn't commit anything because it's not finished and the code needs to be cleaned up eventually.

====29/06/2012====
* Looked in the ''src/tclscripts/geometree'' folder with the purpose of understanding how the MVC (model, view, controller) pattern is applied there.

* Been suggested that it would be a good idea to create a graph image instead (for now). Therefore, I started working on the connections between different nodes in the graph.

====25/06/2012====
* Committed my latest changes:
:#Added special cases for when the Adaptagrams library is found or not found. Don't add dag.cpp to ged_ignore_files if the library is not found; i.e., always compile it. -- ''src/libged/CMakeLists.txt''
:#Use the #define HAVE_ADAPTAGRAMS in the src/libged/dag.cpp file in order to be compiled regardless of the fact that libavoid exists or no. Fixed indentation. -- ''src/libged/dag.cpp''
:#Added a compile-time preprocessor #define HAVE_ADAPTAGRAMGS -- ''CMakeLists.txt''

* Started looking for .tcl files that I could use as examples and from which I could get methods for implementing a view. My attemp is to print out the hierachy structure build with the ''dag.cpp'''s methods in a user's window.

===''Week 5''===
====23/06/2012====
* After accessing the ''distcheck-enableall_release.log'' file I found out that the error wasn't generated because of my changes. There are usages of '''strcmp''' in the ''src/conv/g-voxel.c'' file that have to be replaced by '''bu_strcmp'''. After making this change, running the command 
 make distcheck
ended well.

* There was a problem caused by the duplicated existence of a variable named PARALLEL. It was included by both ''libavoid.h'' and ''common.h'' so I had to figure out a way in which my program would compile and none of these two values would be lost/modified during the execution.

====22/06/2012====
* Introduced a '''HAVE_ADAPTAGRAMS''' #define and wrapped most of the code in ''src/libged/dag.cpp'' in a '''#ifdef''' - '''#endif'''. Still need to add the '''#else''' case that would provide a useful note stating that the library is unavailable.

* Altered the ''src/libged/CMakeLists.txt'' file correspondingly.

Compilation is ok but the command 
 make distcheck
generates an error. I haven't yet figured out what the problem is.

====20/06/2012====
* Found a potential solution that could solve the below issue: I've compiled Adaptagrams with the flag '''-fPIC'''.

* Discussed it with one of the mentors (brlcad). I was recommended to rather add a compile-time preprocessor define like '''HAVE_AVOID''' and enable linkage against the LIBAVOID_LIBRARY in the ''src/libged/CMakeLists.txt'' file than add the file to '''ged_ignore_files'''.

====19/06/2012====
* Currently, BRL-CAD doesn't build because my ''src/libged/dag.cpp'' can't access elements from the avoid library. BRL-CAD built in the previous attempts because I added a '''main''' function inside ''dag.cpp'' for which I would add the line
 BRLCAD_ADDEXEC(dag dag.cpp avoid)
inside the ''CMakeLists.txt'' file.

The main function was added just for testing purpose so I didn't commit it. Without the '''main''' function, and adding '''${AVOID_LIBRARY}''' with the '''BRLCAD_ADDLIB''' command generates [http://pastebin.mozilla.org/1668038 this] error.

So far, after doing a little research I came to the conclusion that this is because the libavoid library is static.

====18/06/2012====
* Fixed src/libged/CMakeLists.txt because make distcheck wouldn't work.

* Added reference to the dag.cpp file for the OLD build system.

===''Week 4''===
====17/06/2012====
* Implemented methods that are used for adding a rectangle to the construction of the graph for each object in the database (please see ''src/libged/dag.cpp'' file).
For this, I have modified my previous implementation, more exactly, simplified it.

* Eliminated search for the libavoid library from ''src/conv/CMakeLists.txt'' and added it into the folder ''src/libged/CMakeLists.txt''.

====16/06/2012====
Started implementing the model for a directed acyclic graph in the ''src/libged'' folder. So far, it contains a structure and a method that initializes elements of such a structure.

====15/06/2012====
Looked through the ''src/libged'', ''src/gtools'' and ''src/tclscripts'' folders for MVC pattern implementation. Still have doubts about how to structure the pattern in BRL-CAD.

====13/06/2012====
Corrected the implementation mentioned below. Had a discussion about the proper locations for MVC implementation files.

===''Week 3''===
====10/06/2012====
Worked on the C++ implementation of a class that contains methods similar to the ones in ''src/conv/g-dot.c''. This approach remains to be debated.

====08/06/2012====
By using the ''src/conv/g-dot.c'' I generated a .svg file that contains information about the graph's nodes, i.e., for each node that appears in a '''.dot''' file I generated a corresponding one by using libavoid.

The .svg file was generated and opened in a visual mode for checkup purposes: one rectangle per object in the hierarchy can be observed.

====07/06/2012====
Managed to run a C++ Adaptagrams example(that uses libavoid) inside BRL-CAD.

====05/06/2012====
*Added helper script ''misc/CMake/FindADAPTAGRAMS.cmake'' to check for libavoid's existence as a system-installed library and mark as advanced the set variables.

*Modified the cmake check for libavoid in ''src/conv/CMakeLists.txt'' accordingly.

====04/06/2012====
Added a cmake check in ''src/conv/CMakeLists.txt'' in order to find the system-installed version of libavoid. If it doesn't find it, it prints a status message saying it couldn't find it - no error occurs in either cases (found or not found). 

===''Week 2''===
====03/06/2012====
Compilation of BRL-CAD failed because of some 'set but unused variable' warnings treated as errors. Commited a fix for one of them.

Started work on checking the existence of the libavoid library as a system-installed dependecy.

====02/06/2012====
Started working on a file that would take each element of the tree and process it with libavoid's methods. As a support example I found the ''src/conv/g-dot.c'' file.

Failed attempt to integrate libavoid into BRL-CAD. After further discussions (03/06/2012) it was established that it's best to do this after I have the functionality going, somewhere in late July.

====01/06/2012====
Tried to recompile an ''example.cpp'' file where the Adaptagrams' library is used outside its main folder. Previous attempt to do this was unsuccessful.
I Managed to compile it after all.

Looked for a location where I could implement functions that would traverse a tree and construct a DAG with Adaptagrams' library.

I'm still trying to understand how ''librt/db_tree.c'' and ''db_walk.c'' work in the background.

====30/05/2012====
Adaptagrams will be used as the library of tools.

I've made a plan that sketches what will happend on each side of the MVC pattern for this project.

The process behind the, let's call it for now, ''''igl'''' (Interactive Graph Layout) command that lauches the GUI is the following:
*access the geometry's hierarchy by using the ''''tree'''' command with an additional option ''''g'''' that returns the corresponding DAG.

*traverse this graph and construct it with the help of Adaptagram's library ''libavoid''. Libavoid provides polyline connector routing in order to avoid obstacle objects. The result is passed on to the Tcl/Tk implementation where it will be outputted (View).

*on user action (for example: ''''move'''' or ''''delete'''' command is called), announce the Controller, apply modifications onto the graph by using libavoid.

Remark: other uses of Adaptagram's libraries should/may be added.

====28/05/2012====
Used Adaptagrams' static libraries as external ones by creating a source code file that calls methods from these libraries.

===''Week 1''===
====27/05/2012====
Studied Adaptagrams' documentation.
Listed strong and weak points of both graph libraries, GOBLIN and Adaptagrams.

====26/05/2012====
Compiled Adaptagrams; studied and ran examples provided for libcola and libavoid.

====25/05/2012====
#Worked on compiling GOBLIN. However, I get a lot of errors. You can find them [http://pastebin.mozilla.org/1650086 here]. I am assuming it's because of the c++ standard and their latest update which was made in 2010. Submitted a bug on their sourceforge bug tracker and am waiting for a reply.
#Meanwhile, I'm having a look at the Adaptagrams' source code.

====24/05/2012====
Made comparisons between Adaptagrams and GOBLIN.

====22/05/2012====
Discussed with one of the mentors how to approach the implementation behind the command that would launch the GUI.

Talked about the possible locations where command-line functionality can be developed. 

As a first step, looked for proper already existent functions in BRL-CAD that would allow me to ge the directed acyclic graph structure of a tree.

====21/05/2012====
Read about [http://adaptagrams.sourceforge.net/ Adaptagrams] library.

=Community bonding period=

===General progress===
====19/05/2012====
Studied some aspects of the [http://goblin2.sourceforge.net/ GOBLIN] graph library.

====17/05/2012====
Commit access was gained. My first commit was for the src/libbu/test_booleanize.c file; it included style and formatting corrections.

====16/05/2012====
Patch for the file src/libbu/booleanize.c was accepted and applied in the revision r50566.

====15/05/2012====
I have modified my first patch, the one meant to create a test_booleanize.c with unit tests for the file src/libbu/booleanize.c. At the same time, I found a small bug in the booleanize.c code.
The patch can be found [https://sourceforge.net/tracker/index.php?func=detail&aid=3519874&group_id=105292&atid=640804 here].

====14/05/2012====
I have created an alternative patch for the one that is meant to separate out LIBNMG from LIBRT. This one 'moves' the files from the src/primitives/nmg location to src/libnmg without being needed an extra help from someone with commit access.

Here is a [http://dl.dropbox.com/u/3425790/separate_nmg.patch.bz2 link] to a temporary location for the patch since it exceeds the size limit provided by Sourceforge.

====12/05/2012====
I have finished a patch meant to separate out LIBNMG from LIBRT. You can find the patch [https://sourceforge.net/tracker/?func=detail&aid=3526143&group_id=105292&atid=640804 here].
Build system modifications have been made in the following files:
*''src/librt/CMakeLists.txt''
*''src/librt/Makefile.am''
and the following 2 files have been correspondingly added for libnmg:
*''src/libnmg/CMakeLists.txt''
*''src/librt/Makefile.am''

One thing needs to be made by a person with commit access: move the ''src/librt/primitives/nmg'' source code into ''src/libnmg'' and apply the provided patch.

Reminder: there's also [https://sourceforge.net/tracker/?func=detail&aid=3519874&group_id=105292&atid=640804 this] patch that I've made and needs to be reviewed. It contains unit tests for the ''src/libbu/booleanize.c'' file and it fixes a small bug that wouldn't have passed one of the tests.

====10/05/2012====
I've studied the ''src/mged'', ''src/librt'' and ''src/conv'' folders, looking for methods that can be used to access the elements of a CSG tree.

Methods that got my attention:
*in the ''src/librt/db_tree.c'' file:
 int db_tree_list(struct bu_vls *vls, const union tree *tp)
which fills a bu_vls with a representation of a given tree appropriate for processing by Tcl scripts. Could be useful in constructing the interactive graph.

 union tree *db_tree_parse(struct bu_vls *vls, const char *str, struct resource *resp)
which takes a TCL-style string description of a binary tree, as produced * by db_tree_list(), and reconstruct the in-memory form of that tree. Could be useful after the structure of the graph is modified and the CSG needs to be updated.

===2. Get commit access===
====08/05/2012====

Worked on the patch for the NMG migration task (create a separate library LIBNMG outside LIBRT). This time, because BRL-CAD previously built without errors, things go smoother.

===1. Compile & install BRL-CAD===
====28/04/2012====

After discussing my problem with one of the mentors and finding the cause for these errors, BRL-CAD completely built.

====27/04/2012====

I created my first patch for BRL-CAD by using the virtual machine disk image so now I want to compile and install BRL-CAD from source (from a svn checkout).

I've followed the instructions with respect to the dependencies (the ones from here http://brlcad.org/wiki/Compiling and from the '''doc/README.Linux'''). I've used the command

''cmake  -DCMAKE_BUILD_TYPE=Debug -DBRLCAD_BUNDLED_LIBS=Bundled .''

but after using 

''make''

, I kept getting these errors http://pastebin.mozilla.org/1602696.

Afterwards, I decided to try the command
 
''cmake  -DCMAKE_BUILD_TYPE=Debug .''

but then I encountered another error while running it: http://pastebin.mozilla.org/1602697. I managed to solve the problem by installing itk3 and itk3-dev. However, while running the make command I bumped into the previously mentioned ''make'' errors and this one: http://pastebin.mozilla.org/1602700. The first ones refer to fontconfig symbols.
@@ Line 1: / Line 1: @@
 =Coding period=
-===''Week 14''===
-====Firm pencils down day: 20/08/2012====
-* Adjusted the ''doc/docbook/system/mann/en/graph.xml'' according to the changes made on the subcommands and added a brief documentation for the '''igraph''' command.
 ===''Week 13''===
-====19/08/2012====
-* Added two subcommands for the '''graph''' command: '''show''' and '''positions'''.
-* Removed the previous ''graph_objects_positions'' and ''graph_structure'' commands.
-* Renamed the previously named Tcl ''graph'' procedure into '''igraph''' - this command launches the interactive graph; along with this procedure, the ''src/tclscripts/graph'' was renamed into ''src/tclscripts/'''igraph''''', and the file ''src/tclscripts/graph/graph.tcl'' was renamed into ''src/tclscripts/'''igraph/igraph.tcl'''''.
-* The '''igraph''' command works in MGED; when launched in Archer, an error message in outputted saying that the command is not available yet.
-* Took care of some command error cases (C and Tcl).
-====18/08/2012====
-* Again tried to integrate the previously mentioned command in Archer - Didn't find an example that would suit me. I found commands that would have procedures that use C wrapped commands but they were either working strictly for Archer or for MGED, not for both.
 ====17/08/2012====
 * Introduced a '''graph''' command and its '''show''' subcommand.