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Final Update?
I graduated and started working at the MathWorks on Sept. 29, 2006. I very much enjoy working there,
not least because I get to play around with yet more GUI's. All contact information
above should be considered null and invalid. My address is currently:
1296 Worcester Rd. Apt. 2407 (pronounced Worster in that New England accent)
Framingham, MA, USA
01702
Cell: Five-Oh-Eight Eight-One-Six Three-Oh-Six-Oh
Office: Five-Oh-Eight Six-Four-Seven Eight-Oh-Six-One
AToM3 Download Area
Download AToM3 (Build Feb. 13, 2007) , Additional AToM3 files, and Recent Changes List
AToM3 Documentation
AToM3 installation readme (txt),
and
AToM3 Help Guide (HTML but old)
Illustrated AToM3 Tutorials (HTML Format, Updated: Sept. 5, 2006):
Basic,
Advanced
Graph Grammars
M.Sc. thesis (final): Graph Layout for Domain-Specific Modeling and some AToM3 Automatic Layout Pictures
If you have problems with AToM3 e-mail denkkar@gmail.com
and watch the recent change list)
What is AToM3?
Official answer, main AToM3 page
It's a tool that lets you make an editor for models... fast. Instead of building
a whole application, you just specify what can be connected to what, what they
look like, and what attributes they aught to have (such as names or number of
tokens).
Sound like just any other drawing tool? Well it's not! Once you've specified the
type of models you want to draw, you can draw just that kind of model, so you
won't insert inconsistent elements into it like you could in a general drawing
tool. Moreover, AToM 3 takes care of details like placing arrows nicely, and
offers a good selection of automatic layout tools so you don't waste time prettying
up your diagrams.
In case you were wondering, the multi-formalism part of AToM 3 means that if you
specifying two types of models (lets call these formalisms), then you can draw
a model containg components from both simultaneously. Throw in graph grammars,
and this gets much more interesting, as you can use these grammars to transform
one type of model into another. AToM 3 lets you specify these grammars in a mostly
visual fashion (specifying exactly what happens to attributes tends to involve code),
and even lets you automatically generate latex documentation of the entire grammar.
Where do I come into the picture? Well, basically AToM 3 was stone-age in
the user-interface department (
see AToM3 version 0.2.2 if you don't believe me). So I pretty much changed the
entire GUI, modeled the reactive behaviour parts of it and generated the code
from this model that is used AToM 3 0.3, implemented all the layouting algorithms, latex documentor, added menus, help messages, debugging info,
and fixed bugs and inconsistent behaviour.
Can anyone use AToM 3? Well, you actually need to read the guide (not that it's
terribly complete), to figure out how to use it. Knowledge of Python (programming
language in which AToM 3 is implemented) is not needed for low-level use of AToM 3
but as soon as you want condition/action code, or better yet a code generator,
you'll feel the need for brushing up on Python.
Logo done entirely in AToM3 using 5-6 formalisms at once
Download AToM3 external utility pack: LPSolve, SVM, and yED
About:
These "external" utilities add extra functionality to AToM3. They only need to be
installed once since they do not change (unlike the main AToM3 distribution).
LPSolve is used for solving linear programming problems.
SVM is especially important if you plan on using statecharts in AToM3, since this
utility is responsible for simulating and generating code.
yED is used when the best quality layout of a model is desired. In this case the
model graphics are exported to yED which then does the layout. The model can
then be re-imported into AToM3 (i.e., the position, height, and width info). Note
that the arrows tend to have slightly incorrect offsets when re-importing though.
Installation instructions:
The simplist method to install them is to place the external utility folders in
your User area (this is created the first time AToM3 is started) in the
'User_External' directory. You can also place them arbitrarily, but then you'll
have to edit the ExternalUserPaths.py file to point to it.
Modifed the uniqueFormalismNamer.py to be more effective and added the correct
usage of it to the advanced tutorial (i.e.: to re-name an entire formalism for
re-use purposes).
Added a big warning in the basic tutorial with regards to the correct directory
for putting formalisms in.
-- Sep 1, 2006
Fixed bug in graph grammar editor when top menubar is enabled in the options.
Debug console now prints a traceback when commands result in an exception.
-- Aug 30, 2006
Improved the Debug Console to make it useable! It is now possible to type either
"self" or "atom3i" to get an instance of ATOM3 and then trigger an incredible
number of methods directly during run-time. The console can now be re-sized. If
your code crashes, the console can now handle it. If you exit AToM3, the debug
console no longer causes exceptions (that would force you to control-break).
Improved the error dialog encountered when AToM3 cannot find a meta-model
Fixed bug in the Advanced Modelling Tutorial (a picture showed the "EDIT" instead of "SELECT" trigger)
-- Aug 29, 2006
Added a GG tutorial.
Re-designed the UI for modifying Graph Grammar rules. Instead of having to click
on a button to edit the LHS and then the RHS, both sides of the rule are shown
in the same dialog with the "Name", "Order", etc. of the rule. Better yet, the
dialog window (for the rule) has full support for re-sizing as well as scrollbars.
Modified the UI for the primary Graph Grammar editing dialog.
Added an "Isolate Association" button, to make getting an association without
the entities it is normally connected to, easy.
Fixed bugs in the Graph Grammar that were causing "Subtype Matching" not to work.
-- Aug 25, 2006
Fixed bug in Icon Editor introduced when I added Font sorting.
-- Aug 18, 2006
Modified the code generator for CD_ClassDiagramsV3 formalism. Associations are
now inherited by subclasses from their superclass.
Modified the code generator for CD_ClassDiagramsV3 formalism. Error messages given
for classes without a visual representation have been streamlined so you only get
hit once with a dialog. Note: if a class has no visual representation, attempting
to instantiate it (such as by pushing the corresponding button in the generated
formalism) will result in an exception. Perhaps a default icon should be provided?
Modified the error dialog shown when a formalism is not in the correct directory.
It should now be absolutely clear where the formalism should be.
-- Aug 15, 2006
Added a C++ STL layout server Win32 executable and a Python pipe that make it useable
within AToM3 by pressing the HOME key. Implemented: Spring, Tree-like, FTA,
Circle, and Random (the last 2 are useful in conjunction with Spring). The speed
increase in porting the Python implementations to C++ are over 2 orders of
magnitude, but don't quote me on that, I ran a very skimpy benchmark.
Fixed some bugs in Tree-like layout under some graphs and added a new tip-over
style tree layout.
Fixed bugs in the custom type model code generator
Fixed SVG exporter so it always exports unique "id" tags for each item.
-- Aug 12, 2006
SVG exporter: improved text anchor support by exhaustive tweaking
View the exported text test:
AllTextAnchorsTest.svg (SVG capable browser needed)
SVG exporter: added support for the "Image" primitive
View the exported primitives test:
AllPrimitivesTest.svg (SVG capable browser needed)
-- June 21, 2006
Implemented a SVG (Scalable Vector Graphic) exporter (works on any AToM3 model
loaded on the canvas). It is accessible via the Postscript exporter.
Added a small Digital Watch formalism to demonstrate scoped UI event handling.
Modified the scoped UI event handler to better deal with statechart event locks.
Improved DChartsV3 formalism layout behaviour.
Fixed more bugs in the DChartsV3 formalism code generator
(All the constructs, except priorities, have now been tested in compiled code).
Added one-click layouting buttons to the CD_ClassDiagramsV3 formalism.
-- June 19, 2006
Improved the formalism-specific buttons... formalism. Currently used in conjunction
with DChartsV3. Combines behaviour statecharts and layout (layered drawing technique)
very naturally.
Fixed bugs in the new DChartsV3 formalism code generator. Since the DChartsV3
formalism is bootstrapped using itself, the formalism itself was previously
buggy due to incorrect code generation.
-- May 10, 2006
Added DChartsV3 formalism to the distribution. Simulation and code generation are
working.
Fixed bugs in the automatic layout interface module with hyperedges or with
directed edges that are upgraded to hyperedges.
-- May 10, 2006
Fixed bugs related to starting AToM3 with no default meta-model. The bugs caused the model menu and the types list not to display.
-- Apr 5, 2006
Added a new scaling and dragging user-interface layer. Should be more intuitive.
Modified a number of things, including addition of a method to show/hide links.
Updated FAQ
-- Apr 3, 2006
Fixed a data-structure bug in Hierarchical layout that was causing graphs with
many cycles (and hence reversed edges) to be layed out incorrectly.
Fixed a bug in graphLink.py when dealing with a link that has arrows in both directions.
Modified the cardinality dialog to be user-friendly instead of doing the exact
opposite of what one would expect...
-- Feb 11, 2006
Modified ATOM3Text type so that you can set the height of a text box and it
will stay that height after you save/load a model with an entity which has
an attribute of the ATOM3Text type. No more tiny text windows!!!
Modified the exception logger to log files in the user options area (.AToM3)
This was neccessary for central installations of AToM3
Updated main AToM3 options. Removed obsolete stuff.
AToM3 no longer starts with formalisms open unless the USER asks for them.
Updated atom3/FAQ.txt
-- Feb 10, 2006
Re-built the Class Diagram formalism. It is now called CD_classDiagramsV3.
NOTE:
I did not make it the default yet, so you'll have to either manually load it or
set it up in AToM3 options to load when you start.
Class diagram attributes now propagate from superclasses to subclasses
instantly after editing.
The method employed is simple but robust.
Derived attributes are internally marked so they are never confused
with normal attributes.
The derived attributes are consistent under load/save cycles.
They are also consistent under any changes made to the inheritance structure. (so long as Edit and Disconnect/Connect triggers report said changes, might be a problem in graph grammar situations?)
SIDE-EFFECT: All attributes are now alphabetically sorted by name
Graphical icons are propagated from superclasses to subclasses if the subclass
has no icon of it's own.
I killed the buttons grammar system. It annoyed me for the last time.
(1) It was a gross miss-use of a grammar system
(2) With no model-evolution capabilities it had a huge PITA factor
Therefore I'm sure you'll all appreciate my new system... (works for all generative meta-models without any changes!)
Updated atom3/FAQ.txt
-- Feb 4, 2006
Modified the core event handler loop to take into account that Tkinter is
multi-threaded and may suddenly stop handling one event to start working on
another event while the first event isn't done executing yet.
Added some postaction "create" triggers. In particular, meta-models with that
register for the create postaction trigger will now recieve it when loading
transformations! Hopefully all hell won't break loose... but I had to do this
because some formalisms need their initilization routines triggered by this!
Added an animated move method to graphEntity.py, allows for linear or
acceleration based movement. Assuming self is a semantic object, and you want
to move to pixel coordinates x=100, y=100, use it as
follows: self.graphObject_.animatedMoveTo((100, 100), acceleration=9.8))
or self.graphObject_.animatedMoveTo((100, 100), timeSecInt=4)) to do the linear
movement in 4 seconds. NOTE: acceleration method does not allow you to determine
the time the animation takes. The animation ends when the entity has moved to
the target location.
Added some new methods to GraphicalForm.py for more Tkinter canvas manipulation power.
Updated atom3/FAQ.txt
-- Feb 2, 2006
Improved all automatic layout algorithms. Layouters are accessible through the
regular layout menu (shortcut key... L).
Layouter specific shortcuts are shown in the layout menu.
Improvements are made in terms of layout quality, convergence
speed, code simplicity, and an additional sub-algorithm for crossing minimization.
Added ability to turn all invisible links orange. Press Control-6.
Should be especially useful for those poor people trying to write
visual graph grammars with invisible links...
Added extra command-line functionality.
Command help and ability to load models (not just meta-models)
directly from the command-line.
Added external scripting functionality.
This allows you to run AToM3 via a script and no user-intervention.
Perfect for batch testing... see atom3/scriptedAToM3.py
Updated atom3/FAQ.txt
-- Jan 25, 2006
Numerous changes to the graph grammar system (and I don't remember them all).
Added help messages, debug messages,
changed the latex documentation generator to give more info for Specify, to scale
the LHS and RHS drawings properly, and to use GG labels that are visible to the
naked eye!
Changed the way low level user interface events are handled.
Massively overhauled the automatic layout algorithms. The old algorithms still
exist and are untouched for compatiblity reasons. The new ones all work through
a common interface to AToM3 (so they don't know about AToM3 and AToM3 does not
know about them). Spring layout actually converges! The hierarchical crossing
reducer actually works non-randomly! Access to these improved layout algorithms
is currently through the HOME key, until inspiration strikes me.
Added some random bugs... just joking. We really need a version control
system at MSDL though...
-- Nov 25
Added ability to turn specify code on/off in a graph grammar RHS rule.
-- Aug 31
Rolled back the GGRule.py found in the Aug 19 version of AToM3. Was causing
extremely nasty bugs in graph grammars. This means super-ugly layout during
GG execution once again.
Redid all the keybindings, moving towards a scoped UI environment.
Added all the new layouts to the layout menu.
Added an uninstall script to make fixing your AToM3 installation easier.
-- Aug 30
Fixed arrow connected to arrow drawing problems.
Added a shift-delete binding to delete an entity but not the arrows it is
connected to. This allows you to create partially connected arrows in graph
grammars.
Added Copy LHS error handler
-- Aug 19
Added "template code" when creating new graph grammar rules,
so that you don't have to hunt down for the arcane bits
of code neccessary for making a graph grammar.
Added automatic sorting of graph grammar rules by their "Order" attribute.
Added a duplicate GG label checker that nabs duplicates immediately
Updated the version of Causal Block Diagrams in the distribution
Added a warning if attempting to generate a formalism from a meta-model (ie:
with Entity Relationships) when
multiple meta-models are opened (As Ernest discovered, it won't work properly).
Modified the generator for Class Diagrams V3, will now work even with multiple
formalisms open :)
Improved the Model Menu a bit, should work better when multiple-formalisms are
open and you want to use it to drop stuff not in the toolbar buttons. Still
very very shaky though... and impossible to improve further without
re-generating all older formalisms (speaking of which, formalisms from before
2004 will undoubtedly not show up on the menu at all).
Modified the "Generate code" item in the Model Menu. Will now show a warning
to the effect that you should use the "Generate" button in the toolbar instead.
Made it possible to enable/disable actions and conditions in grammars.
-- Aug 11
Improved startup behaviour when AToM3 is run for the first time.
Added a dialog to the icon editor that warns if a visual icon has no connectors,
thus saving the unwary meta-modeller the agony of not knowing why arrows are
failing to connect
Improved the behaviour of the code generator for both ER and Class Diagram
formalisms in the event that no name has been given to the metamodel.
(These last 3 changes brought to my attention by Ernesto)
Improved arrow creation code so that it is now possible to create formalisms
where edges can themselves contain connection points in their center drawing,
thus making it possible to connect an edge in a grammar with a generic edge...
It is now possible to save a visual icon that contains only a connector, such
as for the center object of an edge.
(These last 2 changes brought to my attention by Sagar)
Added a dialog when AToM3 is closed that asks the user if they want to trash
all the temporary files that have accumulated (if the temporary files have not
been automatically deleted already... this happens when AToM3 crashes).
-- Aug 8
Added new error messages to the graph grammar re-writing system to make
debugging easier. (Brought to my attention by Sagar)
Improved graph grammar transfromation visualization. Previously transformations
resulted in randomly placed nodes. Now they are placed near the nodes they
connect to. I can't do much better than this without requiring graph grammar
authors to input quite a bit of layout specification.
Improved automatic arrow optimizations to handle self-looping links.
Improved named port support by adding messages that tell you want named port
you started your arrow at and terminated your arrow at. Can also be disabled
easily if you don't like dialog windows...
Fixed arrow optimizer issues with named ports
Fixed arrow editor issues with named ports
QOCA layout is now possible, though disabled by default. Uses are limited to
very specific diagrams... unfortunately QOCA simply doesn't have that much
power for general layout, and even worse, does not hybridize well with other
layout techniques.
Added simple circle layout, operates on entire graph or selection
Added tree-like layout, operates on entire graph or selection
Added hieararchical layout, operates on entire graph or selection, very
powerful. Works well on most diagram types, although Causal Block Diagrams
don't look very natural with it. They would need Orthogonal layout...
NOTE: new layouts are not in the Layout Menu yet in this release. If you wish
to test them, try "Control-X" where X is in the range 1 <= X <= 6
-- Aug 4
Added QOCA incremental linear constraint support for graphical layout. This is
disabled by default in the main options. Do not use yet, still changing things...
Fixed a bug in the graphical entity easyScale() method
Disabled option database locking. Can now run multiple copies of AToM3 at once
with no popup messages :)
-- July 7
Fixed a bug with the GEN button for Class Diagrams version 3 (did not work properly
if you did not specify all the visual icons first).
Experimented with timed StateCharts and AToM3. Polling worked but was far too
slow, especially when dragging multiple objects. Instead used a comprimise
solution: events are handled as they come in (unless an event is already being
handled, then it is queued and executed right after, fixing nastiness that used
to occur in the old version), and timed events are triggered by a polling
mechanism that depends on Tkinter after method. The Central model directory
in "DCharts_TkinterFriendlyTest" has an example of how this works... no loss
of functionality over the threaded version that I know of, and it is fast and
stable! Yay.
-- May 25
Changed the default formalism for generating formalisms from Entity Relationship version 3
to Class Diagrams version 3. The addition of the inheritance mechanism should be of great use.
Caveat: you can inherit attributes, but if you do, you can't use them as dynamaically displayed
visual attributes. Also, graphical icons are not inherited.
Added Simon's fix for saving models with large numbers of connections.
Fixed a bug with regard to cardinalities when generating new formalisms. NOTE: do not use ER or CD
original versions to create new formalisms, as they are still "broken".
Miscallaneous stuff: made the save/open dialogs a bit nicer, added a warning after generating
formalisms that you need to reboot AToM3, and added an incomplete HTML help guide to AToM3.
-- May 17
Made a new logo for AToM3... modeled in AToM3 :D
In the process, I identified 3 exceptional cases that caused Save/Load failure in a massively
multi-formalism environment (I had 6 formalisms open at once!). They are now fixed!
I fixed the issue with the buttons graph grammar not generating buttons for Relationships.
I think this was a *very* serious bug, and would affect all graph grammars had I not fixed it!
Ernesto didn't like my dynamically re-sizing buttons in the toolbar (on mouse over event), so I
removed that behaviour... now they just turn red...
I fixed up the behaviour of the main Options Dialog when you change which Formalisms you want active
and press Okay.
-- March 29
Implemented a secondary data structure to keep track of ASGroots (formalisms) ATTRIBUTES
Apparently, just having a clear knowlege of which ASGroots were active was insufficient,
I had to also make a copy of all the ASGroot attributes, and then figure out a way to LOAD them,
MODIFY them, and SAVE them. Considerable amount of work in the juicy innards of AToM3 :p
Hopefully, AToM3 is now completely multi-formalism! I know I'm able to modify buttons models at will
even if I have X number of other meta-models open at the same time... so happiness :D
I added some methods in graphEntity.py that make Hierarchical connect/disconnect in a drag-n-drop
situation very easy. IE: checks bounding box to see if other entities are under it, dialogs, etc.
Added a Help Document system to AToM3. Most notable is the one sported by the ERV3 formalism... a
nice big question mark button! The system makes it *very* easy to add Help Documents to AToM3 inline.
Indeed, I modified the button generating graph grammar to give you a new "HELP" button automatically.
At the moment though, documents are still a bit sketchy, but the ways of using scripts in the Icon
Editor, what exactly a Contraint/Action in the ER Model is, what all the colors & stipples in Tk are,
are all explained in gory detail :D
Discovered a bug in the ERV3 button grammar, it doesn't generate buttons for relationships.
I personally like it that way, so I'm having trouble building up motivation to fix it...
Also, if you desperately want to drop an unsuable relationship on the canvas, you don't need a button,
use the popup-menu and go to the 'Model' menu. You'll find it all there...
I juiced up the buttons model slightly... it now has a Help button, and an Edit button (so you can set
formerly hard to find parameters!). Also, I've got buttons working very nicely, BUT *WARNING*, you must
load buttons models with ONLY the buttons formalism active, for all buttons models created prior to
this release of AToM3!!! This is stated in the Help file for buttons.
-- March 28
Implemented a secondary data structure to keep track of ASGroots (formalisms)
The benefit: much better chances that if you save a model you'll be able to load it up again :D
Added try/except statements to save model code (specifically for generated ASGroot attributes).
This is a very partial solution, but I can't seem to get my hands on the generated attributes before
AToM3 squashes them into an unrecongizable pile of %$*@!.
It is now possible for an entity to lookup info in the ASGroot (ie: the model attributes you set through
the M menu). This makes configuring parameters for all entities in a diagram very easy. If your
interested in this, see ASG.py method getASGbyName(), or wait for me to release DevsV2 to see it in
action...
Modified the Buttons model to warn users of the bad things that will happen if they start working
on a Buttons model and another formalism is already open (Until I figure out the generated attributes
problem, your going to have to walk on your tip toes on this one).
Fixed up the stipples for the indentation guide in the Text widgets
-- March 21
Fixed a few problems when saving models and then they don't want to load after.
Added the ability to easily specify a ERV3 relationship as being non-visual (ie: for insideness relations)
Miscallaneous other small changes... especially to graphEntity.py and graphLink.py
(added stuff useful for layout, scaling, etc.)
-- March 20
Fixed yet another bug with the button creation grammar.
This was a really really tough bug to track down. I'm surprised it wasn't revealed earlier...
I guess that's because no one ever created new ER formalisms before though. Anyway, it's sooo
handled.
-- March 19
Sagar found a few bugs in AToM 3... but no worries, I killed them :D
Fixed a bug involving the creation of new formalisms and editing visual icons,
when the Transformation toolbar is open.
Fixed the Model menu system (Shortcut key is 'M').
Newly created formalisms will now have usable Model
menu entries with which you can drop all entities in the formalisms, regardless
of the fact that you might omit arrows from the buttons menu. (ie: This lets you use
arrows for Graph Grammar transformations, even if no button is available).
Currently supported by: EntityRelationV3 and Annotation
Fixed out of date Graph Grammar for creating buttons for new formalisms. The power
of being able to edit the ERV3 Meta-Model must be tempered with caution :p
Fixed a bug when generating formalism buttons files (META file). The formalism
file is now simply the name, with no path. Paths like: someDir\testing_MM.py
were being interpreted as \t = tab, leading to bad things.
Improved the Graph Grammar transformation editor: now assumes 'Set to any' and
'Copy from LHS', since this is the most common case.
Changed edit entity --> Now shows the name of the entity being edited
Changed copy/paste attributes --> Now works between entities of any type, so long
as they have some subset of attributes in common (ie: if they both have 'name' and
nothing else in common, then only the 'name' attribute is copied). Also added a
dialog box that shows you exactly what attributes have been copied. This feature
is in the popup menu when hovering over an entity, or you can press Alt-C/Alt-V.
-- March 18
Fixed a bug where the text/code editing tool was causing exceptions because it couldn't
find stipple files (xbm graphics). If it can't find them, you'll see a solid grey indentation
guide instead of a nice dotted line. The horror.
-- March 17,2005
AToM3 now has its own IDE for Python coding. Everything you *need* is implemented.
Most of what your *want* is implemented too
I like it better than IDLE, although much of the code is taken from IDLE, but IDLE has no
tab indentation guide!!! A must have!
Also, you may wonder why the popup menu looks a tad wierd... that's because it's
being automatically generated from the event-keybinds map
(so keybinds & menus are always in sync). I find it kind of neat how the popup-menu
is actually just generating the event the keypress would have generated
-- March 14,2005
Modified the AToM3 text widgets to support Python coding
1) Syntax highlighting
2) Tabs are spaces (but can still be deleted easily, as if they were tabs)
3) Tabs are colored with a stipple line, makes indentation obvious
4) # of spaces in a tab can be set easily (same button also re-calculates tab coloring)
5) Todo: Add undo/redo and search/replace capabilities. Multi-line indent/unindent would be nice too
Discovered a bug whereby if you crash AToM3 alot, temp files build up, until WinXP refuses to make more!
Therefore, from now on, whenever you exit AToM3 and choose 'Overide lock' for the options, ALL temporary
files will be cleaned out, instead of just those associated with the current AToM3 process ID.
-- March 13, 2005
Modified Entity Relationship model: Entities and Relationships can now display exactly as
much information as you want them to (example: you can make your entities visually abstract
by displaying only the name, or you can make them very concrete by showing everything:
Name, Attributes, Conditions, Actions, and Cardinalities).
I expect AToM3 formalism makers to look carefully at what I have done here...
Added the ability to specify customized UI behavior model and keybindings code
to make AToM3 work exactly as you like it
Added improved multi-formalism support, see options
Fixed Top Menubar option not working.
The top menubar can now only be activated from the Options (since this works now!)
AToM3 logo in the top left now pops up the Options dialog (better use for the logo no?)
Graph grammar manual execution
(where user must select where in the model the GG will operate), now uses the UI statechart
Added nice headers for automatically generated files
Fixed Icon Editor bugs with respect to editing arrow decorations
Added an arrow preview when designing arrow shapes
-- March 6, 2005
Fixed bug in the Graph Grammar execution code (was looping infinitely).
Added a new Entity Relationship formalism that fully boostraps itself,
making its modification trivial.
-- March 3, 2005
I overhauled the Graph Grammar execution code. The 'Animate' option is now disabled until someone
explains to me what it should be doing (crash in under 1 sec is probably not it...). All other
combination of Graph Grammar execution option should now work better than ever. This means that
if you have multiple rules of the same execution order, they will now be picked RANDOMLY! And if you
use the Sequential-Manual mode, you can select the subgraph transformation target by simply
left-clicking on it (I think the old AToM3 did this, but I have no idea how, so I re-implemented it).
BUG WARNING: I think there may be a bug hidden away somewhere. I was able to duplicate the bug
without fail until I setup a barage of print statements (nothing else), and it completely
disapeared...
BTW: The 'LetEntitiesMove' option seems to move each transformed entity by 100 pixels southeast.
Is this what it is supposed to do? Is this useful?
Added 2 new editing methods, Edit Overlapping and Drag Overlapping which present a menu of all
entities/links around the mouse cursor and let you choose one, and then either popup the edit
dialog or initiate dragging mode. Previously, overlapping entities could be very difficult to
select and operate on. You can find these new methods in the Right-Click popup menu when your
mouse is over/near some object on the canvas. Or you could just press E for edit, D for drag.
Improved AToM3 initial installation setup (after watching the misadventures of fellow MSDL'ers).
Also it has become apparent to me that the current AToM3 does not work with Python 2.2 nor with
Python 2.3 on Win98 due to the fact that they treat import statements like
"from LocalScript import SomceClass" as meaning LocalScript is in the directory where the first
application boostrapping script is located. This would be simple to fix if I had either of these
configurations available to me, but I no longer have Win98, and I can't get Tkinter to work on my
Red Hat Linux 8. I'll find the neccessary setup sometime...
Bug that caused Graph Grammars to 'pretend to save' but actually not save, has been fixed after
causing me untold agony.
AToM3 now strictly enforces naming conventions for:
Models --> _MDL.py
Meta-Models --> _META.py (Button model but it loads a formalism too)
Graph Grammar Model --> _GG_mdl.py
Executable Graph Grammar --> _GG_exec.py
Graph Grammar Rule --> _GG_rule.py (Rules of the executable grammar)
Uncaught exception handlers have been added, they provide a GUI notification and log error to file,
additionally, they assign each error a unique identification number to ease bug tracking.
NOTE: This is applicable to any error that is passed to the standard Python exception handler,
which I have overridden. If the error bypasses the exception handler and goes directly to STDERR,
a GUI notice will still popup, but it will not generate a log entry at this time
(since I believe this to be a very rare occurence).
Automatic generation of text and latex documentation from Graph Grammars is now supported
Graph Grammars are now supported (Do not use the Animate option when executing though...)
-- Sometime in 2005
Coverability Graph via Automatic Layout (Summer 2004)
I added an export function to AToM3 which allows it to export coverability graphs,
such as those automatically generated for Petri-Nets, into some standardized graph langagues.
The first is a human readable ascii descriptive
language called GML (Graph Modeling Language).
GraphViz and yED are two graph visualization tools that can read this format.
The second is GXL (Graph Exchange Language), that can be imported by the open source JGraphpad tool.
The third is DOT, which is recognized by the open source GraphViz visualization tool.
See the links section for more information about these tools.
The modifications to AToM3 are minimal, I merely extended an existing model specific menu to call
my own python exporter file. A screenshot, for the curious, of what this looks like in AToM3 can
be downloaded here.
The most complex example of a coverability graph available to me at the moment is the one AToM3
automatically generates from a Petri Net model of a simple traffic system I made
last year as part of a Modeling and Simulation course. It turns out that this coverability graph
is extremely hard to represent well. The following algorithms were set loose on it:
JGraphpad:
GEM : Best JGraphpad algorithm, but node-node and edge-node overlaps are rampant, not to mention edge-edge crossings. Compactness is okay.
Spring : Graph isn't compact enough, making it hard to read. Also suffers from node-node and edge-node overlap.
Simulated Annealing : Extremely slow, the other algorithms were virtually real-time (on a 2700+ Athlon).
I didn't stick around to see how long it took, but I estimate about 5-10 minutes to do the Petri-Net coverability graph.
The results didn't warrant the running time at all either.
Sugiyama : Applicable only to DAGs, and for some reason the DAG property got lost in the GXL translation.
Note: this is a problem in the JGraphpad import mechanism, not inherent to the GXL language.
GraphViz:
Dot (Hierarchical) : Fairly nice, the spline curved edges in particular, but not the most compact representation.
Neato (Force-Directed) : Too compact, everything overlapped.
yED:
Hierarchical : Not only reveals the underlying structure of the problem, but does in a near optimally compact fashion! Of course, this requires tweaking the settings a bit.
Organic : Relatively compact graph, but edge-node crossings are rampant.
Circular : Graph compactness is a major issue with this one.
Orthogonal : Graph compactness is a problem, some edges in particular must be followed very far.
The original model and coverability graph, along
with the new automated hierarchical layouts can be viewed via the following links:
Traffic Model Petri-Net
Hand Done
Coverability Graph
Hierachical
Coverability Graph
Hierachical
Coverability Graph (Abbreviated labels for greater compactness)
Hierachical
Coverability Graph (no intermediate nodes for edge labeling, uses a label placement post-processing step)
Hierachical
Coverability Graph (using the dot engine in GraphViz)
Thus the hierarchical layout algorithm from yED appears to be the best suited for the task of laying
out a coverability graph. Indeed, it looks considerably better than what I've done by hand. However,
does it work as well for smaller graphs? To test this, I generated a coverability graph for the
venerable producer-consumer model. The results show that the orthogonal layout algorithm has an
edge in this case, as it is far more compact. Note: a label placing post processing step was applied
in both these layouts.
Hierachical
coverability graph of a producer-consumer model
Orthogonal
coverability graph of a producer-consumer model
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