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Roeland Merks
In response to referee's comment:

"I am also afraid that

the ‘snapshot’ and the ‘Export cell data’ functions do not seem to work very
well in my hands, could the program be changed so that the correct file
extension (.jpg, .tif, .txt, .dat, .xls, .csv…) is given automatically."

I corrected the "export cell data" dialog (it did not actually write the file in the submitted version). Also we now assume default file extensions (.jpg for snapshot and .csv for data export) if none is given.

--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed src/VirtualLeaf.pro
changed src/canvas.cpp
removed src/miscq.cpp
removed src/miscq.h
2010-10-19    <guravage@caterpie.sen.cwi.nl>

	* mainbase.cpp (Save): Use format specified in function prototype.

	* VirtualLeaf.cpp (Plot): Render PNG instead of JPEG. Write image
	and XML files dependent only on getTime().

2010-10-18    <guravage@caterpie.sen.cwi.nl>

	* mainbase.cpp (Save): QDir::toNativeSeparators(fname). Invoke
	save with format argument set to zero to force QImage to guess the
	format by looking at fileName's suffix.

	* VirtualLeaf-install.nsi: Put uninstaller in top directory.

	* modelcatalogue.cpp (InstallModel): For all OS-es. Move from "bin" directory to root application folder.

	* VirtualLeaf.pro: MAXOSX, look for gpl3.txt in the ../doc directory.

	* Makefile (Makefile.libplugin): Removed -makefile qmake option.

	* VirtualLeaf.cpp (TIMESTEP): Removed getIterations().

	* mesh.h (Mesh): Removed {increment,get}Iterations().

	* canvas.cpp (TimeStepWrap): Replaced getIterations() with getTime().

2010-10-15    <guravage@caterpie.sen.cwi.nl>

	* mesh.h (Mesh): Added iterations. incrementIterations() and
	getIterations().

	* VirtualLeaf.cpp (Plot): Replaced local frame counter with
	mesh.incrementIterations().

	* canvas.cpp (TimeStepWrap): Replaced local counter with
	mesh.incrementIterations().

2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Turned debug off to make all profiles must be
	consistant.

	* VirtualLeaf-install.nsi: Tweaked paths to coincide with UNIX
	distribution, i.e. VirtualLeaf.exe, its libraries, models, and the
	uninstaller all go in the bin directory. And leaves directory
	placed under data directory.

	* canvas.cpp (exportCellData): Added a check to inquire before
	overwritting an existing file.


2010-10-14    <merks@cwi.nl>

	* mesh.cpp: In response to referees' comments, added new parameter
	"yield_threshold" instead of fixed parameter '4' for yield
	threshold.

	* wallitem.cpp: when clicking a wall, both the wall type was
	cycled and the transporterdialog popped up. Corrected this - for
	wall type cycling, hold the Control button while left
	clicking. TransporterDialog only pops up for left click. Also made
	sure the wall is redrawn after changing the transporter values.

	* cell.cpp (DivideWalls): accomodated for rename of Circumference -> WallCircumference

	* hull.h: added an operator< to sort Points

	* hull.cpp: added an operator< to sort Points

	* cellbase.cpp (ExactCircumference): I added a new function
	ExactCircumference, yielding the circumference of the cell along
	its wall_elements

	* VirtualLeaf.cpp: adjust info_string to accomodate for new name
	of function CellBase::Circumference -> CellBase::WallCircumference

	* mesh.cpp: corrected Mesh::Compactness, the boundary coordinates
	need to be sorted in x,y order for the convex hull algorithm
	(thanks Margriet!). I updated CSVExportCellData so it exports the
	circumferences of hull and boundary_polygon.


2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeafpar.tmpl (export_fn_prefix): changed to 'cell.'

	* canvas.cpp (TimeStepWrap): Removed TimeStamp(). Cell data
	filename now incorporates iteration number.

	* canvas.h (MainBase): Removed TimeStamp().


2010-10-08    <guravage@caterpie.sen.cwi.nl>


	* pardialog.h:
	* pardialog.cpp:
	* parameter.h:
	* parameter.cpp: Regenerated to include export_interval and export_fn_prefix.

	* VirtualLeafpar.tmpl: Appended export_interval and export_fn_prefix.

	* canvas.h (MainBase): Declared polymorphic exportCellData() functions.

	* canvas.cpp:
	(TimeStamp): New private TimeStamp() function.
	(TimeStepWrap): Added invocation of exportCellData().
	(exportCellData): Created two polymorphic functions: one with a
	single QString argument, the other with no argument. The former is
	called from TimeStepWrap() while the latter is called from the
	"Export cell areas" item in the file menu.


2010-10-07    <guravage@caterpie.sen.cwi.nl>

	* canvas.cpp (exportCellData): Added a Q3FileDialog to inquire
	where to write the exportCellData.

2010-06-28    <guravage@caterpie.sen.cwi.nl>


	* VirtualLeaf-install.nsi: Grab gpl3.txt from doc directory.

	* canvas.cpp (gpl): gpl3.txt can be either in an ancestor doc
	directory (Linux) or a decedent doc directory (Windows, via the
	binary installer).

	* VirtualLeaf-install.nsi: Add VirtualLeaf doc directory.

2010-06-25    <guravage@caterpie.sen.cwi.nl>


	* gpl3.txt: Moved gpl3.txt from doc to src directory.

	* VirtualLeaf.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

	* libplugin.pro: Ditto.

	* parameter.cpp: Result of adding datadir changes to make_parameter_source.pl.
	* parameter.h: Ditto.

	* output.h: Declared new function (AppendHomeDirIfPathRelative).

	* output.cpp (AppendHomeDirIfPathRelative): Added new function.

	* canvas.cpp (gpl): Moving gpl3.txt from doc to src obviates the need to docDir.cd("../doc").

	* VirtualLeaf-install.nsi: Grab gpl3.txt from src directory.
	Add missing libiconv/bin, libxml2bin and libz/bin directories.
	Copy libiconv-2.dll, libxml2.dll and zlib1.dll from relative paths.

	* VirtualLeaf.pro: copy gpl3.txt as part of QMAKE_POST_LINK.

2010-06-24    <guravage@caterpie.sen.cwi.nl>

	* libplugin.pro: Use correct library path.
	* VirtualLeaf.pro: Ditto.

	* VirtualLeaf.cpp (DrawCell): Iterate over NChem to construct info_string.

2010-06-23    <guravage@caterpie.sen.cwi.nl>

	* simitembase.cpp: Removed NULL assignments to unused variables.
	* VirtualLeaf.cpp: Ditto.
	* apoplastitem.cpp: Ditto.
	* canvas.cpp: Ditto.
	* cell.cpp: Ditto.
	* cellbase.h: Ditto.
	* forwardeuler.cpp: Ditto.
	* mainbase.h: Ditto.
	* nodeitem.cpp: Ditto.
	* qcanvasarrow.h: Ditto.
	* simitembase.cpp: Ditto.


	* Makefile (clean): Add -f Makefile argument to each make invocation.

	* VirtualLeaf-install.nsi: New gpl license text.

	* VirtualLeaf.pro: Disabled console mode.

	* mesh.cpp (Clear): Added parentheses to qDebug statments.
	(TestIllegalWalls): Replaced qDebug().

	* canvas.cpp (mouseReleaseEvent): Replaced qDebug() with cerr since qDebug complains about *node_set.

	* wall.cpp (CorrectWall): Rplaced gDebug() with cerr in transform call and when printing *this.

2010-06-22    <guravage@caterpie.sen.cwi.nl>

	* Makefile (tutorials): Add tutorials target.

2010-06-21    <guravage@caterpie.sen.cwi.nl>

	* parameter.cpp: Added particular reassignment of datadir.

	* canvas.cpp (gpl): Added GPL3 License text. Display detail text only if the source text file exists.

2010-06-18    <guravage@caterpie.sen.cwi.nl>

	* canvas.cpp (gpl): Added gpl slot to display GPL license.

	* VirtualLeaf.pro: Changed default LIBXML2DIR, LIBICONVDIR and LIBZDIR to corresponding distribution lib directories.
	* libplugin.pro: Ditto.

	* Makefile (clean): add if stmt not to `touch` on windows.

2010-06-17    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed perl references.
	* libplugin.pro: Ditto.

2010-06-15    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed xmlwritecode.cpp from SOURCES list.

	* xmlwrite.cpp (XMLSave): Removed references to XMLWriteLeafSourceCode and XMLWriteReactionsCode.
	* xmlwrite.h (XMLIO): Ditto!

	* mesh.cpp (findNextBoundaryNode): Initialize Node *next_boundary_node = NULL;

	* xmlwrite.cpp (XMLReadSimtime): Removed unused variable cur
	(XMLReadWalls): viz_flux need not be declared twice; default value of 0.0.
	(XMLReadCells): Removed unused count variable.
	(XMLReadSimtime): Removed unused cur variable.
	(XMLRead): Removed unused v_str variable.

	* simitembase.cpp (userMove): Use assignment merely to obviate compilation warning.
	(SimItemBase) Ditto.

	* qcanvasarrow.h (QGraphicsLineItem): Use assignment merely to obviate compilation warning.

	* output.cpp (OpenWriteFile): Removed unused par variable.

	* nodeitem.cpp (paint): Use assignment merely to obviate compilation warning.

	* forwardeuler.cpp (odeint): Use assignment merely to obviate compilation warning.

	* cell.cpp (DivideOverGivenLine): Use assignment merely to obviate compilation warning.

	* canvas.cpp (FigureEditor): Use assignments merely to obviate compilation errors.
	(mousePressEvent): Removed unused item variable.

	* apoplastitem.cpp
	(ApoplastItem): Removed unused par variable.
	(OnClick): Use NULL assignment merely to obviate compilation warning.

	* mainbase.h (MainBase): Use assignment merely to obviate compilation warning.

	* cellbase.h (CellsStaticDatamembers): Use assignment merely to obviate compilation warning.


	* cell.cpp: Wrapped diagnostic output in QDEBUG blocks.
	* VirtualLeaf.cpp ditto.
	* canvas.cpp ditto.
	* cell.cpp ditto.
	* data_plot.cpp ditto.
	* forwardeuler.cpp ditto.
	* mesh.cpp ditto.
	* mesh.h
	* random.cpp ditto.
	* wall.cpp ditto.
	* wallbase.cpp ditto.
	* wallitem.cpp ditto.


2010-06-07    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed explicit perl invocation to regerenerate parameter files.
	* libplugin.pro: ditto.

2010-06-03    <guravage@caterpie.sen.cwi.nl>

	* pardialog.h: Added default versions of this automatically generated file.
	* pardialog.cpp: ditto.
	* parameter.h: ditto.
	* parameter.cpp: ditto.

	* VirtualLeaf.pro: delete/generate  parameter.{h,cpp}and pardialog.{h,cpp} only if perl is installed.
 	* libplugin.pro: dito.

	* Makefile: Added top-level Makefile

2010-05-10    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Added -fPIC option to QMAKE_CXXFLAGS.