Merged Branch-FW-0.1 into trunk, using command

"svn merge -r850:1193 https://svn.janelia.org/penglab/projects/v3d/branches/Branch-FW-0.1"
I clumsily resolved conflicts in files mainwindow.cpp, v3d_commandlineparser.h, mainwindow.h, main.cpp, and the webservices/ directory.
I also created a couple of tags under https://svn.janelia.org/penglab/projects/v3d/tags/ representing the two code bases being merged:
  /Branch-FW-0.1_before_merge_into_trunk_18May2011/
  /trunk_before_neuron_annotator_merge_18May2011/
(all but webservice folder this time)

build.hudson

@@ -0,0 +1,25 @@
+#!/bin/bash
+# 2010-08-07 by Hanchuan Peng
+# a convenience script for building teh system on Linux (Redhat and Ubuntu)
+#
+# examples: 
+#    sh build.linux
+#    sh build.linux -B -j4   #rebuild the entire system using 4 processors
+
+cd v3d_main
+
+sh ./build.redhat $*
+
+cd ../
+
+# Check for the executable file
+if [ -e "./v3d/v3d" ]
+then
+    echo "Found executable"
+    exit 0;
+else
+    echo "ERROR: did not find executable"
+    exit 1;
+fi
+
+

released_plugins/v3d_plugins/HDRfilter/hdrfilter.cpp

@@ -0,0 +1,216 @@
+/* hdrfilter.cpp
+ * 2011-03-21: create this program by Yang Yu
+ */
+
+//
+#include <cmath>
+#include <stdlib.h>
+#include <ctime>
+
+#include <iostream>
+
+#include "hdrfilter.h"
+
+#include "stackutil.h"
+#include "mg_utilities.h"
+#include "mg_image_lib.h"
+
+
+// redefine loadimage function copy from stackutil.h remove size constrains
+bool loadImageWSC(char imgSrcFile[], unsigned char *& data1d, V3DLONG * &sz, int & datatype)
+{
+	if (data1d)
+	{
+		printf("Warning: The pointer for 1d data storage is not empty. This pointer will be freed first and the  reallocated. \n");
+		delete []data1d; data1d=0;
+	}
+	if (sz)
+	{
+		printf("Warning: The pointer for size is not empty. This pointer will be freed first and the  reallocated. \n");
+		delete []sz; sz=0;
+	}
+	else
+	{
+		sz = new V3DLONG [4];
+		if (!sz)
+		{
+			printf("Fail to alocate memory for the size variable.\n");
+			return false;
+		}
+	}
+
+	unsigned char *tmp_data1d =0;
+	V3DLONG * tmp_sz = 0; /* note that this variable must be initialized as NULL. */
+	int tmp_datatype = 0;
+	bool b_5d=false;
+
+	char * curFileSuffix = getSurfix(imgSrcFile);
+	if (strcasecmp(curFileSuffix, "tif")==0 || strcasecmp(curFileSuffix, "tiff")==0) //read tiff stacks
+	{
+		if (loadTif2Stack(imgSrcFile, tmp_data1d, tmp_sz, tmp_datatype))
+		{
+			printf("Error happens in TIF file reading. Stop. \n");
+			return false;
+		}
+	}
+	else if ( strcasecmp(curFileSuffix, "lsm")==0 ) //read lsm stacks
+	{
+		if (loadLsm2Stack(imgSrcFile, tmp_data1d, tmp_sz, tmp_datatype))
+		{
+			printf("Error happens in LSM file reading. Stop. \n");
+			return false;
+		}
+	}
+	else if ( strcasecmp(curFileSuffix, "raw5")==0 ) //read lsm stacks
+	{
+		if (loadRaw5d2Stack(imgSrcFile, tmp_data1d, tmp_sz, tmp_datatype))
+		{
+			printf("Error happens in V3D .raw5 (5D) file reading. Stop. \n");
+			return false;
+		}
+		b_5d = true;
+	}
+	else //then assume it is Hanchuan's RAW format
+	{
+		if (loadRaw2Stack(imgSrcFile, tmp_data1d, tmp_sz, tmp_datatype))
+		{
+			if (loadRaw2Stack_2byte(imgSrcFile, tmp_data1d, tmp_sz, tmp_datatype))
+			{
+				printf("Error happens in reading 2-byte-size RAW file. Stop. \n");
+				return false;
+			}
+		}
+	}
+
+
+	//copy output data
+	switch (tmp_datatype)
+	{
+		case 1:
+			datatype = 1;
+			break;
+
+		case 2:
+			datatype = 2;
+			break;
+
+		case 4:
+			datatype = 4;
+			break;
+
+		default:
+			printf("Something wrong with the program, -- should NOT display this message at all. Check your program. \n");
+			if (data1d) {delete []data1d; data1d=0;}
+			if (tmp_sz) {delete []tmp_sz; tmp_sz=0;}
+			if (sz) {delete []sz; sz=0;}
+			return false;
+	}
+
+	sz = new V3DLONG [5];
+	sz[0] = tmp_sz[0];
+	sz[1] = tmp_sz[1];
+	sz[2] = tmp_sz[2];
+	sz[3] = tmp_sz[3]; //no longer merge the 3rd and 4th dimensions
+	sz[4] = (b_5d) ? tmp_sz[4] : 1; //090802
+
+	data1d = tmp_data1d;
+
+	/* clean all workspace variables */
+	if (tmp_sz) {delete []tmp_sz; tmp_sz=0;}
+
+	return true;
+}
+
+
+//Q_EXPORT_PLUGIN2 ( PluginName, ClassName )
+//The value of PluginName should correspond to the TARGET specified in the plugin's project file.
+Q_EXPORT_PLUGIN2(hdrfilter, HDRFilterPlugin);
+
+// func datatype converting main
+int hdr_filtering(V3DPluginCallback2 &callback, QWidget *parent);
+
+// func convering kernel
+template <class Tpre, class Tpost>
+int convering(void *subject1d, ImagePixelType v3d_dt, ImagePixelType dt);
+
+//plugin funcs
+const QString title = "HDR Filtering";
+QStringList HDRFilterPlugin::menulist() const
+{
+    return QStringList() << tr("HDR Filtering")
+						 << tr("About");
+}
+
+void HDRFilterPlugin::domenu(const QString &menu_name, V3DPluginCallback2 &callback, QWidget *parent)
+{
+    if (menu_name == tr("HDR Filtering"))
+    {
+    	hdr_filtering(callback, parent);
+    }
+	else if (menu_name == tr("About"))
+	{
+		QMessageBox::information(parent, "Version info", QString("HDR Filtering Plugin %1 (March 21, 2011) developed by Yang Yu. (Janelia Research Farm Campus, HHMI)").arg(getPluginVersion()));
+		return;
+	}
+}
+
+// show different datatype data in V3D
+int hdr_filtering(V3DPluginCallback2 &callback, QWidget *parent)
+{
+	qDebug()<<"run hdr filtering ...";
+
+	// get image
+	HDRFilerDialog dialog(callback, parent);
+	if (dialog.exec()!=QDialog::Accepted)	return -1;
+
+	QString fn_image = dialog.fn_image;
+
+	qDebug()<<"input is ... "<<dialog.fn_image;
+
+	// load image
+	unsigned char *data1d=NULL;
+	V3DLONG *imgsz=NULL, sx, sy, sz, sc;
+	int datatype;
+
+	if(QFile::exists(fn_image))
+	{
+		if (loadImageWSC(const_cast<char *>( fn_image.toStdString().c_str() ), data1d, imgsz, datatype)!=true)
+		{
+			std::cout << "The image loading fails."<<endl;
+			return false;
+		}
+
+		sx= imgsz[0], sy = imgsz[1], sz = imgsz[2]; sc = imgsz[3];
+
+	}
+	else
+	{
+		std::cout << "The image does not exist."<<endl;
+		return false;
+	}
+
+	Image4DSimple p4DImage;
+
+	if(datatype==1)
+	{
+		p4DImage.setData((unsigned char *)data1d, sx,sy,sz,sc, V3D_UINT8);
+	}
+	else if(datatype==2)
+	{
+		p4DImage.setData((unsigned char *)data1d, sx,sy,sz,sc, V3D_UINT16);
+	}
+	else if(datatype==4)
+	{
+		p4DImage.setData((unsigned char *)data1d, sx,sy,sz,sc, V3D_FLOAT32);
+	}
+
+
+	// HDR filtering
+	HDRwidget *pHDRwidget = new HDRwidget(parent, p4DImage);
+	pHDRwidget->show();
+
+	//
+	return 0;
+
+}
+