Vaa3D v3.131 / TeraFly version 2.1.41

- Dev: added TeraStitcher submodule
Vaa3D · Mar 8, 2016 · 5a68cc0 · 5a68cc0
1 parent 6443089
commit 5a68cc0
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Showing 126 changed files with 183 additions and 41,389 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "v3d_main/terafly/src/terarepo"]
+	path = v3d_main/terafly/src/terarepo
+	url = https://github.com/abria/TeraStitcher.git
diff --git a/v3d_main/terafly/CMakeLists.txt b/v3d_main/terafly/CMakeLists.txt
@@ -58,41 +58,43 @@ include_directories(${Boost_INCLUDE_DIR})
 # add internal include directories
 include_directories(./src/presentation)
 include_directories(./src/control)
-include_directories(./src/core/imagemanager)
-include_directories(./src/core/volumeconverter)
-include_directories(./src/core/volumemanager)
-include_directories(./src/core/stitcher)
-include_directories(./src/core/crossmips)
-include_directories(./src/core/tinyxml)
-include_directories(./src/core/iomanager)
-include_directories(./src/core/iomanager/plugins/tiff2D)
-include_directories(./src/core/iomanager/plugins/tiff3D)
+include_directories(./src/terarepo/imagemanager)
+include_directories(./src/terarepo/utils/volumeconverter)
+include_directories(./src/terarepo/volumemanager)
+include_directories(./src/terarepo/stitcher)
+include_directories(./src/terarepo/crossmips)
+include_directories(./src/terarepo/tinyxml)
+include_directories(./src/terarepo/iomanager)
+include_directories(./src/terarepo/iomanager/plugins/tiff2D)
+include_directories(./src/terarepo/iomanager/plugins/tiff3D)
 
 # add internal header files
 file(GLOB presentation_h 		./src/presentation/*.h)
 file(GLOB control_h 			./src/control/*.h)
-file(GLOB imagemanager_h 		./src/core/imagemanager/*.h)
-file(GLOB volumeconverter_h 	./src/core/volumeconverter/*.h)
-file(GLOB volumemanager_h 		./src/core/volumemanager/*.h)
-file(GLOB stitcher_h 			./src/core/stitcher/*.h)
-file(GLOB crossmips_h 			./src/core/crossmips/*.h)
-file(GLOB tinyxml_h 			./src/core/tinyxml/*.h)
-file(GLOB iomanager_h 			./src/core/iomanager/*.h)
-file(GLOB plugin_tiff2D_h 		./src/core/iomanager/plugins/tiff2D/*.h)
-file(GLOB plugin_tiff3D_h 		./src/core/iomanager/plugins/tiff3D/*.h)
+file(GLOB imagemanager_h 		./src/terarepo/imagemanager/*.h)
+file(GLOB volumeconverter_h 	./src/terarepo/utils/volumeconverter/*.h)
+file(GLOB volumemanager_h 		./src/terarepo/volumemanager/*.h)
+file(GLOB stitcher_h 			./src/terarepo/stitcher/*.h)
+file(GLOB crossmips_h 			./src/terarepo/crossmips/*.h)
+file(GLOB tinyxml_h 			./src/terarepo/tinyxml/*.h)
+file(GLOB iomanager_h 			./src/terarepo/iomanager/*.h)
+file(GLOB plugin_tiff2D_h 		./src/terarepo/iomanager/plugins/tiff2D/*.h)
+file(GLOB plugin_tiff3D_h 		./src/terarepo/iomanager/plugins/tiff3D/*.h)
+file(GLOB common_h 				./src/terarepo/common/*.h)
 
 # add internal source files
 file(GLOB presentation_src 		./src/presentation/*.cpp)
 file(GLOB control_src 			./src/control/*.cpp)
-file(GLOB imagemanager_src 		./src/core/imagemanager/*.cpp)
-file(GLOB volumeconverter_src 	./src/core/volumeconverter/*.cpp)
-file(GLOB volumemanager_src 	./src/core/volumemanager/*.cpp)
-file(GLOB stitcher_src 			./src/core/stitcher/*.cpp)
-file(GLOB crossmips_src 		./src/core/crossmips/*.cpp)
-file(GLOB tinyxml_src 			./src/core/tinyxml/*.cpp)
-file(GLOB iomanager_src 		./src/core/iomanager/*.cpp)
-file(GLOB plugin_tiff2D_src 	./src/core/iomanager/plugins/tiff2D/*.cpp)
-file(GLOB plugin_tiff3D_src 	./src/core/iomanager/plugins/tiff3D/*.cpp)
+file(GLOB imagemanager_src 		./src/terarepo/imagemanager/*.cpp)
+file(GLOB volumeconverter_src 	./src/terarepo/utils/volumeconverter/*.cpp)
+file(GLOB volumemanager_src 	./src/terarepo/volumemanager/*.cpp)
+file(GLOB stitcher_src 			./src/terarepo/stitcher/*.cpp)
+file(GLOB crossmips_src 		./src/terarepo/crossmips/*.cpp)
+file(GLOB tinyxml_src 			./src/terarepo/tinyxml/*.cpp)
+file(GLOB iomanager_src 		./src/terarepo/iomanager/*.cpp)
+file(GLOB plugin_tiff2D_src 	./src/terarepo/iomanager/plugins/tiff2D/*.cpp)
+file(GLOB plugin_tiff3D_src 	./src/terarepo/iomanager/plugins/tiff3D/*.cpp)
+file(GLOB common_src 			./src/terarepo/common/*.cpp)
 
 # look for "Q_OBJECT" in headers to determine which ones to MOC
 message(STATUS "TeraFly: finding header files containing 'Q_OBJECT' macro...")
@@ -129,6 +131,7 @@ add_library(terafly STATIC
 	${stitcher_src}
 	${crossmips_src}
 	${tinyxml_src}
+	${common_src}
 	${presentation_h}
 	${control_h}
 	${imagemanager_h}
@@ -140,6 +143,7 @@ add_library(terafly STATIC
 	${stitcher_h}
 	${crossmips_h}
 	${tinyxml_h}
+	${common_h}
 )
 
 target_link_libraries(terafly ${HDF5_LIBRARY} ${z_LIBRARY} ${szip_LIBRARY})

diff --git a/v3d_main/terafly/changelog.txt b/v3d_main/terafly/changelog.txt
@@ -11,6 +11,12 @@ ties names are:
 - Rem: a feature no longer available
 
 ============================================================================================
+Vaa3D v3.131 / TeraFly version 2.1.41
+March 8th, 2016
+--------------------------------------------------------------------------------------------
+- Dev: added TeraStitcher submodule
+--------------------------------------------------------------------------------------------
+
 Vaa3D v3.113 / TeraFly version 2.1.4
 December 12th, 2015
 --------------------------------------------------------------------------------------------

diff --git a/v3d_main/terafly/src/control/CConverter.h b/v3d_main/terafly/src/control/CConverter.h
@@ -33,7 +33,7 @@
 #include <string>
 #include "CPlugin.h"
 #include "../presentation/PConverter.h"
-#include "../core/volumeconverter/VolumeConverter.h"
+#include "VolumeConverter.h"
 
 class teramanager::CConverter : public QThread
 {

diff --git a/v3d_main/terafly/src/control/CPlugin.cpp b/v3d_main/terafly/src/control/CPlugin.cpp
@@ -47,7 +47,7 @@ namespace teramanager
     *    PARAMETERS    *
     ********************
     ---------------------------------------------------------------------------------------------------------------------------*/
-    std::string version = "2.1.4";         //software version
+    std::string version = "2.1.41";         //software version
     int DEBUG = LEV_MAX;                    //debug level
     bool DEBUG_TO_FILE = false;             //whether debug messages should be printed on the screen or to a file (default: screen)
     std::string DEBUG_FILE_PATH = "/home/alex/Scrivania/terafly_debug.log";   //filepath where to save debug information

diff --git a/v3d_main/terafly/src/control/CPlugin.h b/v3d_main/terafly/src/control/CPlugin.h
@@ -37,6 +37,7 @@
 #include <limits>
 #include <sstream>
 #include <algorithm>
+#include <QThread>
 
 class V3DPluginCallback2;
 
@@ -334,6 +335,14 @@ namespace teramanager
         return (b - a) * step_index / static_cast<float>(steps_number) + a;
     }
 
+    class Sleeper : public QThread
+    {
+        public:
+            static void usleep(unsigned long usecs){QThread::usleep(usecs);}
+            static void msleep(unsigned long msecs){QThread::msleep(msecs);}
+            static void sleep(unsigned long secs){QThread::sleep(secs);}
+    };
+
     //cross-platform current function macro
     #if defined(__GNUC__) || (defined(__MWERKS__) && (__MWERKS__ >= 0x3000)) || (defined(__ICC) && (__ICC >= 600))
     # define __itm__current__function__ __PRETTY_FUNCTION__

diff --git a/v3d_main/terafly/src/core/crossmips/CMakeLists.txt b/v3d_main/terafly/src/core/crossmips/CMakeLists.txt
diff --git a/v3d_main/terafly/src/core/crossmips/CrossMIPs.h b/v3d_main/terafly/src/core/crossmips/CrossMIPs.h