New features

- path and name of metadata file of unstitched datasets (mdata.bin) can be changed using command line option --mdata_bin
- loading of special cases of unstitched subvolumes has been optimized

cmake/Version.cmake

@@ -1,6 +1,6 @@
 set(TeraStitcher_VERSION_MAJOR 1)
 set(TeraStitcher_VERSION_MINOR 10)
-set(TeraStitcher_VERSION_PATCH 11)
+set(TeraStitcher_VERSION_PATCH 12)
 set(TeraStitcher_VERSION
   "${TeraStitcher_VERSION_MAJOR}.${TeraStitcher_VERSION_MINOR}.${TeraStitcher_VERSION_PATCH}")
 add_definitions( -DTERASTITCHER_MAJOR=${TeraStitcher_VERSION_MAJOR} )

src/imagemanager/VirtualVolume.h

@@ -88,7 +88,7 @@ class iim::VirtualVolume {
 				src += totalChanSize;
 				cc++;
 			}
-			memcpy(dst,src,totalChanSize);
+			memcpy(dst,src,(size_t)totalChanSize);
 		}
 	}
 

src/iomanager/ioplugins.h

@@ -1,5 +1,5 @@
-// Include plugins headers
-#include "plugins/dcimg/dcimg.h"
-#include "plugins/IMS_HDF5/IMS_HDF5.h"
-#include "plugins/tiff2D/tiff2D.h"
-#include "plugins/tiff3D/tiff3D.h"
+// Include plugins headers
+#include "plugins/dcimg/dcimg.h"
+#include "plugins/IMS_HDF5/IMS_HDF5.h"
+#include "plugins/tiff2D/tiff2D.h"
+#include "plugins/tiff3D/tiff3D.h"

src/ui/CLI.cpp

@@ -28,6 +28,7 @@
 /******************
 *    CHANGELOG    *
 *******************
+* 2018-03-02. Giulio.     @ADDED an option to set a path and a name for the mdata.bin file generated when volumes are created from data
 * 2018-01-30. Giulio.     @FIXED flags disabling last row and colum were not initialized in non-parallel executions
 * 2018-01-28. Giulio.     @CHANGED the checks about the image input channel
 * 2018-01-23. Giulio.     @ADDED check to set always the input format of a MultiVolume dataset as a non-interleaved input format
@@ -84,6 +85,7 @@ void TeraStitcherCLI::readParams(int argc, char** argv) throw (iom::exception)
 	TCLAP::SwitchArg p_isotropic("","isotropic","Generate lowest resolution with voxels as much isotropic as possible. Use this flag when the high resolution image has highy anistropic voxels",false);
 	TCLAP::SwitchArg p_dump("d","dump","Print the entire content of metadata file mdata.bin",false);
 	TCLAP::SwitchArg p_pluginsinfo("p","pluginsinfo","Display plugins informations",false);
+	TCLAP::ValueArg<std::string> p_mdata_fname("","mdata_bin","Path and name of mdata.bin file.",false,"","string");
 	TCLAP::ValueArg<std::string> p_vol_in_path("","volin","Directory path where the volume is stored.",false,"null","string");
 	TCLAP::ValueArg<std::string> p_vol_out_path("","volout","Directory path where to save the stitched volume.",false,"null","string");
 	TCLAP::ValueArg<std::string> p_vol_in_plugin("","volin_plugin",vm::strprintf("Plugin that manages the input volume format/organization. Available plugins are: {%s}. Default is \"%s\".", vm::VirtualVolumeFactory::registeredPlugins().c_str(), vm::VOLUME_INPUT_FORMAT_PLUGIN.c_str()),false,vm::VOLUME_INPUT_FORMAT_PLUGIN,"string");
@@ -211,6 +213,7 @@ void TeraStitcherCLI::readParams(int argc, char** argv) throw (iom::exception)
 	cmd.add(p_vol_out_path);
 	cmd.add(p_vol_in_plugin);
 	cmd.add(p_vol_in_path);
+	cmd.add(p_mdata_fname);
 	cmd.add(p_pluginsinfo);
 	cmd.add(p_dump);
 	cmd.add(p_stitch);
@@ -520,6 +523,7 @@ void TeraStitcherCLI::readParams(int argc, char** argv) throw (iom::exception)
 	this->thresholddisplacements = p_thresholdisplacements.getValue();
 	this->placetiles = p_placetiles.getValue();
 	this->mergetiles = p_merge.getValue();
+	this->mdata_fname = p_mdata_fname.getValue();
 	this->volume_load_path = p_vol_in_path.getValue();
 	this->volume_save_path = p_vol_out_path.getValue();
 	this->projfile_load_path = p_proj_in_path.getValue();

src/ui/CLI.h

@@ -28,6 +28,7 @@
 /******************
 *    CHANGELOG    *
 *******************
+* 2018-03-02. Giulio.     @ADDED an option to set a path and a name for the mdata.bin file generated when volumes are created from data
 * 2018-01-23. Giulio.     @ADDED include of MCVolume.h
 * 2017-06-30. Giulio.     @ADDED control over displacement computation of last row and last column of tiles
 * 2016-09-04. Giulio.     @ADDED the options for setting the configuration of the LibTIFF library
@@ -66,6 +67,7 @@ class TeraStitcherCLI
         bool isotropic;                         //generate lowest resolutiona with voxels as much isotropic as possible
 
 		//STITCHING pipeline parameters
+		string mdata_fname;						//path  & file mane of mdata.bin file
 		string volume_load_path;				//directory path where the volume is stored used during the volume import step
 		string volume_save_path;				//directory path where to save the stitched volume
 		string projfile_load_path;				//file path of the project XML file to be loaded

src/ui/main.cpp

@@ -28,6 +28,7 @@
 /******************
 *    CHANGELOG    *
 *******************
+* 2018-03-02. Giulio.     @ADDED the possibility to set a path and a name for the mdata.bin file generated when volumes are created from data
 * 2018-01-23. Giulio.     @ADDED check to set always the input format of a MultiVolume dataset as a non-interleaved input format
 * 2017-12-01. Giulio      @ADDED conditional code to activate the new merge step 
 * 2017-06-30. Giulio.     @FIXED the coding of iom::CHANS was not coherent with the one used internally by vmVirtualVolume
@@ -190,7 +191,7 @@ int main(int argc, char** argv)
 				throw iom::exception(vm::strprintf("Volume \"%s\" is incomplete or not coherent", volume->getSTACKS_DIR()).c_str());
 		}
 		else if(cli.import || (cli.computedisplacements && cli.projfile_load_path.compare("null")==0) || cli.stitch || cli.test) {
-			volume = volumemanager::VirtualVolumeFactory::createFromData(vm::VOLUME_INPUT_FORMAT_PLUGIN, cli.volume_load_path.c_str(), cli.reference_system, cli.VXL_1, cli.VXL_2, cli.VXL_3, true);
+		volume = volumemanager::VirtualVolumeFactory::createFromData(vm::VOLUME_INPUT_FORMAT_PLUGIN, cli.volume_load_path.c_str(), cli.reference_system, cli.VXL_1, cli.VXL_2, cli.VXL_3, true, cli.mdata_fname);
 			if ( !volume->check(fillPath(cli.errlogfile_path, volume->getSTACKS_DIR(), "err_log_file", "txt").c_str()) ) {
 				// save xml for further checking
 				volume->saveXML(0, fillPath(cli.projfile_save_path, volume->getSTACKS_DIR(), "xml_import", "xml").c_str());

src/volumemanager/vmBlockVolume.cpp

@@ -25,6 +25,7 @@
 /******************
 *    CHANGELOG    *
 *******************
+* 2018-03-02. Giulio.     @ADDED the possibility to set a path and a name for the mdata.bin file
 * 2018-02-03. Giulio.     @ADDED call to 'adjustDisplacements' in method reading the xml file to force all displacements of adjacent tile symmetric
 * 2017-06-27. Giulio.     @CHANGED If the attributes 'resolution' and 'timepoint' in section 'subimage' of xml file are present additional parameters are always enabled 
 * 2017-04-27. Giulio.     @ADDED code to get and initialize the input plugin from the xml if specified
@@ -90,7 +91,7 @@ const std::string BlockVolume::creator_id1 = volumemanager::VirtualVolumeFactory
 const std::string BlockVolume::creator_id2 = volumemanager::VirtualVolumeFactory::registerPluginCreatorData(&createFromData, BlockVolume::id);
 
 
-BlockVolume::BlockVolume(const char* _stacks_dir, vm::ref_sys _reference_system, float VXL_1, float VXL_2, float VXL_3, bool overwrite_mdata) throw (iom::exception)
+BlockVolume::BlockVolume(const char* _stacks_dir, vm::ref_sys _reference_system, float VXL_1, float VXL_2, float VXL_3, bool overwrite_mdata, std::string mdata_fname) throw (iom::exception)
 	: VirtualVolume(_stacks_dir, _reference_system, VXL_1, VXL_2, VXL_3)
 {
 	#if VM_VERBOSE > 3
@@ -104,7 +105,12 @@ BlockVolume::BlockVolume(const char* _stacks_dir, vm::ref_sys _reference_system,
 
 	//trying to unserialize an already existing metadata file, if it doesn't exist the full initialization procedure is performed and metadata is saved
     char mdata_filepath[VM_STATIC_STRINGS_SIZE];
-    sprintf(mdata_filepath, "%s/%s", stacks_dir, vm::BINARY_METADATA_FILENAME.c_str());
+	if ( mdata_fname == "" ) { // no metadata file name present in xml file, use default folder and name
+		sprintf(mdata_filepath, "%s/%s", stacks_dir, vm::BINARY_METADATA_FILENAME.c_str());
+	}
+	else {
+		strcpy(mdata_filepath,mdata_fname.c_str());
+	}
     if(fileExists(mdata_filepath) && !overwrite_mdata)
             loadBinaryMetadata(mdata_filepath);
     else
@@ -164,7 +170,16 @@ BlockVolume::BlockVolume(const char *xml_filepath, bool overwrite_mdata) throw (
 
 	//trying to unserialize an already existing metadata file, if it doesn't exist the full initialization procedure is performed and metadata is saved
 	char mdata_filepath[2000];
-	sprintf(mdata_filepath, "%s/%s", stacks_dir, vm::BINARY_METADATA_FILENAME.c_str());
+	pelem = hRoot.FirstChildElement("mdata_bin").Element();
+
+	if ( pelem == ((TiXmlElement *)0) ) { // no metadata file name present in xml file, use default folder and name
+		sprintf(mdata_filepath, "%s/%s", stacks_dir, vm::BINARY_METADATA_FILENAME.c_str());
+	}
+	else {
+		strcpy(mdata_filepath, pelem->Attribute("value"));
+	}
+
+	xml.Clear();
 
     // 2014-09-20. Alessandro. @ADDED overwrite_mdata flag
     if(fileExists(mdata_filepath) && !overwrite_mdata)

src/volumemanager/vmBlockVolume.h

@@ -25,6 +25,7 @@
 /******************
 *    CHANGELOG    *
 *******************
+* 2018-03-02. Giulio.     @ADDED the possibility to set a path and a name for the mdata.bin file
 * 2017-06-26. Giulio.     @ADDED methods to set active resolution and active timepoint
 * 2017-04-12. Giulio.     @ADDED method to release all buffers allocated in VirtualStack
 * 2016-10-27. Giulio.     @ADDED string fields for control over the subimage to be exposed through the xml import file  
@@ -54,8 +55,8 @@ class vm::BlockVolume : public vm::VirtualVolume
 		// 2014-09-10. Alessandro. @ADDED plugin creation/registration functions to make 'StackedVolume' a volume format plugin.
 		static const std::string creator_id1, creator_id2;							
         static vm::VirtualVolume* createFromXML(const char* xml_path, bool ow_mdata) { return new BlockVolume(xml_path, ow_mdata); }
-		static vm::VirtualVolume* createFromData(const char* data_path, vm::ref_sys ref, float vxl1, float vxl2, float vxl3, bool ow_mdata) { 
-			return new BlockVolume(data_path, ref, vxl1, vxl2, vxl3, ow_mdata); 
+		static vm::VirtualVolume* createFromData(const char* data_path, vm::ref_sys ref, float vxl1, float vxl2, float vxl3, bool ow_mdata, std::string mdata_fname) { 
+			return new BlockVolume(data_path, ref, vxl1, vxl2, vxl3, ow_mdata,mdata_fname); 
 		}
 
 		vm::Block ***BLOCKS;			    //2-D array of <Block*>
@@ -96,7 +97,7 @@ class vm::BlockVolume : public vm::VirtualVolume
 
 		//CONSTRUCTORS-DECONSTRUCTOR
 		BlockVolume() : vm::VirtualVolume(){}
-        BlockVolume(const char* _stacks_dir, vm::ref_sys reference_system, float VXL_1=0, float VXL_2=0, float VXL_3=0, bool overwrite_mdata=false) throw (iom::exception);
+        BlockVolume(const char* _stacks_dir, vm::ref_sys reference_system, float VXL_1=0, float VXL_2=0, float VXL_3=0, bool overwrite_mdata=false, std::string mdata_fname="") throw (iom::exception);
         BlockVolume(const char *xml_filepath, bool overwrite_mdata=false) throw (iom::exception);
 		~BlockVolume();
 

src/volumemanager/vmMCVolume.cpp

@@ -25,6 +25,7 @@
 /******************
 *    CHANGELOG    *
 *******************
+* 2018-03-01. Giulio. @FIXED global variable 'vm::VOLUME_INPUT_FORMAT_PLUGIN' is set to vm::MCVolume::id in the constructor to signal that it is a non interleaved channel representation
 * 2018-01-20. Giulio. @CREATED
 */
 
@@ -77,6 +78,9 @@ MCVolume::MCVolume(const char* _stacks_dir, vm::ref_sys _reference_system, float
 		  _stacks_dir,reference_system.first, reference_system.second, reference_system.third, VXL_1, VXL_2, VXL_3);
 	#endif
 
+	// 2018-03-01. Giulio. @FIXED global variable 'vm::VOLUME_INPUT_FORMAT_PLUGIN' has to be set to vm::MCVolume::id to signal that it is a non interleaved channel representation
+	vm::VOLUME_INPUT_FORMAT_PLUGIN = vm::MCVolume::id;
+
 	checked = false;
 	aligned = false; // no guarantee that subvolumes are aligned
 
@@ -118,6 +122,9 @@ MCVolume::MCVolume(const char *xml_filepath, bool overwrite_mdata) throw (iom::e
 	#if VM_VERBOSE > 3
 	printf("\t\t\t\tin MCVolume::MCVolume(xml_filepath=%s)\n", xml_filepath);
 	#endif
+
+	// 2018-03-01. Giulio. @FIXED global variable 'vm::VOLUME_INPUT_FORMAT_PLUGIN' has to be set to vm::MCVolume::id to signal that it is a non interleaved channel representation
+	vm::VOLUME_INPUT_FORMAT_PLUGIN = vm::MCVolume::id;
 
  	checked = false;
 	aligned = false; // no guarantee that subvolumes are aligned

src/volumemanager/vmMCVolume.h

@@ -25,6 +25,7 @@
 /******************
 *    CHANGELOG    *
 *******************
+* 2018-03-02. Giulio. @ADDED a parameter to set a path and a name for the mdata.bin file for compatibility, but it is not used
 * 2018-01-20. Giulio. @CREATED
 */
 
@@ -47,8 +48,8 @@ class vm::MCVolume : public vm::VirtualVolume
 		static const std::string creator_id1, creator_id2;							
         static vm::VirtualVolume* createFromXML(const char* xml_path, bool ow_mdata = false) { return new MCVolume(xml_path, ow_mdata); }
 		// 2018-01-21. Giulio @ADDED default parameters to support creation from data (folder containing xml import files)
-		static vm::VirtualVolume* createFromData(const char* data_path, vm::ref_sys ref = vm::ref_sys(vm::axis(0),vm::axis(0),vm::axis(0)), float vxl1 = 0, float vxl2 = 0, float vxl3 = 0, bool ow_mdata = false) { 
-			return new MCVolume(data_path, ref, vxl1, vxl2, vxl3, ow_mdata); 
+		static vm::VirtualVolume* createFromData(const char* data_path, vm::ref_sys ref = vm::ref_sys(vm::axis(0),vm::axis(0),vm::axis(0)), float vxl1 = 0, float vxl2 = 0, float vxl3 = 0, bool ow_mdata = false, std::string mdata_fname = "") { 
+			return new MCVolume(data_path, ref, vxl1, vxl2, vxl3, ow_mdata); // the mdata_fname parameter is not used for MCVolumes
 		}
 
 		vm::VirtualVolume **subvolumes;

src/volumemanager/vmStackedVolume.cpp

@@ -28,6 +28,7 @@
 /******************
 *    CHANGELOG    *
 *******************
+* 2018-03-02. Giulio.     @ADDED the possibility to set a path and a name for the mdata.bin file
 * 2018-02-03. Giulio.     @ADDED call to 'adjustDisplacements' in method reading the xml file to force all displacements of adjacent tile symmetric
 * 2017-04-27. Giulio.     @ADDED code to get and initialize the input plugin from the xml if specified
 * 2017-04-12. Giulio.     @ADDED method to release all buffers allocated in VirtualStack
@@ -91,7 +92,7 @@ const std::string StackedVolume::id = "TiledXY|2Dseries";
 const std::string StackedVolume::creator_id1 = volumemanager::VirtualVolumeFactory::registerPluginCreatorXML(&createFromXML, StackedVolume::id);
 const std::string StackedVolume::creator_id2 = volumemanager::VirtualVolumeFactory::registerPluginCreatorData(&createFromData, StackedVolume::id);
 
-StackedVolume::StackedVolume(const char* _stacks_dir, vm::ref_sys _reference_system, float VXL_1, float VXL_2, float VXL_3, bool overwrite_mdata) throw (iom::exception)
+StackedVolume::StackedVolume(const char* _stacks_dir, vm::ref_sys _reference_system, float VXL_1, float VXL_2, float VXL_3, bool overwrite_mdata, std::string mdata_fname) throw (iom::exception)
 	: VirtualVolume(_stacks_dir, _reference_system, VXL_1, VXL_2, VXL_3)
 {
 	#if VM_VERBOSE > 3
@@ -100,8 +101,13 @@ StackedVolume::StackedVolume(const char* _stacks_dir, vm::ref_sys _reference_sys
 	#endif
 
 	//trying to unserialize an already existing metadata file, if it doesn't exist the full initialization procedure is performed and metadata is saved
-    char mdata_filepath[VM_STATIC_STRINGS_SIZE];
-    sprintf(mdata_filepath, "%s/%s", stacks_dir, vm::BINARY_METADATA_FILENAME.c_str());
+	char mdata_filepath[VM_STATIC_STRINGS_SIZE];
+	if ( mdata_fname == "" ) { // no metadata file name present in xml file, use default folder and name
+		sprintf(mdata_filepath, "%s/%s", stacks_dir, vm::BINARY_METADATA_FILENAME.c_str());
+	}
+	else {
+		strcpy(mdata_filepath,mdata_fname.c_str());
+	}
     if(fileExists(mdata_filepath) && !overwrite_mdata)
         loadBinaryMetadata(mdata_filepath);
     else
@@ -155,13 +161,21 @@ StackedVolume::StackedVolume(const char *xml_filepath, bool overwrite_mdata) thr
     TiXmlElement * pelem = hRoot.FirstChildElement("stacks_dir").Element();
     this->stacks_dir = new char[strlen(pelem->Attribute("value"))+1];
     strcpy(this->stacks_dir, pelem->Attribute("value"));
-	xml.Clear();
 
-	//trying to unserialize an already existing metadata file, if it doesn't exist the full initialization procedure is performed and metadata is saved
-	char mdata_filepath[2000];
-	sprintf(mdata_filepath, "%s/%s", stacks_dir, vm::BINARY_METADATA_FILENAME.c_str());
+ 	//trying to unserialize an already existing metadata file, if it doesn't exist the full initialization procedure is performed and metadata is saved
+	char mdata_filepath[VM_STATIC_STRINGS_SIZE];
+	pelem = hRoot.FirstChildElement("mdata_bin").Element();
+
+	if ( pelem == ((TiXmlElement *)0) ) { // no metadata file name present in xml file, use default folder and name
+		sprintf(mdata_filepath, "%s/%s", stacks_dir, vm::BINARY_METADATA_FILENAME.c_str());
+	}
+	else {
+		strcpy(mdata_filepath, pelem->Attribute("value"));
+	}
+
+	xml.Clear();
 
-    // 2014-09-20. Alessandro. @ADDED overwrite_mdata flag
+	// 2014-09-20. Alessandro. @ADDED overwrite_mdata flag
     if(fileExists(mdata_filepath) && !overwrite_mdata)
 	{
 		// load mdata.bin content and xml content, also perform consistency check between mdata.bin and xml content

src/volumemanager/vmStackedVolume.h

@@ -28,6 +28,7 @@
 /******************
 *    CHANGELOG    *
 *******************
+* 2018-03-02. Giulio.     @ADDED the possibility to set a path and a name for the mdata.bin file
 * 2017-04-12. Giulio.     @ADDED method to release all buffers allocated in VirtualStack
 * 2015-06-12. Giulio      @ADDED 'check' method to check completeness and coherence of a volume
 * 2015-02-26. Giulio.     @ADDED initChannels private method to initialize fields DIM_C and BYTESxCHAN
@@ -58,8 +59,8 @@ class vm::StackedVolume : public vm::VirtualVolume
 		// 2014-09-10. Alessandro. @ADDED plugin creation/registration functions to make 'StackedVolume' a volume format plugin.
 		static const std::string creator_id1, creator_id2;							
         static vm::VirtualVolume* createFromXML(const char* xml_path, bool ow_mdata) { return new StackedVolume(xml_path, ow_mdata); }
-		static vm::VirtualVolume* createFromData(const char* data_path, vm::ref_sys ref, float vxl1, float vxl2, float vxl3, bool ow_mdata) { 
-			return new StackedVolume(data_path, ref, vxl1, vxl2, vxl3, ow_mdata); 
+		static vm::VirtualVolume* createFromData(const char* data_path, vm::ref_sys ref, float vxl1, float vxl2, float vxl3, bool ow_mdata, std::string mdata_fname) { 
+			return new StackedVolume(data_path, ref, vxl1, vxl2, vxl3, ow_mdata, mdata_fname); 
 		}
 
 
@@ -91,7 +92,7 @@ class vm::StackedVolume : public vm::VirtualVolume
 
 		//CONSTRUCTORS-DECONSTRUCTOR
 		StackedVolume() : vm::VirtualVolume(){}
-        StackedVolume(const char* _stacks_dir, vm::ref_sys reference_system, float VXL_1=0, float VXL_2=0, float VXL_3=0, bool overwrite_mdata=false) throw (iom::exception);
+        StackedVolume(const char* _stacks_dir, vm::ref_sys reference_system, float VXL_1=0, float VXL_2=0, float VXL_3=0, bool overwrite_mdata=false, std::string mdata_fname="") throw (iom::exception);
         StackedVolume(const char *xml_filepath, bool overwrite_mdata=false) throw (iom::exception);
 		~StackedVolume();
 

src/volumemanager/vmVirtualStack.h

@@ -28,6 +28,7 @@
 /******************
 *    CHANGELOG    *
 *******************
+* 2018-03-03. Giulio.     @ADDED method 'releaseImageSteckOwnership' to manage cases when the ownership of the internal buffer must be given to other modules
 * 2017-07-06. Giulio.     @ADDED method 'loadImageStack2' to enable selective reads of data
 * 2015-02-28. Giulio.     @ADDED fields N_CHANS and BYTESxCHAN
 * 2015-01-17. Alessandro. @ADDED support for all-in-one-folder data (import from xml only).
@@ -179,6 +180,7 @@ class vm::VirtualStack
         virtual iom::real_t* loadImageStack(int first_file=-1, int last_file=-1) throw (iom::exception) = 0;
         virtual iom::real_t* loadImageStack2(int first_file=-1, int last_file=-1, int V0=-1, int V1=-1, int H0=-1, int H1=-1) throw (iom::exception) = 0;
 		virtual void releaseImageStack()= 0;
+		void releaseImageStackOwnership() { STACKED_IMAGE = 0; }
 
         // return true if the given range [z0,z1] does not contain missing slices/blocks
         virtual bool isComplete(int z0, int z1);