Merge pull request #991 from I2PC/jmk_new_residuals

first version of new continuous_create_residuals

Author: albertmena

CHANGELOG.md

@@ -1,7 +1,7 @@
 ## Release 3.24.X - 
    ### Xmipp Programs 
    - New programs
-        - 
+      - continuous_create_residuals: Make better residuals by continuous assignment updates to projections
 
    - Programs updated
       - 

src/xmipp/applications/programs/continuous_create_residuals/continuous_create_residuals_main.cpp

@@ -0,0 +1,29 @@
+/***************************************************************************
+ *
+ * Authors:    Carlos Oscar S. Sorzano (coss@cnb.csic.es)
+ *             James Krieger                jamesmkrieger@gmail.com
+ *
+ * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+ * 02111-1307  USA
+ *
+ *  All comments concerning this program package may be sent to the
+ *  e-mail address 'xmipp@cnb.csic.es'
+ ***************************************************************************/
+
+#include <reconstruction/continuous_create_residuals.h>
+
+RUN_XMIPP_PROGRAM(ProgContinuousCreateResiduals)

src/xmipp/applications/programs/mpi_continuous_create_residuals/mpi_continuous_create_residuals_main.cpp

@@ -0,0 +1,29 @@
+/***************************************************************************
+ *
+ * Authors:  Carlos Oscar Sanchez Sorzano coss@cnb.csic.es
+ *           James Krieger                jamesmkrieger@gmail.com
+ *
+ * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+ * 02111-1307  USA
+ *
+ *  All comments concerning this program package may be sent to the
+ *  e-mail address 'xmipp@cnb.uam.es'
+ ***************************************************************************/
+
+#include <parallel/mpi_continuous_create_residuals.cpp>
+
+RUN_XMIPP_PROGRAM(MpiProgContinuousCreateResiduals)

src/xmipp/libraries/parallel/mpi_continuous_create_residuals.cpp

@@ -0,0 +1,121 @@
+/***************************************************************************
+ *
+ * Authors:  Carlos Oscar Sanchez Sorzano coss@cnb.csic.es
+ *           James Krieger                jamesmkrieger@gmail.com
+ *
+ * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+ * 02111-1307  USA
+ *
+ *  All comments concerning this program package may be sent to the
+ *  e-mail address 'xmipp@cnb.uam.es'
+ ***************************************************************************/
+
+#include <mpi.h>
+#include <parallel/xmipp_mpi.h>
+#include <reconstruction/continuous_create_residuals.h>
+
+
+class MpiProgContinuousCreateResiduals: public ProgContinuousCreateResiduals, public MpiMetadataProgram
+{
+public:
+
+    void defineParams()
+    {
+        ProgContinuousCreateResiduals::defineParams();
+        MpiMetadataProgram::defineParams();
+    }
+    void readParams()
+    {
+        MpiMetadataProgram::readParams();
+        ProgContinuousCreateResiduals::readParams();
+    }
+    void read(int argc, char **argv, bool reportErrors = true)
+    {
+        MpiMetadataProgram::read(argc,argv);
+    }
+    void preProcess()
+    {
+    	rank=node->rank;
+        ProgContinuousCreateResiduals::preProcess();
+   		node->barrierWait();
+
+   		// Get the volume padded size from rank 0
+   		int realSize, origin;
+   		if (node->rank==0)
+   		{
+   			realSize = XSIZE(projector->VfourierRealCoefs);
+   			origin = STARTINGX(projector->VfourierRealCoefs);
+   		}
+        MPI_Bcast(&realSize, 1, MPI_INT, 0, MPI_COMM_WORLD);
+        MPI_Bcast(&origin, 1, MPI_INT, 0, MPI_COMM_WORLD);
+        MPI_Bcast(&(projector->volumePaddedSize), 1, MPI_INT, 0, MPI_COMM_WORLD);
+        MPI_Bcast(&(projector->volumeSize), 1, MPI_INT, 0, MPI_COMM_WORLD);
+
+        if (rank!=0)
+        {
+        	projector->VfourierRealCoefs.resizeNoCopy(realSize,realSize,realSize);
+        	projector->VfourierImagCoefs.resizeNoCopy(realSize,realSize,realSize);
+        	STARTINGX(projector->VfourierRealCoefs)=STARTINGY(projector->VfourierRealCoefs)=STARTINGZ(projector->VfourierRealCoefs)=origin;
+        	STARTINGX(projector->VfourierImagCoefs)=STARTINGY(projector->VfourierImagCoefs)=STARTINGZ(projector->VfourierImagCoefs)=origin;
+        }
+        MPI_Bcast(MULTIDIM_ARRAY(projector->VfourierRealCoefs), MULTIDIM_SIZE(projector->VfourierRealCoefs), MPI_DOUBLE, 0, MPI_COMM_WORLD);
+        MPI_Bcast(MULTIDIM_ARRAY(projector->VfourierImagCoefs), MULTIDIM_SIZE(projector->VfourierImagCoefs), MPI_DOUBLE, 0, MPI_COMM_WORLD);
+    	if (rank!=0)
+        	projector->produceSideInfoProjection();
+
+        MetaData &mdIn = *getInputMd();
+        mdIn.addLabel(MDL_GATHER_ID);
+        mdIn.fillLinear(MDL_GATHER_ID,1,1);
+        createTaskDistributor(mdIn, blockSize);
+    }
+    void startProcessing()
+    {
+        if (node->rank==1)
+        {
+        	verbose=1;
+            ProgContinuousCreateResiduals::startProcessing();
+        }
+        node->barrierWait();
+    }
+    void showProgress()
+    {
+        if (node->rank==1)
+        {
+            time_bar_done=first+1;
+            ProgContinuousCreateResiduals::showProgress();
+        }
+    }
+
+    virtual bool getImageToProcess(size_t &objId, size_t &objIndex) override
+    {
+        return getTaskToProcess(objId, objIndex);
+    }
+    void finishProcessing()
+    {
+        node->gatherMetadatas(getOutputMd(), fn_out);
+    	MetaDataVec MDaux;
+    	MDaux.sort(getOutputMd(), MDL_GATHER_ID);
+        MDaux.removeLabel(MDL_GATHER_ID);
+        getOutputMd()=MDaux;
+        if (node->isMaster())
+            ProgContinuousCreateResiduals::finishProcessing();
+    }
+    void wait()
+    {
+		distributor->wait();
+    }
+};