Geradus patch for Clarity v1.0.0 which, amongst other things, allows it to compile under Ubuntu 11.10

clarity-ubuntu.patch

Index: apps/DeconvolveRawImages/DeconvolveRawImages.cxx
===================================================================
--- apps/DeconvolveRawImages/DeconvolveRawImages.cxx	(.../cquammen-Clarity-v1.0.0-5-c9d0889)	(revision 643)
+++ apps/DeconvolveRawImages/DeconvolveRawImages.cxx	(.../cquammen-Clarity)	(revision 658)
@@ -21,6 +21,13 @@
  * Author: Cory Quammen <cquammen@cs.unc.edu>
  */
 
+/*
+ * This is a derivative work of Clarity provided as a third-party
+ * library in Gerardus
+ *
+ *  Minor fixes by Ramon Casero <rcasero@gmail.com>
+ */
+
 /* This example shows how to read unsigned short images, run a deconvolution
  * routine on them, and write the result. */
 
@@ -61,7 +68,7 @@
     if (!psfFp) 
       printf("ERROR: Could not open PSF file '%s'\n'", psfFileName);
     if (!outputFp) 
-      printf("ERROR: Could not open file '%' for writing\n", outputFileName);
+      printf("ERROR: Could not open file '%s' for writing\n", outputFileName);
 
     if (inputFp)  fclose(inputFp);
     if (psfFp)    fclose(psfFp);
@@ -75,9 +82,17 @@
   unsigned short *inputImage  = new unsigned short[inputImageSize];
   unsigned short *psfImage    = new unsigned short[psfImageSize];
 
-  fread(inputImage, sizeof(unsigned short), inputImageSize, inputFp);
+  if ((size_t)inputImageSize 
+      != fread(inputImage, sizeof(unsigned short), inputImageSize, inputFp)) {
+    printf("Error reading input image file\n");
+    return 1;
+  }
   fclose(inputFp);
-  fread(psfImage, sizeof(unsigned short), psfImageSize, psfFp);
+  if ((size_t)psfImageSize 
+      != fread(psfImage, sizeof(unsigned short), psfImageSize, psfFp)) {
+    printf("Error reading PSF file\n");
+    return 1;
+  }
   fclose(psfFp);
   
   // Cast to floats
Index: include/internal/Stopwatch.h
===================================================================
--- include/internal/Stopwatch.h	(.../cquammen-Clarity-v1.0.0-5-c9d0889)	(revision 643)
+++ include/internal/Stopwatch.h	(.../cquammen-Clarity)	(revision 658)
@@ -20,6 +20,13 @@
 // $Id: Stopwatch.h,v 1.1 2008/09/11 14:56:35 cquammen Exp $
 //------------------------------------------------------------------------------
 
+/*
+ * This is a derivative work of Clarity provided as a third-party
+ * library in Gerardus
+ *
+ *  Minor fixes by Ramon Casero <rcasero@gmail.com>
+ */
+
 //------------------------------------------------------------------------------
 //  The interface is as follows:
 //   The first call to Start() begins the timer counting.
@@ -118,8 +125,8 @@
   float elapsedTime;     // the accumulated elapsed time
   int numStarts;         // number of calls to Start since last Reset
   char sw_name[STOPWATCH_MAX_NAME];  // a name for the stopwatch
+  bool running;
   const char *sw_type;
-  bool running;
 
   // THESE ARE THE METHODS SUBCLASSES NEED TO IMPLEMENT
   virtual void markTime()=0;   // jot down the current timestamp
Index: src/WienerDeconvolve.cxx
===================================================================
--- src/WienerDeconvolve.cxx	(.../cquammen-Clarity-v1.0.0-5-c9d0889)	(revision 643)
+++ src/WienerDeconvolve.cxx	(.../cquammen-Clarity)	(revision 658)
@@ -21,9 +21,17 @@
  * Author: Cory Quammen <cquammen@cs.unc.edu>
  */
 
+/*
+ * This is a derivative work of Clarity provided as a third-party
+ * library in Gerardus
+ *
+ *  Minor fixes by Ramon Casero <rcasero@gmail.com>
+ */
 
 #include "Clarity.h"
 
+#include <cstdlib>
+
 #include <iostream>
 #include <fftw3.h>
 #include <math.h>
Index: src/FFT.cxx
===================================================================
--- src/FFT.cxx	(.../cquammen-Clarity-v1.0.0-5-c9d0889)	(revision 643)
+++ src/FFT.cxx	(.../cquammen-Clarity)	(revision 658)
@@ -21,6 +21,12 @@
  * Author: Cory Quammen <cquammen@cs.unc.edu>
  */
 
+/*
+ * This is a derivative work of Clarity provided as a third-party
+ * library in Gerardus
+ *
+ *  Minor fixes by Ramon Casero <rcasero@gmail.com>
+ */
 
 #include "Clarity.h"
 
@@ -105,7 +111,7 @@
   fftTimer.Start();
 #endif // TIME_FFT
 
-  int numVoxels = nx*ny*nz;
+  //  int numVoxels = nx*ny*nz;
 
 #ifdef BUILD_WITH_CUDA
   if (g_CUDACapable) {
Index: src/MaximumLikelihoodDeconvolve.cxx
===================================================================
--- src/MaximumLikelihoodDeconvolve.cxx	(.../cquammen-Clarity-v1.0.0-5-c9d0889)	(revision 643)
+++ src/MaximumLikelihoodDeconvolve.cxx	(.../cquammen-Clarity)	(revision 658)
@@ -21,6 +21,12 @@
  * Author: Cory Quammen <cquammen@cs.unc.edu>
  */
 
+/*
+ * This is a derivative work of Clarity provided as a third-party
+ * library in Gerardus
+ *
+ *  Minor fixes by Ramon Casero <rcasero@gmail.com>
+ */
 
 #include "Clarity.h"
 
@@ -133,7 +139,7 @@
   Clarity_ReduceSum(&energy, inImage, nx*ny*nz);
 
   // Iterate
-  int numVoxels = nx*ny*nz;	 
+  //  int numVoxels = nx*ny*nz;	 
   for (unsigned k = 0; k < iterations; k++) {
     float* currentGuess = (k == 0 ? inImage : iPtr);
     float* newGuess     = (k == iterations-1 ? outImage : iPtr);
Index: src/Clarity.cxx
===================================================================
--- src/Clarity.cxx	(.../cquammen-Clarity-v1.0.0-5-c9d0889)	(revision 643)
+++ src/Clarity.cxx	(.../cquammen-Clarity)	(revision 658)
@@ -22,8 +22,17 @@
  */
 
 
+/*
+ * This is a derivative work of Clarity provided as a third-party
+ * library in Gerardus
+ *
+ *  Minor fixes by Ramon Casero <rcasero@gmail.com>
+ */
+
 #include "Clarity.h"
 
+#include <cstdlib>
+
 #include <fftw3.h>
 #include <iostream>
 
Index: src/Memory.cxx
===================================================================
--- src/Memory.cxx	(.../cquammen-Clarity-v1.0.0-5-c9d0889)	(revision 643)
+++ src/Memory.cxx	(.../cquammen-Clarity)	(revision 658)
@@ -21,6 +21,12 @@
  * Author: Cory Quammen <cquammen@cs.unc.edu>
  */
 
+/*
+ * This is a derivative work of Clarity provided as a third-party
+ * library in Gerardus
+ *
+ *  Minor fixes by Ramon Casero <rcasero@gmail.com>
+ */
 
 #include "Clarity.h"
 #include "Memory.h"
@@ -46,9 +52,9 @@
 
   ClarityResult_t result = CLARITY_SUCCESS;
 
-  size_t totalSize = size*2*nz*ny*(nx/2 + 1);
 #ifdef BUILD_WITH_CUDA
   if (g_CUDACapable) {
+    size_t totalSize = size*2*nz*ny*(nx/2 + 1);
     cudaError_t cudaResult = cudaMalloc(buffer, totalSize);
     if (cudaResult != cudaSuccess) {
       return CLARITY_DEVICE_OUT_OF_MEMORY;
@@ -56,6 +62,7 @@
   } else 
 #endif // BUILD_WITH_CUDA
   {
+    size_t totalSize = size*2*nz*ny*(nx/2 + 1);
     *buffer = fftwf_malloc(totalSize);
     if (*buffer == NULL) {
       result = CLARITY_OUT_OF_MEMORY;
@@ -72,9 +79,9 @@
 
   ClarityResult_t result = CLARITY_SUCCESS;
 
-  size_t totalSize = size*nz*ny*nx;
 #ifdef BUILD_WITH_CUDA
   if (g_CUDACapable) {
+    size_t totalSize = size*nz*ny*nx;
     cudaError_t cudaResult = cudaMalloc(buffer, totalSize);
     if (cudaResult != cudaSuccess) {
       return CLARITY_DEVICE_OUT_OF_MEMORY;
Index: src/IDivergenceDeconvolve.cxx
===================================================================
--- src/IDivergenceDeconvolve.cxx	(.../cquammen-Clarity-v1.0.0-5-c9d0889)	(revision 643)
+++ src/IDivergenceDeconvolve.cxx	(.../cquammen-Clarity)	(revision 658)
@@ -21,6 +21,12 @@
  * Author: Cory Quammen <cquammen@cs.unc.edu>
  */
 
+/*
+ * This is a derivative work of Clarity provided as a third-party
+ * library in Gerardus
+ *
+ *  Minor fixes by Ramon Casero <rcasero@gmail.com>
+ */
 
 #include "Clarity.h"
 
@@ -30,29 +36,30 @@
 #include <omp.h>
 #endif // BUILD_WITH_OPENMP
 
-static float IDIVFunctional(
-   float* g, float* gHat, float* sHat, float alpha, 
-   int nx, int ny, int nz) {
+// comment out these undefined functions, to avoid compilation warnings
+// static float IDIVFunctional(
+//    float* g, float* gHat, float* sHat, float alpha, 
+//    int nx, int ny, int nz) {
 
-   float sum = 0.0f;
-   int numVoxels = nx*ny*nz;
+//    float sum = 0.0f;
+//    int numVoxels = nx*ny*nz;
 
-#ifdef BUILD_WITH_OPENMP
-#pragma omp parallel for reduction(+:sum)
-#endif // BUILD_WITH_OPENMP
-   for (int i = 0; i < numVoxels; i++) {
-      sum += (g[i]*log(g[i]/gHat[i])) + gHat[i] - g[i] + (alpha*sHat[i]*sHat[i]);
-   }
-   return sum;
-}
+// #ifdef BUILD_WITH_OPENMP
+// #pragma omp parallel for reduction(+:sum)
+// #endif // BUILD_WITH_OPENMP
+//    for (int i = 0; i < numVoxels; i++) {
+//       sum += (g[i]*log(g[i]/gHat[i])) + gHat[i] - g[i] + (alpha*sHat[i]*sHat[i]);
+//    }
+//    return sum;
+// }
 
 
-static void IDIVGradient(
-   float* g, float* gHat, float* sHat, float* flippedPSFtf, 
-   float alpha, float* gradient) {
+// static void IDIVGradient(
+//    float* g, float* gHat, float* sHat, float* flippedPSFtf, 
+//    float alpha, float* gradient) {
 
 
-}
+// }
 
 
 
Index: CMakeLists.txt
===================================================================
--- CMakeLists.txt	(.../cquammen-Clarity-v1.0.0-5-c9d0889)	(revision 643)
+++ CMakeLists.txt	(.../cquammen-Clarity)	(revision 658)
@@ -1,10 +1,12 @@
 PROJECT(Clarity)
 
-CMAKE_MINIMUM_REQUIRED(VERSION 2.4)
-IF(COMMAND cmake_policy)
-  CMAKE_POLICY(SET CMP0003 OLD)
-ENDIF(COMMAND cmake_policy)
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+#IF(COMMAND cmake_policy)
+#  CMAKE_POLICY(SET CMP0003 OLD)
+#ENDIF(COMMAND cmake_policy)
 
+# options can we set from the command line as
+#  $ cmake -DBUILD_WITH_CUDA:BOOL=ON ..
 OPTION(BUILD_SHARED_LIBS "Build Clarity with shared libraries." ON)
 OPTION(BUILD_WITH_OPENMP "Build with OpenMP." ON)
 OPTION(BUILD_WITH_CUDA "Build with CUDA FFT acceleration." OFF)
@@ -15,7 +17,7 @@
 OPTION(TIME_DECONVOLVE "Time deconvolution operation only." OFF)
 OPTION(TIME_TOTAL "Time total deconvolution operation (includes image padding and clipping." OFF)
 
-SET(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/CMake/")
+SET(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/CMake/")
 
 IF(BUILD_WITH_CUDA)
   # Load CUDA macros
@@ -75,7 +77,8 @@
   ADD_LIBRARY( Clarity ${Clarity_SRCS})
 ENDIF(BUILD_WITH_CUDA)
 
-TARGET_LINK_LIBRARIES(Clarity ${FFTW_LIBRARIES} ${FFTW_EXECUTABLE_LIBRARIES})
+TARGET_LINK_LIBRARIES(Clarity ${FFTW_LIBRARIES} 
+  ${FFTW_EXECUTABLE_LIBRARIES})
 
 # Enable linking with OpenMP when compiling with gcc
 SET (USE_GOMP ${CMAKE_COMPILER_IS_GNUCXX}
@@ -91,5 +94,22 @@
   SOVERSION ${Clarity_MAJOR_VERSION}.${Clarity_MINOR_VERSION}
 )
 
-ADD_SUBDIRECTORY(apps)
-ADD_SUBDIRECTORY(tests)
+# Gerardus doesn't need to build the apps and tests of Clarity
+#ADD_SUBDIRECTORY(apps)
+#ADD_SUBDIRECTORY(tests)
+
+################################################################
+## installation of library
+################################################################
+
+IF(WIN32)
+  INSTALL(TARGETS
+    Clarity
+    RUNTIME
+    DESTINATION ${CMAKE_INSTALL_PREFIX})
+ELSE(WIN32)
+  INSTALL(TARGETS
+    Clarity
+    LIBRARY
+    DESTINATION ${CMAKE_INSTALL_PREFIX})
+ENDIF(WIN32)