moved files and sub-directories from src to more logical destinations

- moved scripts and *txt files one level up - moved samples, examples and samples/PET_simulation to new sub-dir examples in the top-level directory - created CMakeLists.txt in top-level directory (and moved PROJECT and other main statements there from src/CMakeLists.txt). - moved CMake helper files to src/cmake, adjust many CMakeLists.txt to rely on module path for these files (by no longer specifying location using paths)
UCL · Mar 17, 2014 · 23a68bb · 23a68bb
1 parent d6f78bf
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -0,0 +1,33 @@
+# This file is part of STIR.
+#
+# This file is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation; either version 2.1 of the License, or
+# (at your option) any later version.
+#
+# This file 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 Lesser General Public License for more details.
+#
+# See STIR/LICENSE.txt for details
+
+# cmake file for building STIR. See the STIR User's Guide and http://www.cmake.org.
+
+# avoid warning about WIN32 no longer defined in CYGWIN
+set(CMAKE_LEGACY_CYGWIN_WIN32 0) 
+
+PROJECT(STIR)
+
+SET_PROPERTY(GLOBAL PROPERTY USE_FOLDERS ON)
+# require 2.8.3 to get FOLDER properties support (without that, we only need cmake 2.6)
+cmake_minimum_required(VERSION 2.8.3)
+
+# add project source to cmake path such that it can use our find_package modules and .cmake files
+set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/src/cmake)
+
+#### enable support for ctest
+ENABLE_TESTING()
+
+ADD_SUBDIRECTORY(src)
+ADD_SUBDIRECTORY(scripts)
diff --git a/src/GPL.txt → GPL.txt b/src/GPL.txt → GPL.txt
diff --git a/src/LGPL.txt → LGPL.txt b/src/LGPL.txt → LGPL.txt
diff --git a/src/LICENSE.txt → LICENSE.txt b/src/LICENSE.txt → LICENSE.txt
diff --git a/src/PARAPETLICENSE.txt → PARAPETLICENSE.txt b/src/PARAPETLICENSE.txt → PARAPETLICENSE.txt
diff --git a/src/VERSION.txt → VERSION.txt b/src/VERSION.txt → VERSION.txt
diff --git a/documentation/release_3.0.htm b/documentation/release_3.0.htm
@@ -1,11 +1,11 @@
 <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
 <html>
   <head>
-    <title>Summary of changes in STIR release 3.0 alpha (dated 13/01/2014)</title>
+    <title>Summary of changes in STIR release 3.0 beta (dated 17/03/2014)</title>
   </head>
 
   <body>
-    <h1>Summary of changes in STIR release 3.0 alpha (dated 13/01/2014)</h1>
+    <h1>Summary of changes in STIR release 3.0 beta (dated 17/03/2014)</h1>
 
 <p>This version is almost backwards compatible with STIR 2.4 for the user (see below), but <strong>not for 
 developers</strong>. Required code changes are minor however and detailed below.
@@ -83,6 +83,15 @@ <h3>Changes that break backwards compatibility</h3>
 </li>
 </ul>
 
+<h3>New directory structure</h3>
+<ul>
+<li>Top-level directories are now <tt>src</tt>, <tt>scripts</tt>, <tt>examples</tt>, <tt>documentation</tt>, <tt>doximages</tt>. The <tt>samples</tt> directory is now a
+sub-directory of <tt>examples</tt>, and the old <tt>examples</tt> is now
+<tt>examples/src</tt>.</li>
+<li><tt>recon_test_pack</tt> and <tt>documentation</tt> are now distributed in
+zip files that unpack as <tt>STIR/recon_test_pack</tt> and <tt>STIR/documentation</tt>.</li>
+</ul>
+
 <h3>New functionality</h3>
 <ul>
 <li> new projection matrix for SPECT (called <code>SPECT UB</code>) supporting parallel hole collimators 
@@ -103,7 +112,7 @@ <h3>New functionality</h3>
 <li>The <tt>list_projdata_info</tt> utilities has an extra option <tt>--exam</tt> to
 list some exam information (patient position and timing).
 </li>
-<li>The distribution now includes sample scripts  (in the <tt>samples</tt> folder) 
+<li>The distribution now includes sample scripts  (in the <tt>examples/PET_simulation</tt> folder) 
 for simulating PET data, adding Poisson noise
 and reconstructing the data.</li>
 </ul>
@@ -130,7 +139,8 @@ <h3>Build system</h3>
 for Visual Studio are no longer distributed. Hand-crafted Unix Makefiles are still there but 
 getting out-of date (no ITK for instance).
 </li>
-<li>compilation when using CMake is speeded-up a bit as dependencies of the tests on STIR libraries are reduced.</li>
+<li>Compilation when using CMake is speeded-up a bit as dependencies of the tests on STIR libraries are reduced.</li>
+<li>You should now point cmake to the STIR main directory, not <tt>STIR/src</tt>.
 </ul>
 
 
@@ -211,7 +221,7 @@ <H2>What's new for developers (aside from what should be obvious
 
 <h3>Major bugs fixed</h3>
 <ul>
-<li>none</li>
+<li>see above</li>
 </ul>
 
 <h3>New functionality</h3>
@@ -236,7 +246,7 @@ <h3>New functionality</h3>
   <li> removed <ocde>CListModeData::get_scan_start_time_in_secs_since_1970()</code>. Get it via its <code>ExamInfo</code>.</li>
   </ul>
 </li>
-<li> Using the above changes, <code>LmToProjData</code> properly writes time frame information to the projection data.</li>
+<li> using the above changes, <code>LmToProjData</code> properly writes time frame information to the projection data.</li>
 
 <li>changes to <code>ProjDataInfoCylindrical</code> to allow different radii for different views, useful for SPECT (or an elliptical PET scanner?)</li>
 </ul>
@@ -265,6 +275,12 @@ <h3>Build system</h3>
  add_subdirectory(${STIR_LOCAL})
 </code>
 </li>
+<li> All CMake help-fules have been moved to a spearate sub-directory  <tt>src/cmake</tt> which is 
+added to the CMazke module path. That means that you should use them for instance as
+<pre>
+include(stir_lib_target)
+</pre>
+</li>
 </ul>
 </body>
 

diff --git a/src/samples/PET_simulation/FBP2D.par → examples/PET_simulation/FBP2D.par b/src/samples/PET_simulation/FBP2D.par → examples/PET_simulation/FBP2D.par
diff --git a/src/samples/PET_simulation/OSMAPOSL_QP.par → examples/PET_simulation/OSMAPOSL_QP.par b/src/samples/PET_simulation/OSMAPOSL_QP.par → examples/PET_simulation/OSMAPOSL_QP.par
diff --git a/src/samples/PET_simulation/OSSPS_QP.par → examples/PET_simulation/OSSPS_QP.par b/src/samples/PET_simulation/OSSPS_QP.par → examples/PET_simulation/OSSPS_QP.par
diff --git a/src/samples/PET_simulation/README.txt → examples/PET_simulation/README.txt b/src/samples/PET_simulation/README.txt → examples/PET_simulation/README.txt
diff --git a/...PET_simulation/Shell-scripting-primer.txt → ...PET_simulation/Shell-scripting-primer.txt b/...PET_simulation/Shell-scripting-primer.txt → ...PET_simulation/Shell-scripting-primer.txt
diff --git a/...ard_projector_proj_matrix_ray_tracing.par → ...ard_projector_proj_matrix_ray_tracing.par b/...ard_projector_proj_matrix_ray_tracing.par → ...ard_projector_proj_matrix_ray_tracing.par
diff --git a/...les/PET_simulation/generate_input_data.sh → ...les/PET_simulation/generate_input_data.sh b/...les/PET_simulation/generate_input_data.sh → ...les/PET_simulation/generate_input_data.sh
diff --git a/..._simulation/generate_uniform_cylinder.par → ..._simulation/generate_uniform_cylinder.par b/..._simulation/generate_uniform_cylinder.par → ..._simulation/generate_uniform_cylinder.par
diff --git a/src/samples/PET_simulation/recon_FBP2D.sh → examples/PET_simulation/recon_FBP2D.sh b/src/samples/PET_simulation/recon_FBP2D.sh → examples/PET_simulation/recon_FBP2D.sh
diff --git a/...samples/PET_simulation/recon_iterative.sh → examples/PET_simulation/recon_iterative.sh b/...samples/PET_simulation/recon_iterative.sh → examples/PET_simulation/recon_iterative.sh
diff --git a/src/samples/PET_simulation/run_simulation.sh → examples/PET_simulation/run_simulation.sh b/src/samples/PET_simulation/run_simulation.sh → examples/PET_simulation/run_simulation.sh
diff --git a/src/samples/PET_simulation/scatter.par → examples/PET_simulation/scatter.par b/src/samples/PET_simulation/scatter.par → examples/PET_simulation/scatter.par
diff --git a/...amples/PET_simulation/scatter_template.hs → examples/PET_simulation/scatter_template.hs b/...amples/PET_simulation/scatter_template.hs → examples/PET_simulation/scatter_template.hs
diff --git a/src/samples/PET_simulation/simulate_data.sh → examples/PET_simulation/simulate_data.sh b/src/samples/PET_simulation/simulate_data.sh → examples/PET_simulation/simulate_data.sh
diff --git a/...amples/PET_simulation/simulate_scatter.sh → examples/PET_simulation/simulate_scatter.sh b/...amples/PET_simulation/simulate_scatter.sh → examples/PET_simulation/simulate_scatter.sh
diff --git a/src/samples/FBP2D.par → examples/samples/FBP2D.par b/src/samples/FBP2D.par → examples/samples/FBP2D.par
diff --git a/src/samples/FBP2D_SPECT.par → examples/samples/FBP2D_SPECT.par b/src/samples/FBP2D_SPECT.par → examples/samples/FBP2D_SPECT.par
diff --git a/...amples/FBP2D_using_ITK_to_write_image.par → ...amples/FBP2D_using_ITK_to_write_image.par b/...amples/FBP2D_using_ITK_to_write_image.par → ...amples/FBP2D_using_ITK_to_write_image.par
diff --git a/src/samples/FBP3DRP.par → examples/samples/FBP3DRP.par b/src/samples/FBP3DRP.par → examples/samples/FBP3DRP.par
diff --git a/src/samples/MCIR.par → examples/samples/MCIR.par b/src/samples/MCIR.par → examples/samples/MCIR.par
diff --git a/src/samples/OSEM_SPECT.par → examples/samples/OSEM_SPECT.par b/src/samples/OSEM_SPECT.par → examples/samples/OSEM_SPECT.par
diff --git a/src/samples/OSMAPOSL_MRP.par → examples/samples/OSMAPOSL_MRP.par b/src/samples/OSMAPOSL_MRP.par → examples/samples/OSMAPOSL_MRP.par
diff --git a/src/samples/OSMAPOSL_QuadraticPrior.par → examples/samples/OSMAPOSL_QuadraticPrior.par b/src/samples/OSMAPOSL_QuadraticPrior.par → examples/samples/OSMAPOSL_QuadraticPrior.par
diff --git a/...les/OSMAPOSL_emml_with_projector_pair.par → ...les/OSMAPOSL_emml_with_projector_pair.par b/...les/OSMAPOSL_emml_with_projector_pair.par → ...les/OSMAPOSL_emml_with_projector_pair.par
diff --git a/...samples/OSMAPOSL_emml_with_projmatrix.par → ...samples/OSMAPOSL_emml_with_projmatrix.par b/...samples/OSMAPOSL_emml_with_projmatrix.par → ...samples/OSMAPOSL_emml_with_projmatrix.par
diff --git a/src/samples/OSMAPOSL_osem_SPECT.par → examples/samples/OSMAPOSL_osem_SPECT.par b/src/samples/OSMAPOSL_osem_SPECT.par → examples/samples/OSMAPOSL_osem_SPECT.par
diff --git a/...les/OSMAPOSL_osem_with_interfiltering.par → ...les/OSMAPOSL_osem_with_interfiltering.par b/...les/OSMAPOSL_osem_with_interfiltering.par → ...les/OSMAPOSL_osem_with_interfiltering.par
diff --git a/src/samples/OSSPS_QuadraticPrior.par → examples/samples/OSSPS_QuadraticPrior.par b/src/samples/OSSPS_QuadraticPrior.par → examples/samples/OSSPS_QuadraticPrior.par
diff --git a/src/samples/POSMAPOSL.par → examples/samples/POSMAPOSL.par b/src/samples/POSMAPOSL.par → examples/samples/POSMAPOSL.par
diff --git a/src/samples/POSSPS.par → examples/samples/POSSPS.par b/src/samples/POSSPS.par → examples/samples/POSSPS.par
diff --git a/src/samples/PatlakPlot.par → examples/samples/PatlakPlot.par b/src/samples/PatlakPlot.par → examples/samples/PatlakPlot.par
diff --git a/src/samples/SPECT_Interfile_header.hs → examples/samples/SPECT_Interfile_header.hs b/src/samples/SPECT_Interfile_header.hs → examples/samples/SPECT_Interfile_header.hs
diff --git a/src/samples/correct_projdata.par → examples/samples/correct_projdata.par b/src/samples/correct_projdata.par → examples/samples/correct_projdata.par
diff --git a/src/samples/fore.par → examples/samples/fore.par b/src/samples/fore.par → examples/samples/fore.par
diff --git a/src/samples/forward_project_SPECT.par → examples/samples/forward_project_SPECT.par b/src/samples/forward_project_SPECT.par → examples/samples/forward_project_SPECT.par
diff --git a/...ard_projector_proj_matrix_ray_tracing.par → ...ard_projector_proj_matrix_ray_tracing.par b/...ard_projector_proj_matrix_ray_tracing.par → ...ard_projector_proj_matrix_ray_tracing.par
diff --git a/...samples/forward_projector_ray_tracing.par → ...samples/forward_projector_ray_tracing.par b/...samples/forward_projector_ray_tracing.par → ...samples/forward_projector_ray_tracing.par
diff --git a/src/samples/generate_image.par → examples/samples/generate_image.par b/src/samples/generate_image.par → examples/samples/generate_image.par
diff --git a/src/samples/list_ROI_values.par → examples/samples/list_ROI_values.par b/src/samples/list_ROI_values.par → examples/samples/list_ROI_values.par
diff --git a/src/samples/lm_to_projdata.par → examples/samples/lm_to_projdata.par b/src/samples/lm_to_projdata.par → examples/samples/lm_to_projdata.par
diff --git a/src/samples/postfilter_Metz.par → examples/samples/postfilter_Metz.par b/src/samples/postfilter_Metz.par → examples/samples/postfilter_Metz.par
diff --git a/src/samples/postfilter_median3x3x3.par → examples/samples/postfilter_median3x3x3.par b/src/samples/postfilter_median3x3x3.par → examples/samples/postfilter_median3x3x3.par
diff --git a/src/samples/scatter.par → examples/samples/scatter.par b/src/samples/scatter.par → examples/samples/scatter.par
diff --git a/src/samples/stir_math_output_file_format.par → .../samples/stir_math_output_file_format.par b/src/samples/stir_math_output_file_format.par → .../samples/stir_math_output_file_format.par
diff --git a/src/samples/write_proj_matrix_by_bin.par → ...ples/samples/write_proj_matrix_by_bin.par b/src/samples/write_proj_matrix_by_bin.par → ...ples/samples/write_proj_matrix_by_bin.par
diff --git a/src/examples/CMakeLists.txt → examples/src/CMakeLists.txt b/src/examples/CMakeLists.txt → examples/src/CMakeLists.txt
@@ -9,4 +9,4 @@ set(${dir_EXE_SOURCES}
 )
 
 
-include(../stir_exe_targets.cmake)
+include(stir_exe_targets)
diff --git a/src/examples/README.txt → examples/src/README.txt b/src/examples/README.txt → examples/src/README.txt
@@ -43,7 +43,7 @@ exe.mk
 Supporting files
 ----------------
 extra_dirs.mk
-	A sub-makefile that needs to be moved to STIR/local. This way, it
+	A sub-makefile that needs to be moved to STIR/src/local. This way, it
 	will be picked up by the Makefile. Its contents simply say
 	that there is an exe.mk sub-makefile in examples/.
 
@@ -73,13 +73,15 @@ small.*s
 
 How to compile using the "hand-made" Makefiles
 -----------------------------------------------
-cp extra_dirs.mk ../local/
+mkdir -p ../src/local
+cp extra_dirs.mk ../src/local/
 cd ..
 make examples
 
 How to compile using CMake (on Unix-type systems)
 -----------------------------------------------
-cp extra_stir_dirs.cmake ../local/
+mkdir -p ../src/local
+cp extra_stir_dirs.cmake ../src/local/
 cd your-build-dir
 # reconfigure your project
 ccmake .
@@ -95,8 +97,8 @@ First you need to create some data.
 #Generate an image
       generate_image generate_image.par
 
-#Generate projection data (you will have to answer questions by fwdtest)
-      fwdtest sino.hs small.hs image.hv
+#Generate projection data
+      forward_project sino.hs image.hv  small.hs
 
 # Run the demos.
 DEST=../opt
@@ -127,3 +129,4 @@ Good luck
 
 Kris Thielemans
 12 November 2004
+(with minor updates until 2014)
diff --git a/src/examples/demo.par → examples/src/demo.par b/src/examples/demo.par → examples/src/demo.par
diff --git a/src/examples/demo1.cxx → examples/src/demo1.cxx b/src/examples/demo1.cxx → examples/src/demo1.cxx
diff --git a/src/examples/demo2.cxx → examples/src/demo2.cxx b/src/examples/demo2.cxx → examples/src/demo2.cxx
diff --git a/src/examples/demo3.cxx → examples/src/demo3.cxx b/src/examples/demo3.cxx → examples/src/demo3.cxx
diff --git a/src/examples/demoPM.par → examples/src/demoPM.par b/src/examples/demoPM.par → examples/src/demoPM.par
diff --git a/src/examples/exe.mk → examples/src/exe.mk b/src/examples/exe.mk → examples/src/exe.mk
diff --git a/src/examples/extra_dirs.mk → examples/src/extra_dirs.mk b/src/examples/extra_dirs.mk → examples/src/extra_dirs.mk
diff --git a/src/examples/extra_stir_dirs.cmake → examples/src/extra_stir_dirs.cmake b/src/examples/extra_stir_dirs.cmake → examples/src/extra_stir_dirs.cmake
diff --git a/src/examples/generate_image.par → examples/src/generate_image.par b/src/examples/generate_image.par → examples/src/generate_image.par
diff --git a/src/examples/small.hs → examples/src/small.hs b/src/examples/small.hs → examples/src/small.hs
diff --git a/src/examples/small.s → examples/src/small.s b/src/examples/small.s → examples/src/small.s
diff --git a/src/scripts/CMakeLists.txt → scripts/CMakeLists.txt b/src/scripts/CMakeLists.txt → scripts/CMakeLists.txt
@@ -30,7 +30,7 @@ set(${dir_scripts}
 
 
 
-#include(../stir_test_exe_targets.cmake)
+#include(stir_test_exe_targets)
 
 install(PROGRAMS ${${dir_scripts}} DESTINATION bin)
 
diff --git a/src/scripts/count → scripts/count b/src/scripts/count → scripts/count
diff --git a/src/scripts/exe.mk → scripts/exe.mk b/src/scripts/exe.mk → scripts/exe.mk
diff --git a/src/scripts/stir_divide → scripts/stir_divide b/src/scripts/stir_divide → scripts/stir_divide
diff --git a/src/scripts/stir_print_voxel_sizes.sh → scripts/stir_print_voxel_sizes.sh b/src/scripts/stir_print_voxel_sizes.sh → scripts/stir_print_voxel_sizes.sh
diff --git a/src/scripts/stir_subtract → scripts/stir_subtract b/src/scripts/stir_subtract → scripts/stir_subtract
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -18,18 +18,6 @@
 
 # cmake file for building STIR. See the STIR User's Guide and http://www.cmake.org.
 
-# avoid warning about WIN32 no longer defined in CYGWIN
-set(CMAKE_LEGACY_CYGWIN_WIN32 0) 
-
-PROJECT(STIR)
-
-SET_PROPERTY(GLOBAL PROPERTY USE_FOLDERS ON)
-# require 2.8.3 to get FOLDER properties support (without that, we only need cmake 2.6)
-cmake_minimum_required(VERSION 2.8.3)
-
-# add project source to cmake path such that it can use our find_package modules
-list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR})
-
 INCLUDE(${CMAKE_ROOT}/Modules/CheckFunctionExists.cmake)
 
 option(STIR_MPI 
@@ -162,15 +150,12 @@ if(STIR_OPENMP)
 
 endif()
 
-#### enable support for ctest
-ENABLE_TESTING()
-
 #### STIR library
-include(stir_dirs.cmake)
+include(stir_dirs)
 
 # see if there's a local subdirectory.
 if(NOT DISABLE_STIR_LOCAL)
-  find_path(STIR_LOCAL NAME "extra_stir_dirs.cmake" PATHS "${PROJECT_SOURCE_DIR}/local/" NO_DEFAULT_PATH)
+  find_path(STIR_LOCAL NAME "extra_stir_dirs.cmake" PATHS "${PROJECT_SOURCE_DIR}/src/local/" NO_DEFAULT_PATH)
   if (STIR_LOCAL)
     include(${STIR_LOCAL}/extra_stir_dirs.cmake)
   endif()

diff --git a/src/IO/CMakeLists.txt b/src/IO/CMakeLists.txt
@@ -60,7 +60,7 @@ if(AVW_FOUND)
   )
 endif()
 
-include(../stir_lib_target.cmake)
+include(stir_lib_target)
 
 if (LLN_FOUND)
   target_link_libraries(IO ${LLN_LIBRARIES})

diff --git a/src/Shape_buildblock/CMakeLists.txt b/src/Shape_buildblock/CMakeLists.txt
@@ -15,6 +15,6 @@ set(${dir_LIB_SOURCES}
 
 #$(dir)_REGISTRY_SOURCES:= $(dir)_registries
 
-include(../stir_lib_target.cmake)
+include(stir_lib_target)
 
 target_link_libraries(Shape_buildblock buildblock IO )
diff --git a/src/SimSET/CMakeLists.txt b/src/SimSET/CMakeLists.txt
@@ -28,7 +28,7 @@ set(${dir_EXE_SOURCES}
 	conv_to_SimSET_att_image
 )
 
-include(../stir_exe_targets.cmake)
+include(stir_exe_targets)
 
 # stand-alone
 add_executable(write_phg_image_info write_phg_image_info.c)

diff --git a/src/SimSET/scripts/CMakeLists.txt b/src/SimSET/scripts/CMakeLists.txt
@@ -32,7 +32,7 @@ stir_image_to_simset_object.sh
 )
 
 
-#include(../stir_test_exe_targets.cmake)
+#include(stir_test_exe_targets)
 
 install(PROGRAMS ${${dir_scripts}} DESTINATION bin)
 
diff --git a/src/analytic/FBP2D/CMakeLists.txt b/src/analytic/FBP2D/CMakeLists.txt
@@ -12,7 +12,7 @@ set(${dir_LIB_SOURCES}
 
 #$(dir)_REGISTRY_SOURCES:= 
 
-include(../../stir_lib_target.cmake)
+include(stir_lib_target)
 target_link_libraries(analytic_FBP2D recon_buildblock IO )
 
 set (dir_EXE_SOURCES ${dir}_EXE_SOURCES)
@@ -21,4 +21,4 @@ set(${dir_EXE_SOURCES}
 	FBP2D
 )
 
-include(../../stir_exe_targets.cmake)
+include(stir_exe_targets)
diff --git a/src/analytic/FBP3DRP/CMakeLists.txt b/src/analytic/FBP3DRP/CMakeLists.txt
@@ -12,7 +12,7 @@ set(${dir_LIB_SOURCES}
 
 #$(dir)_REGISTRY_SOURCES:= 
 
-include(../../stir_lib_target.cmake)
+include(stir_lib_target)
 target_link_libraries(analytic_FBP3DRP analytic_FBP2D recon_buildblock  )
 
 set (dir_EXE_SOURCES ${dir}_EXE_SOURCES)
@@ -21,5 +21,5 @@ set(${dir_EXE_SOURCES}
 	FBP3DRP
 )
 
-include(../../stir_exe_targets.cmake)
+include(stir_exe_targets)
 
diff --git a/src/buildblock/CMakeLists.txt b/src/buildblock/CMakeLists.txt
@@ -75,7 +75,7 @@ if (NOT HAVE_SYSTEM_GETOPT)
   list(APPEND ${dir_LIB_SOURCES} getopt)
 endif()
 
-include(../stir_lib_target.cmake)
+include(stir_lib_target)
 
 # TODO Remove but currently needed for ProjData.cxx, DynamicDisc*cxx, TimeFrameDef
 if (LLN_FOUND)

diff --git a/src/FindAVW.cmake → src/cmake/FindAVW.cmake b/src/FindAVW.cmake → src/cmake/FindAVW.cmake
@@ -15,7 +15,7 @@
 #  message(STATUS "AVW_INCLUDE_DIRS ${AVW_INCLUDE_DIRS}")
 
   find_library(AVW_LIBRARIES NAME AVW
-        HINTS ${AVW_ROOT_DIR}/$ENV(TARGET)/lib/
+        HINTS ${AVW_ROOT_DIR}/$ENV{TARGET}/lib/
         DOC "location of AVW library")
 
 # handle the QUIETLY and REQUIRED arguments and set AVW_FOUND to TRUE if 

diff --git a/src/FindLLN.cmake → src/cmake/FindLLN.cmake b/src/FindLLN.cmake → src/cmake/FindLLN.cmake
diff --git a/src/FindRDF.cmake → src/cmake/FindRDF.cmake b/src/FindRDF.cmake → src/cmake/FindRDF.cmake
diff --git a/src/stir_dirs.cmake → src/cmake/stir_dirs.cmake b/src/stir_dirs.cmake → src/cmake/stir_dirs.cmake
@@ -24,16 +24,18 @@
 
 
 # add the STIR include directory to the search path for the compiler
-include_directories ("${PROJECT_SOURCE_DIR}/include")
+include_directories ("${PROJECT_SOURCE_DIR}/src/include")
+
+SET( STIR_IO_REGISTRIES ${PROJECT_SOURCE_DIR}/src/IO/IO_registries.cxx)
 
 SET ( STIR_REGISTRIES
-${CMAKE_HOME_DIRECTORY}/buildblock/buildblock_registries.cxx
-${CMAKE_HOME_DIRECTORY}/data_buildblock/data_buildblock_registries.cxx
-${CMAKE_HOME_DIRECTORY}/IO/IO_registries.cxx
-${CMAKE_HOME_DIRECTORY}/recon_buildblock/recon_buildblock_registries.cxx
-${CMAKE_HOME_DIRECTORY}/Shape_buildblock/Shape_buildblock_registries.cxx
-${CMAKE_HOME_DIRECTORY}/modelling_buildblock/modelling_registries.cxx
-${CMAKE_HOME_DIRECTORY}/spatial_transformation_buildblock/spatial_transformation_registries.cxx
+${PROJECT_SOURCE_DIR}/src/buildblock/buildblock_registries.cxx
+${PROJECT_SOURCE_DIR}/src/data_buildblock/data_buildblock_registries.cxx
+${STIR_IO_REGISTRIES}
+${PROJECT_SOURCE_DIR}/src/recon_buildblock/recon_buildblock_registries.cxx
+${PROJECT_SOURCE_DIR}/src/Shape_buildblock/Shape_buildblock_registries.cxx
+${PROJECT_SOURCE_DIR}/src/modelling_buildblock/modelling_registries.cxx
+${PROJECT_SOURCE_DIR}/src/spatial_transformation_buildblock/spatial_transformation_registries.cxx
 )
 
 SET( STIR_LIBRARIES analytic_FBP3DRP analytic_FBP2D       iterative_OSMAPOSL  
@@ -69,7 +71,6 @@ SET( STIR_DIRS
      iterative/OSSPS
      iterative/POSMAPOSL  
      iterative/POSSPS
-     scripts
      SimSET
      SimSET/scripts
 )

diff --git a/src/stir_exe_targets.cmake → src/cmake/stir_exe_targets.cmake b/src/stir_exe_targets.cmake → src/cmake/stir_exe_targets.cmake
diff --git a/src/stir_lib_target.cmake → src/cmake/stir_lib_target.cmake b/src/stir_lib_target.cmake → src/cmake/stir_lib_target.cmake
diff --git a/src/stir_test_exe_targets.cmake → src/cmake/stir_test_exe_targets.cmake b/src/stir_test_exe_targets.cmake → src/cmake/stir_test_exe_targets.cmake
diff --git a/src/data_buildblock/CMakeLists.txt b/src/data_buildblock/CMakeLists.txt
@@ -34,6 +34,6 @@ if (HAVE_ECAT)
   )
 endif()
 
-include(../stir_lib_target.cmake)
+include(stir_lib_target)
 
 target_link_libraries(${dir} buildblock)
diff --git a/src/display/CMakeLists.txt b/src/display/CMakeLists.txt
@@ -42,7 +42,7 @@ else()
         message(FATAL_ERROR "GRAPHICS has to be X, PGM or None")
 endif()
 
-include(../stir_lib_target.cmake)
+include(stir_lib_target)
 
 if( "${GRAPHICS}" STREQUAL "X")
 	find_package(Curses REQUIRED)

diff --git a/src/eval_buildblock/CMakeLists.txt b/src/eval_buildblock/CMakeLists.txt
@@ -13,7 +13,7 @@ set(${dir_LIB_SOURCES}
 
 #$(dir)_REGISTRY_SOURCES:= $(dir)_registries.cxx
 
-include(../stir_lib_target.cmake)
+include(stir_lib_target)
 
 target_link_libraries(eval_buildblock buildblock )
 

diff --git a/src/iterative/OSMAPOSL/CMakeLists.txt b/src/iterative/OSMAPOSL/CMakeLists.txt
@@ -9,15 +9,15 @@ set(${dir_LIB_SOURCES}
 
 #$(dir)_REGISTRY_SOURCES:= 
 
-include(${PROJECT_SOURCE_DIR}/stir_lib_target.cmake)
+include(stir_lib_target)
 
 set (dir_EXE_SOURCES ${dir}_EXE_SOURCES)
 
 set(${dir_EXE_SOURCES}
 	OSMAPOSL
 )
 
-include(../../stir_exe_targets.cmake)
+include(stir_exe_targets)
 
 if (STIR_MPI)
   SET_PROPERTY(TARGET OSMAPOSL PROPERTY LINK_FLAGS ${MPI_CXX_LINK_FLAGS})

diff --git a/src/iterative/OSSPS/CMakeLists.txt b/src/iterative/OSSPS/CMakeLists.txt
@@ -9,7 +9,7 @@ set(${dir_LIB_SOURCES}
 
 #$(dir)_REGISTRY_SOURCES:= 
 
-include(${PROJECT_SOURCE_DIR}/stir_lib_target.cmake)
+include(stir_lib_target)
 
 set (dir_EXE_SOURCES ${dir}_EXE_SOURCES)
 
@@ -18,7 +18,7 @@ set(${dir_EXE_SOURCES}
 )
 
 
-include(../../stir_exe_targets.cmake)
+include(stir_exe_targets)
 
 if (STIR_MPI)
   SET_PROPERTY(TARGET OSSPS PROPERTY LINK_FLAGS ${MPI_CXX_LINK_FLAGS})

diff --git a/src/iterative/POSMAPOSL/CMakeLists.txt b/src/iterative/POSMAPOSL/CMakeLists.txt
@@ -26,4 +26,4 @@ set(${dir_EXE_SOURCES}
    POSMAPOSL
 )
 
-include(../../stir_exe_targets.cmake)
+include(stir_exe_targets)