adapted for cases where HighFive is not installed on the system

.gitmodules

+[submodule "HighFive"]
+	path = fitcc/HighFive
+	url = https://github.com/BlueBrain/HighFive.git

fitcc/CMakeLists.txt

@@ -11,8 +11,15 @@ include(CheckLanguage)
 
 
 
-find_package(HighFive REQUIRED)
-
+find_package(HighFivee )
+
+if (HighFive_FOUND)
+  message(STATUS "found high five")
+else()
+  ## manual fix
+  set( hfive_include_dir  ${PROJECT_SOURCE_DIR}/HighFive/include/  "/usr/include/hdf5/serial/" ) 
+  set( hfive_libs  /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so ) 
+endif()
 
 
 find_package(MPI )
@@ -104,6 +111,11 @@ set(CMAKE_CXX_FLAGS_PIPPO "-g -Wextra -Wall   ${CMAKE_CXX_FLAGS}"     )
 
 add_executable (frsv frsv.cc)
 
-target_link_libraries( frsv  PRIVATE yaml-cpp  Boost::filesystem Boost::system   HighFive )
-target_include_directories ( frsv  PRIVATE   "${PROJECT_SOURCE_DIR}")
+if (HighFivee_FOUND)
+  target_link_libraries( frsv  PRIVATE yaml-cpp  Boost::filesystem Boost::system )  
+  target_include_directories ( frsv  PRIVATE   "${PROJECT_SOURCE_DIR}" )
+else()
+  target_link_libraries( frsv  PRIVATE yaml-cpp  Boost::filesystem Boost::system   ${hfive_libs}  )  
+  target_include_directories ( frsv  PRIVATE   "${PROJECT_SOURCE_DIR}"      ${hfive_include_dir}    )
+endif()
 

HighFive @ e582076f

+Subproject commit e582076fb5b4dd654738c24c2d40517d11512ca6

fitcc/frsv.cc

@@ -740,7 +740,7 @@ int main(int argc, char ** argv)  {
     }
 
 
-    for(int iter = 0; iter<10; iter++) {
+    for(int iter = 0; iter<40; iter++) {
 
       pb.settozero(grad);
       

nonregressions/volumes/esrf_scans/fourmis/interp/batch_extraction_interp.py

@@ -12,15 +12,11 @@ from XRStools import xrs_read,  xrs_rois
 
 import os
 def main():
-    
-    ## os.system("xz -dk ../mask.h5.xz --stdout > mask.h5 ")
-
     filter_path = None
     # filter_path = "mask.h5:/FILTER_MASK/filter"
 
     roi_scan_num   = list(range(592,600))
     reference_scan_list = list(range(592,600))
-
     
     monitor_column = "izero/0.000001"
     
@@ -34,36 +30,25 @@ def main():
 
     datadir =   "/data/id20/inhouse/data/run5_17/run7_ihr/"
 
-    # If reference_clip is not None, then a smaller part of the reference scan is considered
-    # This may be usefule to obtain smaller volumes containing the interesting part
-    # The used reference scan  will the correspond to the positions from reference_clip[0] to reference_clip[1]-1 included
-    ###########
     reference_clip = None
-    # reference_clip = [ 90, 180 ]
 
-    ## in the reference scan for each position there is a spot with a maximum. We set zero the background which is further than
-    ## such radius from the maximum
     isolate_spot_by = 7
 
-    #### For the fit of the response function based on reference scans
     response_fit_options = dict( [
         ["niter_optical" , 40],
         ["beta_optical"  , 0.1],
         ["niter_global"  , 1  ]
     ])
 
-    resynth_z_square = 8
+    resynth_z_square = 0
 
     selected_rois = list(range(0,24)) + list( range(36,60) ) 
 
-
     scal_prod_use_optional_solution = False
 
-
     volume_retrieval_beta  = 0.12
     volume_retrieval_niter = 100 
-    
-    
+        
     steps_to_do = {
         "do_step_make_roi":                      False,
         "do_step_sample_extraction":             False,