Commit 5e390289 authored by myron's avatar myron
Browse files

adapted for cases where HighFive is not installed on the system

parent 0fea5ab9
[submodule "HighFive"]
path = fitcc/HighFive
url = https://github.com/BlueBrain/HighFive.git
......@@ -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()
Subproject commit e582076fb5b4dd654738c24c2d40517d11512ca6
......@@ -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);
......
......@@ -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,
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment