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Commit 1b6b1360 authored by myron's avatar myron
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It works iwth NNM components

parent af25b46e
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XRStools/XRS_swissknife.py
View file @ 1b6b1360
......@@ -2725,10 +2725,10 @@ def superR_getVolume_Esynt(mydata):
coefficients[iE, iv, roi_map[rk]] = c
yamlname = output_prefix+"inputforcpp.yaml"
DSname = output_prefix+"DS.raw"
DDname = output_prefix+"DD.raw"
SSname = output_prefix+"SS.raw"
COEFname = output_prefix+"coefficients.raw"
DSname = output_prefix+"DS.h5"
DDname = output_prefix+"DD.h5"
SSname = output_prefix+"SS.h5"
COEFname = output_prefix+"coefficients.h5"
DSname_relative = os.path.basename(DSname)
DDname_relative = os.path.basename(DDname)
......@@ -2736,27 +2736,27 @@ def superR_getVolume_Esynt(mydata):
coeffname_relative = os.path.basename(COEFname)
f=open(yamlname,"w")
f.write("NE : %d\n"%NE)
f.write("NV : %d\n"%NV)
f.write("NROI : %d\n"%NROI)
f.write("DIMZ : %d\n"%DIMZ)
f.write("DIMY : %d\n"%DIMY)
f.write("DIMX : %d\n"%DIMX)
# f.write("NE : %d\n"%NE)
# f.write("NV : %d\n"%NV)
# f.write("NROI : %d\n"%NROI)
# f.write("DIMZ : %d\n"%DIMZ)
# f.write("DIMY : %d\n"%DIMY)
# f.write("DIMX : %d\n"%DIMX)
f.write("DSname : %s\n"%DSname_relative)
f.write("DDname : %s\n"%DDname_relative)
f.write("SSname : %s\n"%SSname_relative)
f.write("COEFFSname : %s\n"%coeffname_relative)
f.close()
coefficients.tofile(COEFname)
DS.tofile(DSname)
DD.tofile(DDname)
SS.tofile(SSname)
# coefficients.tofile(COEFname)
# DS.tofile(DSname)
# DD.tofile(DDname)
# SS.tofile(SSname)
h5py.File(DSname +".h5","w")["data"] = DS.astype("f")
h5py.File(DDname +".h5","w")["data"] = DD.astype("f")
h5py.File(SSname +".h5","w")["data"] = SS.astype("f")
h5py.File(COEFname+".h5","w")["data"] = coefficients.astype("f")
h5py.File(DSname ,"w")["data"] = DS.astype("f")
h5py.File(DDname ,"w")["data"] = DD.astype("f")
h5py.File(SSname ,"w")["data"] = SS.astype("f")
h5py.File(COEFname,"w")["data"] = coefficients.astype("f")
......
fitcc/frsv.cc
View file @ 1b6b1360
......@@ -38,7 +38,7 @@ typedef InputFileNames_struct InputFileNames;
float * read_volume(std::string fn, std::vector<size_t> &dims) {
float * result;
std::string testh5_name(fn+".h5" ) ;
std::string testh5_name(fn) ;
h5::File test_file( testh5_name , h5::File::ReadOnly);
h5::DataSet test_dataset = test_file.getDataSet("data");
dims = test_dataset.getDimensions();
......@@ -52,7 +52,7 @@ float * read_volume(std::string fn, std::vector<size_t> &dims) {
void save_volume(std::string fn, float * X , std::vector<size_t> dims) {
std::string testh5_name(fn+".h5" ) ;
std::string testh5_name(fn) ;
h5::File test_file( testh5_name , h5::File::ReadWrite | h5::File::Create | h5::File::Truncate );
h5::DataSet dataset = test_file.createDataSet<float>("data", h5::DataSpace(dims));
dataset.write_raw(X);
......@@ -597,16 +597,10 @@ int main(int argc, char ** argv) {
" -h prints this help \n"
" arguments :\n"
" input_file : a yaml file containing \n"
" NE : 7 \n"
" NV : 7 \n"
" NROI : 72 \n"
" DIMZ : 10 \n"
" DIMY : 41 \n"
" DIMX : 241 \n"
" DSname : test0_DS.raw \n"
" DDname : test0_DD.raw \n"
" SSname : test0_SS.raw \n"
" COEFFSname : coefficients.raw \n";
" DSname : test0_DS.h5 \n"
" DDname : test0_DD.h5 \n"
" SSname : test0_SS.h5 \n"
" COEFFSname : coefficients.h5 \n";
int hflag = 0;
// char *cvalue = NULL;
......@@ -646,12 +640,6 @@ int main(int argc, char ** argv) {
YAML::Node mockup_config;
mockup_config = YAML::LoadFile(argv[index_input]);
assert( mockup_config["NE"] ) ;
assert( mockup_config["NV"] ) ;
assert( mockup_config["NROI"] ) ;
assert( mockup_config["DIMZ"] ) ;
assert( mockup_config["DIMY"] ) ;
assert( mockup_config["DIMX"] ) ;
assert( mockup_config["DSname"] ) ;
assert( mockup_config["DDname"] ) ;
assert( mockup_config["SSname"] ) ;
......@@ -764,7 +752,7 @@ int main(int argc, char ** argv) {
printf(" iter %d %e\n", iter, merit);
}
pb.save(X, "solution.raw");
pb.save(X, "solution.h5");
pb.setFreeFacts( ffacts , X) ;
......@@ -775,7 +763,7 @@ int main(int argc, char ** argv) {
printf(" set ok \n");
}
pb.save(X, "solution.raw");
pb.save(X, "solution.h5");
}
nonregressions/volumes/test2/batch_extraction_esynth1.py
View file @ 1b6b1360
# newfactors e' gia pronto , dopo verifica fuzionalita di roi_sel in ximages
import numpy as np
import h5py
import glob
......@@ -87,6 +85,45 @@ def extract_sample_givenrois(
process_input( inputstring, exploit_slurm_mpi = 0)
def InterpInfo_Esynt_components(cenom , energy_exp_grid = None, custom_ene_list = None ):
components = h5py.File("components.h5","r")["components"] [()]
info_dict = {}
for i_interval in range(len(components)):
info_dict[str(i_interval)] = {}
info_dict[str(i_interval)]["E"] = custom_ene_list[ i_interval ]
info_dict[str(i_interval)]["coefficients"]={}
for i_n in range(len(energy_exp_grid)):
info_dict[str(i_interval)]["coefficients" ][ str(i_n) ]={}
for roi_num, de in enumerate( cenom ):
info_dict[str(i_interval)]["coefficients" ][ str(i_n) ][ str(roi_num) ] = 0
for ic in range(len(components)):
for i_interval in range(len(custom_ene_list)-1):
cE1 = custom_ene_list[ i_interval ]
cE2 = custom_ene_list[ i_interval+1 ]
for i_ene, t_ene in enumerate( energy_exp_grid) :
for roi_num, de in enumerate( cenom ):
if t_ene+de < cE1 or t_ene+de > cE2:
continue
alpha = (cE2-(t_ene+de) )/(cE2-cE1)
info_dict[str(ic)]["coefficients" ][ str(i_ene) ][ str(roi_num) ] += alpha * components[ic][ i_interval ]
info_dict[str(ic)]["coefficients" ][ str(i_ene) ][ str(roi_num) ] += (1-alpha)*components[ic][ i_interval+1 ]
return info_dict
def InterpInfo_Esynt( cenom , energy_exp_grid = None, custom_ene_list = None):
info_dict = {"energy_exp_grid":list(energy_exp_grid), "de_list": list(cenom)}
......@@ -155,6 +192,27 @@ def InterpInfo_Esynt( cenom , energy_exp_grid = None, custom_ene_list = Non
self.interp_file=interp_file
self.source= source
self.cenom=cenom
# interpolation_infos_file = "interpolation_infos.json"
# info_dict={}
# for i in range(NC):
# dizio = {}
# info_dict[str(i)] = {"coefficients":dizio}
# c = model.components_[i]
# np = len(c)
# for j in range(np):
# dizio[str(j)] = float(c[j])
# json.dump(info_dict,open( interpolation_infos_file,"w"), indent=4)
def interpola_Esynt(self, roi_sel=roi_sel ):
print ( " ECCO I DATI ")
......@@ -163,7 +221,6 @@ def InterpInfo_Esynt( cenom , energy_exp_grid = None, custom_ene_list = Non
info_dict = {}
for i_intervallo in range(len(self.custom_ene_list)):
info_dict[str(i_intervallo)] = {}
info_dict[str(i_intervallo)]["E"] = self.custom_ene_list[ i_intervallo ]
......@@ -171,7 +228,6 @@ def InterpInfo_Esynt( cenom , energy_exp_grid = None, custom_ene_list = Non
for t_vn, t_sn, t_ene in list(zip(self.volum_list, self.scan_num_list, self.ene_list )):
info_dict[str(i_intervallo)]["coefficients" ][ t_vn ]={}
for i_intervallo in range(len(self.custom_ene_list)-1):
cE1 = self.custom_ene_list[ i_intervallo ]
cE2 = self.custom_ene_list[ i_intervallo+1 ]
......@@ -297,7 +353,7 @@ monitor_path_template = datadir + filename_template +"_monitor.hd5:/monitor"
# energy_custom_grid = np.array([6746.0,6754.0,6755.5,6756.2,6757.5,6759.3,6762.5,6770.0,6790.5])
energy_custom_grid = np.array([6745.0,6754.0,6755.5,6756.2,6757.5,6759.3,6762.5,6770.0,6791])
energy_custom_grid = np.array([6745.0,6754.0,6755.5,6756.2,6757.5,6759.3,6762.5,6770.0,6792])
energy_exp_grid = h5py.File( datadir +(filename_template%1)+".nxs" ,"r")["/root.spyc.config1d_RIXS_0024/scan_data/actuator_1_1"][()]
......@@ -347,7 +403,8 @@ interpolation_infos_file = "interpolation_infos.json"
if(1): # INTERPOLATION ESYNTH
info_dict = InterpInfo_Esynt( cenom , energy_exp_grid = energy_exp_grid, custom_ene_list = energy_custom_grid )
# info_dict = InterpInfo_Esynt( cenom , energy_exp_grid = energy_exp_grid, custom_ene_list = energy_custom_grid )
info_dict = InterpInfo_Esynt_components( cenom , energy_exp_grid = energy_exp_grid, custom_ene_list = energy_custom_grid )
json.dump(info_dict,open( interpolation_infos_file,"w"), indent=4)
......
nonregressions/volumes/test2/colletta.py 0 → 100644
View file @ 1b6b1360
from numpy import *
import h5py
f=h5py.File("results/extracted.h5","r")
res=[ [0 for i in range(9) ] for r in range(5)]
for ie in range(9):
he = f["E%d"%ie]
for iscan in range(19):
for ir in range(4):
m = he["Scan%d/%02d/matrix"%(iscan, ir)][()]
res[ir+1][ie] += m.sum()
h5py.File("plot.h5","w")["plot"] = array( res)
R = array(res)
R[0,:] = array( [ 6745.981087876128,
6754.004616913128,
6755.549616942595,
6756.206827194552,
6757.550552579804,
6759.304498100658,
6762.542644309955,
6770.0295586460825,
6790.5063595030115
])
savetxt( "plot.txt" , R.T )
nonregressions/volumes/test2/extract_components.py 0 → 100644
View file @ 1b6b1360
from h5py import *
from sklearn.decomposition import NMF
from pylab import *
import json
NC = 3
model = NMF(n_components=NC, init='random', random_state=0, max_iter = 200)
d=File("solution.h5","r") ["data"][()]
d.shape = 9,-1
W = model.fit_transform(d.T)
for i in range(NC):
plot(model.components_[i])
show()
File("components.h5","w")["components"] = model.components_
interpolation_infos_file = "interpolation_infos.json"
info_dict={}
for i in range(NC):
dizio = {}
info_dict[str(i)] = {"coefficients":dizio}
c = model.components_[i]
np = len(c)
for j in range(np):
dizio[str(j)] = float(c[j])
json.dump(info_dict,open( interpolation_infos_file,"w"), indent=4)
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