From 86165938aba81d2d6c2a1f6678bfc7cf416cd714 Mon Sep 17 00:00:00 2001
From: pospelov <pospelov@fz-juelich.de>
Date: Mon, 1 Oct 2012 14:17:52 +0200
Subject: [PATCH] FresnelCoeff now takes roughness in the account
---
App/src/TestFresnelCoeff.cpp | 8 ++--
Core/Algorithms/inc/OpticalFresnel.h | 4 +-
Core/Algorithms/src/OpticalFresnel.cpp | 14 +++++--
Core/Tools/src/FitMultiParameter.cpp | 5 ++-
Core/Tools/src/FitParameter.cpp | 3 +-
.../ex02_fitspheres/edf_reader.py | 40 ++++---------------
6 files changed, 31 insertions(+), 43 deletions(-)
diff --git a/App/src/TestFresnelCoeff.cpp b/App/src/TestFresnelCoeff.cpp
index c1f4591b888..033228cd38b 100644
--- a/App/src/TestFresnelCoeff.cpp
+++ b/App/src/TestFresnelCoeff.cpp
@@ -240,8 +240,8 @@ void TestFresnelCoeff::draw_standard_samples()
/* ************************************************************************* */
void TestFresnelCoeff::test_roughness_set()
{
-// m_sample = dynamic_cast<MultiLayer *>(SampleFactory::createSample("MultilayerOffspecTestcase1a"));
- m_sample = dynamic_cast<MultiLayer *>(SampleFactory::createSample("SubstrateOnSubstrate"));
+ m_sample = dynamic_cast<MultiLayer *>(SampleFactory::createSample("MultilayerOffspecTestcase1a"));
+// m_sample = dynamic_cast<MultiLayer *>(SampleFactory::createSample("SubstrateOnSubstrate"));
std::cout << *m_sample << std::endl;
std::cout << "-----" << std::endl;
@@ -257,7 +257,7 @@ void TestFresnelCoeff::test_roughness_set()
// multipar.addMatchedParametersFromPool("/multilayer/interface0/roughness/sigma",newpool);
multipar.addMatchedParametersFromPool("/*/*/*/sigma",newpool);
- std::cout << multipar << std::endl;
+ std::cout << "multipar: " << multipar << std::endl;
// multipar.setValue(0.0);
std::cout << *m_sample << std::endl;
@@ -275,7 +275,7 @@ void TestFresnelCoeff::test_roughness_set()
kvec.setLambdaAlphaPhi(1.54*Units::angstrom, -alpha_i, 0.0);
OpticalFresnel::MultiLayerCoeff_t coeffs;
OpticalFresnel fresnelCalculator;
- fresnelCalculator.execute(*m_sample, kvec, coeffs, true);
+ fresnelCalculator.execute(*m_sample, kvec, coeffs);
m_coeffs->next() = coeffs;
//std::cout << alpha_i << " " << roughness << " " << coeffs[0].R << std::endl;
}
diff --git a/Core/Algorithms/inc/OpticalFresnel.h b/Core/Algorithms/inc/OpticalFresnel.h
index c92ddbbaf9e..9f2bbd1dd01 100644
--- a/Core/Algorithms/inc/OpticalFresnel.h
+++ b/Core/Algorithms/inc/OpticalFresnel.h
@@ -52,10 +52,10 @@ public:
MultiLayerCoeff_t m_data;
};
- int execute(const MultiLayer &sample, const kvector_t &k, MultiLayerCoeff_t &coeff, bool useRoughness=false);
- int execute(const MultiLayer &sample, const kvector_t &k, MultiLayerCoeff &coeff, bool useRoughness=false) { return execute(sample,k,coeff.m_data, useRoughness); }
+ int execute(const MultiLayer &sample, const kvector_t &k, MultiLayerCoeff_t &coeff);
private:
+ bool m_use_roughness;
void calculateKZ(const MultiLayer &sample, const kvector_t &k, MultiLayerCoeff_t &coeff);
void calculateFresnelCoefficients(MultiLayerCoeff_t &coeff);
diff --git a/Core/Algorithms/src/OpticalFresnel.cpp b/Core/Algorithms/src/OpticalFresnel.cpp
index aa677f905ce..6849fc8ce35 100644
--- a/Core/Algorithms/src/OpticalFresnel.cpp
+++ b/Core/Algorithms/src/OpticalFresnel.cpp
@@ -5,19 +5,27 @@
-OpticalFresnel::OpticalFresnel()
+OpticalFresnel::OpticalFresnel() : m_use_roughness(false)
{
}
-int OpticalFresnel::execute(const MultiLayer &sample, const kvector_t &kvec, MultiLayerCoeff_t &coeff, bool useRoughness)
+int OpticalFresnel::execute(const MultiLayer &sample, const kvector_t &kvec, MultiLayerCoeff_t &coeff)
{
coeff.clear();
coeff.resize(sample.getNumberOfLayers());
calculateKZ(sample, kvec, coeff);
- if(useRoughness) {
+ // check if there is a roughness
+ for (size_t i=0; i<sample.getNumberOfInterfaces(); ++i) {
+ if(sample.getLayerInterface(i)->getRoughness() ) {
+ m_use_roughness = true;
+ break;
+ }
+ }
+
+ if(m_use_roughness) {
calculateFresnelCoefficientsWithRoughness(sample, coeff);
} else{
calculateFresnelCoefficients(coeff);
diff --git a/Core/Tools/src/FitMultiParameter.cpp b/Core/Tools/src/FitMultiParameter.cpp
index 93267732b22..709ca7f07ec 100644
--- a/Core/Tools/src/FitMultiParameter.cpp
+++ b/Core/Tools/src/FitMultiParameter.cpp
@@ -3,7 +3,7 @@
FitMultiParameter::FitMultiParameter()
{
-
+ setName("FitMultiParameter");
}
/* ************************************************************************* */
@@ -34,13 +34,16 @@ void FitMultiParameter::addParameterFromPool(std::string parkey, const Parameter
void FitMultiParameter::addMatchedParametersFromPool(std::string wildcards, const ParameterPool *pool)
{
// loop over all parameters in the pool
+ int n_added_pars(0);
for(ParameterPool::const_iterator_t it=pool->begin(); it!= pool->end(); it++) {
// (*it).first - parameter key, (*it).second - parameter itself
// parameters whose key match pattern is added to the FitMultiParameter container
if( Utils::StringMatchText::WildcardPattern( (*it).first, wildcards ) ) {
addParameter((*it).second);
+ n_added_pars++;
}
}
+ if(n_added_pars==0) std::cout << "FitMultiParameter::addMatchedParametersFromPool() -> Warning! No parameters satisfying criteria'" << wildcards << "' have been found" << std::endl;
}
diff --git a/Core/Tools/src/FitParameter.cpp b/Core/Tools/src/FitParameter.cpp
index ab122f0b1ed..c2aa5581af8 100644
--- a/Core/Tools/src/FitParameter.cpp
+++ b/Core/Tools/src/FitParameter.cpp
@@ -4,12 +4,13 @@
FitParameter::FitParameter() : m_value(0), m_error(0), m_lower_limit(0), m_upper_limit(0)
{
-
+ setName("FitParameter");
}
FitParameter::FitParameter(const FitParameter &other) : INamed(other)
{
+ setName("FitParameter");
m_value = other.m_value;
m_error = other.m_error;
m_lower_limit = other.m_lower_limit;
diff --git a/Examples/MesoCrystals/ex02_fitspheres/edf_reader.py b/Examples/MesoCrystals/ex02_fitspheres/edf_reader.py
index a87922917e8..48317f83665 100644
--- a/Examples/MesoCrystals/ex02_fitspheres/edf_reader.py
+++ b/Examples/MesoCrystals/ex02_fitspheres/edf_reader.py
@@ -1,9 +1,8 @@
#-*- coding: utf8 -*-
-import os
-import sys
from numpy import *
-h_c=1.23984193*1e-6/1e-10
+h_c=1.239842E4 #eV⋅Å
+
def read_edf_header(file_handler):
'''
@@ -19,7 +18,7 @@ def read_edf_header(file_handler):
key=key.strip()
value=value.strip().rstrip(';').strip()
settings[key]=value
- #header_lines.append(line)
+ header_lines.append(line)
line=file_handler.readline()
header_lines.append(line)
# Read some settings
@@ -33,14 +32,13 @@ def read_edf_header(file_handler):
settings['SampleDistance']=float(settings['SampleDistance'].rstrip('m'))*1000.
if 'Monochromator_energy' in settings:
energy=float(settings['Monochromator_energy'].rstrip('keV'))*1000.
- print "XXX",energy
settings['lambda']=h_c/energy
if 'WaveLength' in settings:
settings['lambda']=float(settings['WaveLength'].rstrip('m'))*1e10
- if 'Exposure_time' in settings:
- settings['Exposure_time']=float(settings['Exposure_time'].rstrip('ms'))/1000.
if 'ExposureTime' in settings:
settings['ExposureTime']=float(settings['ExposureTime'].rstrip('s (Seconds)'))
+ if 'Exposure_time' in settings:
+ settings['ExposureTime']=float(settings['Exposure_time'].rstrip('ms'))/1000.
if 'NormalizationFactor' in settings:
settings['NormalizationFactor']=float(settings['NormalizationFactor'])
if 'Center_1' in settings:
@@ -71,11 +69,11 @@ def import_edf_file(file_name):
input_array=array_module.array('H')
input_array=fromstring(file_handler.read(header_settings['xdim']*header_settings['ydim']*2),
uint16).astype(float)
- input_array-=-200
+ input_array-=200
elif header_settings['DataType']=='SignedInteger':
# load data as binary integer values
- input_array=fromstring(file_handler.read(header_settings['xdim']*header_settings['ydim']*2),
- int16).astype(float)
+ input_array=fromstring(file_handler.read(header_settings['xdim']*header_settings['ydim']*4),
+ int32).astype(float)
elif header_settings['DataType']=='FloatValue':
# load data as binary integer values
input_array=fromstring(file_handler.read(header_settings['xdim']*header_settings['ydim']*4),
@@ -85,25 +83,3 @@ def import_edf_file(file_name):
raise IOError, 'Unknown data format in header: %s'%header_settings['DataType']
file_handler.close()
return input_array.reshape(header_settings['ydim'], header_settings['xdim']), header_settings
-
-
-def main():
- if len(sys.argv)!=2:
- print "Usage: 'python edf_reader.py FileName' "
- print " "
-
- else:
- data=import_edf_file( sys.argv[1] )
- print data[1]
- print data[0].shape
- #savetxt("foo.csv.gz", data[0], fmt='%1.10e', delimiter=" ")
-
-
-
-
-#-------------------------------------------------------------
-# main()
-#-------------------------------------------------------------
-if __name__ == '__main__':
- main()
-
--
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