Readme update and fix in spectral data generator files

mzeegers · Oct 5, 2022 · b937c98 · b937c98
1 parent 02944e2
commit b937c98
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Showing 3 changed files with 11 additions and 11 deletions.
diff --git a/README.md b/README.md
@@ -91,7 +91,7 @@ These scripts are written in Python (version 3.7 or higher). Apart from this, ph
 
 ## References
 
-The algorithms implemented in this MATLAB package are described in following [paper](https://iopscience.iop.org/article/10.1088/1361-6420/ac932e):
+The algorithms implemented in this MATLAB package are described in following [paper](https://iopscience.iop.org/article/10.1088/1361-6420/ac932e). If you use (parts of) this code in a publication, we would appreciate it if you would refer to:
 
 ```
 @article{

diff --git a/python_spectral/SpectralDataGenerator_AllOtherPhantoms.py b/python_spectral/SpectralDataGenerator_AllOtherPhantoms.py
@@ -65,7 +65,7 @@
 def computeMaterialEnergyMatrixXray(materials):
 
     #Collect the attenuation spectra for each material
-    AttenuationSpectra = collectAttenuationSpectra(RootDataPath, materials)
+    AttenuationSpectra = collectAttenuationSpectra(materials)
 
     #Setup the energy discretization
     EnergyBounds = np.linspace(MinEnergy, MaxEnergy, num = energies)
@@ -79,7 +79,7 @@ def computeMaterialEnergyMatrixXray(materials):
 
     return energyatts
 
-def collectAttenuationSpectra(Rootdatapath, Labels):
+def collectAttenuationSpectra(Labels):
     AttenuationSpectra = []
     print("\nLoading attenuation spectra...")
 
@@ -88,10 +88,10 @@ def collectAttenuationSpectra(Rootdatapath, Labels):
             if (mat[1] in [i[1] for i in ElementaryData]):                      #Elementary material
                 AtNo = elementToAtomic(mat[1])
                 if (AtNo > 0):
-                    attData = getAttenuationSpectrum(AtNo, Rootdatapath)
+                    attData = getAttenuationSpectrum(AtNo)
                     AttenuationSpectra.append((mat[0],)+(mat[1],) + attData)
             else:
-                attData = getAttenuationSpectrum(mat[1], Rootdatapath)          #Mixture material
+                attData = getAttenuationSpectrum(mat[1])          #Mixture material
                 AttenuationSpectra.append((mat[0],)+(mat[1],) + attData)
         elif(mat[0] != 0 and mat[1] == "Void"):
             #Make the zero attenuation spectrum
@@ -111,7 +111,7 @@ def elementToAtomic(materialname):
     else:
         return next(x for x in ElementaryData if x[1] == materialname)[0]
 
-def getAttenuationSpectrum(materialno, rootdatapath):
+def getAttenuationSpectrum(materialno):
 
     data = np.array(physdata.xray.fetch_coefficients(materialno))
 

diff --git a/python_spectral/SpectralDataGenerator_Thorax.py b/python_spectral/SpectralDataGenerator_Thorax.py
@@ -60,7 +60,7 @@
 
 def computeMaterialEnergyMatrixXray(materials):
     #Collect the attenuation spectra for each material
-    AttenuationSpectra = collectAttenuationSpectra(RootDataPath, materials)
+    AttenuationSpectra = collectAttenuationSpectra(materials)
 
     #Setup the energy discretization
     EnergyBounds = np.linspace(MinEnergy, MaxEnergy, num = energies)
@@ -74,7 +74,7 @@ def computeMaterialEnergyMatrixXray(materials):
 
     return energyatts
 
-def collectAttenuationSpectra(Rootdatapath, Labels):
+def collectAttenuationSpectra(Labels):
     AttenuationSpectra = []
     print("\nLoading attenuation spectra...")
 
@@ -83,10 +83,10 @@ def collectAttenuationSpectra(Rootdatapath, Labels):
             if (mat[1] in [i[1] for i in ElementaryData]):                      #Elementary material
                 AtNo = elementToAtomic(mat[1])
                 if (AtNo > 0):
-                    attData = getAttenuationSpectrum(AtNo, Rootdatapath)
+                    attData = getAttenuationSpectrum(AtNo)
                     AttenuationSpectra.append((mat[0],)+(mat[1],) + attData)
             else:
-                attData = getAttenuationSpectrum(mat[1], Rootdatapath)          #Mixture material
+                attData = getAttenuationSpectrum(mat[1])                        #Mixture material
                 AttenuationSpectra.append((mat[0],)+(mat[1],) + attData)
         elif(mat[0] != 0 and mat[1] == "Void"):
             #Make the zero attenuation spectrum
@@ -106,7 +106,7 @@ def elementToAtomic(materialname):
     else:
         return next(x for x in ElementaryData if x[1] == materialname)[0]
 
-def getAttenuationSpectrum(materialno, rootdatapath):
+def getAttenuationSpectrum(materialno):
 
     data = np.array(physdata.xray.fetch_coefficients(materialno)) #Density taken from array