From 967e46a18b00f1a55612ff58d35af88300a6e5de Mon Sep 17 00:00:00 2001
From: dmayerich <dmayerich@gmail.com>
Date: Fri, 27 Sep 2013 14:44:28 -0500
Subject: [PATCH] added spectral script

---
 fileout.cu    |  2 ++
 microscope.cu |  9 ++++++---
 nfScalarUf.cu |  1 +
 options.h     |  2 ++
 specimage.py  | 61 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 5 files changed, 72 insertions(+), 3 deletions(-)
 create mode 100755 specimage.py

diff --git a/fileout.cu b/fileout.cu
index 076ea1a..8fdd091 100644
--- a/fileout.cu
+++ b/fileout.cu
@@ -114,6 +114,8 @@ void fileoutStruct::saveDetector(microscopeStruct* scope)
 
         if(is_binary(intFile))
             I.toEnvi(intFile, scope->nf.lambda, append);
+		else
+			I.toImage(intFile);
     }
     //absorbance
     if(absFile != "")
diff --git a/microscope.cu b/microscope.cu
index e6197f3..21b5253 100644
--- a/microscope.cu
+++ b/microscope.cu
@@ -295,9 +295,12 @@ void microscopeStruct::LoadExtendedSource(std::string filename)
             //get the amplitude of the focal point
             QRgb rgb = sourceImage.pixel(x, y);
             //float A = qGray(rgb);
-            p.A = (ptype) qGray(rgb) / 255;
+			if(qGray(rgb) != 0)
+			{
+				p.A = (ptype) qGray(rgb) / 255;
 
-            //insert the point source into the list
-            focalPoints.push_back(p);
+				//insert the point source into the list
+				focalPoints.push_back(p);
+			}
         }
 }
diff --git a/nfScalarUf.cu b/nfScalarUf.cu
index 6bc0724..c19d767 100644
--- a/nfScalarUf.cu
+++ b/nfScalarUf.cu
@@ -151,6 +151,7 @@ __global__ void gpuScalarUf(bsComplex* Uf, bsVector k, ptype kmag, bsPoint f, pt
 		}
 
 		sumUf += il * jl * Pl * (Palpha[1] - Palpha[2] - Pbeta[1] + Pbeta[2]);
+		//sumUf += il * Pl * (Palpha[1] - Palpha[2] - Pbeta[1] + Pbeta[2]);
 
 		il *= im;
 	}
diff --git a/options.h b/options.h
index dfe29f5..d16d520 100644
--- a/options.h
+++ b/options.h
@@ -298,6 +298,8 @@ static void OutputOptions()
 {
 	cout<<SCOPE->nf.toStr();
 
+	cout<<"# of source points: "<<SCOPE->focalPoints.size()<<endl;
+
 }
 
 static void SetOptions(po::options_description &desc)
diff --git a/specimage.py b/specimage.py
new file mode 100755
index 0000000..522ccf3
--- /dev/null
+++ b/specimage.py
@@ -0,0 +1,61 @@
+#!/usr/bin/python3
+import subprocess
+
+command = "bimsim"
+
+#images
+intImage = "out_i.bmp"
+absImage = "out_a"
+#detector specs
+dsize = 208
+dsample = 6.5
+res = int(dsize / dsample)
+sampling = 4
+#incident field
+#nu = 800
+source = "central.bmp"
+order = 100
+#sphere
+x = 0
+y = 0
+z = 0
+a = 5
+#spectral samples
+nuStart = 800
+nuStop = 4000
+nuStep = 10
+iters = int((nuStop - nuStart) / nuStep)
+
+
+#set the position of the image plane
+command += " -u " + str(-dsize/2)
+command += " -v " + str(-dsize/2)
+command += " -w " + str(a)
+command += " -U " + str(dsize/2)
+command += " -V " + str(dsize/2)
+command += " -W " + str(a)
+command += " --plane-norm-x " + str(0)
+command += " --plane-norm-y " + str(0)
+command += " --plane-norm-z " + str(1)
+command += " -R " + str(res)
+command += " --supersample " + str(sampling)
+command += " -X " + source
+command += " --field-order " + str(order)
+command += " -I " + intImage
+command += " -A " + absImage
+command += " --append"
+command += " -x " + str(x)
+command += " -y " + str(y)
+command += " -z " + str(z)
+command += " -r " + str(a)
+
+for inu in range(0, iters):
+    print("Iteration # " + str(inu + 1) + "/" + str(iters))
+    nu = nuStart + inu * nuStep
+    lam = 10000.0/nu
+    
+    runcommand = command + " -l " + str(lam)
+    print(runcommand)
+    subprocess.call(runcommand, shell=True)
+
+#print("Hello world!")
\ No newline at end of file
--
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