diff --git a/JFMC_CuFluoPeakFit.cpp b/JFMC_CuFluoPeakFit.cpp
index 5230325..c80f985 100644
--- a/JFMC_CuFluoPeakFit.cpp
+++ b/JFMC_CuFluoPeakFit.cpp
@@ -39,6 +39,10 @@ int main(int argc, char* argv[]) {
   sprintf(savename,"/mnt/pcmoench_jungfrau_data/jungfrau_ana_sophie/M%s_CalibAna/Fluo_comb.root", module_str.c_str());
   TFile* comb_file = new TFile((const char *)(savename),"READ");
 
+  jungfrauPixelMask *pixelMaskObject = new jungfrauPixelMask();
+  static int pixel_mask [NCH];
+  pixelMaskObject->initialisePixelMask(pixel_mask);
+
   TH1F* peak_fit_pos = new TH1F("peak_fit_pos","",100,250,400);
   TH1F* peak_fit_poserr = new TH1F("peak_fit_poserr","",100,0,2);
   TH2F* peak_fit_pos_2d = new TH2F("peak_fit_pos_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
@@ -61,8 +65,10 @@ int main(int argc, char* argv[]) {
   TH1F* gain_fit_isQuad = new TH1F("gain_fit_isQuad","",100,250,400);
   TH1F* gain_fit_isBulk = new TH1F("gain_fit_isBulk","",100,250,400);
 
-  float noise_pos;
-  float noise_err;
+  int low_bin_noise = 101;
+  int high_bin_noise = 301;
+  int low_bin_peak = 301;
+  int high_bin_peak = 601;
 
   for (int j=1; j<9; j++) {
     cout << "slice " << j << endl;
@@ -76,67 +82,30 @@ int main(int argc, char* argv[]) {
       if (i%10000==0){cout << "another 10k" << endl;}
 
       TH1D* proj = adc2d_j->ProjectionX("bin1",i-(65536*(j-1))+1,i-(65536*(j-1))+1);
-      proj->Draw();
-	
-      if (proj->Integral(100,300)!=0 && proj->Integral(300,600)!=0) {
 
-	proj->Rebin(4);
-	proj->SetStats(kTRUE);
+      if (proj->Integral(low_bin_noise,high_bin_noise)!=0 && proj->Integral(low_bin_peak,high_bin_peak)!=0) {
 
 	// noise
-	proj->GetXaxis()->SetRangeUser(-100,100);
-	proj->Fit("gaus","Q","",-50,50);
-	proj->Draw();
-	c1->Update();
-	TF1 *fit = proj->GetFunction("gaus");
-	noise_pos = fit->GetParameter(1);
-	noise_err = fit->GetParError(1);
-	noise_fit_pos->Fill(noise_pos);
-	noise_fit_pos_2d->Fill(i%NC,i/NC,noise_pos);
-	noise_fit_poserr->Fill(noise_err);
-	noise_fit_poserr_2d->Fill(i%NC,i/NC,noise_err);
+	TH1D *proj_noise = dynamic_cast<TH1D*>(proj->Rebin(4,"proj_noise"));
+	proj_noise->SetStats(kTRUE);
+	proj_noise->GetXaxis()->SetRangeUser(proj->GetBinLowEdge(low_bin_noise),proj->GetBinLowEdge(high_bin_noise+1));
+	proj_noise->Fit("gaus","Q","",-50,50);
+	TF1 *fit = proj_noise->GetFunction("gaus");
 
-	if ((i >= 58000 && i < 58000+10) || // bulk
-	    (i >= 10 && i < 10+10) || // edge
-	    (i >= 1024+10 && i < 1024+10+10) || // inner edge
-	    (i >= (256*1024)+10 && i < (256*1024)+10+10) || // double
-	    (i >= (257*1024)+10 && i < (257*1024)+10+10) || // next to double
-	    (i == (255*1024)+255) // quad
-	    ) {
-
-	  string pixel_type = "x";
-	  if (i >= 58000 && i < 58000+10) {
-	    pixel_type = "b";
-	  } else if (i >= 10 && i < 10+10) {
-	    pixel_type = "e";
-	  } else if (i >= 1024+10 && i < 1024+10+10) {
-	    pixel_type = "ie";
-	  } else if (i >= (256*1024)+10 && i < (256*1024)+10+10) {
-	    pixel_type = "d";
-	  } else if (i >= (257*1024)+10 && i < (257*1024)+10+10) {
-	    pixel_type = "ntd";
-	  } else if (i == (255*1024)+255) {
-	    pixel_type = "q";
-	  }
-
-	  proj->GetXaxis()->SetTitle("Pedestal corrected ADC [ADU]");
-	  TPaveStats *st0 = (TPaveStats*)proj->FindObject("stats");
-	  st0->SetX1NDC(0.65);
-	  st0->SetX2NDC(0.94);
-	  st0->SetY1NDC(0.75);
-	  st0->SetY2NDC(0.94);
-	  st0->SetBorderSize(0);
-	  sprintf(savename,"plots/M%s/CuFluo/proj_noise_%s_%d.png", module_str.c_str(), pixel_type.c_str(), i);
-	  c1->SaveAs((const char *)(savename));
-	}
+	noise_fit_pos->Fill(fit->GetParameter(1));
+	noise_fit_pos_2d->Fill(i%NC,i/NC,fit->GetParameter(1));
+	noise_fit_poserr->Fill(fit->GetParError(1));
+	noise_fit_poserr_2d->Fill(i%NC,i/NC,fit->GetParError(1));
 
 	// peak
-	proj->GetXaxis()->SetRangeUser(100,400);
+	TH1D *proj_peak = dynamic_cast<TH1D*>(proj->Rebin(4,"proj_peak"));
+	proj_peak->SetStats(kTRUE);
+	proj_peak->GetXaxis()->SetRangeUser(proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));
 
 	Double_t mypar[6];
 	mypar[0] = 0.0;
 	mypar[1] = 0.0;
-	mypar[2] = proj->GetBinCenter(proj->GetMaximumBin());
+	mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
 	mypar[3] = 19.;
 	mypar[4] = 60.;
 	mypar[5] = 0.18;
@@ -147,7 +116,7 @@ int main(int argc, char* argv[]) {
 	thiscalibration->setStartParametersKb(mypar);
 	thiscalibration->fixParameter(0,0.); // no background
 	thiscalibration->fixParameter(1,0.);
-	TF1* fittedfun = thiscalibration->fitSpectrum(proj,mypar,emypar);
+	TF1* fittedfun = thiscalibration->fitSpectrum(proj_peak,mypar,emypar);
 
 	peak_fit_pos->Fill(mypar[2]);
 	peak_fit_poserr->Fill(emypar[2]);
@@ -177,11 +146,23 @@ int main(int argc, char* argv[]) {
 	    pixel_type = "q";
 	  }
 	    
-	  proj->Draw();
+	  proj_noise->Draw();
+	  c1->Update();
+	  proj_noise->GetXaxis()->SetTitle("Pedestal corrected ADC [ADU]");
+	  TPaveStats *st0 = (TPaveStats*)proj_noise->FindObject("stats");
+	  st0->SetX1NDC(0.65);
+	  st0->SetX2NDC(0.94);
+	  st0->SetY1NDC(0.75);
+	  st0->SetY2NDC(0.94);
+	  st0->SetBorderSize(0);
+	  sprintf(savename,"plots/M%s/CuFluo/proj_noise_%s_%d.png", module_str.c_str(), pixel_type.c_str(), i);
+	  c1->SaveAs((const char *)(savename));
+
+	  proj_peak->Draw();
 	  fittedfun->Draw("same");
 	  c1->Update();
-	  proj->GetXaxis()->SetTitle("Pedestal corrected ADC [ADU]");
-	  TPaveStats *st = (TPaveStats*)proj->FindObject("stats");
+	  proj_peak->GetXaxis()->SetTitle("Pedestal corrected ADC [ADU]");
+	  TPaveStats *st = (TPaveStats*)proj_peak->FindObject("stats");
 	  st->SetX1NDC(0.22);
 	  st->SetX2NDC(0.55);
 	  st->SetY1NDC(0.55);
@@ -192,36 +173,44 @@ int main(int argc, char* argv[]) {
 	}
 
 	// gain
-	gain_fit->Fill(mypar[2] - noise_pos);
-	gain_fiterr->Fill(sqrt(pow(emypar[2],2) + pow(noise_err,2)));
-	gain_fit_2d->Fill(i%NC,i/NC,mypar[2] - noise_pos);
-	gain_fiterr_2d->Fill(i%NC,i/NC,sqrt(pow(emypar[2],2) + pow(noise_err,2)));
+	gain_fit->Fill(mypar[2] - fit->GetParameter(1));
+	gain_fiterr->Fill(sqrt(pow(emypar[2],2) + pow(fit->GetParError(1),2)));
+	gain_fit_2d->Fill(i%NC,i/NC,mypar[2] - fit->GetParameter(1));
+	gain_fiterr_2d->Fill(i%NC,i/NC,sqrt(pow(emypar[2],2) + pow(fit->GetParError(1),2)));
 
 	if (isEdge(i)) {
-	  gain_fit_isEdge->Fill(mypar[2] - noise_pos);
+	  gain_fit_isEdge->Fill(mypar[2] - fit->GetParameter(1));
 	}
 	if (isInnerEdge(i)) {
-	  gain_fit_isInnerEdge->Fill(mypar[2] - noise_pos);
+	  gain_fit_isInnerEdge->Fill(mypar[2] - fit->GetParameter(1));
 	}
 	if (isDouble(i)) {
-	  gain_fit_isDouble->Fill(mypar[2] - noise_pos);
+	  gain_fit_isDouble->Fill(mypar[2] - fit->GetParameter(1));
 	}
 	if (isNextToDouble(i)) {
-	  gain_fit_isNextToDouble->Fill(mypar[2] - noise_pos);
+	  gain_fit_isNextToDouble->Fill(mypar[2] - fit->GetParameter(1));
 	}
 	if (isQuad(i)) {
-	  gain_fit_isQuad->Fill(mypar[2] - noise_pos);
+	  gain_fit_isQuad->Fill(mypar[2] - fit->GetParameter(1));
 	}
 	if (isBulk(i)) {
-	  gain_fit_isBulk->Fill(mypar[2] - noise_pos);
+	  gain_fit_isBulk->Fill(mypar[2] - fit->GetParameter(1));
 	}
 	  
 	delete thiscalibration;
+	delete proj_noise;
+	delete proj_peak;
+	delete proj;
 
+      } else {
+	pixel_mask[i] = 0;
       }
     }
   }
 
+  sprintf(savename,"plots/M%s/CuFluo/pixelmask_afterfit.png", module_str.c_str());
+  pixelMaskObject->plotPixelMask(pixel_mask,savename);
+
   TCanvas *mapcanvas = new TCanvas("mapcanvas","",150,10,800,400);
   mapcanvas->SetLeftMargin(0.1);
   mapcanvas->SetRightMargin(0.13);
diff --git a/run_JFModuleCalib_CuFBDCS.txt b/run_JFModuleCalib_CuFBDCS.txt
index 3cff3be..1eca76e 100644
--- a/run_JFModuleCalib_CuFBDCS.txt
+++ b/run_JFModuleCalib_CuFBDCS.txt
@@ -35,10 +35,12 @@ Module 022 - 1M	bottom LCLS, PX
 
 Module 027 - old HDI (no current source scan). sent to ESRF with Paolo
 ./JFMC_CuFluoPeak 027 /data_pool/Module_027_Calib FCu_40kvp_60mA_10us_500Hz_QS_pede FCu_40kvp_60mA_10us_500Hz_QS_beam
+./JFMC_CuFluoPeakFit 027
 
 
 Module 040 - partly etched. sent to ESRF with Paolo
 ./JFMC_CuFluoPeak 040 /data_pool/Module_040_Calib Cu_FLuo_240317_500Hz_10us_QS_pede Cu_FLuo_240317_500Hz_10us_QS_beam
+./JFMC_CuFluoPeakFit 040
 ./JFMC_CurrentSourceScan 040 /data_pool/Module_040_Calib CS_240322_scan