.

restoration/restoration.cpp

@@ -84,7 +84,7 @@ int main(int argc, char *argv[])
 		cout << "<in_file>:  Raw input file in seaMass Input format (smi)" << endl;
 		cout << "            guidelines: Use pwiz-seamass to convert from mzML or vendor format" << endl;
 		cout << "<mz_res>:   MS resolution given as: \"b-splines per Th = 2^mz_res * 60 / 1.0033548378\"" << endl;
-		cout << "            guidelines: between 0 to 1 for ToF, 3 for Orbitrap" << endl;
+		cout << "            guidelines: between 0 to 1 for ToF (e.g. 1 is suitable for 30,000 resolution), 3 for Orbitrap" << endl;
 		cout << "<rt_res>:   LC resolution given as: \"b-splines per minute = 2^rt_res\"" << endl;
 		cout << "            guidelines: around 4" << endl;
 		cout << "<shrink>:   Amount of denoising given as: \"L1 shrinkage = 2^shrinkage\"" << endl;

seamass/SMOWriter.cpp

@@ -28,13 +28,17 @@
 SMOWriter::
 SMOWriter(const string& filename)
 {
-    file = H5Fcreate(filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
-    if (file < 0)
-    {
-            // throw exception
-            cerr << "problem opening smo" << endl;
-            throw "problem opening smo";
-    }
+	file = H5Fcreate(filename.c_str(), H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
+	if (file < 0)
+	{
+		file = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
+		if (file < 0)
+		{
+			// throw exception
+			cerr << "problem opening smo" << endl;
+			throw "problem opening smo";
+		}
+	}
 }
 
 
@@ -46,7 +50,8 @@ SMOWriter::
     {
         // throw exception
         cerr << "problem closing smo" << endl;
-    }
+		throw "problem closing smo";
+	}
 }
 
 

seamass/core.cpp

@@ -92,6 +92,23 @@ print(ostream& out) const
 ////////////////////////////////////////////////////////////////////////////////
 
 
+double CatmullRomInterpolate(
+	double y0, double y1,
+	double y2, double y3,
+	double mu)
+{
+	double a0, a1, a2, a3, mu2;
+
+	mu2 = mu*mu;
+	a0 = -0.5*y0 + 1.5*y1 - 1.5*y2 + 0.5*y3;
+	a1 = y0 - 2.5*y1 + 2 * y2 - 0.5*y3;
+	a2 = -0.5*y0 + 0.5*y2;
+	a3 = y1;
+
+	return a0*mu*mu2 + a1*mu2 + a2*mu + a3;
+}
+
+
 void bin_mzs_intensities(vector< vector<double> >& mzs,
                          vector< vector<double> >& intensities,
 						 ii instrument_type,