McXtrace Filter.comp: Better handling of non-standard inputfiles

mcxtrace-comps/examples/NBI/NBI_Lab_TOMO/NBI_Lab_TOMO.instr

@@ -101,7 +101,7 @@ ROTATED (0,Omega,0) RELATIVE Origin
 
 //chess king
 COMPONENT king =Filter(
-    material_datafile="Glass.dat", geometry="king.off",xwidth=1.5e-2,yheight=1.5e-2,zdepth=1.5e-2)
+    material_datafile="Glass.dat", mu_col=1, geometry="king.off",xwidth=1.5e-2,yheight=1.5e-2,zdepth=1.5e-2)
 AT(0,0,0) RELATIVE sample_mnt
 ROTATED (rx,ry,rz) RELATIVE sample_mnt
 
@@ -111,7 +111,7 @@ COMPONENT e_mon1 = E_monitor(
 AT(0,0,d_sample_det-15e-3) RELATIVE sample_mnt
 
 COMPONENT filter_air=Filter(
-    material_datafile="FilterAir_1mm.dat",xwidth=detw,yheight=deth,zdepth=1e-3*10)
+    material_datafile="FilterAir_1mm.dat", mu_col=1,xwidth=detw,yheight=deth,zdepth=1e-3*10)
 AT(0,0,d_sample_det-20e-3+1e-3-0.2) RELATIVE sample_mnt
 
 COMPONENT filter_Al=Filter(

mcxtrace-comps/examples/Tests_optics/Test_Filter/Test_Filter.instr

@@ -16,24 +16,25 @@
 * Test instrument for checking the Filter.comp component 
 *
 * %Parameters
-* filter_mat: []   Chemical symbol of the filter material
-* thickness:  [m]  thickness of the filter block
-* L0:         [AA] centre wavlength of the source
-* DL:         [AA] half width of the (uniform) wavelength distribution
-* F2:         [1]  add a 2nd filter component further away
+* filter_mat: []    Chemical symbol / datafile of the filter material
+* thickness:  [m]   thickness of the filter block
+* L0:         [AA]  centre wavlength of the source
+* DL:         [AA]  half width of the (uniform) wavelength distribution
+* F2:         [1]   add a 2nd filter component further away
+* mu_col:     [idx] Index of mu-column (from 0) in datafile (required for some inputs).
 *
 * %Example: DL=4.9 L0=5 filter_mat="Si.txt" Detector: l_mon1_I=1.31502e-07
 * %Example: DL=4.9 L0=5 filter_mat="Rh.txt" Detector: l_mon1_I=4.04921e-29
 * %Example: -n5e6 DL=4.9 L0=5 filter_mat="Ti.txt" F2=1 Detector: l_mon1_I=1.14111e-08
 * %Example: DL=4.9 L0=5 filter_mat="Al.txt" Detector: l_mon1_I=1.04427e-07
-* %Example: DL=4.9 L0=5 filter_mat="Glass.dat" Detector: l_mon1_I=1.645e-06
+* %Example: DL=4.9 L0=5 filter_mat="Glass.dat" mu_col=1 Detector: l_mon1_I=1.645e-06
 * %Example: DL=4.9 L0=5 filter_mat="Be.txt" Detector: l_mon1_I=0.000412661
-* %Example: DL=4.9 L0=5 filter_mat="FilterAir_1mm.dat" Detector: l_mon1_I=4.96145e-05
+* %Example: DL=4.9 L0=5 filter_mat="FilterAir_1mm.dat" mu_col=1 Detector: l_mon1_I=4.96145e-05
 *
 * %End
 *******************************************************************************/
 
-DEFINE INSTRUMENT Test_Filter(string filter_mat="Rh.txt",thickness=100e-6,L0=1,DL=0.1, F2=0)
+DEFINE INSTRUMENT Test_Filter(string filter_mat="Rh.txt",thickness=100e-6,L0=1,DL=0.1, F2=0, int mu_col=-1)
 
 DECLARE
 %{
@@ -61,12 +62,12 @@ COMPONENT l_mon0 = L_monitor(
 AT (0,0,1e-6) RELATIVE Source
 
 COMPONENT filter = Filter(
-    material_datafile=filter_mat, xwidth=0.1,yheight=0.1,zdepth=thickness
+    material_datafile=filter_mat, mu_col=mu_col, xwidth=0.1, yheight=0.1, zdepth=thickness
 )
 AT (0,0,0.5) RELATIVE Source
 
 COMPONENT filter2 = Filter(
-    material_datafile=filter_mat,xwidth=0.1, yheight=0.1, zdepth=thickness
+    material_datafile=filter_mat, mu_col=mu_col, xwidth=0.1, yheight=0.1, zdepth=thickness
 )
 WHEN(F2) AT (0,0,0.5+thickness+1e-3) RELATIVE Source
 

mcxtrace-comps/optics/Filter.comp

@@ -42,26 +42,22 @@
 * material_datafile: [str] File where the material parameters for the filter may be found. Format is similar to what may be found off the NIST website. [Be.txt]
 * geometry:   [str] File containing the polygon definition of a general shape object. When xwidth is also given, the object is rescaled accordingly (OFF/PLY)
 * fixed_delta:[0/1] Use a fixed delta to compute refraction - useful for debugging.
-* refraction: [0/1] If nonzero, refraction is enabled. (Only functional for box-geometery.)
+* mu_col:     [idx] Column index to pick up absorption length mu, counted from 0. Use with non-standard input file, e.g. 2-3 column files. -1 means attempt autodetect.
+* refraction: [0/1] If nonzero, refraction is enabled. (Only functional for basic geometries, does not yet work for OFF)
 *
 * %Link
-* Meshlab https://www.meshlab.net/
-* %Link
-* Geomview and Object File Format (OFF) <http://www.geomview.org>
-* %Link
-* Java version of Geomview (display only) jroff.jar <http://www.holmes3d.net/graphics/roffview/>
-* %Link
-* qhull <http://qhull.org>
-* %Linkink
-* Powercrust https://www.cs.ucdavis.edu/~amenta/powercrust.html
-* %Link
-* material datafile obtained from http://physics.nist.gov/cgi-bin/ffast/ffast.pl
+* <a href="https://www.meshlab.net/">Meshlab</a> - viewer for OFF files
+* <a href="http://www.geomview.org">Geomview and Object File Format (OFF)</a> - OFF file definition and examples
+* <a href="http://www.holmes3d.net/graphics/roffview/">jroff.jar - Java version of Geomview (display only)</a>
+* <a href="http://qhull.org">Qhull</a> - for calculating a convex hull from points.
+* <a href="https://www.cs.ucdavis.edu/~amenta/powercrust.html">Powercrust</a> - for reconstructing a solid geometry from a point cloud.
+* Most material datafile inpus may obtained from <a href="https://physics.nist.gov/PhysRefData/FFast/form.html<https://physics.nist.gov/PhysRefData/FFast/form.html">NIST FFast</a>
 * %End
 *******************************************************************************/
 DEFINE COMPONENT Filter
 
 SETTING PARAMETERS (refraction=0,fixed_delta=0,string material_datafile="Be.txt",
-    string geometry=0,xwidth=0,yheight=0,zdepth=0,radius=0)
+    string geometry=0,xwidth=0,yheight=0,zdepth=0,radius=0, int mu_col=-1)
 
 /* X-ray parameters: (x,y,z,kx,ky,kz,phi,t,Ex,Ey,Ez,p) */
 
@@ -163,23 +159,28 @@ INITIALIZE
     fprintf (stderr, "Warning(%s): %s not found in header of %s, set to 1\n", NAME_CURRENT_COMP, "rho", material_datafile);
     rho = 1;
   }
-  if (table.columns == 2) {
-    /*If we are using a 2 column format assume only attenuation and read from last column.
-      I.e. set the delta prefactor to 0*/
-     mu_c = 1;
-     delta_prefactor = 0;
-  } else if (table.columns == 3) {
-    /*If we are using a 3 column format assume only attenuation and read from second column.
-      I.e. set the delta prefactor to 0*/
-     mu_c = 1;
-     delta_prefactor = 0;
-  } else if (table.columns == 4) {
-    /*If we are using a 4 column format assume only attenuation and read from last column.
-      I.e. set the delta prefactor to 0*/
-     mu_c = 3;
-     delta_prefactor = 0;
-  } else {
-    mu_c = 5;
+  if (table.columns < 6) {
+    // "Few or many" columns, use mu_col to pinpoint mu column location
+    if (mu_col == -1 || mu_col >= table.columns) {
+      fprintf (stderr,
+               "Error(%s): Found %i columns in %s. Did NOT detect known NIST file format. Please give a relevant mu_col value to define the mu-column! Exit!\n",
+               NAME_CURRENT_COMP, table.columns, material_datafile);
+      exit (-1);
+    } else {
+      mu_c = mu_col;
+      delta_prefactor = 0;
+    }
+  } else if (table.columns >= 6) {
+    // ... fingers crossed this is "Legacy" NIST format
+    if (mu_col == -1) {
+      mu_c = 5;
+    } else if (mu_col < table.columns) {
+      mu_c = mu_col;
+    } else {
+      fprintf (stderr, "Error(%s): Found %i columns in %s and you gave a mu_col of %i. Please correct. Exit!\n", NAME_CURRENT_COMP, table.columns,
+               material_datafile, mu_col);
+      exit (-1);
+    }
     delta_prefactor = NA * (rho * 1e-24) / Ar * 2.0 * M_PI * RE;
   }
   if (10 * (double)mcget_ncount () > (table.max_x - table.min_x) / (table.step_x)) {
@@ -191,7 +192,7 @@ INITIALIZE
   if (shape != CUBE) {
     if (refraction) {
       fprintf (stderr, "Warning(%s): refraction=1 not supported with chosen geometry\n", NAME_CURRENT_COMP);
-      refraction=0;
+      refraction = 0;
     }
   }
 %}