invert mu_map and add filtering to recon script

mu_map/recon/recon.py

@@ -67,18 +67,18 @@ OSMAPOSLParameters :=
 
   ; keywords that specify the filtering that occurs after every subiteration
   ; warning: do not normally use together with a prior
-  ;inter-iteration filter subiteration interval := 4
-  ;inter-iteration filter type := Separable Gaussian
+  inter-iteration filter subiteration interval := 4
+  inter-iteration filter type := Separable Gaussian
   ;post-filter type := Separable Gaussian
-  ;separable gaussian filter parameters :=
-    ;x-dir filter fwhm (in mm) := 6
-    ;y-dir filter fwhm (in mm) := 6
-    ;z-dir filter fwhm (in mm) := 6
-    ;x-dir maximum kernel size := 129
-    ;y-dir maximum kernel size := 129
-    ;z-dir maximum kernel size := 31
-    ;Normalise filter to 1 := 1
-  ;end separable gaussian filter parameters :=
+  separable gaussian filter parameters :=
+    x-dir filter fwhm (in mm) := 9.6
+    y-dir filter fwhm (in mm) := 9.6
+    z-dir filter fwhm (in mm) := 9.6
+    x-dir maximum kernel size := 128
+    y-dir maximum kernel size := 128
+    z-dir maximum kernel size := 33
+    Normalise filter to 1 := 1
+  end separable gaussian filter parameters :=
 
 END :=
 """
@@ -189,6 +189,11 @@ if __name__ == "__main__":
         type=str,
         help="a mu map for attenuation correction in DICOM or INTERFILE format",
     )
+    parser.add_argument(
+        "--skip_mu_map_z_inv",
+        action="store_true",
+        help="per default mu maps need to be inverted in z direction for attenuation correction to work correctly - this parameter can skip this",
+    )
     parser.add_argument(
         "--out", type=str, help="the filename to store the reconstruction"
     )
@@ -215,6 +220,8 @@ if __name__ == "__main__":
     stir.Verbosity_set(args.verbosity)
 
     mu_map = load_as_interfile(args.mu_map) if args.mu_map else None
+    if not args.skip_mu_map_z_inv:
+        mu_map = (mu_map[0], mu_map[1][::-1])
     mu_map_slices = None if mu_map is None else mu_map[1].shape[0]
 
     if args.recon: