Julia: Add peak search algorithms

2 files changed, 78 insertions, 0 deletions

diff --git a/julia/CrystFEL/src/CrystFEL.jl b/julia/CrystFEL/src/CrystFEL.jl
index daea5284..230def00 100644
--- a/julia/CrystFEL/src/CrystFEL.jl
+++ b/julia/CrystFEL/src/CrystFEL.jl
@@ -82,4 +82,8 @@ include("millepede.jl")
 using .Millepede
 export Mille
 
+include("peaksearch.jl")
+using .PeakSearch
+export zaefpeaks, peakfinder8, peakfinder9
+
 end  # of module
diff --git a/julia/CrystFEL/src/peaksearch.jl b/julia/CrystFEL/src/peaksearch.jl
new file mode 100644
index 00000000..aaaee16c
--- /dev/null
+++ b/julia/CrystFEL/src/peaksearch.jl
@@ -0,0 +1,74 @@
+module PeakSearch
+
+import ..CrystFEL: libcrystfel
+import ..CrystFEL.Images: InternalImage
+import ..CrystFEL.PeakLists: PeakList, InternalPeakList
+
+export zaefpeaks, peakfinder8, peakfinder9
+
+
+function tf10(val)
+    if val
+        return 1
+    else
+        return 0
+    end
+end
+
+
+function zaefpeaks(image; threshold=100, mingrad=100000, minsnr=5,
+        radiusinn=4, radiusmid=5, radiusout=7, usesaturated=true)
+    out = @ccall libcrystfel.search_peaks(image.internalptr::Ptr{InternalImage},
+                                          threshold::Cfloat,
+                                          mingrad::Cfloat,
+                                          minsnr::Cfloat,
+                                          radiusinn::Cdouble,
+                                          radiusmid::Cdouble,
+                                          radiusout::Cdouble,
+                                          tf10(usesaturated)::Cint)::Ptr{InternalPeakList}
+    if out == C_NULL
+        throw(ErrorException("Peak search failed"))
+    end
+    PeakList(out)
+end
+
+
+
+function peakfinder8(image; threshold=100, minsnr=5, minpix=2, maxpix=200,
+        localbg=3, minres=0, maxres=5000, usesaturated=true, maxpeaks=2000)
+    out = @ccall libcrystfel.peakfinder8(image.internalptr::Ptr{InternalImage},
+                                         maxpeaks::Cint,
+                                         threshold::Cfloat,
+                                         minsnr::Cfloat,
+                                         minpix::Cint,
+                                         maxpix::Cint,
+                                         localbg::Cint,
+                                         minres::Cint,
+                                         maxres::Cint,
+                                         tf10(usesaturated)::Cint,
+                                         0::Cint,
+                                         C_NULL::Ptr{Cvoid})::Ptr{InternalPeakList}
+    if out == C_NULL
+        throw(ErrorException("Peak search failed"))
+    end
+    PeakList(out)
+end
+
+
+function peakfinder9(image; minsnrbig=7, minsnrpeak=6, minsnrwhole=5, minbgsig=11,
+        brightpxcut=-Inf, window=5)
+    out = @ccall libcrystfel.search_peaks_peakfinder9(image.internalptr::Ptr{InternalImage},
+                                                      minsnrbig::Cfloat,
+                                                      minsnrpeak::Cfloat,
+                                                      minsnrwhole::Cfloat,
+                                                      minbgsig::Cfloat,
+                                                      brightpxcut::Cfloat,
+                                                      window::Cint)::Ptr{InternalPeakList}
+    if out == C_NULL
+        throw(ErrorException("Peak search failed"))
+    end
+    PeakList(out)
+end
+
+
+end   # of module