Fixed conflict

clig/accelsearch.1

@@ -11,7 +11,7 @@
 .\" it edited by clig, remove the respective pair of cligPart-lines.
 .\"
 .\" cligPart TITLE
-.TH "accelsearch" 1 "07Dec16" "Clig-manuals" "Programmer's Manual"
+.TH "accelsearch" 1 "19Sep17" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -26,6 +26,7 @@ accelsearch \- Search an FFT or short time series for pulsars using a Fourier do
 [-lobin lobin]
 [-numharm numharm]
 [-zmax zmax]
+[-wmax wmax]
 [-sigma sigma]
 [-rlo rlo]
 [-rhi rhi]
@@ -69,6 +70,10 @@ The max (+ and -) Fourier freq deriv to search,
 1 Int value between 0 and 1200.
 .br
 Default: `200'
+.IP -wmax
+The max (+ and -) Fourier freq double derivs to search,
+.br
+1 Int value between 0 and 4000.
 .IP -sigma
 Cutoff sigma for choosing candidates,
 .br

clig/accelsearch_cmd.cli

@@ -18,6 +18,8 @@ Int -numharm numharm    {The number of harmonics to sum (power-of-two)}\
 	-r 1 32 -d 8
 Int -zmax    zmax       {The max (+ and -) Fourier freq deriv to search} \
 	-r 0 1200  -d 200
+Int -wmax    wmax       {The max (+ and -) Fourier freq double derivs to search} \
+	-r 0 4000
 Float -sigma sigma      {Cutoff sigma for choosing candidates}\
 	-r 1.0 30.0 -d 2.0
 Double -rlo     rlo     {The lowest Fourier frequency (of the highest harmonic!) to search} \

docs/accelsearch.1

@@ -11,7 +11,7 @@
 .\" it edited by clig, remove the respective pair of cligPart-lines.
 .\"
 .\" cligPart TITLE
-.TH "accelsearch" 1 "07Dec16" "Clig-manuals" "Programmer's Manual"
+.TH "accelsearch" 1 "19Sep17" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -26,6 +26,7 @@ accelsearch \- Search an FFT or short time series for pulsars using a Fourier do
 [-lobin lobin]
 [-numharm numharm]
 [-zmax zmax]
+[-wmax wmax]
 [-sigma sigma]
 [-rlo rlo]
 [-rhi rhi]
@@ -69,6 +70,10 @@ The max (+ and -) Fourier freq deriv to search,
 1 Int value between 0 and 1200.
 .br
 Default: `200'
+.IP -wmax
+The max (+ and -) Fourier freq double derivs to search,
+.br
+1 Int value between 0 and 4000.
 .IP -sigma
 Cutoff sigma for choosing candidates,
 .br

include/accel.h

@@ -25,94 +25,112 @@
 #define ACCEL_DZ  2
 /* Reciprocal of ACCEL_DZ */
 #define ACCEL_RDZ 0.5
+/* Stepsize in Fourier F-dot-dot */
+#define ACCEL_DW 20
+/* Reciprocal of ACCEL_DW */
+#define ACCEL_RDW 0.05
 /* Closest candidates we will accept as independent */
 #define ACCEL_CLOSEST_R 15.0
 /* Padding for .dat file reading so that we don't SEGFAULT */
 #define ACCEL_PADDING 2000
 
 typedef struct accelobs{
-  long long N;         /* Number of data points in observation */
-  long long numbins;   /* Number of spectral bins in the file */
-  long long lobin;     /* Lowest spectral bin present in the file */
-  long long highestbin;/* Highest spectral bin present in the file */
-  int fftlen;          /* Length of short FFTs to us in search */
-  int numharmstages;   /* Number of stages of harmonic summing */
-  int numz;            /* Number of f-dots searched */
-  int numbetween;      /* Highest fourier freq resolution (2=interbin) */
-  int numzap;          /* Number of birdies to zap */
-  int dat_input;       /* The input file is a short time series */
-  int mmap_file;       /* The file number if using MMAP */
-  int inmem;           /* True if we want to keep the full f/fdot plan in RAM */
-  int norm_type;       /* 0 = old-style block median, 1 = local-means power norm */
-  double dt;           /* Data sample length (s) */           
-  double T;            /* Total observation length */
-  double rlo;          /* Minimum fourier freq to search */
-  double rhi;          /* Maximum fourier freq to search */
-  double dr;           /* Stepsize in fourier freq (1/numbetween) */
-  double zlo;          /* Minimum fourier fdot to search */
-  double zhi;          /* Maximum fourier fdot to search */
-  double dz;           /* Stepsize in fourier fdot */
-  double baryv;        /* Average barycentric velocity during observation */
-  float nph;           /* Freq 0 level if requested, 0 otherwise */
-  float sigma;         /* Cutoff sigma to choose a candidate */
-  float *powcut;       /* Cutoff powers to choose a cand (per harmsummed) */
-  float *ffdotplane;   /* The full F-Fdot plane if working in memory */
-  double *lobins;      /* The low Fourier freq boundaries to zap (RFI) */
-  double *hibins;      /* The high Fourier freq boundaries to zap (RFI) */
-  long long *numindep; /* Number of independent spectra (per harmsummed) */
-  FILE *fftfile;       /* The FFT file that we are analyzing */
-  FILE *workfile;      /* A text file with candidates as they are found */
-  fcomplex *fft;       /* A pointer to the FFT for MMAPing or input time series */
-  char *rootfilenm;    /* The root filename for associated files. */
-  char *candnm;        /* The fourierprop save file for the fundamentals */
-  char *accelnm;       /* The filename of the final candidates in text */
-  char *workfilenm;    /* The filename of the working candidates in text */
-  int use_harmonic_polishing; /* Should we force harmonics to be related */
+    long long N;         /* Number of data points in observation */
+    long long numbins;   /* Number of spectral bins in the file */
+    long long lobin;     /* Lowest spectral bin present in the file */
+    long long highestbin;/* Highest spectral bin present in the file */
+    int maxkernlen;      /* Maximum full width (in points, not Fourier bins) of corr kernels */
+    int corr_uselen;     /* Number of good data points we will get from high-harm correlations */
+    int fftlen;          /* Length of short FFTs to us in search */
+    int numharmstages;   /* Number of stages of harmonic summing */
+    int numz;            /* Number of f-dots searched */
+    int numw;            /* Number of f-dot-dots searched */
+    int numbetween;      /* Highest fourier freq resolution (2=interbin) */
+    int numzap;          /* Number of birdies to zap */
+    int dat_input;       /* The input file is a short time series */
+    int mmap_file;       /* The file number if using MMAP */
+    int inmem;           /* True if we want to keep the full f-fdot plane in RAM */
+    int norm_type;       /* 0 = old-style block median, 1 = local-means power norm */
+    double dt;           /* Data sample length (s) */
+    double T;            /* Total observation length */
+    double rlo;          /* Minimum fourier freq to search */
+    double rhi;          /* Maximum fourier freq to search */
+    double dr;           /* Stepsize in fourier freq (1/numbetween) */
+    double zlo;          /* Minimum fourier fdot to search */
+    double zhi;          /* Maximum fourier fdot to search */
+    double dz;           /* Stepsize in fourier fdot */
+    double wlo;          /* Minimum fourier f-dot-dot to search */
+    double whi;          /* Maximum fourier f-dot-dot to search */
+    double dw;           /* Stepsize in fourier f-dot-dot */
+    double baryv;        /* Average barycentric velocity during observation */
+    float nph;            /* Freq 0 level if requested, 0 otherwise */
+    float sigma;          /* Cutoff sigma to choose a candidate */
+    float *powcut;        /* Cutoff powers to choose a cand (per harmsummed) */
+    float *ffdotplane;    /* The full f-fdot-fdotdot plane if working in memory */
+    double *lobins;      /* The low Fourier freq boundaries to zap (RFI) */
+    double *hibins;      /* The high Fourier freq boundaries to zap (RFI) */
+    long long *numindep;  /* Number of independent spectra (per harmsummed) */
+    FILE *fftfile;       /* The FFT file that we are analyzing */
+    FILE *workfile;      /* A text file with candidates as they are found */
+    fcomplex *fft;       /* A pointer to the FFT for MMAPing or input time series */
+    char *rootfilenm;    /* The root filename for associated files. */
+    char *candnm;        /* The fourierprop save file for the fundamentals */
+    char *accelnm;       /* The filename of the final candidates in text */
+    char *workfilenm;    /* The filename of the working candidates in text */
+    int use_harmonic_polishing; /* Should we force harmonics to be related */
 } accelobs;
 
 typedef struct accelcand{
-  float power;         /* Summed power level (normalized) */
-  float sigma;         /* Equivalent sigma based on numindep (above) */
-  int numharm;         /* Number of harmonics summed */
-  double r;            /* Fourier freq of first harmonic */
-  double z;            /* Fourier f-dot of first harmonic */
-  double *pows;        /* Optimized powers for the harmonics */
-  double *hirs;        /* Optimized freqs for the harmonics */
-  double *hizs;        /* Optimized fdots for the harmonics */
-  rderivs *derivs;     /* An rderivs structure for each harmonic */
+    float power;         /* Summed power level (normalized) */
+    float sigma;         /* Equivalent sigma based on numindep (above) */
+    int numharm;         /* Number of harmonics summed */
+    double r;            /* Fourier freq of first harmonic */
+    double z;            /* Fourier f-dot of first harmonic */
+    double w;            /* Fourier f-dot-dot of first harmonic */
+    double *pows;        /* Optimized powers for the harmonics */
+    double *hirs;        /* Optimized freqs for the harmonics */
+    double *hizs;        /* Optimized f-dots for the harmonics */
+    double *hiws;        /* Optimized f-dot-dots for the harmonics */
+    rderivs *derivs;     /* An rderivs structure for each harmonic */
 } accelcand;
 
 typedef struct kernel{
-  int z;               /* The fourier f-dot of the kernel */
-  int fftlen;          /* Number of complex points in the kernel */
-  int numgoodbins;     /* The number of good points you can get back */
-  int numbetween;      /* Fourier freq resolution (2=interbin) */
-  int kern_half_width; /* Half width (bins) of the raw kernel. */
-  fcomplex *data;      /* The FFTd kernel itself */
+    int z;               /* The fourier f-dot of the kernel */
+    int w;               /* The fourier f-dot-dot of the kernel */
+    int fftlen;          /* Number of complex points in the kernel */
+    int numgoodbins;     /* The number of good points you can get back */
+    int numbetween;      /* Fourier freq resolution (2=interbin) */
+    int kern_half_width; /* Half width (bins) of the raw kernel. */
+    fcomplex *data;      /* The FFTd kernel itself */
 } kernel;
 
 typedef struct subharminfo{
-  int numharm;       /* The number of sub-harmonics */
-  int harmnum;       /* The sub-harmonic number (fundamental = numharm) */
-  int zmax;          /* The maximum Fourier f-dot for this harmonic */
-  int numkern;       /* Number of kernels in the vector */
-  kernel *kern;      /* The kernels themselves */
-  unsigned short *rinds; /* Table of indices for Fourier Freqs */
+    int numharm;       /* The number of sub-harmonics */
+    int harmnum;       /* The sub-harmonic number (fundamental = numharm) */
+    int zmax;          /* The maximum Fourier f-dot for this harmonic */
+    int wmax;          /* The maximum Fourier f-dot-dot for this harmonic */
+    int numkern_zdim;  /* Number of kernels calculated in the z dimension */
+    int numkern_wdim;  /* Number of kernels calculated in the w dimension */
+    int numkern;       /* Total number of kernels in the vector */
+    kernel **kern;     /* A 2D array of the kernels themselves, with dimensions of z and w */
+    unsigned short *rinds; /* Table of lookup indices for Fourier Freqs: subharmonic r values corresponding to "fundamental" r values */
+    unsigned short *zinds; /* Table of lookup indices for Fourier F-dots */
 } subharminfo;
 
 typedef struct ffdotpows{
-  int numrs;          /* Number of Fourier freqs present */
-  int numzs;          /* Number of Fourier f-dots present */
-  int rlo;            /* Lowest Fourier freq present */
-  int zlo;            /* Lowest Fourier f-dot present */
-  float **powers;     /* Matrix of the powers */
-  unsigned short *rinds; /* Table of indices for Fourier Freqs */
+    long long rlo;      /* Lowest Fourier freq present */
+    int zlo;            /* Lowest Fourier f-dot present */
+    int wlo;            /* Lowest Fourier f-dot-dot present */
+    int numrs;          /* Number of Fourier freqs present */
+    int numzs;          /* Number of Fourier f-dots present */
+    int numws;          /* Number of Fourier f-dot-dots present */
+    float ***powers;     /* 3D Matrix of the powers */
+    unsigned short *rinds; /* Table of lookup indices for Fourier Freqs */
+    unsigned short *zinds; /* Table of lookup indices for Fourier f-dots */
 } ffdotpows;
 
 /* accel_utils.c */
 
-/* accel_utils.c */
-
 subharminfo **create_subharminfos(accelobs *obs);
 void free_subharminfos(accelobs *obs, subharminfo **shis);
 void create_accelobs(accelobs *obs, infodata *idata, 
@@ -127,7 +145,7 @@ void output_harmonics(GSList *list, accelobs *obs, infodata *idata);
 void free_accelcand(gpointer data, gpointer user_data);
 void print_accelcand(gpointer data, gpointer user_data);
 fcomplex *get_fourier_amplitudes(long long lobin, int numbins, accelobs *obs);
-ffdotpows *subharm_ffdot_plane(int numharm, int harmnum, 
+ffdotpows *subharm_fderivs_vol(int numharm, int harmnum, 
 			       double fullrlo, double fullrhi, 
 			       subharminfo *shi, accelobs *obs);
 ffdotpows *copy_ffdotpows(ffdotpows *orig);

include/accelsearch_cmd.h

@@ -25,6 +25,10 @@ typedef struct s_Cmdline {
   char zmaxP;
   int zmax;
   int zmaxC;
+  /***** -wmax: The max (+ and -) Fourier freq double derivs to search */
+  char wmaxP;
+  int wmax;
+  int wmaxC;
   /***** -sigma: Cutoff sigma for choosing candidates */
   char sigmaP;
   float sigma;