Merge branch 'float_internals'. This is the new "master" branch of

PRESTO.
masonng-astro · Jan 29, 2014 · b890d10 · b890d10
2 parents 6b49859 + e2e7d41
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diff --git a/clig/accelsearch.1 b/clig/accelsearch.1
@@ -11,7 +11,7 @@
 .\" it edited by clig, remove the respective pair of cligPart-lines.
 .\"
 .\" cligPart TITLE
-.TH "accelsearch" 1 "03Jul11" "Clig-manuals" "Programmer's Manual"
+.TH "accelsearch" 1 "10Nov13" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -22,6 +22,7 @@ accelsearch \- Search an FFT or short time series for pulsars using a Fourier do
 .\" cligPart SYNOPSIS
 .SH SYNOPSIS
 .B accelsearch
+[-ncpus ncpus]
 [-lobin lobin]
 [-numharm numharm]
 [-zmax zmax]
@@ -30,19 +31,26 @@ accelsearch \- Search an FFT or short time series for pulsars using a Fourier do
 [-rhi rhi]
 [-flo flo]
 [-fhi fhi]
+[-inmem]
 [-photon]
 [-median]
 [-locpow]
 [-zaplist zaplist]
 [-baryv baryv]
-[-harmpolish]
+[-otheropt]
 [-noharmpolish]
 [-noharmremove]
 infile
 .\" cligPart SYNOPSIS end
 
 .\" cligPart OPTIONS
 .SH OPTIONS
+.IP -ncpus
+Number of processors to use with OpenMP,
+.br
+1 Int value between 1 and oo.
+.br
+Default: `1'
 .IP -lobin
 The first Fourier frequency in the data file,
 .br
@@ -68,11 +76,11 @@ Cutoff sigma for choosing candidates,
 .br
 Default: `2.0'
 .IP -rlo
-The lowest Fourier frequency to search,
+The lowest Fourier frequency (of the highest harmonic!) to search,
 .br
 1 Double value between 0.0 and oo.
 .IP -rhi
-The highest Fourier frequency to search,
+The highest Fourier frequency (of the highest harmonic!) to search,
 .br
 1 Double value between 0.0 and oo.
 .IP -flo
@@ -87,6 +95,8 @@ The highest frequency (Hz) (of the highest harmonic!) to search,
 1 Double value between 0.0 and oo.
 .br
 Default: `10000.0'
+.IP -inmem
+Compute full f-fdot plane in memory.  Very fast, but only for short time series..
 .IP -photon
 Data is poissonian so use freq 0 as power normalization.
 .IP -median
@@ -103,8 +113,8 @@ The radial velocity component (v/c) towards the target during the obs,
 1 Double value between -0.1 and 0.1.
 .br
 Default: `0.0'
-.IP -harmpolish
-Constrain harmonics to be harmonically related during polishing (on by default).
+.IP -otheropt
+Use the alternative optimization (for testing/debugging).
 .IP -noharmpolish
 Do not use 'harmpolish' by default.
 .IP -noharmremove

diff --git a/clig/accelsearch_cmd.cli b/clig/accelsearch_cmd.cli
@@ -10,6 +10,8 @@ Commandline full_cmd_line
 
 # Options (in order you want them to appear)
 
+Int -ncpus   ncpus      {Number of processors to use with OpenMP} \
+	-r 1 oo  -d 1
 Int -lobin   lobin      {The first Fourier frequency in the data file} \
 	-r 0 oo  -d 0
 Int -numharm numharm    {The number of harmonics to sum (power-of-two)}\
@@ -18,14 +20,15 @@ Int -zmax    zmax       {The max (+ and -) Fourier freq deriv to search} \
 	-r 0 1200  -d 200
 Float -sigma sigma      {Cutoff sigma for choosing candidates}\
 	-r 1.0 30.0 -d 2.0
-Double -rlo     rlo     {The lowest Fourier frequency to search} \
+Double -rlo     rlo     {The lowest Fourier frequency (of the highest harmonic!) to search} \
 	-r 0.0 oo
-Double -rhi     rhi     {The highest Fourier frequency to search} \
+Double -rhi     rhi     {The highest Fourier frequency (of the highest harmonic!) to search} \
 	-r 0.0 oo
 Double -flo     flo     {The lowest frequency (Hz) (of the highest harmonic!) to search} \
 	-r 0.0 oo -d 1.0
 Double -fhi     fhi     {The highest frequency (Hz) (of the highest harmonic!) to search} \
 	-r 0.0 oo -d 10000.0
+Flag   -inmem   inmem   {Compute full f-fdot plane in memory.  Very fast, but only for short time series.}
 Flag   -photon  photon  {Data is poissonian so use freq 0 as power normalization}
 Flag   -median  median  {Use block-median power normalization (default)}
 Flag   -locpow  locpow  {Use double-tophat local-power normalization (not usually recommended)}
@@ -34,7 +37,7 @@ String  -zaplist    zaplist \
 Double  -baryv      baryv \
         {The radial velocity component (v/c) towards the target during the obs} \
         -r -0.1 0.1  -d 0.0
-Flag   -harmpolish  harmpolish  {Constrain harmonics to be harmonically related during polishing (on by default)}
+Flag   -otheropt otheropt  {Use the alternative optimization (for testing/debugging)}
 Flag   -noharmpolish noharmpolish  {Do not use 'harmpolish' by default}
 Flag   -noharmremove noharmremove  {Do not remove harmonically related candidates (never removed for numharm = 1)}
 

diff --git a/clig/mpiprepsubband.1 b/clig/mpiprepsubband.1
@@ -11,7 +11,7 @@
 .\" it edited by clig, remove the respective pair of cligPart-lines.
 .\"
 .\" cligPart TITLE
-.TH "mpiprepsubband" 1 "14Oct11" "Clig-manuals" "Programmer's Manual"
+.TH "mpiprepsubband" 1 "31Aug12" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -38,8 +38,9 @@ mpiprepsubband \- Converts a raw radio data file into many de-dispersed time-ser
 [-if ifs]
 [-clip clip]
 [-noclip]
-[-runavg]
+[-invert]
 [-zerodm]
+[-runavg]
 [-numout numout]
 [-nobary]
 [-DE405]
@@ -98,10 +99,12 @@ Time-domain sigma to use for clipping (0.0 = no clipping, 6.0 = default,
 Default: `6.0'
 .IP -noclip
 Do not clip the data.  (The default is to _always_ clip!).
-.IP -runavg
-Running mean subtraction from the input data.
+.IP -invert
+For rawdata, flip (or invert) the band.
 .IP -zerodm
 Subtract the mean of all channels from each sample (i.e. remove zero DM).
+.IP -runavg
+Running mean subtraction from the input data.
 .IP -numout
 Output this many values.  If there are not enough values in the original data file, will pad the output file with the average value,
 .br

diff --git a/clig/mpiprepsubband_cmd.cli b/clig/mpiprepsubband_cmd.cli
@@ -30,8 +30,9 @@ Int    -if      ifs     {A specific IF to use if available (summed IFs is the de
 Float  -clip    clip    {Time-domain sigma to use for clipping (0.0 = no clipping, 6.0 = default} \
 	-r 0 1000.0  -d 6.0
 Flag   -noclip  noclip  {Do not clip the data.  (The default is to _always_ clip!)}
-Flag   -runavg  runavg  {Running mean subtraction from the input data}
+Flag   -invert  invert  {For rawdata, flip (or invert) the band}
 Flag   -zerodm  zerodm  {Subtract the mean of all channels from each sample (i.e. remove zero DM)}
+Flag   -runavg  runavg  {Running mean subtraction from the input data}
 Int    -numout  numout  {Output this many values.  If there are not enough values in the original data file, will pad the output file with the average value} \
 	-r 1 oo
 Flag   -nobary  nobary  {Do not barycenter the data}

diff --git a/clig/prepdata.1 b/clig/prepdata.1
@@ -11,7 +11,7 @@
 .\" it edited by clig, remove the respective pair of cligPart-lines.
 .\"
 .\" cligPart TITLE
-.TH "prepdata" 1 "23Mar10" "Clig-manuals" "Programmer's Manual"
+.TH "prepdata" 1 "31Aug12" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -38,6 +38,8 @@ prepdata \- Prepares a raw data file for pulsar searching or folding (conversion
 [-if ifs]
 [-clip clip]
 [-noclip]
+[-invert]
+[-zerodm]
 [-numout numout]
 [-downsamp downsamp]
 [-nobary]
@@ -94,6 +96,10 @@ Time-domain sigma to use for clipping (0.0 = no clipping, 6.0 = default,
 Default: `6.0'
 .IP -noclip
 Do not clip the data.  (The default is to _always_ clip!).
+.IP -invert
+For rawdata, flip (or invert) the band.
+.IP -zerodm
+Subtract the mean of all channels from each sample (i.e. remove zero DM).
 .IP -numout
 Output this many values.  If there are not enough values in the original data file, will pad the output file with the average value,
 .br

diff --git a/clig/prepdata_cmd.cli b/clig/prepdata_cmd.cli
@@ -30,6 +30,8 @@ Int    -if      ifs     {A specific IF to use if available (summed IFs is the de
 Float  -clip    clip    {Time-domain sigma to use for clipping (0.0 = no clipping, 6.0 = default} \
 	-r 0 1000.0  -d 6.0
 Flag   -noclip  noclip  {Do not clip the data.  (The default is to _always_ clip!)}
+Flag   -invert  invert  {For rawdata, flip (or invert) the band}
+Flag   -zerodm  zerodm  {Subtract the mean of all channels from each sample (i.e. remove zero DM)}
 Int    -numout  numout  {Output this many values.  If there are not enough values in the original data file, will pad the output file with the average value} \
 	-r 1 oo
 Int    -downsamp downsamp {The number of neighboring bins to co-add} \

diff --git a/clig/prepfold.1 b/clig/prepfold.1
@@ -11,7 +11,7 @@
 .\" it edited by clig, remove the respective pair of cligPart-lines.
 .\"
 .\" cligPart TITLE
-.TH "prepfold" 1 "10Dec12" "Clig-manuals" "Programmer's Manual"
+.TH "prepfold" 1 "21Feb13" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -36,6 +36,7 @@ prepfold \- Prepares (if required) and folds raw radio data, standard time serie
 [-window]
 [-topo]
 [-invert]
+[-zerodm]
 [-absphase]
 [-numwapps numwapps]
 [-if ifs]
@@ -133,6 +134,8 @@ Window correlator lags with a Hamming window before FFTing.
 Fold the data topocentrically (i.e. don't barycenter).
 .IP -invert
 For rawdata, flip (or invert) the band.
+.IP -zerodm
+Subtract the mean of all channels from each sample (i.e. remove zero DM).
 .IP -absphase
 Use the absolute phase associated with polycos.
 .IP -numwapps

diff --git a/clig/prepfold_cmd.cli b/clig/prepfold_cmd.cli
@@ -24,6 +24,7 @@ Flag   -wapp    wapp    {Raw data in Wideband Arecibo Pulsar Processor (WAPP) fo
 Flag   -window  window  {Window correlator lags with a Hamming window before FFTing}
 Flag   -topo    topo    {Fold the data topocentrically (i.e. don't barycenter)}
 Flag   -invert  invert  {For rawdata, flip (or invert) the band}
+Flag   -zerodm  zerodm  {Subtract the mean of all channels from each sample (i.e. remove zero DM)}
 Flag   -absphase absphase  {Use the absolute phase associated with polycos}
 Int    -numwapps numwapps  {Number of WAPPs used with contiguous frequencies} \
 	-r 1 8    -d 1

diff --git a/clig/prepsubband.1 b/clig/prepsubband.1
@@ -11,7 +11,7 @@
 .\" it edited by clig, remove the respective pair of cligPart-lines.
 .\"
 .\" cligPart TITLE
-.TH "prepsubband" 1 "08Feb12" "Clig-manuals" "Programmer's Manual"
+.TH "prepsubband" 1 "31Aug12" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -38,8 +38,9 @@ prepsubband \- Converts a raw radio data file into many de-dispersed time-series
 [-if ifs]
 [-clip clip]
 [-noclip]
-[-runavg]
+[-invert]
 [-zerodm]
+[-runavg]
 [-sub]
 [-subdm subdm]
 [-numout numout]
@@ -100,10 +101,12 @@ Time-domain sigma to use for clipping (0.0 = no clipping, 6.0 = default,
 Default: `6.0'
 .IP -noclip
 Do not clip the data.  (The default is to _always_ clip!).
-.IP -runavg
-Running mean subtraction from the input data.
+.IP -invert
+For rawdata, flip (or invert) the band.
 .IP -zerodm
 Subtract the mean of all channels from each sample (i.e. remove zero DM).
+.IP -runavg
+Running mean subtraction from the input data.
 .IP -sub
 Write subbands instead of de-dispersed data.
 .IP -subdm

diff --git a/clig/prepsubband_cmd.cli b/clig/prepsubband_cmd.cli
@@ -30,8 +30,9 @@ Int    -if      ifs     {A specific IF to use if available (summed IFs is the de
 Float  -clip    clip    {Time-domain sigma to use for clipping (0.0 = no clipping, 6.0 = default} \
 	-r 0 1000.0  -d 6.0
 Flag   -noclip  noclip  {Do not clip the data.  (The default is to _always_ clip!)}
-Flag   -runavg  runavg  {Running mean subtraction from the input data}
+Flag   -invert  invert  {For rawdata, flip (or invert) the band}
 Flag   -zerodm  zerodm  {Subtract the mean of all channels from each sample (i.e. remove zero DM)}
+Flag   -runavg  runavg  {Running mean subtraction from the input data}
 Flag   -sub     sub     {Write subbands instead of de-dispersed data}
 Double -subdm   subdm   {The DM to use when de-dispersing subbands for -sub} \
 	-r 0 4000.0  -d 0.0

diff --git a/clig/rfifind.1 b/clig/rfifind.1
@@ -11,7 +11,7 @@
 .\" it edited by clig, remove the respective pair of cligPart-lines.
 .\"
 .\" cligPart TITLE
-.TH "rfifind" 1 "14Oct11" "Clig-manuals" "Programmer's Manual"
+.TH "rfifind" 1 "31Aug12" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -38,6 +38,8 @@ rfifind \- Examines radio data for narrow and wide band interference as well as
 [-if ifs]
 [-clip clip]
 [-noclip]
+[-invert]
+[-zerodm]
 [-xwin]
 [-nocompute]
 [-rfixwin]
@@ -100,6 +102,10 @@ Time-domain sigma to use for clipping (0.0 = no clipping, 6.0 = default,
 Default: `6.0'
 .IP -noclip
 Do not clip the data.  (The default is to _always_ clip!).
+.IP -invert
+For rawdata, flip (or invert) the band.
+.IP -zerodm
+Subtract the mean of all channels from each sample (i.e. remove zero DM).
 .IP -xwin
 Draw plots to the screen as well as a PS file.
 .IP -nocompute

diff --git a/clig/rfifind_cmd.cli b/clig/rfifind_cmd.cli
@@ -30,6 +30,8 @@ Int    -if      ifs     {A specific IF to use if available (summed IFs is the de
 Float  -clip    clip    {Time-domain sigma to use for clipping (0.0 = no clipping, 6.0 = default} \
 	-r 0 1000.0  -d 6.0
 Flag   -noclip  noclip  {Do not clip the data.  (The default is to _always_ clip!)}
+Flag   -invert  invert  {For rawdata, flip (or invert) the band}
+Flag   -zerodm  zerodm  {Subtract the mean of all channels from each sample (i.e. remove zero DM)}
 Flag   -xwin    xwin    {Draw plots to the screen as well as a PS file}
 Flag   -nocompute nocompute {Just plot and remake the mask}
 Flag   -rfixwin rfixwin {Show the RFI instances on screen}

diff --git a/docs/accelsearch.1 b/docs/accelsearch.1
@@ -11,7 +11,7 @@
 .\" it edited by clig, remove the respective pair of cligPart-lines.
 .\"
 .\" cligPart TITLE
-.TH "accelsearch" 1 "03Jul11" "Clig-manuals" "Programmer's Manual"
+.TH "accelsearch" 1 "10Nov13" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -22,6 +22,7 @@ accelsearch \- Search an FFT or short time series for pulsars using a Fourier do
 .\" cligPart SYNOPSIS
 .SH SYNOPSIS
 .B accelsearch
+[-ncpus ncpus]
 [-lobin lobin]
 [-numharm numharm]
 [-zmax zmax]
@@ -30,19 +31,26 @@ accelsearch \- Search an FFT or short time series for pulsars using a Fourier do
 [-rhi rhi]
 [-flo flo]
 [-fhi fhi]
+[-inmem]
 [-photon]
 [-median]
 [-locpow]
 [-zaplist zaplist]
 [-baryv baryv]
-[-harmpolish]
+[-otheropt]
 [-noharmpolish]
 [-noharmremove]
 infile
 .\" cligPart SYNOPSIS end
 
 .\" cligPart OPTIONS
 .SH OPTIONS
+.IP -ncpus
+Number of processors to use with OpenMP,
+.br
+1 Int value between 1 and oo.
+.br
+Default: `1'
 .IP -lobin
 The first Fourier frequency in the data file,
 .br
@@ -68,11 +76,11 @@ Cutoff sigma for choosing candidates,
 .br
 Default: `2.0'
 .IP -rlo
-The lowest Fourier frequency to search,
+The lowest Fourier frequency (of the highest harmonic!) to search,
 .br
 1 Double value between 0.0 and oo.
 .IP -rhi
-The highest Fourier frequency to search,
+The highest Fourier frequency (of the highest harmonic!) to search,
 .br
 1 Double value between 0.0 and oo.
 .IP -flo
@@ -87,6 +95,8 @@ The highest frequency (Hz) (of the highest harmonic!) to search,
 1 Double value between 0.0 and oo.
 .br
 Default: `10000.0'
+.IP -inmem
+Compute full f-fdot plane in memory.  Very fast, but only for short time series..
 .IP -photon
 Data is poissonian so use freq 0 as power normalization.
 .IP -median
@@ -103,8 +113,8 @@ The radial velocity component (v/c) towards the target during the obs,
 1 Double value between -0.1 and 0.1.
 .br
 Default: `0.0'
-.IP -harmpolish
-Constrain harmonics to be harmonically related during polishing (on by default).
+.IP -otheropt
+Use the alternative optimization (for testing/debugging).
 .IP -noharmpolish
 Do not use 'harmpolish' by default.
 .IP -noharmremove