Added ability to ignore channels in raw data files (-ignorechan)

leafwell · Jun 3, 2017 · 2fade8e · 2fade8e
1 parent 6d23e56
commit 2fade8e
Show file tree

Hide file tree

Showing 34 changed files with 6,000 additions and 5,972 deletions.
diff --git a/clig/mpiprepsubband_cmd.cli b/clig/mpiprepsubband_cmd.cli
@@ -47,6 +47,7 @@ Int     -nsub   nsub    {The number of sub-bands to use} \
 Int     -downsamp downsamp {The number of neighboring bins to co-add} \
 	-r 1 128 -d 1
 String -mask    maskfile {File containing masking information to use}
+String -ignorechan ignorechanstr {Comma separated string (no spaces!) of channels to ignore (or file containing such string).  Ranges are specified by min:max[:step]}
 
 # Rest of command line:
 

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 "17Mar15" "Clig-manuals" "Programmer's Manual"
+.TH "prepdata" 1 "03Jun17" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -47,6 +47,7 @@ prepdata \- Prepares a raw data file for pulsar searching or folding (conversion
 [-shorts]
 [-dm dm]
 [-mask maskfile]
+[-ignorechan ignorechanstr]
 infile ...
 .\" cligPart SYNOPSIS end
 
@@ -130,6 +131,10 @@ Default: `0'
 File containing masking information to use,
 .br
 1 String value
+.IP -ignorechan
+Comma separated string (no spaces!) of channels to ignore (or file containing such string).  Ranges are specified by min:max[:step],
+.br
+1 String value
 .IP infile
 Input data file name.  If the data is not in a known raw format, it should be a single channel of single-precision floating point data.  In this case a '.inf' file with the same root filename must also exist (Note that this means that the input data file must have a suffix that starts with a period).
 .\" cligPart OPTIONS end

diff --git a/clig/prepdata_cmd.cli b/clig/prepdata_cmd.cli
@@ -43,6 +43,7 @@ Flag   -shorts  shorts  {Use short ints for the output data instead of floats}
 Double  -dm      dm      {The dispersion measure to de-disperse (cm^-3 pc)} \
 	-r 0 oo  -d 0
 String -mask    maskfile {File containing masking information to use}
+String -ignorechan ignorechanstr {Comma separated string (no spaces!) of channels to ignore (or file containing such string).  Ranges are specified by min:max[:step]}
 
 # Rest of command line:
 

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 "21Apr15" "Clig-manuals" "Programmer's Manual"
+.TH "prepfold" 1 "03Jun17" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -95,6 +95,7 @@ prepfold \- Prepares (if required) and folds raw radio data, standard time serie
 [-w w]
 [-wdot wdot]
 [-mask maskfile]
+[-ignorechan ignorechanstr]
 [-events]
 [-days]
 [-mjds]
@@ -373,6 +374,10 @@ Default: `0'
 File containing masking information to use,
 .br
 1 String value
+.IP -ignorechan
+Comma separated string (no spaces!) of channels to ignore (or file containing such string).  Ranges are specified by min:max[:step],
+.br
+1 String value
 .IP -events
 Use a event file instead of a time series (.dat) file.
 .IP -days

diff --git a/clig/prepfold_cmd.cli b/clig/prepfold_cmd.cli
@@ -119,6 +119,8 @@ Double -wdot wdot    {Rate of advance of periastron (deg/yr)} \
 
 String -mask    maskfile   {File containing masking information to use}
 
+String -ignorechan ignorechanstr {Comma separated string (no spaces!) of channels to ignore (or file containing such string).  Ranges are specified by min:max[:step]}
+
 # Parameters if we are using events instead of a timeseries
 
 Flag -events events  {Use a event file instead of a time series (.dat) file}

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 "17Mar15" "Clig-manuals" "Programmer's Manual"
+.TH "prepsubband" 1 "03Jun17" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -53,6 +53,7 @@ prepsubband \- Converts a raw radio data file into many de-dispersed time-series
 [-downsamp downsamp]
 [-dmprec dmprec]
 [-mask maskfile]
+[-ignorechan ignorechanstr]
 infile ...
 .\" cligPart SYNOPSIS end
 
@@ -168,6 +169,10 @@ Default: `2'
 File containing masking information to use,
 .br
 1 String value
+.IP -ignorechan
+Comma separated string (no spaces!) of channels to ignore (or file containing such string).  Ranges are specified by min:max[:step],
+.br
+1 String value
 .IP infile
 Input data file name.  If the data is not in a known raw format, it should be a single channel of single-precision floating point data.  In this case a '.inf' file with the same root filename must also exist (Note that this means that the input data file must have a suffix that starts with a period).
 .\" cligPart OPTIONS end

diff --git a/clig/prepsubband_cmd.cli b/clig/prepsubband_cmd.cli
@@ -54,6 +54,7 @@ Int     -downsamp downsamp {The number of neighboring bins to co-add} \
 Int     -dmprec dmprec  {The number of decimals in the precision of the DM in the filename.} \
         -r 2 4 -d 2
 String -mask    maskfile {File containing masking information to use}
+String -ignorechan ignorechanstr {Comma separated string (no spaces!) of channels to ignore (or file containing such string).  Ranges are specified by min:max[:step]}
 
 # Rest of command line:
 

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 "17Mar15" "Clig-manuals" "Programmer's Manual"
+.TH "rfifind" 1 "03Jun17" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -54,6 +54,7 @@ rfifind \- Examines radio data for narrow and wide band interference as well as
 [-zapchan zapchanstr]
 [-zapints zapintsstr]
 [-mask maskfile]
+[-ignorechan ignorechanstr]
 infile ...
 .\" cligPart SYNOPSIS end
 
@@ -156,17 +157,21 @@ The fraction of bad intervals that will mask a full channel,
 .br
 Default: `0.3'
 .IP -zapchan
-Comma separated string (no spaces!) of channels to explicitly remove from analysis (zero-offset).  Ranges are specified by min:max[:step],
+Comma separated string (no spaces!) of channels to explicitly mask.  Ranges are specified by min:max[:step],
 .br
 1 String value
 .IP -zapints
-Comma separated string (no spaces!) of intervals to explicitly remove from analysis (zero-offset).  Ranges are specified by min:max[:step],
+Comma separated string (no spaces!) of intervals to explicitly mask.  Ranges are specified by min:max[:step],
 .br
 1 String value
 .IP -mask
 File containing masking information to use,
 .br
 1 String value
+.IP -ignorechan
+Comma separated string (no spaces!) of channels to ignore (or file containing such string).  Ranges are specified by min:max[:step],
+.br
+1 String value
 .IP infile
 Input data file name(s)..
 .\" cligPart OPTIONS end

diff --git a/clig/rfifind_cmd.cli b/clig/rfifind_cmd.cli
@@ -50,9 +50,10 @@ Float  -chanfrac chantrigfrac {The fraction of bad channels that will mask a ful
 	-r 0.0 1.0 -d 0.7
 Float  -intfrac  inttrigfrac  {The fraction of bad intervals that will mask a full channel} \
 	-r 0.0 1.0 -d 0.3
-String -zapchan zapchanstr {Comma separated string (no spaces!) of channels to explicitly remove from analysis (zero-offset).  Ranges are specified by min:max[:step]}
-String -zapints zapintsstr {Comma separated string (no spaces!) of intervals to explicitly remove from analysis (zero-offset).  Ranges are specified by min:max[:step]}
+String -zapchan zapchanstr {Comma separated string (no spaces!) of channels to explicitly mask.  Ranges are specified by min:max[:step]}
+String -zapints zapintsstr {Comma separated string (no spaces!) of intervals to explicitly mask.  Ranges are specified by min:max[:step]}
 String -mask    maskfile {File containing masking information to use}
+String -ignorechan ignorechanstr {Comma separated string (no spaces!) of channels to ignore (or file containing such string).  Ranges are specified by min:max[:step]}
 
 # Rest of command line:
 

diff --git a/clig/show_pfd.1 b/clig/show_pfd.1
@@ -11,7 +11,7 @@
 .\" it edited by clig, remove the respective pair of cligPart-lines.
 .\"
 .\" cligPart TITLE
-.TH "show_pfd" 1 "03Apr14" "Clig-manuals" "Programmer's Manual"
+.TH "show_pfd" 1 "03Jun17" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME

diff --git a/docs/prepdata.1 b/docs/prepdata.1
@@ -11,7 +11,7 @@
 .\" it edited by clig, remove the respective pair of cligPart-lines.
 .\"
 .\" cligPart TITLE
-.TH "prepdata" 1 "17Mar15" "Clig-manuals" "Programmer's Manual"
+.TH "prepdata" 1 "03Jun17" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -47,6 +47,7 @@ prepdata \- Prepares a raw data file for pulsar searching or folding (conversion
 [-shorts]
 [-dm dm]
 [-mask maskfile]
+[-ignorechan ignorechanstr]
 infile ...
 .\" cligPart SYNOPSIS end
 
@@ -130,6 +131,10 @@ Default: `0'
 File containing masking information to use,
 .br
 1 String value
+.IP -ignorechan
+Comma separated string (no spaces!) of channels to ignore (or file containing such string).  Ranges are specified by min:max[:step],
+.br
+1 String value
 .IP infile
 Input data file name.  If the data is not in a known raw format, it should be a single channel of single-precision floating point data.  In this case a '.inf' file with the same root filename must also exist (Note that this means that the input data file must have a suffix that starts with a period).
 .\" cligPart OPTIONS end

diff --git a/docs/prepfold.1 b/docs/prepfold.1
@@ -11,7 +11,7 @@
 .\" it edited by clig, remove the respective pair of cligPart-lines.
 .\"
 .\" cligPart TITLE
-.TH "prepfold" 1 "21Apr15" "Clig-manuals" "Programmer's Manual"
+.TH "prepfold" 1 "03Jun17" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -95,6 +95,7 @@ prepfold \- Prepares (if required) and folds raw radio data, standard time serie
 [-w w]
 [-wdot wdot]
 [-mask maskfile]
+[-ignorechan ignorechanstr]
 [-events]
 [-days]
 [-mjds]
@@ -373,6 +374,10 @@ Default: `0'
 File containing masking information to use,
 .br
 1 String value
+.IP -ignorechan
+Comma separated string (no spaces!) of channels to ignore (or file containing such string).  Ranges are specified by min:max[:step],
+.br
+1 String value
 .IP -events
 Use a event file instead of a time series (.dat) file.
 .IP -days

diff --git a/docs/prepsubband.1 b/docs/prepsubband.1
@@ -11,7 +11,7 @@
 .\" it edited by clig, remove the respective pair of cligPart-lines.
 .\"
 .\" cligPart TITLE
-.TH "prepsubband" 1 "17Mar15" "Clig-manuals" "Programmer's Manual"
+.TH "prepsubband" 1 "03Jun17" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -53,6 +53,7 @@ prepsubband \- Converts a raw radio data file into many de-dispersed time-series
 [-downsamp downsamp]
 [-dmprec dmprec]
 [-mask maskfile]
+[-ignorechan ignorechanstr]
 infile ...
 .\" cligPart SYNOPSIS end
 
@@ -168,6 +169,10 @@ Default: `2'
 File containing masking information to use,
 .br
 1 String value
+.IP -ignorechan
+Comma separated string (no spaces!) of channels to ignore (or file containing such string).  Ranges are specified by min:max[:step],
+.br
+1 String value
 .IP infile
 Input data file name.  If the data is not in a known raw format, it should be a single channel of single-precision floating point data.  In this case a '.inf' file with the same root filename must also exist (Note that this means that the input data file must have a suffix that starts with a period).
 .\" cligPart OPTIONS end

diff --git a/docs/rfifind.1 b/docs/rfifind.1
@@ -11,7 +11,7 @@
 .\" it edited by clig, remove the respective pair of cligPart-lines.
 .\"
 .\" cligPart TITLE
-.TH "rfifind" 1 "17Mar15" "Clig-manuals" "Programmer's Manual"
+.TH "rfifind" 1 "03Jun17" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME
@@ -54,6 +54,7 @@ rfifind \- Examines radio data for narrow and wide band interference as well as
 [-zapchan zapchanstr]
 [-zapints zapintsstr]
 [-mask maskfile]
+[-ignorechan ignorechanstr]
 infile ...
 .\" cligPart SYNOPSIS end
 
@@ -156,17 +157,21 @@ The fraction of bad intervals that will mask a full channel,
 .br
 Default: `0.3'
 .IP -zapchan
-Comma separated string (no spaces!) of channels to explicitly remove from analysis (zero-offset).  Ranges are specified by min:max[:step],
+Comma separated string (no spaces!) of channels to explicitly mask.  Ranges are specified by min:max[:step],
 .br
 1 String value
 .IP -zapints
-Comma separated string (no spaces!) of intervals to explicitly remove from analysis (zero-offset).  Ranges are specified by min:max[:step],
+Comma separated string (no spaces!) of intervals to explicitly mask.  Ranges are specified by min:max[:step],
 .br
 1 String value
 .IP -mask
 File containing masking information to use,
 .br
 1 String value
+.IP -ignorechan
+Comma separated string (no spaces!) of channels to ignore (or file containing such string).  Ranges are specified by min:max[:step],
+.br
+1 String value
 .IP infile
 Input data file name(s)..
 .\" cligPart OPTIONS end

diff --git a/docs/show_pfd.1 b/docs/show_pfd.1
@@ -11,7 +11,7 @@
 .\" it edited by clig, remove the respective pair of cligPart-lines.
 .\"
 .\" cligPart TITLE
-.TH "show_pfd" 1 "03Apr14" "Clig-manuals" "Programmer's Manual"
+.TH "show_pfd" 1 "03Jun17" "Clig-manuals" "Programmer's Manual"
 .\" cligPart TITLE end
 
 .\" cligPart NAME

diff --git a/include/backend_common.h b/include/backend_common.h
@@ -67,19 +67,22 @@ struct spectra_info {
     int remove_zerodm;      // Do zero-DM substraction?
     int use_poln;           // The number of the specific polarization to use 0-num_polns-1
     int flip_bytes;         // Hack to flip the order of the bits in a byte of data
+    int num_ignorechans;    // Number of channels to explicitly ignore (set to zero)
     float zero_offset;      // A DC zero-offset value to apply to all the data
     float clip_sigma;       // Clipping value in standard deviations to use
     long double *start_MJD; // Array of long double MJDs for the file starts
     char **filenames;       // Array of the input file names
     FILE **files;           // Array of normal file pointers if needed
-    fitsfile **fitsfiles;   // Array of FITS file pointers if needed
+    fitsfile **fitsfiles;    // Array of FITS file pointers if needed
     float *padvals;         // Array of length num_channels for current padding values
     int *header_offset;     // Number of bytes to skip in each file to get to spectra
     int *start_subint;      // Starting ISUBINT in each file (for PSRFITS)
     int *num_subint;        // Number of subints per file
-    long long *start_spec;  // Starting spectra for each file (zero offset)
-    long long *num_spec;    // Number of spectra per file
-    long long *num_pad;     // Number of padding samples after each file
+    int *ignorechans;       // Array of channels to explicitly ignore (set to zero)
+    char *ignorechans_str; // String describing the ignorechans
+    long long *start_spec; // Starting spectra for each file (zero offset)
+    long long *num_spec;   // Number of spectra per file
+    long long *num_pad;    // Number of padding samples after each file
     int (*get_rawblock)(float *, struct spectra_info *, int *);  // Raw data block function pointer
     long long (*offset_to_spectra)(long long, struct spectra_info *);  // Shift into file(s) function pointer
 };
@@ -101,6 +104,7 @@ void get_channel(float chandat[], int channum, int numsubints, float rawdata[],
 int prep_subbands(float *fdata, float *rawdata, int *delays, int numsubbands, struct spectra_info *s, int transpose, int *maskchans, int *nummasked, mask *obsmask);
 int read_subbands(float *fdata, int *delays, int numsubbands, struct spectra_info *s, int transpose, int *padding, int *maskchans, int *nummasked, mask *obsmask);
 void flip_band(float *fdata, struct spectra_info *s);
+int *get_ignorechans(char *ignorechans_str, int minchan, int maxchan, int *num_ignorechans, char **filestr);
 
 /* zerodm.c */
 void remove_zerodm(float *fdata, struct spectra_info *s);
diff --git a/include/prepdata_cmd.h b/include/prepdata_cmd.h
@@ -77,6 +77,10 @@ typedef struct s_Cmdline {
   char maskfileP;
   char* maskfile;
   int maskfileC;
+  /***** -ignorechan: Comma separated string (no spaces!) of channels to ignore (or file containing such string).  Ranges are specified by min:max[:step] */
+  char ignorechanstrP;
+  char* ignorechanstr;
+  int ignorechanstrC;
   /***** uninterpreted command line parameters */
   int argc;
   /*@null*/char **argv;

diff --git a/include/prepfold_cmd.h b/include/prepfold_cmd.h
@@ -235,6 +235,10 @@ typedef struct s_Cmdline {
   char maskfileP;
   char* maskfile;
   int maskfileC;
+  /***** -ignorechan: Comma separated string (no spaces!) of channels to ignore (or file containing such string).  Ranges are specified by min:max[:step] */
+  char ignorechanstrP;
+  char* ignorechanstr;
+  int ignorechanstrC;
   /***** -events: Use a event file instead of a time series (.dat) file */
   char eventsP;
   /***** -days: Events are in days since the EPOCH in the '.inf' file (default is seconds) */

diff --git a/include/prepsubband_cmd.h b/include/prepsubband_cmd.h
@@ -99,6 +99,10 @@ typedef struct s_Cmdline {
   char maskfileP;
   char* maskfile;
   int maskfileC;
+  /***** -ignorechan: Comma separated string (no spaces!) of channels to ignore (or file containing such string).  Ranges are specified by min:max[:step] */
+  char ignorechanstrP;
+  char* ignorechanstr;
+  int ignorechanstrC;
   /***** uninterpreted command line parameters */
   int argc;
   /*@null*/char **argv;