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| coord_convert.m Coord_latlon.m dfa.m dfa2.m dfam.m dfam2.m loadmag.m loadmsp.m magplot.m make_kappa.m mapper2.m photo.m plotmag.m plotmagv3.m rs1.m rs2.m Rigidity.m T87.m yearmonthday.m |
dfa.c dfa2.c mexT87.c preparephoto.c preparemag.c |
*
PURPOSE:
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OUTPUT:
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NOTES:
*
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*
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*
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* coord_convert.m
PURPOSE: Convert between different
coordinate systems
USAGE:
[out1,out2,out3,GST,SLONG,SRASN,SDEC,PSI,MLT]=coord_convert(initial,final,in1,in2,in3,control1,year,month,day,doy,control2,hour,minute,second)
OUTPUT: r,lat,lon or x,y,z in
the chosen coordinate system
LOCATION: /home/wanliss/matlab/Coordinate_Conversion
NOTES:
%
% [out1,out2,out3,GST,SLONG,SRASN,SDEC,PSI,MLT]=coord_convert(initial,final,in1,in2,in3,control1,year,month,day,doy,control2,hour,minute,second)
%
% Coordinate Systems Available: (use these numbers for 'initial' and 'final')
% 1 - AACGM
% 2 - GEI
% 3 - GEO
% 4 - GSE
% 5 - GSM
% 6 - MAG
% 7 - SM
%
% INPUTS:
% --------
%
% initial - integer value that corresponds to the input coordinate system
% final - integer value that corresponds to the desired output coordinate system
% in1 - input coordinate variable 1 - if input is in Cartesian, this is X in Earth Radii (Re)
% - if input is Spherical, this is height above ground in kilometers (km) (i.e. Radial Distance minus Earth Radius)
% in2 - input coordinate variable 2 - if input is in Cartesian, this is Y in Earth Radii (Re)
% - if input is Spherical, this is latitude in degrees (deg) the range is [-90 90]
% in3 - input coordinate variable 3 - if input is in Cartesian, this is Z in Earth Radii (Re)
% - if input is Spherical, this is longitude in degrees (deg) the range is (-inf inf)
% control1 - integer value that specifies the form for the input and output:
% switch (control1)
% case 1 - in and out are both Cartesian
% case 2 - in is Cartesian, out is Spherical
% case 3 - in is Spherical, out is Cartesian
% case 4 - in and out are both Spherical
% year,month,day,doy - year, month, day, and day of year for the coordinate conversion (integer values only)
% control2 - since (month + day) and (doy) specifies the same information, only one of the two needs to be specified
% control2 = 1 - use month and day, doy becomes a dummy variable and will not be used, input anything for doy
% control2 = 2 - use doy, month and day become dummy variables and will not be used, input anything for month and day
% hour,minute,second - specifies the time for the coordinate conversion (integer values only)
%
%
% OUTPUTS:
% ---------
%
% out1,out2,out3 - output coordinate variables
% - these are in the same format as in1, in2, and in3
%
% GST - Greenwich Mean Sidereal Time (hr)
% SLONG - Solar Longitude Along Ecliptic (deg)
% SRASN - Solar Right Ascension (hr)
% SDEC - Solar Declination (deg)
% PSI - Dipole Tilt Angle (deg)
% MLT - Magnetic Local Time (hr)
%
% Note: if AACGM is not selected as either input or output, then MLT will not be available
% if AACGM is selected as both input or output, then GST, SLONG, SRASN, SDEC, and PSI will not be available
* Coord_latlon.m
PURPOSE: CANOPUS station locations
in various coordinate systems
USAGE: [lat,lon]=Coord_latlon('RANK110','PACE');
OUTPUT: lat,lon in the chosen
coordinate system
LOCATION: /home/wanliss/matlab/CANOPUS.dir/Plotmpa
NOTES: Input a selected latitude
and outputs that latitude
and the correct PACE longitude
station='RANK110','RANK230','GILL110','GILL230',
'PINA110','PINA230','FSMI110','FSMI230'
coord='GEOD','EDFL','AACGM','PACE'
This code will output the correct latitude and longitude in
the
chosen coordinate system for the 1995 epoch.
e.g. [lat,lon]=Coord_latlon('RANK110','PACE');
James Wanliss
November 2000
Was preceeded by PACElon.m
*
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* dfa.m
(superseded by dfa2.m)
PURPOSE: Calculate Hurst exponent via detrended
fluctuation analysis
USAGE: [x,y]=dfa(d,K,h,ii,l,MINBOX,u,MAXBOX,s,data)
OUTPUT: Slope of log(x) versus
log(y) gives the Hurst exponent
LOCATION: /home/wanliss/matlab/Chaos.dir
NOTES: Utilises dfa.c
% -d K detrend using a polynomial
of degree K
% (default: K=1 -- linear detrending)
% -h print this usage summary
% -i input series is already integrated
% -l MINBOX smallest box width (default: 2K+2)
% -u MAXBOX largest box width (default: NPTS/4)
% -s sliding window DFA
% The standard input should contain one column of data in text format.
% The standard output is two columns: log(n) and log(F) [base 10 logarithms],
% where n is the box size and F is the root mean square fluctuation.
%
% fBm is by definition already integrated
% fGm must be integrated
%
% Use MINBOX>=16 because of poor stats for small n
%
% [x,y,dy]=dfa(1,1,0,1,1,16,0,0,0,fBm9);
% x=log10(rs);y=log10(mse);dy=d(log10(y))=delta_y/y/ln(10)
% errorbar(x,y,dy);
% [m,c,dm,dc]=lsqfitydy(x,y,dy)
%
% Wanliss 5/2003
* dfa2.m
(supersedes dfa.m)
PURPOSE: Calculate Hurst exponent
via detrended fluctuation analysis, now with error analysis
USAGE: [x,y,dy]=dfa2(nfit,iflag,minbox,maxbox,sw,err,data)
OUTPUT: Slope of log(x) versus
log(y) gives the Hurst exponent; errorbar is dy./y if natural logs are used
LOCATION: /home/wanliss/matlab/Chaos.dir
NOTES: Utilises dfa2.c
% Err is measuring uncertainty; e.g. 0.1 nT
% -d K detrend using a polynomial of degree K
% (default: K=1 -- linear detrending)
% -h print this usage summary
% -i input series is already integrated
% -l MINBOX smallest box width (default: 2K+2)
% -u MAXBOX largest box width (default: NPTS/4)
% -s sliding window DFA
% The standard input should contain one column of data in text format.
% The standard output is two columns: log(n) and log(F) [base 10 logarithms],
% where n is the box size and F is the root mean square fluctuation.
%
% fBm is by definition already integrated
% fGm must be integrated
%
% Use MINBOX>=16 because of poor stats for small n
%
%[x,y,dy]=dfa2(1,0,16,0,0,0.1,f);
% x=log10(rs);y=log10(mse);dy=d(log10(y))=delta_y/y/ln(10)
% errorbar(x,y,dy);
% [m,c,dm,dc]=lsqfitydy(x,y,dy)
% x=log10(rs);y=log10(mse);dy=d(log10(y))=delta_y/y/ln(10)
* dfam.m
(pure matlab version of dfa2.m)
PURPOSE: Calculate Hurst exponent
via detrended fluctuation analysis, now with error analysis
USAGE: [x,y,dy]=dfam2(nfit,iflag,minbox,maxbox,sw,dely,data)
OUTPUT: Slope of log(x) versus
log(y) gives the Hurst exponent; errorbar is dy./y if natural logs are used
LOCATION: /home/wanliss/matlab/Chaos.dir
NOTES: Uses Peng algorithm
* dfam2.m
(supersedes dfa.m)
PURPOSE: Calculate Hurst exponent
via detrended fluctuation analysis, now with easier error analysis
USAGE: [x,y,dy]=dfam2(nfit,iflag,minbox,maxbox,sw,err,data)
OUTPUT: Slope of log(x) versus
log(y) gives the Hurst exponent; errorbar is dy./y if natural logs are used
LOCATION: /home/wanliss/matlab/Chaos.dir
NOTES: Most mature version of the dfa-series codes
% USAGE: [x,y,dy]=dfam2(nfit,iflag,minbox,maxbox,sw,data)
% Slightly different algorithm than Peng et
al., allows easier computation
% of uncertainty
%
% nfit detrend using a polynomial of degree nfit
% (default: nfit=1 -- linear detrending)
% iflag=1/0 integrate/don't
% minbox smallest box width (default: 2nfit+2)
% maxbox largest box width (default: NPTS/4)
% sw=0/1 sliding window DFA off/on
%
%[x,y,dy]=dfam2(1,0,16,0,0,f);
%[m,c,dm,dc]=lsqfitydy(log(x),log(y),dy./y)
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* loadmag.m
PURPOSE: Load magnetometer data
from CANOPUS (1990-2001) into memory
USAGE: date='950309';loadmag;
OUTPUT: Loads all photometer
files for that date
LOCATION: ~/matlab/CANOPUS.dir/Plotmag/
NOTES: date='yymmdd'
* loadmsp.m
PURPOSE: Load Meridian scanning
photometer data from CANOPUS (1990-2001) into memory
USAGE: date='950309';loadmsp;
OUTPUT: Loads all photometer
files for that date
LOCATION: ~/matlab/CANOPUS.dir/Plotmpa/
NOTES: date='yymmdd'
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* magplot.m/plotmag.m
PURPOSE:
Plot CANOPUS magnetometer data
USAGE: [x2,y2,z2,place,year2,day2,hour2,minute2,second2,interval2,totalvadjust]=plotmag(date,stationvec,[tinitial,tfinal],plottype,variable,readbefore)
OUTPUT:
eg. plotmag('a95138',[0 0 0 1 0 0 0 0 0 0 0 0 1 0],'all',3,'y',0)
LOCATION: /home/wanliss/matlab/CANOPUS.dir/Plotmag/new
NOTES:
date -- in the form yyddd yy=two digit year ddd=three
digit day of year, then add 'a' in front of date (yyddd --> ayyddd)
stationvec -- logical station vector
the station list is:
[TALO RANK ESKI FCHU BACK GILL ISLL PINA CONT
FSIM FSMI RABB MCMU DAWS]
e.g. if stations FCHU and MCMU are desired,
then the logical station vector should be [0 0 0 1 0 0 0 0 0 0 0 0 1
0]
tinitial -- start time for plot in hour of day eg. 1:35:45
== 1.5958333
tfinal -- end time for plot in hour of day formula:
hour+minute/60+second/3600
If the user wishes to plot entire time interval, input "all"
for [tinitial,tfinal]
plottype 1 -- plot data versus data position (avaliable
only for individual stations)
2 -- plot data versus time in seconds of
day (standard) (avaliable only for individual stations)
3 -- plot data versus time in minutes of
day (standard)
4 -- plot data versus time in hours of day
(standard)
be careful when choosing plottype 1 because data
position #1, doesn't automatically mean time=0:00
variable 'x' -- plot x dimensional data
'y' -- plot y dimensional data
'z' -- plot z dimensional data
readbefore -- if the user wishes to plot data from the
same file then the data does not need to be read in twice;
if this is the case, then set readbefore=1;
otherwise readbefore=0;
when readbefore=1, then the user should add
the output arguments:
x2,y2,z2,place,year2,day2,hour2,minute2,second2,interval2
to the end of the 6 input arguments
* make_kappa.m
PURPOSE: Find kappa values K^2=R/rc
where R=radius of curvature, rc=gyroradius
USAGE: [ki,ke]=kappa(x,y,z,Wi,We,model,variables)
OUTPUT: Proton (ki) and electron
(ke) kappa values for given 'model' and particle energies (eV) at a given
position
LOCATION: /home/wanliss/matlab/
NOTES: function [ki,ke]=kappa(x,y,z,Wi,We,model,variables)
% Find kappa parameter
%
% [ki,ke]=kappa(x,y,z,Wi,We,model)
%
% K = sqrt(Rc/r)
%
% Rc is the radius of curvature of the magnetic field
%
% Rc = Bz/(dBx/dz) at y=0
%
% vec{Rc}/Rc^2=-(vec{B} dot grad)vec{B}/B^2
%
% r is gyroradius = mv/q Bz
% W in eV
%
% 26/3/1998 - working version
% Modified 2/2003 Wanliss
* mapper2.m
PURPOSE: Find streamlines (usually
from equator) that end in the ionosphere
USAGE: [x2,y2,z2,lat,lon]=mapper2(x1,y1,z1,model,variables)
OUTPUT: Positions, latitude,
longitude of field lines
LOCATION: /home/wanliss/matlab
NOTES:function [x2,y2,z2,lat,lon]=mapper2(x1,y1,z1,model,variables)
% Calculating magnetic field lines (streamlines)
% Can start anywhere and goes to the ionosphere
% [x2,y2,z2,lat,lon]=mapper2(x1,y1,z1,model,thick)
% e.g. [x,y,z]=mapper2(-15,0,0,@T87,[3,-29]);
% e.g. [x,y,z]=mapper2(-15,0,0,@M1,3);
%
% Wanliss
% Modified March 28/2002
% Modified 2/2003 Wanliss
%
*
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* photo.m
PURPOSE: Plot CANOPUS photometer
data
USAGE: photo
OUTPUT:
LOCATION: /home/wanliss/matlab/CANOPUS.dir/Plotmpa
NOTES: Uses plotmpa.m
1. How to run the GUI
-----------------------
At the command line type:
>> photo
This starts the GUI. Now proceed to the GUI.
2. Data
---------
The GUI can load data from files by pressing the "Load Data"
button. This
will employ the loadmpa GUI. Select the file that needs to
be loaded and
press "Load". Once loaded, the data is stored in variables
which are
visible in the box labelled "Current Available Variables."
The user may
also load the data using the Matlab command window. Press
"Update Current
Variables" to show all the currently available variables.
To select the
data to plot, just double click on the varaible. The variable
will appear
in the "Selected Data" text box. The user may also directly
edit this
box to change the data to plot.
The format of the data files that are loaded has a slight
variation from
the original files that one can obtain from CANOPUS (ASCII
files of photometer
data). The first line of these files gives information about
the station,
date, start time, and interval. This line must be commented
out by placing a
percentage sign (%) at the beginning of this line. If this
is not done, then
the file will not load properly in Matlab.
3. Station
------------
The photometer station name and altitude of where the data
is taken must
be specified in the Station section. The stations to choose
from are:
FCHU, FSIM, FSMI, GILL, ISLL, PINA, and RANK. The avaliable
altitudes
are: 110 and 230.
4. Options
------------
When the program starts, all the options are defaulted. To
edit the
options, the "default everything" checkbox must be clicked
off.
a. Time
--------
The time interval to plot needs to be specified. The units
are in minutes
ranging from 1 min to 1440 min. Setting to "full range" will
automatically select a range from 1 min to 1440 min. Selecting
"manual"
allows the user to select more specific choices. The time
range of the
data might not span the entire interval from 1 min to 1440
min. In this
case, the user must specify a valid range in which data is
avaliable.
b. CLim
--------
This is the color coding range limits for the plot. "Auto"
will
automatically set the range. Selecting "manual" allows the
choice of user
selected ranges.
c. Scale
---------
The scale of the color coding can be in linear ("linear")
or base 10
logarithmic ("log10") form. Usually, the activity levels
within a graph
varies by many orders of magnitude so using "log10" is recommended.
d. Type
--------
This defines the type of 2D interpolation for the photometer
data. Here
are the options:
"nearest" - nearest neighbor interpolation
"linear" - bilinear interpolation
"cubic" - bicubic interpolation
"spline" - spline interpolation
The default type is "cubic." Note that the output is not
the raw data.
e. Advanced
------------
The advanced option is the implementation of border detection
with the
plotting. If "Use Border Detect" is checked, then the program
will enter
border detection mode when "Render" is clicked. (See Plotting)
5. Plotting
------------
After the data, station, and options have been correctly selected,
click
the "Render" button to create the photometer plot. If "Use
Border Detect"
is unchecked, then a photometer plot will be generated. If
this advanced
option is checked, then the user must interact with the command
window to
employ the border detection with Matlab filters.
Using the border detection feature:
CAUTION: Do not use this option unless the meanings of the
various filters
are understood. The filters can be looked up in Matlab help.
Once "Render" is pressed, 3 figures will be created.
The user is prompted in the command window to "Input edge
threshold
parameter:" Usually 1 or 0.9 are fair values for this. Next,
the user is
prompted for the filter type. The available types are: sobel,
prewitt,
roberts, log, zerocross, and canny. The default filter type
is canny. If
the user wishes to use canny, then just press enter. The
user does not
need to explicitly specify "canny." After the filter type
is chosen, the
border plots are created in black and white. The user is
then prompted to
see if he or she is satisfied with the filtered results.
The default is
"y" for yes, and just pressing enter will mean yes. Input
"n" to reselect
the filter threshold and filter type.
The two filtered black and white plots indicate the border
location. BW1
differs from BW2 in that BW2 has reduced noise due to an iterative
process
being applied to it. The user is then prompted to choose
if he/she wants
to use BW1 data or BW2 data for the border detection. BW1
is recommended
and is the default choice. Zoom in to a region of interest
before
selecting BW1 or BW2. Once selected, a crosshair will appear
on one of
the graphs and two input points are expected to be chosen.
These two
points should be the start and end of a continuous border.
The detected
border will appear in red circles.
The user is then prompted to "Try a different fit interval
(y/n/r):"
"y" means accept the detected border and continue to detect
more borders
for the same plot.
"n" means accept the detected border and finish the boarder
detect
process.
"r" means reject the detected border and continue to detect
more borders
for the same plot.
When border detection is completed, the values for the borders
are stored
in the variables "l1" and "t1." The variables "data" contains
the
interpolated data, and the variables "BW1" and "BW2" contains
the data for
the black and white border plots.
5. Other
---------
The help button at the top right corner of the GUI brings
up this help
text.
* plotmag.m
PURPOSE:
Plot CANOPUS magnetometer data
USAGE: [x2,y2,z2,place,year2,day2,hour2,minute2,second2,interval2,totalvadjust]=plotmag(date,stationvec,[tinitial,tfinal],plottype,variable,readbefore)
OUTPUT:
eg. plotmag('a95138',[0 0 0 1 0 0 0 0 0 0 0 0 1 0],'all',3,'y',0)
LOCATION: /home/wanliss/matlab/CANOPUS.dir/Plotmag/new
* plotmagv3.m
PURPOSE:
Plot CANOPUS magnetometer data
USAGE: [x2,y2,z2,place,year2,day2,hour2,minute2,second2,interval2,totalvadjust]=plotmagv3(date,stationvec,[tinitial,tfinal],plottype,variable,readbefore)
OUTPUT: eg. plotmag('950113',[0
0 0 1 0 0 0 0 0 0 0 0 1 0],'all',3,'y',0)
NOTES: Supersedes plotmag.m; date is in the form yymmdd
* plotmpa.m
PURPOSE: Plot CANOPUS photometer
data
USAGE: plotmpa(data,time,STATION,type,CLIM,scale);
OUTPUT: Graph
LOCATION: /home/wanliss/matlab/CANOPUS.dir/Plotmpa
NOTES:
*
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* Rigidity.m
PURPOSE: Find model particle
rigidity for comparison with satellite data.
USAGE: [x,L,Rigidite,Rigiditi]=Rigidity(kappa,model,variables)
OUTPUT: x=positions where rigidity
is calculated; L=corresponding L-shell position; Rigidite=value for electrons
for the chosen value of Kappa, etc.
LOCATION: /home/wanliss/matlab
NOTES: function [x,L,Rigidite,Rigiditi]=Rigidity(kappa,model,variables)
% Calculate particle rigidity for T87
% cf. Popielawska and Zwolakowska, 1991, GRL, 18, 1489-1492
%
% Rigidity=G=B*gyroradius=sqrt(2*m*Ecrit/q)
%
% [x,L,Re,Ri]=Rigidity(sqrt(8),@T87,[4,0]); (units: nt m)
% Wanliss 1/2003
% x10^6 for their units
* rs1.m
PURPOSE: For calculating the
Hurst coefficient for a time series (slope of log-log graph gives H).
USAGE: [n, rs, drs]=rs1(y)
OUTPUT: n=index; rs=rescaled
range; drs=error in rs
LOCATION: /home/wanliss/matlab/Chaos.dir
NOTES:
% For calculating the Hurst coefficient for a time series. The
% method used is from "Complexification," John L. Casti, HarperCollins,
% New York, New York, 1994, ISBN 0-06-016888-9, pp 253, or "Chaos and
% Order in the Capital Markets," Edgar E. Peters, John Wiley & Sons,
New
% York, New York, 1991, ISBN 0-471-53372-6, pp 63, or "Fractals, Chaos,
% Power Laws," Manfred Schroeder, W. H. Freeman and Company, New York,
% New York, 1991, ISBN 0-7167-2136-8, pp 129, or "Applied Chaos Theory:
% A Paradigm for Complexity," A. B. Cambel. Academic Press, San Diego,
% California, 1993, ISBN 0-12-155940-8, pp 172. The time series is
% broken into variable length intervals, which are assumed to be
% independent of each other, and the R/S value is computed for each
% interval based on the deviation from the average over the
% interval. These R/S values are then averaged for all of the intervals.
PURPOSE: For calculating the
Hurst coefficient for a time series (slope of log-log graph gives H).
USAGE: [n, rs, drs]=rs1(y)
OUTPUT: n=index; rs=rescaled
range; drs=error in rs
LOCATION: /home/wanliss/matlab/Chaos.dir
NOTES: Fast version based on
power two math.
% Range Scaling Analysis (Fractal Analysis)
% This program calculates the rescaled range of a time series
% Input: the time series with equal time increments
% Output: the rescaled range
% For more detail see Peters, E.E. 1994, Fractal Market Analysis, John Wiley
and
Sons, New York
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* T87.m
PURPOSE: Calculate Tsyganenko
(1987) model magnetospheric field
USAGE: b=T87([x,y,z,kp,dtilt]
OUTPUT: Magnetic field vector
(nT) in GSM coordinates
LOCATION: /home/wanliss/matlab/MODELS.dir/T87
NOTES:
function b=T87(var)
% Function T87(var)
% var=[x,y,z,kp,dtilt,l]
% Outputs magnetic field in nT
% Wanliss 1/2003
%
*
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* yearmonthday.m
PURPOSE: Calculate the doy given
other parameters, or calculate other
% parameters, given doy
%
% direction = -1 DOY -> MONTH-DAY
% direction = 1 MONTH-DAY -> DOY
USAGE: [doy,m,d]=yearmonthday(yyyy,mm,dd,doy,direction);
OUTPUT: Date
LOCATION: ~/matlab
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*
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* dfa.c
PURPOSE: Detrended fluctuation
analysis (Peng et al. version)
USAGE: ./dfa [OPTIONS ...]
OUTPUT: Outputs to stdio matrix
with 2 columns. Column 1 is log10(n), Column 2 is log10(mse)
LOCATION: /home/wanliss/matlab/Chaos.dir
* dfa2.c
PURPOSE: Detrended fluctuation
analysis (Peng et al. version) with error calculation
USAGE: ./dfa [OPTIONS ...]
OUTPUT: Outputs to stdio matrix
with 2 columns. Column 1 is log10(n), Column 2 is log10(mse), Column 3 is
the error
LOCATION: /home/wanliss/matlab/Chaos.dir
* preparephoto.c
PURPOSE:
Put raw CANOPUS photometer data into a format
compatible with Matlab and plotmpa.m
USAGE: preparephoto filename
OUTPUT: filename
LOCATION: ~/bin
NOTES: The output filename is
idnetical to the input filename, but a % has been put into the first
line, which is the comment sign for Matlab,
*
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