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Programs for Manipulation of Columns and Lines in Data Files

Datafiles usually contain columns of numbers, for example:

# T(K) mu0H(T)  M(mb/T)  [comment lines start with '#' ]
1      1      0.9
2      1      0.6
3      1      0.4
4      1      0.3
5      1      0.25

The following programs manipulate such data files, for example the program delcol deletes a column from a data file, some general features are:

data files are overwritten
multiple files may be handled by one command, e.g. delcol 4 *.dat deletes column 4 in all files ending with .dat
arguments may contain mathematical expressions, e.g.

shifttcol 3x2+27 2xx4 data.dat ...adds to each number in column 33 in file data.dat the number .

factcol 2 sin(3.1415/2) data.dat ...multiplies column 2 in file data.dat with sin(3.1415/2) ,i.e. with 0.999999989

acoscol col[ecolerr] file:

calculates arccosine of a column arccos(col)

add colx1 coly1[ecoly1err] file1 colx2 coly2[ecoly1err] file2:
program to add functions y1(x1) with (optional) y1err and y2(x2) with (optional y2err) taken from data file1 and data file2

input:
file1, file2: filennames
colx, coly, colyerr: columns containing x and y=f(x) and yerror values
output:
file1: contains in coly1=coly1+f2(colx1) and in coly1err=sqrt[coly1err+f2err(colx1)] f2(colx1) is calculated by linear interpolation f2(colx1)= (colx1-colx2(n)*(coly2(n+1)-coly2(n))/(colx2(n+1)-colx2(n)) f2err(colx1)= (colx1-colx2(n)*(coly2err(n+1)-coly2err(n))/(colx2(n+1)-colx2(n))

note: colx2 has to be sorted in file2

addcol colx[ecolxerr] coly[ecolyerr] file:

adds column x and column y of file, result is stored in col y Optional - error is added using the error columns colxerr and colyerr by colyerr=sqrt(colxerr*colxerr+colyerr*colyerr)

asincol col const file:

calculates arcsine of a column arcsine(col)

atancol col const file:

calculates arctangens of a column arctan(col)

chi2 col1 col2 col3 *.*

is used to calculate the chi-squared from 3 columns in a file: if col1, col2 and col3 are calculation, experiment and experimental error, respectively, then chisquared is defined as $\chi^2=\frac{1}{n}\sum_{i=1}^n \frac{({\rm col2}_i-{\rm % col1}_i)^2}{{\rm col3_i}^2}$ . For each datapoint the program outputs a line sta= deviation (experimental error) to stdout. This may be used directly for generating useful input for fitting in simannfit.

comment l1 l2 file:

comments all lines from l1 and l2 (with #) in a file

compare file1 file2:

used to compare data file1 and data file2 all columns and rows are compared and a standard deviation is calculated according to sum_i (file1_i - file2_i)2 this standard deviation is output to stdout, e.g. as sta=143.3

convolute c1 c2 file cx cy convfuncfile [d1 d2 datafile]:

convolutes data given as column c1 vs column c2 in file (data pairs ) with the convolution function given in column cx vs cy of convfuncfile (function ) Range and step width of output file is determined from range and step of convfuncfile unless a datafile is given. If a datafile is given, with data column d1 and d2, the result of the convolution is calculated for x-values of data column d1 and is compared to data in column d2 - a standard deviation sta is calculated as sum of squared deviations.Values out of range of convfile are assumed to be zero, convfile has to be sorted according to ascending x. Formula: $f(x)=\sum_i y_i c(x-x_i)$ , output is written to stdout.

convolute2d c1 c2 c3 file cx cy cz convfuncfile minx maxx Nx miny maxy Ny:

convolutes a 2 dimensional function data given as column c3(c1,c2) in file (data tripls ) with the convolution function given in column cx vs cy vs cz of convfuncfile (function ) Range and number of points of output file is determined from minx maxx Nx and miny, maxy Ny. Formula: $f(x,y)=\sum_i z_i c(x-x_i,y-y_i)$ . In the program the contribution to the sum is evaluated for a discrete triplet cx cy cz of the convolution function, the resulting x,y will not correspond to a point on the grid defined by minx, max Nx, miny,maxy Ny - therefore the contribution is distributed (according to distance) onto the neighbouring grid points. output is written to stdout.

coscol col const file:

calculates cosinus of a column cos(col)

delcol col file:

deletes column col in file

delcols col n file:

deletes column col several (n) times in file

delcomments *.*

removes every comment line (starting with #) from a file and prints the removed lines to screen

delline l1 l2 file:

deletes lines l1 to l2 in file

delnthline n file

remove every nth line (n2) in file

dif colx coly n *.*:

used to calculate d(coly)/d(colx) with differentiation averaging n points

display 5[e7] 6[e8] ./results/mcdisp.qei [colx coly file2]

displays a graphic on screen as xy graph with column 5 as x axis and columns 6 as y axis. By default graphic is a line graph. However, if error columns (in the example x error column is 7 and y error column is 8) are given, then symbols with x and y error bars are shown. Several files can be plotted in the same graph by extending the commandline. If the contents of a file changes, the plot is automatically updated.

displaybubbles 5 6 8 ./results/mcdisp.qei

works similar as display, however a third column is given and the radius of the symbols varied according to the data in this column.

displaycontour 5 6 8 ./results/mcdisp.dsigma.tot

produces a graphical display of a 3 dimensional dataset as a colour and/or contour plot. Here '5 6 8' denote the x,y and z column in file ./results/mcdisp.dsigma.tot, which should be plotted. Figure 17 shows an sample output of this program.

displaytext ./results/mcphas.hkl

monitors the file mcphas.hkl in a text window on screen.

displayhtml calc.bat.html

monitors the file calc.bat.html in a text window on screen.

expcol col const file:

calculates exponent of a column exp(col)

factcol col[ecolerr] const file:

multiplies col with a constant in file, a error colmn may be given and is also multiplied by the absvalue of the constant.

fform col1 col2 format file:

reformats numbers in col1 to col2 in file with a number format given by format. Format is a number format string according to c conventions, for example 8.4f or 4.4g ...

fillcol col expression *.*

used to fill column with numbers in data file
col .... column expression ... e.g. 'tan(c1x7.52)+c2' here c1,c2,.. refer to column 1,2,... operations are multiplication (x), division(/) addition (+), subtraction(-), power (xx) trigonometric functions tan,cos,sin, asin,atan,acos exp,(natural) log *.* .... filenname

fitcol coldata prog col parprog1 parprog2 ... [] in filename:

simple fitting program for data in coldata.
[]=[and prog col parprog1 parprog2 ... [and ...]] coldata ...... column number of data column to be fitted prog ...... program name, e.g. shiftcol col ...... column to which prog should be applied parprog1 ..... parameter of the program prog, which should be fitted filename... filename in order to fit data in column coldata, prog is run many times on the column col with varying parameter set parprog1 ..., the result is scaled to fit best the experimental data. If several programs are combined with option 'and' then the best linear combination of the results is calculated by linear regression to fit coldata. Starting values for the parameters parprog are taken from the commandline. initial Stepwidths are chosen 10percent of parameter value, or may be given by adding them to the parameter with an 's', e.g. 100.3s0.1 If a parameter should not be fitted and kept fix, add an 'f', e.g. 100.3f output: - files can be found in directory results - filename.fit is created with fitted function and parameter values examples: 1) to fit a gaussian to column 2 in datafile expdat (with xvalues in column 1) with starting values 132.3, 0.5 and 10 for position, fwhm and area, respectively: fitcol 2 gausscol 1 132.3 0.5 10 in exp.dat 2) to do the same fit but with a background create a column 3, fill it with constant values and use echo as a fake column manipulation program doing nothing. newcol 3 -c 1.0 exp.dat fitcol 2 gausscol 1 132.3 0.5 10 and rem 3 in exp.dat 3) to do the same with a linear background, put into a column 4 the x values newcol 4 -c 4.0 exp.dat fitcol 2 gausscol 1 132.3 0.5 10 and rem 3 and rem 4 in exp.dat 4) to fit two gaussians with fixed fwhm and stepping in position initially only with 0.1 fitcol 2 gausscol 1 132.3s0.1 0.5f 10 and gausscol 1 100.3s0.1 0.5f 10 and rem 3 and rem 4 in exp.dat

gausscol col position fwhm area *.*:

calculate a gaussian from the x values given in column col.
The formula for a gaussian is: $\sigma={\rm fwhm}/\sqrt{8*log(2)}$ , ${\rm gauss}(x)=\frac{{\rm area} exp(-(x-{\rm position})^2/2 \sigma^2)}{\sqrt{2*\pi}\sigma}$

getvalue colx coly xvalue dx filename

program to get the y-value of a function by averaging over an interval xvalue+-dx, note: colx has to be sorted
output: the y-value is written to stdout and environment variable MCPHASE_YVALUE 1/y-value is written to stdout MCPHASE_YVALUE_INVERSE standarddeviation to stdaout and MCPHASE_STA

getvariable variablename filename

program to get the value of a variable from a file (e.g. somewhere in a file there is a statement T=4.3 and you want to get out this 4.3)
output: the variable value is written to stdout and environment variable MCPHASE_GETVARIABLE_VALUE, the name is stored in MCPHASE_GETVARIABLE_NAME mind lines starting with # are ignored (unless these start with #!)

histcol col [stepwidth|-n steps] *.*:

generates a histogram of a column in a data file and stores it in histcol.out. stepwidth is the stepwidth of the histogram points. Alternatively the number of steps in the histogram may be given by e.g. -n 100.

int [-m] colx coly *.*:

program to integrate columnx vs columny=f(x), integration is done point by point, the result goes to the data file, the total integral INT= $\int f(x)dx$ is printed to stdout and set to the environment variable MCPHASE_INT. option -m: n-th moments are calculated according to $\mu_1=\int x f(x)dx$ /INT, $\mu_n=\int (x-\mu_1)^n f(x)dx$ /INT. The results go to stdout and environment variables MCPHASE_INT_MU_1, MCPHASE_INT_MU_2,MCPHASE_INT_MU_3 ... are set.

linreg col n file:

calculates linear regression of n columns in file
col ...... column containing y_k values followed by n ...... n columns containing x_ik (i=1 to n) filename... filename the program calculates the linear regression, i.e. the best values of coefficients ai such that y_k~sum_i a_i*x_ik for every data line k in the file. The n linear regression equations solved to determin a_i are (i,j=1 ...n): sum_k x_jk y_k = sum_i a_i (sum_k x_ik * x_jk) Output: - sdtoud: best coefficients a_i and standard deviation sta=sum_k (y_k-sum_i a_i*x_ik)^2 - file: new column col+n+1 contining sum_i a_i*x_ik

lorentzcol col position fwhm area:

calculate a lorentzian from a column with x values, the formula for a Lorentz curve is: ${\rm lorentz}(x)=\frac{1.0}{\pi{\rm fwhm}(1.0+(x-{\rm position})^2/fwhm^2)}$

multcol colx coly file:

multiplies column x and column y of file, result is stored in col y

newcol col [options] file:

creates a new column col in file containing the line numbe. option: -c 12.3 ... instead of line number put constant 12.3 into the new column

newcols col n [options] file:

creates n new columns from column col in file. New columns are inserted after column col and contain the same data as column col. options: -c 12.3 ... put constant 12.3 into the new columns, -n ... put line number into the new column.

newline n text file:

creates a new line number n in file containing the text

potcol col const file:

col=col $^{\rm const}$ in file

range col min max file:

deletes (comments out) all data points outside min max in column col of file file (remember to store your full data set in some other file before using this command), # is used to comment lines

rotate xcol ycol angle file:

program rotate used to rotate coordinate axes, xcol,yxol=columns containing x and y , angle=angle $\alpha$ of rotation around z.
The rotation is done using the following formula:

$\displaystyle x'$ $\textstyle =$ $\displaystyle \cos(\alpha)*x+\sin(\alpha)*y$

$\displaystyle y'$ $\textstyle =$ $\displaystyle -\sin(\alpha)*x+\cos(\alpha)*y$ (153)

rpvalue colx coly *.*:

program rpvalue used to calculate the -value from columns number colx and coly in a file *.*. The -value is defined as

$\begin{displaymath} R_p= 100*\frac{\sum_{i=1}^{N} \vert(x(i)-y(i)\vert}{\sum_{i=1}^{N}\vert x(i)\vert} \end{displaymath}$ (154)

denotes the number of data points in the file.

setvalue row column text files:

sets the numerical value in a specified position of a data file.

row : row number column : column number number : text to be placed in file at this position files : one or more filenames example: $0 4 5 3.142 data.dat replaces the number in row 4 and column 5 by 3.142 in file data.dat

shiftcol col const *.*:

used to add a constant (const) to a column (number col) in file(s) *.*

sincol col const file:

calculates sinus of a column sin(col)

sumcol col *.*

prints to stdout number of lines, sum of squares, sum of absolute values of column col in file *.*

swapcol colx coly file:

swaps column x and column y of file

tancol col file:

calculates tangens of a column tan(col)

tanhcol col file:

calculates tangens-hyperbolicus of a column tanh(col)

uvw2fwhm u v w col *.*:

used to calculate the full width half maximum from 2theta in degree according to fullprofs u,v,w parameters ... The column col in file *.* must contain 2theta scattering angle values and is overwritten with the fwhm as calculated by

$\begin{displaymath} {\rm fwhm }= \sqrt {u \tan^2(\theta) + v \tan(\theta) + w} \end{displaymath}$ (155)

zshift constx colx coly *.*:

shifts colx by a constant such that it is zero at a specified value constx of colx.

Next: Programs of General Interest Up: McPhase USERS MANUAL Previous: Programs for Specific Tasks Contents Index

martin rotter 2013-09-19

$\displaystyle x'$	$\textstyle =$	$\displaystyle \cos(\alpha)x+\sin(\alpha)y$
$\displaystyle y'$	$\textstyle =$	$\displaystyle -\sin(\alpha)x+\cos(\alpha)y$	(153)