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Reading in a document full of code

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Chris E.
Chris E. on 19 Oct 2013
Commented: Cedric Wannaz on 22 Oct 2013
I'm building a program to read in some code for Accelerator physics and I really do not know how to start reading the files into MATLAB. I need to make the lines starting with "!" as a comment or for the case of reading it into MATLAB, just ignore any line starting with "!", so it will not show up in MATLAB. All of the names starting with "&", like "&NEWRUN", starts the info that I need. I can handle anything in between, but separating the sections that start with "&NAME" and ending with "/", and there are a few of them, I'm not sure exactly. Any help I can get to make this work well will be very welcomed, even any comments or advice will be great! Thank you!
Here is the document in a .in file format:
! header
!
&NEWRUN
Version=3
Head= 'IAC 44 MeV LINAC'
RUN=1,
Distribution = 'IAC_LASER_1p5ps70mmRISE5000.ini', Xoff=0.0, Yoff=0.0
! Qbunch=1.00
XYrms=0.6900
! Trms=4.0e-3
TRACK_ALL=T, PHASE_SCAN=F, AUTO_PHASE=.T
Lmonitor=.F
check_ref_part=.F
H_max=0.001
H_min=0.000
! MAX_STEP=5000000
debunch=0.0
/
&SCAN
LScan= T,
Scan_para='MaxB(1)',
! Fine Scan
S_min= 0.100, S_max=0.200, S_numb=11
!Scan_para='XYrms',
!rms beam size
!S_min=0.6555, S_max=0.7245, S_numb=11
!Scan_para='MaxB(2)',
! Rough Scan
! S_min=0.0, S_max=0.01, S_numb=17
!Scan_para='MaxB(3)',
! Rough Scan
! S_min=0.02, S_max=0.1, S_numb=12
!Scan_para='S_pos(1)',
!Gun Solenoid Position Scanning
!S_min=0.00, S_max=0.1, S_numb=21
!Scan_para='C_pos(2)',
!1st Cavity Position Scanning
!S_min=2.00, S_max=3.00, S_numb=21
!Scan_para='MaxE(1)' ,
!1st Cavity Gradient
!S_min=38.00, S_max=42.00, S_numb=11,
!Scan_para='Phi(1)' ,
!Gun Phase
!S_min=-2.1147, S_max=-1.9133, S_numb=11,
!Scan_para='MaxE(2)' ,
!1st Cavity Gradient
!S_min=9.975, S_max=11.025, S_numb=11,
!Scan_para='Phi(2)' ,
!1st Linac Cavity Phase
!S_min=-1.00, S_max=1.00, S_numb=16,
!Scan_para='MaxE(3)' ,
!S_min=22.85, S_max=52.85, S_numb=31,
FOM(1)='rms bunch length',
FOM(2)='horizontal rms emittance',
FOM(3)='vertical rms emittance',
FOM(4)='longitudinal rms emittance',
FOM(5)='horizontal rms spot size',
FOM(6)='vertical rms spot size',
FOM(7)='bunch charge',
FOM(8)='mean beam energy',
FOM(9)='horizontal rms emittance minus Z correlation',
FOM(10)='horizontal rms beam divergence'
/
! &ERROR
! /
&CHARGE
Loop=F,
LSPCH=.T,
Nrad=15, Nlong_in=20
Cell_var=2.0
min_grid=0.0
Max_scale=0.05
Lmirror=.T
! N_min=100
/
&FEM
/
&CAVITY
LEfield=.T
! 1.5 cells RF Gun with a symmetric coupler
File_Efield(1) = 'ttf2rfgun.dat',
Nue(1)=1.300, MaxE(1)=40.00, Phi(1)=-2.115, C_pos(1)=0.000000,
! The 1st 2.00 m long L-band Linac Structure with 24 cells
FILE_EFIELD(2) = 'TWS_IAC_Lband_ASTRA.dat'
Nue(2)=1.300, MaxE(2)=10.40, Phi(2)=0.8667, C_pos(2)=2.35, C_Numb(2)=24
! The 2nd 2.75 m long L-band Linac Structure with 33 cells
! Distance between 1st and 2nd L-band Linacs = 0.65 m
FILE_EFIELD(3) = 'TWS_IAC_Lband_ASTRA.dat'
Nue(3)=1.300, MaxE(3)=15, Phi(3)=0.0, C_pos(3)=5.15, C_Numb(3)=33
/
&SOLENOID
LBfield=.T,
! Gun Main Solenoid
File_Bfield(1)='TTF2solenoids.dat', MaxB(1)=0.1585,
S_pos(1)=0.0E-3, S_xoff(1)=0.0, S_yoff(1)=0.0, S_Smooth(1)=150
! 1st Solenoids in the 1st L-band Linac Structure
! distance between center of solenoid and 1st Linac head = 0.13795 m
! distance between center of solenoids = 0.35 m
! -> 2.35 m + 0.13795 m = 2.48795 m
! File_Bfield(2)='IAC_SOLENOID_ASTRA.dat', MaxB(2)=0.04
File_Bfield(2)='IAC_SOLENOID_ASTRA.dat', MaxB(2)=0.005
S_pos(2)=2.48795, S_xoff(2)=0.0, S_yoff(2)=0.0, S_Smooth(2)=150
! 2nd Solenoid = 2.48795 m + 0.35 m = 2.83795 m
File_Bfield(3)='IAC_SOLENOID_ASTRA.dat', MaxB(3)=0.005,
S_pos(3)=2.83795, S_xoff(3)=0.0, S_yoff(3)=0.0, S_Smooth(3)=150
! 3rd Solenoid = 2.83795 m + 0.35 m = 3.18795 m
File_Bfield(4)='IAC_SOLENOID_ASTRA.dat', MaxB(4)=0.005,
S_pos(4)=3.18795, S_xoff(4)=0.0, S_yoff(4)=0.0, S_Smooth(4)=150
! 4th Solenoid = 3.18795 m + 0.35 m = 3.53795 m
File_Bfield(5)='IAC_SOLENOID_ASTRA.dat', MaxB(5)=0.09,
S_pos(5)=3.53795, S_xoff(5)=0.0, S_yoff(5)=0.0, S_Smooth(5)=150
! 5th Solenoid = 3.53795 m + 0.35 m = 3.88795 m
File_Bfield(6)='IAC_SOLENOID_ASTRA.dat', MaxB(6)=0.09,
S_pos(6)=3.88795, S_xoff(6)=0.0, S_yoff(6)=0.0, S_Smooth(6)=150
! 6th Solenoid = 3.88795 m + 0.35 m = 4.23795 m
File_Bfield(7)='IAC_SOLENOID_ASTRA.dat', MaxB(7)=0.09,
S_pos(7)=4.23795, S_xoff(7)=0.0, S_yoff(7)=0.0, S_Smooth(7)=150
! 1st - 8th Solenoids in the 2nd L-band Linac Structure
! distance between center of solenoid and 1st Linac head = 0.13795 m
! distance between center of solenoids = 0.35 m
! -> 5.15 m + 0.13795 m = 5.28795 m
File_Bfield(8)='IAC_SOLENOID_ASTRA.dat', MaxB(8)=0.10,
S_pos(8)=5.28795, S_xoff(8)=0.0, S_yoff(8)=0.0, S_Smooth(8)=150
! 2nd Solenoid = 5.28795 m + 0.35 m = 5.63795 m
File_Bfield(9)='IAC_SOLENOID_ASTRA.dat', MaxB(9)=0.10,
S_pos(9)=5.63795, S_xoff(9)=0.0, S_yoff(9)=0.0, S_Smooth(9)=150
! 3rd Solenoid = 5.63795 m + 0.35 m = 5.98795 m
File_Bfield(10)='IAC_SOLENOID_ASTRA.dat', MaxB(10)=0.10,
S_pos(10)=5.98795, S_xoff(10)=0.0, S_yoff(10)=0.0, S_Smooth(10)=150
! 4th Solenoid = 5.98795 m + 0.35 m = 6.33795 m
File_Bfield(11)='IAC_SOLENOID_ASTRA.dat', MaxB(11)=0.10,
S_pos(11)=6.33795, S_xoff(11)=0.0, S_yoff(11)=0.0, S_Smooth(11)=150
! 5th Solenoid = 6.33795 m + 0.35 m = 6.68795 m
File_Bfield(12)='IAC_SOLENOID_ASTRA.dat', MaxB(12)=0.10,
S_pos(12)=6.68795, S_xoff(12)=0.0, S_yoff(12)=0.0, S_Smooth(12)=150
! 6th Solenoid = 6.68795 m + 0.35 m = 7.03795 m
File_Bfield(13)='IAC_SOLENOID_ASTRA.dat', MaxB(13)=0.10,
S_pos(13)=7.03795, S_xoff(13)=0.0, S_yoff(13)=0.0, S_Smooth(13)=150
! 7th Solenoid = 7.03795 m + 0.35 m = 7.38795 m
File_Bfield(14)='IAC_SOLENOID_ASTRA.dat', MaxB(14)=0.10,
S_pos(14)=7.38795, S_xoff(14)=0.0, S_yoff(14)=0.0, S_Smooth(14)=150
! 8th Solenoid = 7.38795 m + 0.35 m = 7.73795 m
File_Bfield(15)='IAC_SOLENOID_ASTRA.dat', MaxB(15)=0.10,
S_pos(15)=7.73795, S_xoff(15)=0.0, S_yoff(15)=0.0, S_Smooth(15)=150
/
&QUADRUPOLE
/

Accepted Answer

Cedric Wannaz
Cedric Wannaz on 19 Oct 2013
Edited: Cedric Wannaz on 20 Oct 2013
Simple answer below, and a more complete function in comment #3. Code is attached to the comment.
You can use a REGEXP to split blocks/sections, and then post-process each block of data:
content = fileread( 'myFile.in' ) ;
content = regexprep( content, '!.*?\r?\n', '' ) ;
blocks = regexp( content, '&(?<name>[^\n\r]+)(?<data>.+?)/', 'names' ) ;
This creates a struct array blocks with the following type of content:
>> blocks(1)
ans =
name: 'NEWRUN'
data: [1x266 char]
>> blocks(2)
ans =
name: 'SCAN'
data: [1x496 char]
where the field data stores the content of the section as a raw, unprocessed character array. Post-processing seems to be a bit section specific, but here is an example:
for bId = 1 : numel( blocks )
blocks(bId).parsed = regexp( blocks(bId).data, ...
'([^=\s,]+)\s*=\s*''?([^\s,\n\r'']+)', ...
'tokens' ) ;
end
which builds a new field named parsed for each block (you could overwrite blocks(bId).data with parsed data actually, to spare memory, but I kept both at this point for debugging). For example:
>> blocks(1)
ans =
name: 'NEWRUN'
data: [1x266 char]
parsed: {1x15 cell}
shows that 15 parameters were parsed (without commented lines) in block/section 1. Parsed parameters are stored in pairs name/value: ..
>> blocks(1).parsed{1}
ans =
'Version' '3'
>> blocks(1).parsed{4}
ans =
'Distribution' 'IAC_LASER_1p5ps70mmRISE5000.ini'
>> blocks(1).parsed{5}
ans =
'Xoff' '0.0'
This approach holds in ~6 lines of code, which is interesting for such a complex file. However, you have to be familiar enough with regular expressions for fine tuning the mechanism.
The second approach is simply to read the file line by line and build whatever structure or cell array of parameters you need. For example:
sections = {} ;
sId = 0 ;
fid = fopen( 'myFile.in', 'r' ) ;
while ~feof( fid )
line = strtrim( fgetl( fid )) ;
if isempty( line ), continue ; end
if line(1) == '!', continue ; end
if line(1) == '&'
sId = sId + 1 ;
sections{sId}.name = line(2:end) ;
sections{sId}.data = {} ;
elseif line(1) ~= '/'
sections{sId}.data = [sections{sId}.data; {line}] ;
end
end
fclose( fid ) ;
This is simple, but there would still be some post processing..
>> sections{1}
ans =
name: 'NEWRUN'
data: {11x1 cell}
>> sections{1}.data
ans =
'Version=3'
'Head= 'IAC 44 MeV LINAC''
'RUN=1,'
'Distribution = 'IAC_LASER_1p5ps70mmRISE5000.ini', Xoff=0.0, Yoff=0.0'
'XYrms=0.6900'
'TRACK_ALL=T, PHASE_SCAN=F, AUTO_PHASE=.T'
'Lmonitor=.F'
'check_ref_part=.F'
'H_max=0.001'
'H_min=0.000'
'debunch=0.0'
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