Integrated development environment

There are many IDE's available. I use Screen/ Vim/ CTAGS/ GDB to setup my programming environment.

Screen

start a screen session and name it "DavidFuentes"
```
      screen -S DavidFuentes
```
create a new shell,window
```
      CNTL-a c
```
split screen
```
      CNTL-a S
```
cycle through display
```
      CNTL-a n
      CNTL-a p
```
close single window
```
      CNTL-a X
```
vertical split
```
      CNTL-a |
```

change focus

      CNTL-a CNTL-i
      CNTL-a :focus up/down

quit split
```
      CNTL-a Q
```
detach or lost connection
```
      CNTL-a d
```
re-attach
```
      screen -rd DavidFuentes
```

scroll

      CNTL-a [
      CNTL-u
      CNTL-d

copy

      CNTL-a [
      space
      highlight w/ cursor (arrow keys)
      space

paste
```
      CNTL-a ]
```

PETSc

Download code and build.

    wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.5.1.tar.gz
    tar -zxf petsc-lite-3.5.1.tar.gz
    cd petsc-3.5.1
    ./config/configure.py --with-shared-libraries --with-clanguage=c++ --CFLAGS='-O0' --CXXFLAGS='-O0' --download-ctetgen --download-triangle --with-debugging=yes --with-blas-lapack-dir=/opt/apps/MKL/12.1/lib/intel64/ --with-exodusii-lib=[/usr/lib/x86_64-linux-gnu/libexoIIv2.so] --with-netcdf-dir=/usr/lib --with-hdf5-dir=/usr/lib --with-c2html=0 --with-exodusii-include=/usr/include  --with-opencl-include=/usr/include/ --with-opencl-lib=/usr/lib/libOpenCL.so  --download-viennacl=yes
    make

ITK

Download code and build.

    wget http://downloads.sourceforge.net/project/itk/itk/4.6/InsightToolkit-4.6.0.tar.gz
    tar -xvzf InsightToolkit-4.6.0.tar.gz
    mkdir InsightToolkit-4.6.0-build
    cd InsightToolkit-4.6.0-build
    cmake -DBUILD_SHARED_LIBS=OFF  -DCMAKE_BUILD_TYPE=Debug -DBUILD_EXAMPLES=ON -DBUILD_TESTING=OFF -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=../InsightToolkit-4.6.0-install ../InsightToolkit-4.6.0
    make -j 10 ;  make install

ctags

Build tag file

    cd InsightToolkit-4.6.0
    ctags -R --langmap=c++:+.txx --langmap=c++:+.hxx --langmap=c++:+.cl  *

    cd petsc-3.5.1
    ctags -R --langmap=c++:+.txx --langmap=c++:+.hxx --langmap=c++:+.cl  *

Access tag file in vim

  [1] vim /opt/apps/ITK/InsightToolkit-4.6.0/Examples/IO/DicomSeriesReadImageWrite2.cxx
  [2] :set tags=/opt/apps/ITK/InsightToolkit-4.6.0/tags

Search through the code

  [1] Search for function
     /GetSeriesUIDs

  [2] Follow tag
      g] 

  Prints places in source code where you find instances of the function on the
  line you were on. Select the number of the instance you would like to look
  at and press enter. 

  [3] Goes to last tagged instance. 
      CNTL-t

Search for GPU functions
```
  :ta GPU<tab>
```

GDB

Use the debugger to understand the software design.

$ /opt/apps/ITK/InsightToolkit-4.6.0-build/bin/DicomSeriesReadImageWrite2
Usage:
/opt/apps/ITK/InsightToolkit-4.6.0-build/bin/DicomSeriesReadImageWrite2 DicomDirectory  outputFileName  [seriesName]
$ /opt/apps/ITK/InsightToolkit-4.6.0-build/bin/DicomSeriesReadImageWrite2 sample1 sample1.nii.gz

The directory:

sample1

Contains the following DICOM Series:

1.3.12.2.1107.5.2.32.35177.3.2006121409284535196417894.0.0.0.4tfl3d1ns125625620061214
1.3.12.2.1107.5.2.32.35177.3.2006121409371282268118605.0.0.0.5tfl3d1ns125625620061214
1.3.12.2.1107.5.2.32.35177.3.2006121409455295707319315.0.0.0.6spc3d1278ns125625620061214


Now reading series:

1.3.12.2.1107.5.2.32.35177.3.2006121409284535196417894.0.0.0.4tfl3d1ns125625620061214


Writing the image as

sample1.nii.gz

Now run under the debugger

$ gdb --args /opt/apps/ITK/InsightToolkit-4.6.0-build/bin/DicomSeriesReadImageWrite2
sample1 sample1.nii.gz
GNU gdb (GDB) 7.1-ubuntu
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later
<http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from
/opt/apps/ITK/InsightToolkit-4.6.0-build/bin/DicomSeriesReadImageWrite2...done.
(gdb) r
Starting program: /opt/apps/ITK/InsightToolkit-4.6.0-build/bin/DicomSeriesReadImageWrite2
sample1 sample1.nii.gz
[Thread debugging using libthread_db enabled]

The directory:

sample1

Contains the following DICOM Series:

1.3.12.2.1107.5.2.32.35177.3.2006121409284535196417894.0.0.0.4tfl3d1ns125625620061214
1.3.12.2.1107.5.2.32.35177.3.2006121409371282268118605.0.0.0.5tfl3d1ns125625620061214
1.3.12.2.1107.5.2.32.35177.3.2006121409455295707319315.0.0.0.6spc3d1278ns125625620061214


Now reading series:

1.3.12.2.1107.5.2.32.35177.3.2006121409284535196417894.0.0.0.4tfl3d1ns125625620061214


Writing the image as

sample1.nii.gz


Program exited normally.

Run the code but stop by line number or function name.

(gdb) b 183
(gdb) b nifti_image_write
Breakpoint 2 at 0x988513: file /opt/apps/ITK/InsightToolkit-4.6.0/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_io.c, line 5879.
(gdb) r

Produce a stack frame for examination

(gdb) bt
#0  nifti_image_write (nim=0x4b51870) at /opt/apps/ITK/InsightToolkit-4.6.0/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_io.c:5879
#1  0x0000000000770b04 in itk::NiftiImageIO::Write (this=0x4b55190, buffer=0x7ffff1c35010) at /opt/apps/ITK/InsightToolkit-4.6.0/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx:1854
#2  0x00000000005dcfaa in itk::ImageFileWriter<itk::Image<short, 3u> >::GenerateData (this=0x476e0c0) at >/opt/apps/ITK/InsightToolkit-4.6.0/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:421
#3  0x00000000005db21f in itk::ImageFileWriter<itk::Image<short, 3u> >::Write (this=0x476e0c0) at >/opt/apps/ITK/InsightToolkit-4.6.0/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:355
#4  0x00000000005d843d in itk::ImageFileWriter<itk::Image<short, 3u> >::Update (this=0x476e0c0) at >/opt/apps/ITK/InsightToolkit-4.6.0/Modules/IO/ImageBase/include/itkImageFileWriter.h:166
#5  0x00000000005d51ae in main (argc=3, argv=0x7fffffffe5c8) at /opt/apps/ITK/InsightToolkit-4.6.0/Examples/IO/DicomSeriesReadImageWrite2.cxx:316

    up/down move in the stack frame. Just remember that the higher
number called the routine in the frame below it. Or (#7 called #6, #6 called
#5, #5 called #4, and so on).

Regular Expression Breakpoint:

rbreak regex
Set breakpoints on all functions matching the regular expression regex. This command sets an unconditional 
breakpoint on all matches, printing a list of all breakpoints it set. Once these breakpoints are set, they
 are treated just like the breakpoints set with the break command. You can delete them, disable them, or make
them conditional the same way as any other breakpoint.

The syntax of the regular expression is the standard one used with tools like grep. Note that this is different
 from the syntax used by shells, so for instance foo* matches all functions that include an fo followed by zero
 or more os. There is an implicit .* leading and trailing the regular expression you supply, so to match only 
functions that begin with foo, use ^foo.

When debugging C++ programs, rbreak is useful for setting breakpoints on overloaded functions that are not 
members of any special classes.

The rbreak command can be used to set breakpoints in all the functions in a class vtkExodusIIWriter, like this:

          (gdb) rbreak ^vtkExodusIIWriter::
     

rbreak file:regex
If rbreak is called with a filename qualification, it limits the search for functions matching the given regular expression 
to the specified file. This can be used, for example, to set breakpoints on every function in a given file:
          (gdb) rbreak file.c:.
     
The colon separating the filename qualifier from the regex may optionally be surrounded by spaces.

VIM

open the file: vim [filename]

Splits windows horizontally/vertically.
```
    :sp  
    :vsp
```
up/down/left/right switching between screens
```
    CNTL-w then k/j/h/l
```
undo
```
    u
```
re-do
```
    CNTL r
```
move cursor up/down/left/right
```
    k/j/h/l
```
insert at cursor location
```
    i
```
insert after cursor location
```
    a
```
repeat previous command
```
    .
```
Copy line
```
    yy
```
Copy 7 lines
```
    7yy
```
Copy from current cursor location to end of line
```
    y$
```
Copy from current cursor location to beginning of line
```
    y^
```
Delete line
```
    dd
```
Delete 5 lines
```
    5dd
```
Delete from current cursor location to end of line
```
    d$
```
Delete from current cursor location to beginning of line
```
    d^
```
Cut and paste 4 lines
```
    4dd
    p
```

Visual Block insert 10 lines

    CNTL v   ( start visual block        )
    10j         ( move cursor down 10 lines )
    I           ( insert )
    <text>

Visual Block cut and paste 12 lines from cursor to end of line

    CNTL v   ( start visual block          )
    12j         ( move cursor down 10 lines   )
    $           ( move cursor to end of lines )
    x           (            cut              )
    p           (          paste              )

Visual Block search and replace all

    CNTL v   ( start visual block          )
    G           ( move cursor to end of file  )
    $           ( move cursor to end of lines )
    :           ( initialize search i         )
    :'<,'>s/current/replace/g

Go to beginning/end of line
```
    0
    $
```

Search forward

    /[search_term] 

Searches for [search_term] 

When searching it may be useful to use the following command to tell VIM to
ignore the case (case insensitive): :set ic

Search backward
```
    ?
```
Repeat search/ repeat search backward
```
    n
    N
```
Search for "word" at the beginning/end of a line
```
    /^word
    /word$
```
Regular Expression Search for all characters or all numbers
```
    /[a-z]
    /[0-9]
```
Search forward backward for word under the cursor
```
    *
    #
```
Search for "windows end line" ^M
```
    /CNTL v CNTL m
```

Mark line and revisit

[1] m[a,b,c,...(any char)] (Marks that line for later use) 

[2] '[a,b,c,...(char that you marked)] 
    Look to [1]. This takes you to the line you marked. (Use apostrophe)

Go to previous cursor location
```
   
   CNTL  o
```
Go to the first line / line number 11
```
   
   :1
   :11
```
Go to the last line
```
   
   G
```
Mate command that finds end brackets
```
    %
```
Mover cursor to top/middle/bottom of screen
```
    H 
    M 
    L
```
Shift current line to top of screen
```
    z [enter]
```
Shift current line to middle of screen
```
    zz
```
Shift current line to bottom of screen
```
    z-
```
build code within editor, fix error messages
```
    :make 
    :copen
```

Subsections

- - Screen
  - PETSc
  - ITK
  - ctags
  - GDB
  - VIM