Make sure patternstim input file has gid as integers

[pramodk]

See this internal JIRA ticket :

User has input file:

/scatter
1000.15876308    221273.0
1000.16120151    221145.0
1000.1612057     221043.0 

The second column is gid and it should be integer form i.e.

1000.15876308    221273
1000.16120151    221145
1000.1612057     221043 

We should change implementation in

CoreNeuron/coreneuron/mechanism/patternstim.cpp

Line 140 in 5f1c036

while (fscanf(f, "%lf %d\n", &stime, &gid) == 2) {

Possible solutions:

• if not an integer, throw an error
• read as double, if it's integer then it's fine. Otherwise thrown an error

[admud]

Hi Pramod sir, could I work on this?

[singhshivansh244]

What we have to do?Ccannot understand please help.SIr

[pramodk]

hello @muhdmud @singhshivansh244,

sorry for delay here. Let me explain how to reproduce and fix the issue:

• build coreneuron:

# clone repo, create build dir and compile coreneuron
git clone https://github.com/BlueBrain/CoreNeuron coreneuron
mkdir coreneuron/build && cd coreneuron/build
cmake .. -DCMAKE_INSTALL_PREFIX=`pwd`/install -DCORENRN_ENABLE_MPI=OFF
make -j

• create sample pattern.dat stimulus input file:

echo "/scatter" > pattern.dat
echo "10.15876308    221273.0" >> pattern.dat
echo "1000.16120151    221145.0" >> pattern.dat

note that second column is floating point value instead of integer:

$ cat pattern.dat
/scatter
10.15876308    221273.0
1000.16120151    221145.0

• now we can run coreneuron with pattern.dat from build directory:

./bin/x86_64/special-core --tstop 100 --datpath=../tests/integration/ring/ --pattern=./pattern.dat

• now if you look at

  CoreNeuron/coreneuron/mechanism/patternstim.cpp

  Line 140 in 5f1c036

  while (fscanf(f, "%lf %d\n", &stime, &gid) == 2) {

  , the second value is read as integer with %d. In our case, the second column is float (containing integer value) and parsing this with %d is error prone.

So what one can do is:

• read the value as double (%lf)
• if the value read is non-integer : throw an error and abort program
• if value contains integer then static_cast it to int and push to spikes vector

(I think std::modf can be used?)

[singhshivansh244]

So,Sir what I have to do is,change "%d" to "%lf" and add if condition to check var is int or float??
If yes then I can do it.