Difference between revisions of "Kyle's Log"

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=Progress and Task Log for Kyle=
 
=Progress and Task Log for Kyle=
  
[[Image:KyleSched.png|Schedule]]  
+
[[Image:Sched.png|Schedule]]  
  
 
==Tasks==
 
==Tasks==
 +
<pre>
 
Shared G4 libraries - Testing
 
Shared G4 libraries - Testing
 
Single G4 source - Testing
 
Single G4 source - Testing
 +
Review GEMC Output code
 +
Determine coordinate system
 +
Replicate more graphs, put in Elog
 +
</pre>
  
===Log===
+
==Notes==
 
+
'''Getting a histo from GEMC ROOT data'''
====October====
 
'''Tue 23'''
 
 
<pre>
 
<pre>
Off clock - building Sim12 on Fedora 7, some linking errors with JGeant4
+
To get a histogram from GEMC data do something akin to:
 
+
  TH2F *edep_p = new TH2F("edep_p","edep vs p (Protons)",100,0.0,4000.0,100,0.0,2.2);
Arrived 12pm
+
  edep_p->SetMarkerColor(40); 
Familiarizing with batch mode, xml files
+
  edep_p->SetMarkerSize(20.0);
Put together common batch mode commands from http://clasweb.jlab.org/wiki/index.php/Sim12_Manual.
+
  bst->Draw("Edep:p>>edep_p","Edep<2");
Creating log for hours, things done.
+
First we create the histo, set up some attributes, and then finally we pipe a graph into
Read SVT and silicon detector papers
+
it. After this, you probably want to use Clear() in whatever pad your using to remove
Out 3:00pm
+
any graphs it draws in the process.
 
 
tonight: more reading, fix linking problem
 
 
</pre>
 
</pre>
  
'''Thur 25'''
+
'''Specifying exactly which histo to grab'''
 
<pre>
 
<pre>
Off clock - picking up Introduction to Elementary Particles by Griffiths today or tomorrow.
+
In something like:
 
+
  bst->Draw("Edep:p","Edep<2");
Arrived 12pm
+
Edep may be in the bst tree while p is in the generated tree. To specify which ones to use:
Reading through HDDS-1_0.xsd - XML documentation
+
  bst->Draw("Edep:genT.p","Edep<2");
Put together a simulation with just 2 SVTs (or maybe 1 double layered SVT) and a target.
 
Simulation runs a LOT faster with reduced geometry.
 
 
 
Wrote XML guide.
 
Left 2:45pm
 
 
</pre>
 
</pre>
  
'''Fri 26'''
+
'''Drawing A Legend'''
 
<pre>
 
<pre>
Off clock - picking up Introduction to Elementary Particles by Griffiths today or tomorrow.
+
Try something like:
 +
  TLegend *leg = new TLegend(0.4,0.6,0.89,0.89);
 +
  leg->SetTextSize(.03);
 +
  leg->AddEntry(histo,"title","p"); //p specifies marker as key
 +
  leg->SetFillColor(0); //white BG instead of yellow default
 +
  leg->Draw();
 +
And to change the marker color of a histo:
 +
  histo->SetMarkerColor(int color);
 +
</pre>
  
Arrived 10am
+
===Log===
Set up single 'strip' simulation. Trying to figure out color meaning.
 
Color crazy! Perhaps seperated by charge, optical or 'other' emag radiation. All leptons so far are red.
 
Note: I do not get the vertical red lines I did when first running the simulation. Perhaps there is too
 
much geometry when the entire site is loaded and it breaks?
 
  
Applying fields to the region. (Uniform) Seem to have some effect on charged particles in jets but not
+
[[Kyle's Old Logs]]
in incoming beam...not much of an effect though. Need to run more tests, check field strength. I don't think
 
it's doing anything.
 
  
Rotation in the phi dimension is broken for theta = 0.
+
====June====
 +
'''Wed 4'''
 +
<pre>
 +
In 12:00pm
 +
Sarah gave Dan and I example root scripts which we are to modify for use with data collected in GEMC.
 +
Can now open root files from interpreter or program, explore trees and draw histos. I want to be able
 +
to recreate some of these: http://clasweb.jlab.org/wiki/index.php/First_SVT_results
 +
Out 4:00pm
 +
</pre>
  
Sim12 registered hit for an optical photon, gave lots of nice information. Hasn't done that for other
+
'''Thur 5'''
particle hits. Trying to get Sim12 to dump particle info to a file rather than just the terminal.
+
<pre>
Out - 12:30pm
+
In 1:00pm
 +
Made theta dependence event detection graph. Recreated Edep vs. p graph using AddFriend method on TTree svt.
 +
Then everything took a strange turn as root began to fail to do things. Worked with sarah trying to figure
 +
out what was going on. Affecting different programs, different versions of root.
 +
Out 4:00pm
 
</pre>
 
</pre>
  
====November====
+
'''Tue 10'''
 
 
'''Mon 5'''
 
 
<pre>
 
<pre>
Arrived 10:30AM
+
In 1:00pm
Will G4 simulate semicondcutor SVT? - should...simulates photoelectric effect
+
Met with Sarah, Maurik. Frustratingly tried to manipulate GEMC data trees. Finally reached the point
Building detector piece as descriped in the diagrom in the SVT notes. Fixing geometry.
+
where we can create copies of histograms. Many root things not working or working strangely.  
Out 12:15PM
+
Need to get bin content of individual histos and manipulate them manually.
 +
Out 4:00pm
 
</pre>
 
</pre>
  
'''Wed 7'''
+
'''Wed 11'''
 
<pre>
 
<pre>
Arrived 10:00AM
+
In 12:00pm
It seems references to geometry in the xml files use the center of a volume for it's
+
Trying to create one 2d histogram from two 1d histograms...can't find anything similar online.  
referencing index. I've built the first layer of the SVT cross section. What are we
+
Maurizio got back to us, piped output into a 2d histogram and it worked. Changed drawing,  
using for n, n+, and p+? Spoke to Sam about this, he will get back to me.
+
binning options. Looks great! Dan is running a 50000 event simulation with the same inputs
 
+
as our current 5000 event data for further refined data.
For the laser test-bed we are trying to assemble:
 
Is this laserlight polarized? Geant4 cannot yet simulate
 
polarized light.
 
  
Trying to simulate photoelectric effect.
+
gemc_evio2root has been updated and our current version of root does not have RIO libraries.
-what is the opticalphoton wavelength -controlled by energy?
+
Another version did but we found it to be incompatible.  
Out 12:30pm
+
Out 3:45pm
 
</pre>
 
</pre>
  
'''Fri 9'''
+
'''Wed 18'''
 
<pre>
 
<pre>
Arrived 10:15AM
+
In 2:00pm
Met with Sam on thursday, he recommended a great detector book, explaining the + designation on p and n semiconductors.
+
The hub is not working, Hovannes, Dan and I tried to get ennui and benfranklin up to no avail.  
I spoke with grad student Georgi Nenchev on Solid State physics, and he recommended I pick up a book.
+
Hovannes and I just used our laptops, with Dan on benfranklin going direct to an ethernet jack in the wall.
Modeling SVT from the cross section.
+
Talked to sarah, recreating graphs. Have Edep v. p, working on theta with threshold cutting and phi v. z.
What semiconductor materials are we using? (notes: p-gallium,boron,indium n-arsenic,phosphorus,antimony)
+
Our Phi v. z plot is very sparsely populated. I emailed maurizio about this.
How must the geometry be defined for pn junctions?
+
One can see two distinct signals in the proton & pion edep v p graph, however we may need to widen
out 12:45pm
+
our energy scale (lower) to see this more clearly. Running simulation with wider energy allowances.
 +
Out 5:00pm
 
</pre>
 
</pre>
  
'''Wed 14'''
+
'''Tue 24'''
 
<pre>
 
<pre>
Arrived 10:15AM
+
In 1:00
Got scons, qt4, already have mysql, geant4 and python. Building qt4. Need gemc source. Filled out early time sheet.
+
Elog is up but needs a proper template - Dan is on that. Making images of the graphs to put in elog. Fixed wiki log error.
Out 12:45PM
+
Running 500,000 events proton and pion simultaneously. Need more statistics to replicate Maurizio's graphs. Proton data was
 +
damaged and I am running it again. Running another pion experiment to add to our current one.
 +
Out 3:30
 +
Ran to James hall fossil/map giveaway
 +
In 4:15
 +
Creating pion-proton graph with new data
 +
Out 4:30
 
</pre>
 
</pre>
  
'''Thur 15'''
+
'''Thur 26'''
 
<pre>
 
<pre>
Arrived 12:30PM
+
In 11:15am
Needed to set some env vars. Had to recompile qt4 with mysql support, recycling geant4 in sim12 build for gemc.
+
Working on pion-proton graph.
Lunch/Class Out: 2:15PM
+
Out 12:00pm Lunch
  
Arrived 5:00PM
+
In 1:15
make install qt - still getting mysql errors. Rebuild scons.
+
Had Katie sign timesheets
Out 6:15pm
+
I cannot figure out why our data isn't succesfully piping to histograms.
 +
Talked to sarah, she didn't know. Checking root documentation.
 +
Can we directly refer to histograms?
 +
Out 4:30
 
</pre>
 
</pre>
  
'''Fri 16'''
+
'''Mon 30'''
 
<pre>
 
<pre>
Arrived 9:00AM
+
In 12:15
Still getting MYSQL errors. Needed to export MYSQL=/. Getting a library error.
+
Contacted jlab, my password has changed and I can't svn or get my email.
Looking at G4 source. Trying to implement a simple log. I see references to a file stream named LOG_MSG in gemc's source but can't find the file.
+
Dan gone until tommorow, he's in NJ. I shall investigate why my program
Out: 11:30PM
+
isn't working.
 +
Finally fixed the pion & proton edep_p graph! Cool!
 +
Updated some wiki information on availability and versions of programs
 +
in the CLAS12ROOT directory. Created a notes section for me, in this log.
 +
Updated summer, fall schedule.
 +
 
 +
Made theta graph with current data. Maurizio's cuts are different than mine.
 +
Making phi vs. z graph. I need to combine lots of data for a statistical view,
 +
running more proton simulations.
 +
Out 3:15pm
 
</pre>
 
</pre>
  
 
+
====July====
'''Wed 19'''
+
'''Tue 1st'''
 
<pre>
 
<pre>
Arrived 10:00AM
+
In 1:30pm
Compiled GEMC with maurizio's file logging, it works just fine. Checking out the source, brushing up on Qt4
+
Organized goals with Sarah. Dan has elog running on mariecurie, but does Maurik want
Out: 11:30PM
+
us using it? Emailing maurizio for coordinate system and other things.
 +
Maurizio got back to us. /home ran out of space! We alerted matt and spoke with him
 +
about the new server. Organized CLAS12ROOT. Data will now be in CLAS12ROOT/Experiments/data
 +
to keep home directories smaller. Removed older data.
 +
Out 4:45pm
 
</pre>
 
</pre>
  
'''Mon 26'''
+
'''Thur 3rd'''
 
<pre>
 
<pre>
Arrived 10:15AM
+
In 7:45am
Implemented panning with respect to zoom. Compiles fine, but I can't test it as Maurizio must be playing with the geometry server. Implementing buttons for panning.
+
Edited RHEL5_x64 env script to reflect a new $DATA variable pointing to the folder containing
Out: 12:45PM
+
all the data from gemc runs.
 +
 
 +
The data I set running Tue 1st seems to have not been properly closed. Someone must have killed
 +
benfranklin's internet connection before my run finished last night. Rerunning.
 +
 
 +
I created an Index.txt in $DATA in which we can keep the command used to generate data next to
 +
it's filename, alleviating the need for long rootfile names.
 +
 
 +
I don't understand why we register so few hits in layers 2, 3, and 4 in our data, for the theta
 +
graph. You can see it again, in the Edep graphs.
 +
 
 +
I do not know the cause of the phenomenon, but I nearly sure there are 8 layers in total between
 +
all four barrels of the SVT. I would think this would mean 2 per layer but histograms I have
 +
generated beg to differ. Made x_y_z for all 8 layers.
 +
Out 10:30am
 
</pre>
 
</pre>
  
'''Tue 27'''
+
'''Thur 10th'''
 
<pre>
 
<pre>
Arrived 12:30AM
+
In 12:00pm
Implemented test button for panning. Again, geometry server is not functioning, so I can't really test it yet. Trying to compile new version of GEMC, getting EVIO errors
+
Hobo and Ben Franklin are not of good health, so Dan and I are using the physics lounge computers.  
on building.
+
We asked maurizio about the layers confusion and it works as such:
  
Just tested, scale to zoom panning works great!
+
"layer[0] == 1 means "plot all events where the first hit was in layer 1".
Button isn't working. I don't know if I can pass an argument to a function using a slot.
+
layer[1] == 2 means "plot all events where the second hit was in layer 2"  - that means the first hit is somewhere else
Created seperate method for button panning, works great! Now I need to just put it all together so it looks good.
+
layer[4] == 3 means "plot all events where the fifth hit was in layer 3"  - that means the first 4 hits are somewhere else (very unlikely)."
Updated notes and tasks on this page.
+
 
Can't get new GEMC to build, with evio from taro/maurik or evio from jlab. It can't link evioxx. I can't even find anything called evioxx.
+
So my question is how do I specify showing the hits in just a single layer?
Out: 3:00PM
+
out 2:45
 
</pre>
 
</pre>
  
'''Wed 28'''
+
'''Tue 15th'''
 
<pre>
 
<pre>
Arrived 10:15AM
+
In 1:00
Helping Dan with Command line box
+
Prepared for meeting with Maurik. Fixed X_Y_Z graph.
Implemented buttons for panning. Trying to get them in their own box, not working yet.
+
Lunch 2:45
I see maurizio wants a google-maps like interface. I assume he means drag to pan/rotate and scroll zoom.
+
In 3:45
 +
Looking through gemc's output code. Trying to find evio documentation.
 +
Out 4:30
 +
</pre>
  
I'm going to pick up a book on QT.
+
'''16th-19th'''
Left 12:15
+
<pre>
 +
Trying to decipher GEMC and gemc2evio code. Just following it, not producing anything
 +
so I'm not recording any hours.
 
</pre>
 
</pre>
  
'''Fri 30'''
+
'''Tue 22'''
 
<pre>
 
<pre>
Arrived 10:00AM
+
In 1:00
got latest evio/gemc from taro/maurik
+
Checking out GEMC code. Trying to form questions to ask Maurik.
got evio to install, but scons'ing gemc results in the same linking evioxx error
+
Out 2:00
  
reading through qt tutorial
+
Our advisors were busy! Reading code. Perhaps if we can create our own dummy item in gemc and
 +
run it through the processes until we can see it in a root file we will understand more.
 
</pre>
 
</pre>
  
 +
'''Thur 24'''
 +
<pre>
 +
In 3:00pm
 +
Did timesheets for past two weeks.
 +
Inside output/evio_output.cc is an interesting method, called WriteGenerated, which takes a vector<MGeneratedParticle>
 +
called MGP. I'm trying to find where WriteGenerated is called to see where MGP originates.
 +
 +
WriteGenerated is referenced in src/MEventAction.cc
  
====December====
+
More interesting things inside /hitprocess/clas12/svt/BST_hitprocess.cc
'''Mon 3'''
+
Out:4:30
<pre>
 
Arrived 1015
 
built new gemc, sent code to maurizio
 
checking out dan's code
 
future ideas for buttons: pan factor
 
Out 1215
 
 
</pre>
 
</pre>
  
'''Tue 11'''
+
'''Fri 25'''
 
<pre>
 
<pre>
In 1215
+
Supposed to come in 8-11am, stuck in Hanover with brake problems.
Implemented compass-rose type buttons, put into new
+
Will work monday afternoon for three hours.
code with command box
 
Implemented pan factor slider
 
Out 2:15
 
 
</pre>
 
</pre>
  
'''Wed 13'''
+
'''Mon 28'''
 
<pre>
 
<pre>
In 100
+
Came in at 12:15 but the physics lounge computers were inaccessable. Tried to boot up BF but it was
Implemented coord boxes. Displays current x,y and allows
+
taking a long time so I went to an early lunch. Saw Maurik! Meeting with Sarah later. Amrit may have
one to jump to any x,y. What is wrong with phi? Fix it.
+
a student? Also need to coordinate a time to move computers in the nuc server room.
Tommorow add reset button. Move on.
+
 
Out 300
+
In 1:30
 +
Physics lounge still being buffed. Bypassed router in JLAB room, BF booted up fine. It occurred to me
 +
during lunch that MGeneratedParticle is probably a Geant4 object and I can use the G4 documentation.
 +
 
 +
-Strike that. Haven't found anything online. $GEMC/grep -R -i mgeneratedparticle ./
 +
 
 +
Nice find: /src/MHit.cc:
 +
int MHit::mc_number_scheme(string pid)
 +
{
 +
if(pid=="e-")            return 11;
 +
if(pid=="e+")            return -11;
 +
if(pid=="gamma")        return 22;
 +
if(pid=="neutron")      return 2112;
 +
if(pid=="proton")        return 2212;
 +
if(pid=="kaon+")        return 321;
 +
if(pid=="kaon-")        return -321;
 +
if(pid=="kaon0")        return 311;
 +
if(pid=="kaon0L")        return 130;
 +
if(pid=="pi+")          return 211;
 +
if(pid=="pi-")          return -211;
 +
if(pid=="p0")            return 111;
 +
if(pid=="opticalphoton") return -22;
 +
else return 0;
 +
}
 +
 
 +
Made some changes to GEMC code. MHit.cc and MSensitiveDetector.cc. compiled, but not putting my changes into the output.
 +
 
 +
Out 4:30
 +
 
 
</pre>
 
</pre>
  
 
+
'''Tue 29'''
====January====
 
'''Thur 10'''
 
 
<pre>
 
<pre>
 
In 11:30
 
In 11:30
Got updated code from maurik,
 
integrating my gui changes into the new code.
 
Arg! Scons errors. Emailed Maurizio.
 
Out 12:15
 
</pre>
 
  
'''Tue 15'''
+
  "G4Colour colour_touch (0.0, 0.0, 1.0);
<pre>
+
    G4Colour colour_hit  (1.0, 0.0, 0.0);
In 115
+
    G4Colour colour_passby(0.0, 1.0, 0.0);
Built g4.9.1, assembly el4/5 32/64 bit builds of all
+
 
gemc things.
+
    // If the energy is above threshold, red circle.
 +
    // If the energy is below threshold, blue smaller circle.
 +
    // If no energy deposited, green smaller circle."
 +
 
 +
Added extra output to GEMC. Trying to get it through evio2root but getting segfaults.
  
Gemc will not build. There is a linking error with a QT4 .so
+
Met with Maurik at 2:00.  
however QTDIR and QTHOME are specified, QTHOME/lib is in
 
LD_LIBRARY_PATH, and the .so exists within the directory.
 
Out 5:00PM
 
</pre>
 
  
 +
Out 2:30
  
'''Wed 16'''
 
<pre>
 
In 12:30
 
Still trying to figure out this linking error.
 
-seems we need the latest gemc to resolve
 
building RHEL4_x32 gemc dependencies on pumpkin
 
Out 4:45
 
 
</pre>
 
</pre>
  
'''Mon 21'''
+
===August===
 +
'''Move Week'''
 
<pre>
 
<pre>
In 11:00
+
Dan and I were here Mon-Thur for 8-9 hours a day helping, but I'm not sure if it's work or not.  
GEANT built successfully. Building scons. Got BMS and built EVIO.
+
We recorded three hours a day, will check with sarah.
SCons and pyscripts are in the main CLAS12 directory.
 
Getting new GEMC...maurik is writing to JLab for access.
 
Out 1:00
 
SSH:
 
Fixed the scons install. Putting GEMC in my home directory and attempting
 
to build it from the dependencies on pumpkin2/taro
 
I thought dan had compiled qt, has not. Moving source to pumpkin and
 
compiling as in the 'detailed instructions.' http://clasweb.jlab.org/wiki/index.php/Detailed_instructions
 
 
</pre>
 
</pre>
  
'''Tue 22'''
+
'''Mon 11'''
 
<pre>
 
<pre>
In 1:15
+
In 11:30
Recompiling Geant4
+
Dan is investigating Elog problems. Sarah has the guidelines for the electrical output methods
I tried compiling it manually but I must be doing something wrong. Using
+
that we are to implement, but I am still reading the code, trying to write a variable out.
the configure script. Everything seems like it built fine.
+
 
 +
I'm trying to identify a clear chain of events in processing a hit, and writing it out. It's not yet
 +
completely clear where we will need to interrupt this chain to insert our ADC to TDC code
 +
however it has become apparent to me that evio_output.cc has a much higher importance than
 +
I had originally given it in processing and writing an event.
 +
 
 +
2:00 - ran to nesmith, getting a table for dawn.
 +
2:10 - back
 +
 
 +
mariecurie seems to have gone down for some reason. We are trying to transition to Elog.
 +
 
 +
Updating GEMC. I will try to get a variable written out through the generated info tree.
 +
 
 +
Moved desks for Sarah.
  
Whever I scons gemc, it tells me G4UIQt is undeclared, despite G4UIQt.hh being
+
Out 5:10
included in the building of gemc.
 
  
"gemc.cc: In function `int main(int, char**)':
 
gemc.cc:176: error: `G4UIQt' has not been declared
 
scons: *** [gemc.o] Error 1
 
scons: building terminated because of errors."
 
Out 3:30
 
 
</pre>
 
</pre>
  
'''Tue 29'''
+
'''Wed 13'''
 
<pre>
 
<pre>
In 2:00PM
+
In 11:00
This error must lie either in combining the incorrect G4 and gemc versions,
+
 
or in a bad G4 compile. QT I beleive should be compiled correctly.
+
Pumpkin slow for some reason. Using Einstein.
I've recompiled, making manually after setting enviroment variables, G4. Gemc still doesn't compile.
+
 
Out 3:30
+
Ok. So I think most of the actual writing and suck happens inside evio_output.cc|Record_and_Clear(). However, I
</pre>
+
don't yet speak EVIO and will begin reading EVIO's code more in depth.
  
====Febuary====
+
Out 11:30 Lunch
'''Tue 5'''
 
<pre>
 
In 9:30
 
Found some info on GTUI.py. We have the right version of python...
 
Redownloading loadgeant4.py
 
GEMC builds! Doesn't run though.
 
Exporting CLHEP/lib to LD_LIBRARY_PATH
 
Runs! But segfaults. Probably just problems in this GEMC.
 
Interestingly enough, old versions of gemc also build, but then
 
segfault. We need the newest gemc version to be able to tell if
 
this is gemc or G4.
 
Out 10:30
 
  
In 12:00
+
In 1:00
Dan is moving the directory structure as I write a guide.
 
Beginning work on RHEL5_64
 
  
Built:
+
Reading EVIO source files - make that example scripts.
CLHEP
 
XERCESC
 
DAWN
 
EVIO
 
QT
 
  
Out 2:00pm
+
Using Elog
  
 +
Out 3:30
 
</pre>
 
</pre>
  
 
+
'''Tue 19'''
'''Tue 8-12'''
 
 
<pre>
 
<pre>
sshing in from home, building 5_x64
+
In 12:00
 +
I cannot get into elog for some reason. Waiting to talk to sarah-more office drama.
 +
Reading through code, wondering about the << operator. I will email Maurizio.
 +
Out 2:00
 
</pre>
 
</pre>
  
 
+
'''Wed 20'''
'''Thur 14'''
 
 
<pre>
 
<pre>
 
In 10:30
 
In 10:30
Building dependencies RHEL5_x32
+
Checking out Geant4 examples recommended by sarah. Reading M. Brigada's paper.
corn crashed.
+
Out 12:00 Lunch
Out-Class 11:00
+
In 1:00
 +
Reading.
 +
Finished Brigada's paper. Emphasis on part 4.
 +
Out 2:00 - going to financial aid
 +
In 2:15
 +
Read G4 examples sent by Sarah, Simulation study for a single TOF
 +
scintillator using GEANT4. Brigada's paper was more accessible in the fourth part,
 +
which is directly relevant to our interests. I'd like to see the code as well.
  
In 12:00
+
Out 3:30
getting evio linking errors when building gemc.
 
slowly but surely driving me ever closer of the
 
cliff and into the depths of madness.
 
Out 2:15
 
 
</pre>
 
</pre>
  
'''Mon 18'''
+
'''Thur 21'''
 
<pre>
 
<pre>
In 3:00pm
+
In 10:00am
Corn should be good to go.
+
Met with Sarah, discussed questions for her SVT meeting. She recommends I steer clear of the
Compiled CLHEP, XERCESC RHEL5_x32.
+
Brigada code and look at the G4 examples.
  
Got GEMC to build on RHEL5_x64, loadevio.py
+
Reading GammaRayTele example
was linking from EVIO/lib, but libraries are in EVIO/OS_ARCH/lib.
 
Moved my lib to the root directory as the pyscripts are shared.
 
  
On RHEL5_x32:
+
Out Lunch 12:20
Tried to build qt, on running configure script gcc failes as not recognizing the filetype of project.o.
 
Out 5:30pm
 
  
 +
In 12:50
 +
GRT
 +
Out 2:20
 
</pre>
 
</pre>
  
 +
'''Fri 22'''
 +
<pre>
 +
In 10:00am
 +
 +
Creating a method to write out digital info in GEMC.
 +
Success! It writes out a file called digitalouts.txt. With information like:
 +
 +
layer: 1    sector: 5    strip: 18    Edep: 0.215085 MeV
 +
layer: 2    sector: 5    strip: 220    Edep: 0.283442 MeV
 +
layer: 3    sector: 8    strip: 190    Edep: 0.129059 MeV
 +
layer: 3    sector: 8    strip: 191    Edep: 0.177371 MeV
 +
layer: 4    sector: 8    strip: 13    Edep: 0.255779 MeV
 +
layer: 5    sector: 10    strip: 17    Edep: 0.172112 MeV
 +
layer: 6    sector: 10    strip: 170    Edep: 0.160031 MeV
 +
layer: 7    sector: 14    strip: 58    Edep: 0.153398 MeV
 +
 +
Of course, to use this data it is much more likely we will
 +
be organising more like:
 +
 +
layer  sector  strip  Edep
 +
1          5            18      .21508
 +
etc
  
 +
In fact, this system is probably not directly suited for
 +
simulated electronics output as we want to integrate
 +
the energy deposited in a strip over a certain amount
 +
of time, and then read that out. Right?
  
'''Tue 19'''
+
Out 1:30
 +
I think I went .5 hrs over the timesheet.
 +
</pre>
 +
 
 +
'''Tue 26'''
 
<pre>
 
<pre>
In 12:00pm
+
In 1:30pm
Building QT on corn...getting compiler errors. It's trying to compile 64bit???
+
My old routine had a few logical errors, I've fixed those now. Meeting with Maurizio.
Corn does not have mysql. I email npg-admins about this.
+
Out 4:00pm
Out 1:30
 
 
</pre>
 
</pre>
  
'''Mon 25'''
+
'''Wed 27'''
 
<pre>
 
<pre>
In 4:00pm
+
In 9:30
Dan and I edited the Detailed Instructions wiki, and are putting up example environment scripts,
+
 
build steps/commands.
+
Trying to add an ADC variable to the hitprocess. Maurizio confirmed my suspicions that
We downloaded magnetic field info and GEMC starts smoothly.
+
variables have to be added database side.
Out 5:45
+
Waiting for an email back from sarah
 +
Out 12:00pm
 
</pre>
 
</pre>
  
 
'''Thu 28'''
 
'''Thu 28'''
 
<pre>
 
<pre>
In 12:00
+
In 11:15am
Naturally, when showing maurik GEMC it failed to open.
+
What variables do we need added to the banks?
We have deduced this to be a problem with svtgeometry and
+
Out 1:15 Lunch with Sarah, Matt, Dan
not out builds as other geometries function correctly.
+
In 2:30
Out 2:00
+
Trying to print sys-admin flyers. Printer drivers on MarieCurie all messed up.
 +
Put up flyers in Mub, Kingsbury, took down old flyers.
 +
Out 4:00
 +
</pre>
 +
 
 +
'''Fri 29'''
 +
<pre>
 +
In 10:30am
 +
Fleshed out wiki from yesterday. I would like to meet with Sarah and Dan today and decide
 +
which variables we need Maurizio to add to the bank definition so we can create our
 +
digitization methods.
 +
 
 +
Met with Sarah. Moved Furniture.
 +
Out 12:30pm
 
</pre>
 
</pre>
  
 +
===September===
  
====March====
+
'''Wed 3'''
'''Tue 4'''
 
 
<pre>
 
<pre>
In 12:00
+
In 8:30
Built shared libraries for G4 on RH5 64 and 32. 64 did spit out some errors, but it completed successfully. Testing this.
+
Maurizio has not emailed us back. Updated GEMC. Our ADC variable has not
As per Maurik's suggestion, moved the G4 source directory into the main CLAS12 directory and created a simlink in RHEL5_x64/GEANT4.9.1
+
been implemented. We are thinking each step in the electronics chain should be
to point there. Currently building GEMC, testing this.
+
a method called by ProcessHit in BST_hitprocess. Creating blank methods.
 +
Out 9:40
 +
 
 +
in 2:30
 +
We talked to Sarah about the electronics, and if Maurizio doesn't add the
 +
variable soon we will shoot the information to a text file.
 +
out 3:30
 +
</pre>
 +
 
 +
'''Thur 4'''
 +
<pre>
 +
In 8:35
 +
Filling out digi methods
 +
Out 9:35
 
</pre>
 
</pre>
  
'''Sun 23'''
+
'''Fun Fun Friday the 5th'''
 
<pre>
 
<pre>
In 1:45
+
In 11:00am
Trying to get data out of GEMC and into ROOT.
+
 
Got data out into text, evio formats.
+
Talked to Sarah about ADC methods. I've decided to implement all or our
Got xml data from evio data. Need to svn evio2root.
+
changes within our own class, as spaghetti code was beginning to form.
Installing root in CLAS12 on pumpkin2
+
 
Out 5:00
+
Out 12:30pm
 +
 
 +
Lunch with Sarah, Karl
 +
 
 +
In 1:30pm
 +
Implementing class. It's much much easier to maintain this way.
 +
Out 5:45pm
 
</pre>
 
</pre>

Latest revision as of 21:45, 5 September 2008

Progress and Task Log for Kyle

Schedule

Tasks

Shared G4 libraries - Testing
Single G4 source - Testing
Review GEMC Output code
Determine coordinate system
Replicate more graphs, put in Elog

Notes

Getting a histo from GEMC ROOT data

To get a histogram from GEMC data do something akin to:
  TH2F *edep_p = new TH2F("edep_p","edep vs p (Protons)",100,0.0,4000.0,100,0.0,2.2);
  edep_p->SetMarkerColor(40);  
  edep_p->SetMarkerSize(20.0); 
  bst->Draw("Edep:p>>edep_p","Edep<2");
First we create the histo, set up some attributes, and then finally we pipe a graph into
it. After this, you probably want to use Clear() in whatever pad your using to remove
any graphs it draws in the process.

Specifying exactly which histo to grab

In something like:
  bst->Draw("Edep:p","Edep<2");
Edep may be in the bst tree while p is in the generated tree. To specify which ones to use:
  bst->Draw("Edep:genT.p","Edep<2");

Drawing A Legend

Try something like:
  TLegend *leg = new TLegend(0.4,0.6,0.89,0.89);
  leg->SetTextSize(.03);	
  leg->AddEntry(histo,"title","p"); //p specifies marker as key
  leg->SetFillColor(0); //white BG instead of yellow default
  leg->Draw();
And to change the marker color of a histo:
  histo->SetMarkerColor(int color);

Log

Kyle's Old Logs

June

Wed 4

In 12:00pm
Sarah gave Dan and I example root scripts which we are to modify for use with data collected in GEMC.
Can now open root files from interpreter or program, explore trees and draw histos. I want to be able
to recreate some of these: http://clasweb.jlab.org/wiki/index.php/First_SVT_results
Out 4:00pm

Thur 5

In 1:00pm
Made theta dependence event detection graph. Recreated Edep vs. p graph using AddFriend method on TTree svt.
Then everything took a strange turn as root began to fail to do things. Worked with sarah trying to figure 
out what was going on. Affecting different programs, different versions of root.
Out 4:00pm

Tue 10

In 1:00pm
Met with Sarah, Maurik. Frustratingly tried to manipulate GEMC data trees. Finally reached the point 
where we can create copies of histograms. Many root things not working or working strangely. 
Need to get bin content of individual histos and manipulate them manually.
Out 4:00pm

Wed 11

In 12:00pm
Trying to create one 2d histogram from two 1d histograms...can't find anything similar online. 
Maurizio got back to us, piped output into a 2d histogram and it worked. Changed drawing, 
binning options. Looks great! Dan is running a 50000 event simulation with the same inputs 
as our current 5000 event data for further refined data.

gemc_evio2root has been updated and our current version of root does not have RIO libraries.
 Another version did but we found it to be incompatible. 
Out 3:45pm 

Wed 18

In 2:00pm
The hub is not working, Hovannes, Dan and I tried to get ennui and benfranklin up to no avail. 
Hovannes and I just used our laptops, with Dan on benfranklin going direct to an ethernet jack in the wall.
Talked to sarah, recreating graphs. Have Edep v. p, working on theta with threshold cutting and phi v. z. 
Our Phi v. z plot is very sparsely populated. I emailed maurizio about this.
One can see two distinct signals in the proton & pion edep v p graph, however we may need to widen
 our energy scale (lower) to see this more clearly. Running simulation with wider energy allowances.
Out 5:00pm

Tue 24

In 1:00
Elog is up but needs a proper template - Dan is on that. Making images of the graphs to put in elog. Fixed wiki log error.
Running 500,000 events proton and pion simultaneously. Need more statistics to replicate Maurizio's graphs. Proton data was
damaged and I am running it again. Running another pion experiment to add to our current one.
Out 3:30
Ran to James hall fossil/map giveaway
In 4:15
Creating pion-proton graph with new data
Out 4:30

Thur 26

In 11:15am
Working on pion-proton graph.
Out 12:00pm Lunch

In 1:15
Had Katie sign timesheets
I cannot figure out why our data isn't succesfully piping to histograms.
Talked to sarah, she didn't know. Checking root documentation.
Can we directly refer to histograms? 
Out 4:30

Mon 30

In 12:15
Contacted jlab, my password has changed and I can't svn or get my email.
Dan gone until tommorow, he's in NJ. I shall investigate why my program
isn't working.
Finally fixed the pion & proton edep_p graph! Cool!
Updated some wiki information on availability and versions of programs
in the CLAS12ROOT directory. Created a notes section for me, in this log.
Updated summer, fall schedule.

Made theta graph with current data. Maurizio's cuts are different than mine.
Making phi vs. z graph. I need to combine lots of data for a statistical view,
running more proton simulations.
Out 3:15pm

July

Tue 1st

In 1:30pm
Organized goals with Sarah. Dan has elog running on mariecurie, but does Maurik want
us using it? Emailing maurizio for coordinate system and other things.
Maurizio got back to us. /home ran out of space! We alerted matt and spoke with him
about the new server. Organized CLAS12ROOT. Data will now be in CLAS12ROOT/Experiments/data
to keep home directories smaller. Removed older data.
Out 4:45pm

Thur 3rd

In 7:45am
Edited RHEL5_x64 env script to reflect a new $DATA variable pointing to the folder containing
all the data from gemc runs.

The data I set running Tue 1st seems to have not been properly closed. Someone must have killed
benfranklin's internet connection before my run finished last night. Rerunning.

I created an Index.txt in $DATA in which we can keep the command used to generate data next to
it's filename, alleviating the need for long rootfile names.

I don't understand why we register so few hits in layers 2, 3, and 4 in our data, for the theta
graph. You can see it again, in the Edep graphs. 

I do not know the cause of the phenomenon, but I nearly sure there are 8 layers in total between
all four barrels of the SVT. I would think this would mean 2 per layer but histograms I have
generated beg to differ. Made x_y_z for all 8 layers.
Out 10:30am

Thur 10th

In 12:00pm
Hobo and Ben Franklin are not of good health, so Dan and I are using the physics lounge computers. 
We asked maurizio about the layers confusion and it works as such:

"layer[0] == 1 means "plot all events where the first hit was in layer 1".
layer[1] == 2 means "plot all events where the second hit was in layer 2"  - that means the first hit is somewhere else
layer[4] == 3 means "plot all events where the fifth hit was in layer 3"  - that means the first 4 hits are somewhere else (very unlikely)."

So my question is how do I specify showing the hits in just a single layer?
out 2:45

Tue 15th

In 1:00
Prepared for meeting with Maurik. Fixed X_Y_Z graph.
Lunch 2:45
In 3:45
Looking through gemc's output code. Trying to find evio documentation.
Out 4:30

16th-19th

Trying to decipher GEMC and gemc2evio code. Just following it, not producing anything
so I'm not recording any hours.

Tue 22

In 1:00
Checking out GEMC code. Trying to form questions to ask Maurik.
Out 2:00

Our advisors were busy! Reading code. Perhaps if we can create our own dummy item in gemc and 
run it through the processes until we can see it in a root file we will understand more.

Thur 24

In 3:00pm
Did timesheets for past two weeks.
Inside output/evio_output.cc is an interesting method, called WriteGenerated, which takes a vector<MGeneratedParticle>
called MGP. I'm trying to find where WriteGenerated is called to see where MGP originates.

WriteGenerated is referenced in src/MEventAction.cc

More interesting things inside /hitprocess/clas12/svt/BST_hitprocess.cc
Out:4:30

Fri 25

Supposed to come in 8-11am, stuck in Hanover with brake problems.
Will work monday afternoon for three hours.

Mon 28

Came in at 12:15 but the physics lounge computers were inaccessable. Tried to boot up BF but it was 
taking a long time so I went to an early lunch. Saw Maurik! Meeting with Sarah later. Amrit may have
a student? Also need to coordinate a time to move computers in the nuc server room.

In 1:30
Physics lounge still being buffed. Bypassed router in JLAB room, BF booted up fine. It occurred to me
during lunch that MGeneratedParticle is probably a Geant4 object and I can use the G4 documentation.

-Strike that. Haven't found anything online. $GEMC/grep -R -i mgeneratedparticle ./ 

Nice find: /src/MHit.cc:
int MHit::mc_number_scheme(string pid)
{
 if(pid=="e-")            return 11;
 if(pid=="e+")            return -11;
 if(pid=="gamma")         return 22;
 if(pid=="neutron")       return 2112;
 if(pid=="proton")        return 2212;
 if(pid=="kaon+")         return 321;
 if(pid=="kaon-")         return -321;
 if(pid=="kaon0")         return 311;
 if(pid=="kaon0L")        return 130;
 if(pid=="pi+")           return 211;
 if(pid=="pi-")           return -211;
 if(pid=="p0")            return 111;
 if(pid=="opticalphoton") return -22;
 else return 0;
}
  
Made some changes to GEMC code. MHit.cc and MSensitiveDetector.cc. compiled, but not putting my changes into the output.

Out 4:30

Tue 29

In 11:30

   "G4Colour colour_touch (0.0, 0.0, 1.0);
    G4Colour colour_hit   (1.0, 0.0, 0.0);
    G4Colour colour_passby(0.0, 1.0, 0.0);

    // If the energy is above threshold, red circle.
    // If the energy is below threshold, blue smaller circle.
    // If no energy deposited, green smaller circle."

Added extra output to GEMC. Trying to get it through evio2root but getting segfaults.

Met with Maurik at 2:00. 

Out 2:30

August

Move Week

Dan and I were here Mon-Thur for 8-9 hours a day helping, but I'm not sure if it's work or not. 
We recorded three hours a day, will check with sarah.

Mon 11

In 11:30
Dan is investigating Elog problems. Sarah has the guidelines for the electrical output methods 
that we are to implement, but I am still reading the code, trying to write a variable out.

I'm trying to identify a clear chain of events in processing a hit, and writing it out. It's not yet
completely clear where we will need to interrupt this chain to insert our ADC to TDC code
however it has become apparent to me that evio_output.cc has a much higher importance than
I had originally given it in processing and writing an event.

2:00 - ran to nesmith, getting a table for dawn.
2:10 - back

mariecurie seems to have gone down for some reason. We are trying to transition to Elog.

Updating GEMC. I will try to get a variable written out through the generated info tree.

Moved desks for Sarah.

Out 5:10

Wed 13

In 11:00

Pumpkin slow for some reason. Using Einstein.

Ok. So I think most of the actual writing and suck happens inside evio_output.cc|Record_and_Clear(). However, I
don't yet speak EVIO and will begin reading EVIO's code more in depth.

Out 11:30 Lunch

In 1:00

Reading EVIO source files - make that example scripts.

Using Elog

Out 3:30

Tue 19

In 12:00
I cannot get into elog for some reason. Waiting to talk to sarah-more office drama.
Reading through code, wondering about the << operator. I will email Maurizio.
Out 2:00

Wed 20

In 10:30
Checking out Geant4 examples recommended by sarah. Reading M. Brigada's paper.
Out 12:00 Lunch
In 1:00
Reading.
Finished Brigada's paper. Emphasis on part 4.
Out 2:00 - going to financial aid
In 2:15
Read G4 examples sent by Sarah, Simulation study for a single TOF 
scintillator using GEANT4. Brigada's paper was more accessible in the fourth part,
which is directly relevant to our interests. I'd like to see the code as well.

Out 3:30

Thur 21

In 10:00am
Met with Sarah, discussed questions for her SVT meeting. She recommends I steer clear of the
Brigada code and look at the G4 examples.

Reading GammaRayTele example

Out Lunch 12:20

In 12:50
GRT
Out 2:20

Fri 22

In 10:00am

Creating a method to write out digital info in GEMC.
Success! It writes out a file called digitalouts.txt. With information like:

layer: 1    sector: 5    strip: 18    Edep: 0.215085 MeV
layer: 2    sector: 5    strip: 220    Edep: 0.283442 MeV
layer: 3    sector: 8    strip: 190    Edep: 0.129059 MeV
layer: 3    sector: 8    strip: 191    Edep: 0.177371 MeV
layer: 4    sector: 8    strip: 13    Edep: 0.255779 MeV
layer: 5    sector: 10    strip: 17    Edep: 0.172112 MeV
layer: 6    sector: 10    strip: 170    Edep: 0.160031 MeV
layer: 7    sector: 14    strip: 58    Edep: 0.153398 MeV

Of course, to use this data it is much more likely we will
be organising more like:

layer   sector   strip   Edep
1          5            18      .21508
etc

In fact, this system is probably not directly suited for
simulated electronics output as we want to integrate
the energy deposited in a strip over a certain amount
of time, and then read that out. Right?

Out 1:30
I think I went .5 hrs over the timesheet.

Tue 26

In 1:30pm
My old routine had a few logical errors, I've fixed those now. Meeting with Maurizio.
Out 4:00pm

Wed 27

In 9:30

Trying to add an ADC variable to the hitprocess. Maurizio confirmed my suspicions that
variables have to be added database side.
Waiting for an email back from sarah
Out 12:00pm

Thu 28

In 11:15am 
What variables do we need added to the banks?
Out 1:15 Lunch with Sarah, Matt, Dan
In 2:30
Trying to print sys-admin flyers. Printer drivers on MarieCurie all messed up.
Put up flyers in Mub, Kingsbury, took down old flyers.
Out 4:00

Fri 29

In 10:30am
Fleshed out wiki from yesterday. I would like to meet with Sarah and Dan today and decide
which variables we need Maurizio to add to the bank definition so we can create our
digitization methods.

Met with Sarah. Moved Furniture.
Out 12:30pm

September

Wed 3

In 8:30
Maurizio has not emailed us back. Updated GEMC. Our ADC variable has not
been implemented. We are thinking each step in the electronics chain should be
a method called by ProcessHit in BST_hitprocess. Creating blank methods.
Out 9:40

in 2:30
We talked to Sarah about the electronics, and if Maurizio doesn't add the
variable soon we will shoot the information to a text file.
out 3:30

Thur 4

In 8:35
Filling out digi methods
Out 9:35

Fun Fun Friday the 5th

In 11:00am

Talked to Sarah about ADC methods. I've decided to implement all or our
changes within our own class, as spaghetti code was beginning to form.

Out 12:30pm

Lunch with Sarah, Karl

In 1:30pm
Implementing class. It's much much easier to maintain this way.
Out 5:45pm