From 33cc210bbe53d80de16af215e5590b7680b2b62b Mon Sep 17 00:00:00 2001 From: "P.M. Sutter" Date: Wed, 27 Feb 2013 16:28:00 -0600 Subject: [PATCH 01/16] fixed issues with slicing in redshift or real space --- .../pipeline_source/prepareCatalogs.in.py | 22 ++++++++----------- 1 file changed, 9 insertions(+), 13 deletions(-) diff --git a/python_tools/pipeline_source/prepareCatalogs.in.py b/python_tools/pipeline_source/prepareCatalogs.in.py index 7c36497..9157d89 100755 --- a/python_tools/pipeline_source/prepareCatalogs.in.py +++ b/python_tools/pipeline_source/prepareCatalogs.in.py @@ -165,26 +165,22 @@ newSample.addStack(0.0, 5.0, 90, 95, False, False) for i in xrange(len(zVsDY)): zVsDX[i] = vp.angularDiameter(zVsDY[i], Om=Om) - if useLightCone: - boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \ - LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox - dzSafe = 0.03 - else: - boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \ - LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox - #boxWidthZ = lbox*100./LIGHT_SPEED - dzSafe = 0.0 + boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \ + LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox for iSlice in xrange(numSlices): - sliceMin = zBox + dzSafe + iSlice*(boxWidthZ-2.*dzSafe)/numSlices - sliceMax = zBox + dzSafe + (iSlice+1)*(boxWidthZ-2.*dzSafe)/numSlices if useLightCone: + dzSafe = 0.03 + sliceMin = zBox + dzSafe + iSlice*(boxWidthZ-2.*dzSafe)/numSlices + sliceMax = zBox + dzSafe + (iSlice+1)*(boxWidthZ-2.*dzSafe)/numSlices sliceMinMpc = sliceMin*LIGHT_SPEED/100. sliceMaxMpc = sliceMax*LIGHT_SPEED/100. else: - sliceMinMpc = LIGHT_SPEED/100.*vp.angularDiameter(sliceMin, Om=Om) - sliceMaxMpc = LIGHT_SPEED/100.*vp.angularDiameter(sliceMax, Om=Om) + sliceMinMpc = zBoxMpc + iSlice*lbox/numSlices + sliceMaxMpc = zBoxMpc + (iSlice+1)*lbox/numSlices + sliceMin = np.interp(sliceMinMpc*100./LIGHT_SPEED, zVsDX, zVsDY) + sliceMax = np.interp(sliceMaxMpc*100./LIGHT_SPEED, zVsDX, zVsDY) sliceMin = "%0.2f" % sliceMin sliceMax = "%0.2f" % sliceMax From f8c8beafd058a47e61853e2d78fe1d90907c929b Mon Sep 17 00:00:00 2001 From: "P.M. Sutter" Date: Fri, 1 Mar 2013 10:31:07 -0600 Subject: [PATCH 02/16] first attempt at doing multiple subsampling with generateMock --- .../void_python_tools/backend/launchers.py | 97 +++++++++++-------- 1 file changed, 59 insertions(+), 38 deletions(-) diff --git a/python_tools/void_python_tools/backend/launchers.py b/python_tools/void_python_tools/backend/launchers.py index 17acc76..5833c4e 100755 --- a/python_tools/void_python_tools/backend/launchers.py +++ b/python_tools/void_python_tools/backend/launchers.py @@ -105,37 +105,43 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None, datafile = inputDataDir+"/"+sample.dataFile - if regenerate: - inputParameterFlag = "inputParameter " + zobovDir+"/zobov_slice_"+sampleName+".par" - outputFile = zobovDir+"/regenerated_zobov_slice_" + sampleName - else: - inputParameterFlag = "" - outputFile = zobovDir+"/zobov_slice_" + sampleName + prevSubSample = -1 + for thisSubSample in sample.subsample.split(): + + if prevSubSample == -1: + inputParameterFlag = "" + outputFile = zobovDir+"/zobov_slice_" + sampleName + "_ss" + thisSubSample + keepFraction = float(thsSubSample) + subSampleLime = "subsample %g" % keepFraction + else: + inputParameterFlag = "inputParameter " + zobovDir+"/zobov_slice_"+\ + sampleName+"_ss"+prevSubSample+".par" + outputFile = zobovDir+"/_zobov_slice_" + sampleName + "_ss" + tihsSubSample + keepFraction = float(thisSubSample)/float(prevSubSample) + subSampleLime = "resubsample %g" % keepFraction - if sample.usePecVel: - includePecVelString = "peculiarVelocities" - else: includePecVelString = "" + if sample.usePecVel: includePecVelString = "peculiarVelocities" - if sample.useLightCone: - useLightConeString = "cosmo" - else: useLightConeString = "" + if sample.useLightCone: useLightConeString = "cosmo" - if sample.dataFormat == "multidark" or sample.dataFormat == "random": - dataFileLine = "multidark " + datafile - elif sample.dataFormat == "gadget": - dataFileLine = "gadget " + datafile + if sample.dataFormat == "multidark" or sample.dataFormat == "random": + dataFileLine = "multidark " + datafile + elif sample.dataFormat == "gadget": + dataFileLine = "gadget " + datafile + elif sample.dataFormat == "sdf": + dataFileLine = "sdf " + datafile - iX = float(sample.mySubvolume[0]) - iY = float(sample.mySubvolume[1]) + iX = float(sample.mySubvolume[0]) + iY = float(sample.mySubvolume[1]) - xMin = iX/sample.numSubvolumes * sample.boxLen - yMin = iY/sample.numSubvolumes * sample.boxLen - xMax = (iX+1)/sample.numSubvolumes * sample.boxLen - yMax = (iY+1)/sample.numSubvolumes * sample.boxLen + xMin = iX/sample.numSubvolumes * sample.boxLen + yMin = iY/sample.numSubvolumes * sample.boxLen + xMax = (iX+1)/sample.numSubvolumes * sample.boxLen + yMax = (iY+1)/sample.numSubvolumes * sample.boxLen - conf=""" + conf=""" %s output %s outputParameter %s @@ -148,36 +154,51 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None, rangeY_max %g rangeZ_min %g rangeZ_max %g - subsample %g %s """ % (dataFileLine, outputFile, - zobovDir+"/zobov_slice_"+sampleName+".par", + outputFile+".par", includePecVelString, useLightConeString, sample.dataUnit, xMin, xMax, yMin, yMax, sample.zBoundaryMpc[0], sample.zBoundaryMpc[1], - sample.subsample,inputParameterFlag) + subSampleLine,inputParameterFlag) - parmFile = os.getcwd()+"/generate_"+sample.fullName+".par" + parmFile = os.getcwd()+"/generate_"+sample.fullName+".par" - file(parmFile, mode="w").write(conf) + file(parmFile, mode="w").write(conf) - if regenerate or not (continueRun and jobSuccessful(logFile, "Done!\n")): - cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile) - os.system(cmd) - if jobSuccessful(logFile, "Done!\n"): - print "done" + doneLine = "Done %g\n" % keepFraction + if not (continueRun and jobSuccessful(logFile, doneLine)): + if (prevSubSample == -1): + cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile) + else: + cmd = "%s --configFile=%s &>> %s" % (binPath,parmFile,logFile) + os.system(cmd) + if jobSuccessful(logFile, doneLine): + print "done" + else: + print "FAILED!" + exit(-1) + else: - print "FAILED!" - exit(-1) + print "already done!" - else: - print "already done!" + # remove intermediate files + if (prevSubSample != -1): + os.unlink(zobovDir+"/zobov_slice_"+sampleName+"_ss"+prevSubSample+".par") + os.unlink(zobovDir+"/zobov_slice_"+sampleName+"_ss"+prevSubSample) + + prevSubSample = thisSubSample + + # place the final subsample + os.system("mv %s %s" % (zobovDir+"/zobov_slice_"+sampleName+"_ss"+\ + prevSubSample, zobovDir+"/zobov_slice_"+sampleName)) + os.system("mv %s %s" % (zobovDir+"/zobov_slice_"+sampleName+"_ss"+\ + prevSubSample+".par", zobovDir+"/zobov_slice_"+sampleName+".par")) if os.access("comoving_distance.txt", os.F_OK): os.system("mv %s %s" % ("comoving_distance.txt", zobovDir)) - #os.system("mv %s %s" % ("sample_info.txt", zobovDir)) if os.access(parmFile, os.F_OK): os.unlink(parmFile) From df98c86a03fb771791e00c822c322dd2b0e881c7 Mon Sep 17 00:00:00 2001 From: "P.M. Sutter" Date: Sat, 2 Mar 2013 09:40:06 -0600 Subject: [PATCH 03/16] modified scripts to work with new generateMock --- c_tools/stacking/pruneVoids.cpp | 8 +- .../pipeline_source/prepareCatalogs.in.py | 119 +++++++++++------- .../void_python_tools/backend/launchers.py | 25 ++-- 3 files changed, 94 insertions(+), 58 deletions(-) diff --git a/c_tools/stacking/pruneVoids.cpp b/c_tools/stacking/pruneVoids.cpp index b0d33c6..32ee656 100644 --- a/c_tools/stacking/pruneVoids.cpp +++ b/c_tools/stacking/pruneVoids.cpp @@ -548,7 +548,7 @@ int main(int argc, char **argv) { } } voids.resize(iGood); - printf(" 1st filter: reiGoodected %d obviously bad\n", numWrong); + printf(" 1st filter: rejected %d obviously bad\n", numWrong); iGood = 0; for (iVoid = 0; iVoid < voids.size(); iVoid++) { @@ -559,7 +559,7 @@ int main(int argc, char **argv) { } } voids.resize(iGood); - printf(" 2nd filter: reiGoodected %d too small\n", numTooSmall); + printf(" 2nd filter: rejected %d too small\n", numTooSmall); iGood = 0; @@ -572,7 +572,7 @@ int main(int argc, char **argv) { } } voids.resize(iGood); - printf(" 3rd filter: reiGoodected %d too close to high redshift boundaries\n", numNearZ); + printf(" 3rd filter: rejected %d too close to high redshift boundaries\n", numNearZ); numNearZ = 0; iGood = 0; @@ -586,7 +586,7 @@ int main(int argc, char **argv) { } } voids.resize(iGood); - printf(" 4th filter: reiGoodected %d too close to low redshift boundaries\n", numNearZ); + printf(" 4th filter: rejected %d too close to low redshift boundaries\n", numNearZ); for (iVoid = 0; iVoid < voids.size(); iVoid++) { if (voids[iVoid].centralDen > args.maxCentralDen_arg) { diff --git a/python_tools/pipeline_source/prepareCatalogs.in.py b/python_tools/pipeline_source/prepareCatalogs.in.py index 9157d89..d1b6f94 100755 --- a/python_tools/pipeline_source/prepareCatalogs.in.py +++ b/python_tools/pipeline_source/prepareCatalogs.in.py @@ -62,7 +62,7 @@ def getSampleName(setName, redshift, useVel, iSlice=-1, iVol=-1): def writeScript(setName, dataFileNameBase, dataFormat, scriptDir, catalogDir, fileNums, redshifts, numSubvolumes, numSlices, useVel, lbox, minRadius, omegaM, subsample=1.0, - suffix=".dat"): + suffix=".dat", dataFileNameList=None): if useVel: setName += "_pv" @@ -134,7 +134,7 @@ newSample = Sample(dataFile = "{dataFile}", numSubvolumes = {numSubvolumes}, mySubvolume = "{mySubvolume}", useLightCone = {useLightCone}, - subsample = {subsample}) + subsample = "{subsample}") dataSampleList.append(newSample) newSample.addStack(0.0, 5.0, 20, 25, False, False) newSample.addStack(0.0, 5.0, 30, 35, False, False) @@ -187,7 +187,10 @@ newSample.addStack(0.0, 5.0, 90, 95, False, False) sliceMinMpc = "%0.1f" % sliceMinMpc sliceMaxMpc = "%0.1f" % sliceMaxMpc - dataFileName = dataFileNameBase + fileNum + suffix + if (dataFileNameList != None): + dataFileName = dataFileNameList[iFile] + else: + dataFileName = dataFileNameBase + fileNum + suffix for iX in xrange(numSubvolumes): for iY in xrange(numSubvolumes): @@ -212,7 +215,7 @@ newSample.addStack(0.0, 5.0, 90, 95, False, False) numSubvolumes=numSubvolumes, mySubvolume=mySubvolume, useLightCone=useLightCone, - subsample=subsample)) + subsample=str(subsample).strip('[]'))) scriptFile.close() return @@ -229,44 +232,60 @@ if not os.access(catalogDir, os.F_OK): os.mkdir(catalogDir) # ss0.000175 ~ SDSS DR9 mid baseResolution = float(numPart)/lbox/lbox/lbox # particles/Mpc^3 prevSubSample = -1 -for thisSubSample in sorted(subSamples, reverse=True): +subSamples = sorted(subSamples, reverse=True) +for iSubSample in xrange(len(subSamples)): - keepFraction = float(thisSubSample) / baseResolution - maxKeep = keepFraction * numPart + subSampleList = subSamples[0:iSubSample+1] + + keepFractionList = [] + for subSample in subSampleList: + keepFractionList.append(float(subSample) / baseResolution) + thisSubSample = subSamples[iSubSample] + maxKeep = keepFractionList[-1] * numPart minRadius = int(np.ceil(lbox/maxKeep**(1./3))) + partFileList = [] + for (iRedshift, redshift) in enumerate(redshifts): + if particleFileDummy == '': + partFileList.append(particleFileBase+fileNums[iRedshift]) + else: + partFileList.append(particleFileBase.replace(particleFileDummy, + fileNums[iRedshift])) + if args.script or args.all: print " Doing subsample", thisSubSample, "scripts" sys.stdout.flush() setName = prefix+"ss"+str(thisSubSample) - if dataFormat == "multidark": - subSampleToUse = 1.0 - fileToUse = prefix+"ss"+str(thisSubSample)+"_z" - suffix = ".dat" - elif dataFormat == "gadget": - subSampleToUse = keepFraction - #subSampleToUse = thisSubSample - fileToUse = particleFileBase - suffix = "" - elif dataFormat == "lanl": - subSampleToUse = keepFraction - #subSampleToUse = thisSubSample - fileToUse = particleFileBase - suffix = "" - elif dataFormat == "random": + + if dataFormat == "random": subSampleToUse = 1.0 fileToUse = "ran.ss"+str(thisSubSample)+"_z" suffix = ".dat" - writeScript(setName, fileToUse, dataFormat, + writeScript(setName, fileToUse, dataFormat, scriptDir, catalogDir, fileNums, redshifts, numSubvolumes, numSlices, False, lbox, minRadius, omegaM, subsample=subSampleToUse, suffix=suffix) - writeScript(setName, fileToUse, dataFormat, + writeScript(setName, fileToUse, dataFormat, scriptDir, catalogDir, fileNums, redshifts, numSubvolumes, numSlices, True, lbox, minRadius, omegaM, subsample=subSampleToUse, suffix=suffix) - + else: + subSampleToUse = keepFractionList + suffix = "" + fileToUse = partFileList[0] + writeScript(setName, fileToUse, dataFormat, + scriptDir, catalogDir, fileNums, redshifts, + numSubvolumes, numSlices, False, lbox, minRadius, omegaM, + subsample=subSampleToUse, suffix=suffix, + dataFileNameList=partFileList) + writeScript(setName, fileToUse, dataFormat, + scriptDir, catalogDir, fileNums, redshifts, + numSubvolumes, numSlices, True, lbox, minRadius, omegaM, + subsample=subSampleToUse, suffix=suffix, + dataFileNameList=partFileList) + + if args.subsample or args.all: print " Doing subsample", thisSubSample sys.stdout.flush() @@ -407,31 +426,37 @@ if (args.halos or args.all) and haloFileBase != "": sampleName = prefix+"halos_min"+str(minHaloMass)+"_z"+fileNums[iRedshift] outFile = open(catalogDir+"/"+sampleName+".dat", 'w') - outFile.write("%f\n" %(lbox)) outFile.write("%s\n" %(omegaM)) outFile.write("%s\n" %(hubble)) outFile.write("%s\n" %(redshift)) outFile.write("%d\n" %(numPart)) - inFile = open(dataFile, 'r') - for (iHalo,line) in enumerate(inFile): - if iHalo < haloFileNumComLines: continue - line = line.split(haloFileColSep) - if minHaloMass == "none" or float(line[haloFileMCol]) > minHaloMass: - x = float(line[haloFileXCol]) - y = float(line[haloFileYCol]) - z = float(line[haloFileZCol]) - vz = float(line[haloFileVZCol]) - vy = float(line[haloFileVYCol]) - vx = float(line[haloFileVXCol]) + if dataFormat == "sdf": + # TODO process halo file with SDFcvt + outFile = open(catalogDir+"/"+sampleName+".dat", 'w') + outFile.write("-99 -99 -99 -99 -99 -99 -99\n") + outFile.close() + else: + outFile = open(catalogDir+"/"+sampleName+".dat", 'w') + inFile = open(dataFile, 'r') + for (iHalo,line) in enumerate(inFile): + if iHalo < haloFileNumComLines: continue + line = line.split(haloFileColSep) + if minHaloMass == "none" or float(line[haloFileMCol]) > minHaloMass: + x = float(line[haloFileXCol]) + y = float(line[haloFileYCol]) + z = float(line[haloFileZCol]) + vz = float(line[haloFileVZCol]) + vy = float(line[haloFileVYCol]) + vx = float(line[haloFileVXCol]) - # write to output file - outFile.write("%d %e %e %e %e %e %e\n" %(iHalo,x,y,z,vz,vy,vx)) + # write to output file + outFile.write("%d %e %e %e %e %e %e\n" %(iHalo,x,y,z,vz,vy,vx)) - outFile.write("-99 -99 -99 -99 -99 -99 -99\n") - inFile.close() - outFile.close() + outFile.write("-99 -99 -99 -99 -99 -99 -99\n") + outFile.close() + inFile.close() # ----------------------------------------------------------------------------- # now the HOD @@ -506,6 +531,14 @@ if (args.hod or args.all) and haloFileBase != "": else: haloFile = catalogDir+haloFileBase.replace(haloFileDummy, fileNums[iRedshift]) + + if dataFormat == "sdf": + # TODO process halo file with SDFcvt + inFile = haloFile + outFile = haloFile+"_temp" + + haloFile = outFile + parFile.write(parFileText.format(omegaM=omegaM, hubble=hubble, redshift=redshift, @@ -531,4 +564,6 @@ if (args.hod or args.all) and haloFileBase != "": os.system("mv %s/hod.mock %s" % (catalogDir, outFileName)) os.system("rm %s/hod.*" % catalogDir) + os.system("rm %s" % haloFile) + print " Done!" diff --git a/python_tools/void_python_tools/backend/launchers.py b/python_tools/void_python_tools/backend/launchers.py index 5833c4e..9f0e977 100755 --- a/python_tools/void_python_tools/backend/launchers.py +++ b/python_tools/void_python_tools/backend/launchers.py @@ -106,19 +106,19 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None, datafile = inputDataDir+"/"+sample.dataFile prevSubSample = -1 - for thisSubSample in sample.subsample.split(): + for thisSubSample in sample.subsample.split(', '): if prevSubSample == -1: inputParameterFlag = "" outputFile = zobovDir+"/zobov_slice_" + sampleName + "_ss" + thisSubSample - keepFraction = float(thsSubSample) - subSampleLime = "subsample %g" % keepFraction + keepFraction = float(thisSubSample) + subSampleLine = "subsample %g" % keepFraction else: inputParameterFlag = "inputParameter " + zobovDir+"/zobov_slice_"+\ sampleName+"_ss"+prevSubSample+".par" - outputFile = zobovDir+"/_zobov_slice_" + sampleName + "_ss" + tihsSubSample + outputFile = zobovDir+"/_zobov_slice_" + sampleName + "_ss" + thisSubSample keepFraction = float(thisSubSample)/float(prevSubSample) - subSampleLime = "resubsample %g" % keepFraction + subSampleLine = "resubsample %g" % keepFraction includePecVelString = "" if sample.usePecVel: includePecVelString = "peculiarVelocities" @@ -155,6 +155,7 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None, rangeZ_min %g rangeZ_max %g %s + %s """ % (dataFileLine, outputFile, outputFile+".par", includePecVelString, @@ -168,21 +169,18 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None, file(parmFile, mode="w").write(conf) - doneLine = "Done %g\n" % keepFraction + doneLine = "Done! %5.2e\n" % keepFraction + print "TEST", doneLine if not (continueRun and jobSuccessful(logFile, doneLine)): if (prevSubSample == -1): cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile) else: cmd = "%s --configFile=%s &>> %s" % (binPath,parmFile,logFile) os.system(cmd) - if jobSuccessful(logFile, doneLine): - print "done" - else: + + if not jobSuccessful(logFile, doneLine): print "FAILED!" exit(-1) - - else: - print "already done!" # remove intermediate files if (prevSubSample != -1): @@ -191,6 +189,9 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None, prevSubSample = thisSubSample + if (continueRun and jobSuccessful(logFile, doneLine)): print "already done!" + if jobSuccessful(logFile, doneLine): print "done" + # place the final subsample os.system("mv %s %s" % (zobovDir+"/zobov_slice_"+sampleName+"_ss"+\ prevSubSample, zobovDir+"/zobov_slice_"+sampleName)) From 3c9ad41132627004d08ccbbdbb7457308b5d7270 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sat, 2 Mar 2013 09:57:11 -0600 Subject: [PATCH 04/16] Activated call to SDF loader in generateMock --- c_tools/mock/generateMock.cpp | 6 ++++++ c_tools/mock/generateMock.ggo | 4 ++++ 2 files changed, 10 insertions(+) diff --git a/c_tools/mock/generateMock.cpp b/c_tools/mock/generateMock.cpp index 64c1bd9..df72e76 100644 --- a/c_tools/mock/generateMock.cpp +++ b/c_tools/mock/generateMock.cpp @@ -618,6 +618,12 @@ int main(int argc, char **argv) { loader = multidarkLoader(args_info.multidark_arg, preselector); } +#ifdef SDF_SUPPORT + else if (args_info.sdf_given) + { + loader = sdfLoader(args_info.sdf_arg, args_info.sdf_splitting_arg, NEED_POSITION|NEED_VELOCITY|NEED_GADGET_ID, preselector); + } +#endif else { cerr << "A simulation snapshot is required to generate a mock catalog." << endl; diff --git a/c_tools/mock/generateMock.ggo b/c_tools/mock/generateMock.ggo index e8fa8a7..3aa591a 100644 --- a/c_tools/mock/generateMock.ggo +++ b/c_tools/mock/generateMock.ggo @@ -11,6 +11,9 @@ option "gadget" - "Base name of gadget snapshot (without parallel writing ex option "flash" - "Base name for FLASH snapshot" string optional option "multidark" - "Base name for multidark snapshot" string optional +option "sdf" - "SDF snapshot name" string optional +option "sdf_splitting" - "Number of artificial splitting of the SDF snapshot" int optional default="20" + option "axis" - "Redshift axis (X=0, Y=1, Z=2)" int optional default="2" option "output" - "Output filename for particles" string required @@ -37,3 +40,4 @@ option "subsample_seed" - "Seed for random number generation to select the subsa option "resubsample" - "Resubsampling factor compared to the subsampled simulation" double optional option "resubsample_seed" - "Seed for resubsampling from a subsampled simulation" int optional default="20132011" + From 69def32595ea17c8812f36ad25ba2632a17c1496 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sat, 2 Mar 2013 10:44:15 -0600 Subject: [PATCH 05/16] Added more assertion checks. Fixed default value for the subsampling. --- c_tools/mock/generateMock.cpp | 4 +++- c_tools/mock/generateMock.ggo | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/c_tools/mock/generateMock.cpp b/c_tools/mock/generateMock.cpp index df72e76..fb2ce29 100644 --- a/c_tools/mock/generateMock.cpp +++ b/c_tools/mock/generateMock.cpp @@ -349,6 +349,8 @@ void buildBox(SimuData *simu, long num_targets, long loaded, for (uint32_t i = 0; i < num_targets; i++, loaded++) { long pid = particle_id[loaded]; + assert(pid < simu->NumPart); + assert(loaded < boxed->NumPart); for (int j = 0; j < 3; j++) { @@ -513,7 +515,7 @@ void makeBoxFromParameter(SimuData *simu, SimuData* &boxed, generateMock_info& a { particle_id[pid_write] = particle_id[pid_read]; uniqueID[pid_write] = uniqueID[pid_read]; - expansion_fac[pid_write] = uniqueID[pid_read]; + expansion_fac[pid_write] = expansion_fac[pid_read]; pid_write++; } pid_read++; diff --git a/c_tools/mock/generateMock.ggo b/c_tools/mock/generateMock.ggo index 3aa591a..fe441e6 100644 --- a/c_tools/mock/generateMock.ggo +++ b/c_tools/mock/generateMock.ggo @@ -31,7 +31,7 @@ option "peculiarVelocities" - "Added peculiar velocities distortion" flag off option "cosmo" - "Apply cosmological redshift" flag off -option "subsample" - "Subsample the input simulation by the specified amount" double optional +option "subsample" - "Subsample the input simulation by the specified amount" double optional default="1.0" option "inputParameter" - "Input geometry (optional, warning!)" string optional option "gadgetUnit" - "Unit of length in gadget file in Mpc/h" double optional default="0.001" From 51c409a170bd87e2560bf0dff05725a6802ae465 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sat, 2 Mar 2013 10:45:08 -0600 Subject: [PATCH 06/16] Maybe incorrect maxCentralDensity ? --- python_tools/void_python_tools/backend/launchers.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python_tools/void_python_tools/backend/launchers.py b/python_tools/void_python_tools/backend/launchers.py index 17acc76..4d7efe2 100755 --- a/python_tools/void_python_tools/backend/launchers.py +++ b/python_tools/void_python_tools/backend/launchers.py @@ -417,7 +417,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None, maxDen = 0.2*float(maskIndex)/float(totalPart) else: maskIndex = 999999999 - maxDen = -0.8 + maxDen = 0.2 if INCOHERENT: nullTestFlag = "INCOHERENT" From b22257b610682f09db29bb7a966efe65de21f413 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sat, 2 Mar 2013 15:26:55 -0600 Subject: [PATCH 07/16] Added some tools to manipulate source code in bulk --- build_tools/apply_license.py | 26 ++++++++++++++++++++++++++ build_tools/gather_sources.py | 11 +++++++++++ build_tools/header.txt | 19 +++++++++++++++++++ 3 files changed, 56 insertions(+) create mode 100644 build_tools/apply_license.py create mode 100644 build_tools/gather_sources.py create mode 100644 build_tools/header.txt diff --git a/build_tools/apply_license.py b/build_tools/apply_license.py new file mode 100644 index 0000000..2c64077 --- /dev/null +++ b/build_tools/apply_license.py @@ -0,0 +1,26 @@ +import shutil +import tempfile +import sys +import re + +rex = "@FILENAME@" + +filename = sys.argv[1] + + +fh = file("header.txt") +header = fh.read() +header_translated = re.sub(r'@FILENAME@', filename, header) +fh.close() + +f = file(filename) +lines = f.read() +f.close() + +lines = re.sub(r'(?s)/\*\+.*\+\*/','',lines) +lines = header_translated + lines + +with tempfile.NamedTemporaryFile(delete=False) as tmp_sources: + tmp_sources.write(lines) + +shutil.move(tmp_sources.name, filename) diff --git a/build_tools/gather_sources.py b/build_tools/gather_sources.py new file mode 100644 index 0000000..b4fed6c --- /dev/null +++ b/build_tools/gather_sources.py @@ -0,0 +1,11 @@ +from git import Repo + +repo = Repo(".") + +assert repo.bare == False + +t = repo.tree() + + +for entry in t.travers(): + print entry diff --git a/build_tools/header.txt b/build_tools/header.txt new file mode 100644 index 0000000..fa4e972 --- /dev/null +++ b/build_tools/header.txt @@ -0,0 +1,19 @@ +/*+ + VIDE -- Void IDEntification pipeline -- @FILENAME@ + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ From 12ca3bf2e3789ec30194658deb28b406762d5ec1 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sat, 2 Mar 2013 15:27:27 -0600 Subject: [PATCH 08/16] Put the name in README --- README | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/README b/README index ef831be..9a1b6ba 100644 --- a/README +++ b/README @@ -1,5 +1,36 @@ +\ / / |-\ ----- + \ / | | \ | + \ / / | | |-- + \ / | | / | + \/ / |-/ ----- + +*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* + +This is VIDE. The Void IDEntifier pipeline. + + +License/Copyright information +----------------------------- + +Copyright (C) 2010-2013 Guilhem Lavaux, 2011-2013 Paul M. Sutter. +This software is put under the GNU Public License. Please see LICENSE +for further information. + + +Parts of the pipeline includes ZOBOV. See zobov/zobov_readme.txt for +copyright/license information + +Building +-------- + + After compiling, go to the pipeline directory. + +Using the pipeline +------------------ + + Create a dataset parameter file. Look at datasets/multidark.py for an example. Describe the simulation, where to put outputs, how many redshift slices, subvolumes, etc. etc. From 175e746d02f8952d83bbdc05e878d30d17049392 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sat, 2 Mar 2013 16:43:58 -0500 Subject: [PATCH 09/16] Apply license code packed into gather_sources.py --- build_tools/apply_license.py | 26 -------------------------- build_tools/header.txt | 19 ------------------- 2 files changed, 45 deletions(-) delete mode 100644 build_tools/apply_license.py delete mode 100644 build_tools/header.txt diff --git a/build_tools/apply_license.py b/build_tools/apply_license.py deleted file mode 100644 index 2c64077..0000000 --- a/build_tools/apply_license.py +++ /dev/null @@ -1,26 +0,0 @@ -import shutil -import tempfile -import sys -import re - -rex = "@FILENAME@" - -filename = sys.argv[1] - - -fh = file("header.txt") -header = fh.read() -header_translated = re.sub(r'@FILENAME@', filename, header) -fh.close() - -f = file(filename) -lines = f.read() -f.close() - -lines = re.sub(r'(?s)/\*\+.*\+\*/','',lines) -lines = header_translated + lines - -with tempfile.NamedTemporaryFile(delete=False) as tmp_sources: - tmp_sources.write(lines) - -shutil.move(tmp_sources.name, filename) diff --git a/build_tools/header.txt b/build_tools/header.txt deleted file mode 100644 index fa4e972..0000000 --- a/build_tools/header.txt +++ /dev/null @@ -1,19 +0,0 @@ -/*+ - VIDE -- Void IDEntification pipeline -- @FILENAME@ - Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter - - This program is free software; you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License along - with this program; if not, write to the Free Software Foundation, Inc., - 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. -+*/ From a829bbf60bb51a3d1a295257c149a52d007cd7d7 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sat, 2 Mar 2013 16:44:27 -0500 Subject: [PATCH 10/16] Find python/shell/C++ code and add a license header (remove it beforehand if necessary) --- build_tools/gather_sources.py | 95 ++++++++++++++++++++++++++++++++--- 1 file changed, 89 insertions(+), 6 deletions(-) diff --git a/build_tools/gather_sources.py b/build_tools/gather_sources.py index b4fed6c..2b6ff2e 100644 --- a/build_tools/gather_sources.py +++ b/build_tools/gather_sources.py @@ -1,11 +1,94 @@ -from git import Repo +import re +from git import Repo,Tree,Blob -repo = Repo(".") +def apply_license(license, relimit, filename): + header = re.sub(r'@FILENAME@', filename, license) -assert repo.bare == False + f = file(filename) + lines = f.read() + f.close() -t = repo.tree() + lines = re.sub(relimit, '', lines) + lines = header + lines + + with tempfile.NamedTemporaryFile(delete=False) as tmp_sources: + tmp_sources.write(lines) + + shutil.move(tmp_sources.name, filename) -for entry in t.travers(): - print entry +def apply_python_license(filename): + license=""" +#+ +# VIDE -- Void IDEntification pipeline -- @FILENAME@ +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ +""" + + print("Shell/Python file: %s" % filename) + relimit = r'(?s)#\+.*#\+' + apply_license(license, relimit, filename) + + +def apply_cpp_license(filename): + license=""" +/*+ + VIDE -- Void IDEntification pipeline -- @FILENAME@ + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ +""" + relimit = r'(?s)/\*\+.*\+\*/' + print("C++ file: %s" % filename) + apply_license(license, relimit, filename) + + +def analyze_tree(prefix, t): + for ename,entry in t.items(): + if ename == 'external' or ename == 'zobov': + continue + if type(entry) == Tree: + analyze_tree(prefix + "/" + ename, entry) + elif type(entry) == Blob: + if re.match(".*\.(sh|py|pyx)$",ename) != None: + fname=prefix+"/"+ename + apply_python_license(fname) + if re.match('.*\.(cpp|hpp|h)$', ename) != None: + fname=prefix+"/"+ename + apply_cpp_license(fname) + + +if __name__=="__main__": + repo = Repo(".") + assert repo.bare == False + t = repo.tree() + analyze_tree(".", t) From 62dfc736d40ab81b35e989ec2a9c804c9894cdbd Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sat, 2 Mar 2013 16:46:58 -0500 Subject: [PATCH 11/16] Missing imports --- build_tools/gather_sources.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/build_tools/gather_sources.py b/build_tools/gather_sources.py index 2b6ff2e..187bf1e 100644 --- a/build_tools/gather_sources.py +++ b/build_tools/gather_sources.py @@ -1,3 +1,5 @@ +import shutil +import tempfile import re from git import Repo,Tree,Blob @@ -18,8 +20,7 @@ def apply_license(license, relimit, filename): def apply_python_license(filename): - license=""" -#+ + license="""#+ # VIDE -- Void IDEntification pipeline -- @FILENAME@ # Copyright (C) 2010-2013 Guilhem Lavaux # Copyright (C) 2011-2013 Paul M. Sutter @@ -41,13 +42,12 @@ def apply_python_license(filename): """ print("Shell/Python file: %s" % filename) - relimit = r'(?s)#\+.*#\+' + relimit = r'^(?s)#\+.*#\+' apply_license(license, relimit, filename) def apply_cpp_license(filename): - license=""" -/*+ + license="""/*+ VIDE -- Void IDEntification pipeline -- @FILENAME@ Copyright (C) 2010-2013 Guilhem Lavaux Copyright (C) 2011-2013 Paul M. Sutter @@ -67,7 +67,7 @@ def apply_cpp_license(filename): 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ """ - relimit = r'(?s)/\*\+.*\+\*/' + relimit = r'^(?s)/\*\+.*\+\*/' print("C++ file: %s" % filename) apply_license(license, relimit, filename) From edd9c2a45d2d9977761dcc0ebf63a6876e947dde Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sat, 2 Mar 2013 18:29:08 -0500 Subject: [PATCH 12/16] Fixed regular expression to only match the first license notice at the top of the file --- build_tools/gather_sources.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build_tools/gather_sources.py b/build_tools/gather_sources.py index 187bf1e..44c18be 100644 --- a/build_tools/gather_sources.py +++ b/build_tools/gather_sources.py @@ -42,7 +42,7 @@ def apply_python_license(filename): """ print("Shell/Python file: %s" % filename) - relimit = r'^(?s)#\+.*#\+' + relimit=r'^#\+\n(#.*\n)*#\+\n' apply_license(license, relimit, filename) From aa38661b656386585326c0162212834b08b1d1ad Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sat, 2 Mar 2013 18:30:40 -0500 Subject: [PATCH 13/16] Added copyright/license notice --- c_tools/analysis/voidOverlap.cpp | 20 +++++++++++++++++++ c_tools/libzobov/contour_pixels.cpp | 20 +++++++++++++++++++ c_tools/libzobov/contour_pixels.hpp | 20 +++++++++++++++++++ c_tools/libzobov/gslIntegrate.hpp | 20 +++++++++++++++++++ c_tools/libzobov/loadZobov.cpp | 20 +++++++++++++++++++ c_tools/libzobov/loadZobov.hpp | 20 +++++++++++++++++++ c_tools/libzobov/particleInfo.cpp | 20 +++++++++++++++++++ c_tools/libzobov/particleInfo.hpp | 20 +++++++++++++++++++ c_tools/libzobov/voidTree.hpp | 20 +++++++++++++++++++ c_tools/mock/generateFromCatalog.cpp | 20 +++++++++++++++++++ c_tools/mock/generateMock.cpp | 20 +++++++++++++++++++ c_tools/mock/generateTestMock.cpp | 20 +++++++++++++++++++ c_tools/mock/loaders/basic_loader.cpp | 20 +++++++++++++++++++ c_tools/mock/loaders/flash_loader.cpp | 20 +++++++++++++++++++ c_tools/mock/loaders/gadget_loader.cpp | 20 +++++++++++++++++++ c_tools/mock/loaders/multidark_loader.cpp | 20 +++++++++++++++++++ c_tools/mock/loaders/ramses_loader.cpp | 20 +++++++++++++++++++ c_tools/mock/loaders/sdf_loader.cpp | 20 +++++++++++++++++++ c_tools/mock/loaders/sdfloader_internal.hpp | 20 +++++++++++++++++++ c_tools/mock/loaders/simulation_loader.cpp | 20 +++++++++++++++++++ c_tools/mock/loaders/simulation_loader.hpp | 20 +++++++++++++++++++ c_tools/stacking/pruneVoids.cpp | 20 +++++++++++++++++++ crossCompare/analysis/datasetsToAnalyze.py | 19 ++++++++++++++++++ crossCompare/analysis/mergerTree.py | 19 ++++++++++++++++++ crossCompare/plotting/datasetsToPlot.py | 19 ++++++++++++++++++ crossCompare/plotting/plotCompareDensCon.py | 19 ++++++++++++++++++ crossCompare/plotting/plotDensConVsR.py | 19 ++++++++++++++++++ crossCompare/plotting/plotNumberFunc.py | 19 ++++++++++++++++++ pipeline/datasets/mock_dr9mid.py | 19 ++++++++++++++++++ pipeline/datasets/multidark.py | 19 ++++++++++++++++++ pipeline/generateCatalog.py | 19 ++++++++++++++++++ .../pipeline_source/prepareCatalogs.in.py | 19 ++++++++++++++++++ python_tools/setup.py | 19 ++++++++++++++++++ python_tools/void_python_tools/__init__.py | 19 ++++++++++++++++++ .../void_python_tools/apTools/__init__.py | 19 ++++++++++++++++++ .../apTools/chi2/__init__.py | 19 ++++++++++++++++++ .../apTools/chi2/cosmologyTools.py | 19 ++++++++++++++++++ .../apTools/profiles/__init__.py | 19 ++++++++++++++++++ .../apTools/profiles/getSurveyProps.py | 19 ++++++++++++++++++ .../void_python_tools/backend/__init__.py | 19 ++++++++++++++++++ .../void_python_tools/backend/classes.py | 19 ++++++++++++++++++ .../void_python_tools/backend/launchers.py | 19 ++++++++++++++++++ .../void_python_tools/plotting/__init__.py | 19 ++++++++++++++++++ .../void_python_tools/plotting/plotDefs.py | 19 ++++++++++++++++++ .../void_python_tools/plotting/plotTools.py | 19 ++++++++++++++++++ 45 files changed, 877 insertions(+) mode change 100755 => 100644 crossCompare/analysis/datasetsToAnalyze.py mode change 100755 => 100644 crossCompare/analysis/mergerTree.py mode change 100755 => 100644 crossCompare/plotting/datasetsToPlot.py mode change 100755 => 100644 crossCompare/plotting/plotCompareDensCon.py mode change 100755 => 100644 crossCompare/plotting/plotDensConVsR.py mode change 100755 => 100644 crossCompare/plotting/plotNumberFunc.py mode change 100755 => 100644 pipeline/generateCatalog.py mode change 100755 => 100644 python_tools/pipeline_source/prepareCatalogs.in.py mode change 100755 => 100644 python_tools/void_python_tools/backend/classes.py mode change 100755 => 100644 python_tools/void_python_tools/backend/launchers.py diff --git a/c_tools/analysis/voidOverlap.cpp b/c_tools/analysis/voidOverlap.cpp index 37f9a9f..5662bf3 100644 --- a/c_tools/analysis/voidOverlap.cpp +++ b/c_tools/analysis/voidOverlap.cpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/analysis/voidOverlap.cpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + // ============================================================================= // // Program: voidOverlap diff --git a/c_tools/libzobov/contour_pixels.cpp b/c_tools/libzobov/contour_pixels.cpp index 6aa7935..a43f921 100644 --- a/c_tools/libzobov/contour_pixels.cpp +++ b/c_tools/libzobov/contour_pixels.cpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/contour_pixels.cpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #include #include #include diff --git a/c_tools/libzobov/contour_pixels.hpp b/c_tools/libzobov/contour_pixels.hpp index c576477..637a29b 100644 --- a/c_tools/libzobov/contour_pixels.hpp +++ b/c_tools/libzobov/contour_pixels.hpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/contour_pixels.hpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #ifndef __CONTOUR_PIXELS_HPP #define __CONTOUR_PIXELS_HPP diff --git a/c_tools/libzobov/gslIntegrate.hpp b/c_tools/libzobov/gslIntegrate.hpp index 4300085..8c3f03f 100644 --- a/c_tools/libzobov/gslIntegrate.hpp +++ b/c_tools/libzobov/gslIntegrate.hpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/gslIntegrate.hpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #ifndef __MYGSL_INTEGRATE_HPP #define __MYGSL_INTEGRATE_HPP diff --git a/c_tools/libzobov/loadZobov.cpp b/c_tools/libzobov/loadZobov.cpp index 2d5a2ff..490ec03 100644 --- a/c_tools/libzobov/loadZobov.cpp +++ b/c_tools/libzobov/loadZobov.cpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/loadZobov.cpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #include #include #include diff --git a/c_tools/libzobov/loadZobov.hpp b/c_tools/libzobov/loadZobov.hpp index 8734971..9da5f3f 100644 --- a/c_tools/libzobov/loadZobov.hpp +++ b/c_tools/libzobov/loadZobov.hpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/loadZobov.hpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #ifndef __LOAD_ZOBOV_HPP #define __LOAD_ZOBOV_HPP diff --git a/c_tools/libzobov/particleInfo.cpp b/c_tools/libzobov/particleInfo.cpp index d3eb2e8..d7ba09e 100644 --- a/c_tools/libzobov/particleInfo.cpp +++ b/c_tools/libzobov/particleInfo.cpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/particleInfo.cpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #include #include #include diff --git a/c_tools/libzobov/particleInfo.hpp b/c_tools/libzobov/particleInfo.hpp index f6e7a82..f1b42e5 100644 --- a/c_tools/libzobov/particleInfo.hpp +++ b/c_tools/libzobov/particleInfo.hpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/particleInfo.hpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #ifndef _PARTICLE_INFO_HEADER_HPP #define _PARTICLE_INFO_HEADER_HPP diff --git a/c_tools/libzobov/voidTree.hpp b/c_tools/libzobov/voidTree.hpp index bb825dc..14013ba 100644 --- a/c_tools/libzobov/voidTree.hpp +++ b/c_tools/libzobov/voidTree.hpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/voidTree.hpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #ifndef _VOID_TREE_HPP #define _VOID_TREE_HPP diff --git a/c_tools/mock/generateFromCatalog.cpp b/c_tools/mock/generateFromCatalog.cpp index 0a578c0..f66e22b 100644 --- a/c_tools/mock/generateFromCatalog.cpp +++ b/c_tools/mock/generateFromCatalog.cpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/mock/generateFromCatalog.cpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #include #include #include diff --git a/c_tools/mock/generateMock.cpp b/c_tools/mock/generateMock.cpp index fb2ce29..8d12f56 100644 --- a/c_tools/mock/generateMock.cpp +++ b/c_tools/mock/generateMock.cpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/mock/generateMock.cpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #include #include #include diff --git a/c_tools/mock/generateTestMock.cpp b/c_tools/mock/generateTestMock.cpp index 9853c36..62126d0 100644 --- a/c_tools/mock/generateTestMock.cpp +++ b/c_tools/mock/generateTestMock.cpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/mock/generateTestMock.cpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #include #include #include diff --git a/c_tools/mock/loaders/basic_loader.cpp b/c_tools/mock/loaders/basic_loader.cpp index a58bb10..2e22151 100644 --- a/c_tools/mock/loaders/basic_loader.cpp +++ b/c_tools/mock/loaders/basic_loader.cpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/basic_loader.cpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #include #include #include diff --git a/c_tools/mock/loaders/flash_loader.cpp b/c_tools/mock/loaders/flash_loader.cpp index 70a7493..16ebcd5 100644 --- a/c_tools/mock/loaders/flash_loader.cpp +++ b/c_tools/mock/loaders/flash_loader.cpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/flash_loader.cpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #include #include #include diff --git a/c_tools/mock/loaders/gadget_loader.cpp b/c_tools/mock/loaders/gadget_loader.cpp index ff7fd17..5a5230a 100644 --- a/c_tools/mock/loaders/gadget_loader.cpp +++ b/c_tools/mock/loaders/gadget_loader.cpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/gadget_loader.cpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #include #include #include diff --git a/c_tools/mock/loaders/multidark_loader.cpp b/c_tools/mock/loaders/multidark_loader.cpp index 29bd0af..8e2a154 100644 --- a/c_tools/mock/loaders/multidark_loader.cpp +++ b/c_tools/mock/loaders/multidark_loader.cpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/multidark_loader.cpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #include #include #include diff --git a/c_tools/mock/loaders/ramses_loader.cpp b/c_tools/mock/loaders/ramses_loader.cpp index f8f1fef..b70783a 100644 --- a/c_tools/mock/loaders/ramses_loader.cpp +++ b/c_tools/mock/loaders/ramses_loader.cpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/ramses_loader.cpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #include #include #include diff --git a/c_tools/mock/loaders/sdf_loader.cpp b/c_tools/mock/loaders/sdf_loader.cpp index 4b0f8a5..a836971 100644 --- a/c_tools/mock/loaders/sdf_loader.cpp +++ b/c_tools/mock/loaders/sdf_loader.cpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/sdf_loader.cpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #include #include #include diff --git a/c_tools/mock/loaders/sdfloader_internal.hpp b/c_tools/mock/loaders/sdfloader_internal.hpp index 93635ac..3e356db 100644 --- a/c_tools/mock/loaders/sdfloader_internal.hpp +++ b/c_tools/mock/loaders/sdfloader_internal.hpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/sdfloader_internal.hpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #ifndef __VOID_SDF_LOADER_INTERNAL_HPP #define __VOID_SDF_LOADER_INTERNAL_HPP diff --git a/c_tools/mock/loaders/simulation_loader.cpp b/c_tools/mock/loaders/simulation_loader.cpp index 7751885..e95531d 100644 --- a/c_tools/mock/loaders/simulation_loader.cpp +++ b/c_tools/mock/loaders/simulation_loader.cpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/simulation_loader.cpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #include #include #include "simulation_loader.hpp" diff --git a/c_tools/mock/loaders/simulation_loader.hpp b/c_tools/mock/loaders/simulation_loader.hpp index e0d79cb..82c8251 100644 --- a/c_tools/mock/loaders/simulation_loader.hpp +++ b/c_tools/mock/loaders/simulation_loader.hpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/simulation_loader.hpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + #ifndef _MOCK_SIMULATION_LOADER_HPP #define _MOCK_SIMULATION_LOADER_HPP diff --git a/c_tools/stacking/pruneVoids.cpp b/c_tools/stacking/pruneVoids.cpp index 32ee656..0d38ef9 100644 --- a/c_tools/stacking/pruneVoids.cpp +++ b/c_tools/stacking/pruneVoids.cpp @@ -1,3 +1,23 @@ +/*+ + VIDE -- Void IDEntification pipeline -- ./c_tools/stacking/pruneVoids.cpp + Copyright (C) 2010-2013 Guilhem Lavaux + Copyright (C) 2011-2013 Paul M. Sutter + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. ++*/ + // Reads in the void catalog and removes any void that could potentially // be affected by a mock particle. It does this by computing the longest // particle distance within each void and comparing it to the distance diff --git a/crossCompare/analysis/datasetsToAnalyze.py b/crossCompare/analysis/datasetsToAnalyze.py old mode 100755 new mode 100644 index 88452f6..90c0f1e --- a/crossCompare/analysis/datasetsToAnalyze.py +++ b/crossCompare/analysis/datasetsToAnalyze.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./crossCompare/analysis/datasetsToAnalyze.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ #!/usr/bin/env python diff --git a/crossCompare/analysis/mergerTree.py b/crossCompare/analysis/mergerTree.py old mode 100755 new mode 100644 index 89c5e13..b3421bb --- a/crossCompare/analysis/mergerTree.py +++ b/crossCompare/analysis/mergerTree.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./crossCompare/analysis/mergerTree.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ #!/usr/bin/env python # plots cumulative distributions of number counts diff --git a/crossCompare/plotting/datasetsToPlot.py b/crossCompare/plotting/datasetsToPlot.py old mode 100755 new mode 100644 index 124edff..d5a8db7 --- a/crossCompare/plotting/datasetsToPlot.py +++ b/crossCompare/plotting/datasetsToPlot.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./crossCompare/plotting/datasetsToPlot.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ #!/usr/bin/env python diff --git a/crossCompare/plotting/plotCompareDensCon.py b/crossCompare/plotting/plotCompareDensCon.py old mode 100755 new mode 100644 index 068be26..172b48a --- a/crossCompare/plotting/plotCompareDensCon.py +++ b/crossCompare/plotting/plotCompareDensCon.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./crossCompare/plotting/plotCompareDensCon.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ #!/usr/bin/env python # plots cumulative distributions of number counts versus density contrast diff --git a/crossCompare/plotting/plotDensConVsR.py b/crossCompare/plotting/plotDensConVsR.py old mode 100755 new mode 100644 index b9e15f7..0788a2f --- a/crossCompare/plotting/plotDensConVsR.py +++ b/crossCompare/plotting/plotDensConVsR.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./crossCompare/plotting/plotDensConVsR.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ #!/usr/bin/env python # plots cumulative distributions of number counts versus density contrast diff --git a/crossCompare/plotting/plotNumberFunc.py b/crossCompare/plotting/plotNumberFunc.py old mode 100755 new mode 100644 index df85dc1..53e7837 --- a/crossCompare/plotting/plotNumberFunc.py +++ b/crossCompare/plotting/plotNumberFunc.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./crossCompare/plotting/plotNumberFunc.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ #!/usr/bin/env python # plots cumulative distributions of number counts diff --git a/pipeline/datasets/mock_dr9mid.py b/pipeline/datasets/mock_dr9mid.py index cd189f3..e0ce29a 100644 --- a/pipeline/datasets/mock_dr9mid.py +++ b/pipeline/datasets/mock_dr9mid.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./pipeline/datasets/mock_dr9mid.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ import os # ----------------------------------------------------------------------------- diff --git a/pipeline/datasets/multidark.py b/pipeline/datasets/multidark.py index 4672b21..2811e3c 100644 --- a/pipeline/datasets/multidark.py +++ b/pipeline/datasets/multidark.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./pipeline/datasets/multidark.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ import os # ----------------------------------------------------------------------------- diff --git a/pipeline/generateCatalog.py b/pipeline/generateCatalog.py old mode 100755 new mode 100644 index 2b3be60..4ee7a60 --- a/pipeline/generateCatalog.py +++ b/pipeline/generateCatalog.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./pipeline/generateCatalog.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ #!/usr/bin/env python # does full void analysis. Also generates 2d/1d stacked plots and hubble diagram diff --git a/python_tools/pipeline_source/prepareCatalogs.in.py b/python_tools/pipeline_source/prepareCatalogs.in.py old mode 100755 new mode 100644 index d1b6f94..60d2c21 --- a/python_tools/pipeline_source/prepareCatalogs.in.py +++ b/python_tools/pipeline_source/prepareCatalogs.in.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./python_tools/pipeline_source/prepareCatalogs.in.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ #!/usr/bin/env python # prepares input catalogs based on multidark simulations diff --git a/python_tools/setup.py b/python_tools/setup.py index bd2a9e9..61a377c 100644 --- a/python_tools/setup.py +++ b/python_tools/setup.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./python_tools/setup.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ from distutils.core import setup from distutils.extension import Extension from Cython.Distutils import build_ext diff --git a/python_tools/void_python_tools/__init__.py b/python_tools/void_python_tools/__init__.py index d31fbd8..3254e46 100644 --- a/python_tools/void_python_tools/__init__.py +++ b/python_tools/void_python_tools/__init__.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/__init__.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ from void_python_tools.backend import * from void_python_tools.apTools import * from void_python_tools.plotting import * diff --git a/python_tools/void_python_tools/apTools/__init__.py b/python_tools/void_python_tools/apTools/__init__.py index b9744dc..9fc13ce 100644 --- a/python_tools/void_python_tools/apTools/__init__.py +++ b/python_tools/void_python_tools/apTools/__init__.py @@ -1,2 +1,21 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/__init__.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ from chi2 import * from profiles import * diff --git a/python_tools/void_python_tools/apTools/chi2/__init__.py b/python_tools/void_python_tools/apTools/chi2/__init__.py index 06f1f52..4ca64f2 100644 --- a/python_tools/void_python_tools/apTools/chi2/__init__.py +++ b/python_tools/void_python_tools/apTools/chi2/__init__.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/chi2/__init__.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ from velocityProfileFitNative import * from likelihood import * from cosmologyTools import * diff --git a/python_tools/void_python_tools/apTools/chi2/cosmologyTools.py b/python_tools/void_python_tools/apTools/chi2/cosmologyTools.py index 69626cf..b2de95c 100644 --- a/python_tools/void_python_tools/apTools/chi2/cosmologyTools.py +++ b/python_tools/void_python_tools/apTools/chi2/cosmologyTools.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/chi2/cosmologyTools.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ # a suite of functions to compute expansion rates, angular diameter # distances, and expected void stretching diff --git a/python_tools/void_python_tools/apTools/profiles/__init__.py b/python_tools/void_python_tools/apTools/profiles/__init__.py index 0f04a3e..b73f4f0 100644 --- a/python_tools/void_python_tools/apTools/profiles/__init__.py +++ b/python_tools/void_python_tools/apTools/profiles/__init__.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/profiles/__init__.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ from build import * from draw import * from fit import * diff --git a/python_tools/void_python_tools/apTools/profiles/getSurveyProps.py b/python_tools/void_python_tools/apTools/profiles/getSurveyProps.py index 764a115..f4e93ab 100644 --- a/python_tools/void_python_tools/apTools/profiles/getSurveyProps.py +++ b/python_tools/void_python_tools/apTools/profiles/getSurveyProps.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/profiles/getSurveyProps.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ import numpy as np import healpy as healpy import scipy.integrate diff --git a/python_tools/void_python_tools/backend/__init__.py b/python_tools/void_python_tools/backend/__init__.py index 95cddfa..e11599a 100644 --- a/python_tools/void_python_tools/backend/__init__.py +++ b/python_tools/void_python_tools/backend/__init__.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/backend/__init__.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ from classes import * from launchers import * from catalogPrep import * diff --git a/python_tools/void_python_tools/backend/classes.py b/python_tools/void_python_tools/backend/classes.py old mode 100755 new mode 100644 index a6d2052..6e164ec --- a/python_tools/void_python_tools/backend/classes.py +++ b/python_tools/void_python_tools/backend/classes.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/backend/classes.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ # classes and routines used to support scripts import os diff --git a/python_tools/void_python_tools/backend/launchers.py b/python_tools/void_python_tools/backend/launchers.py old mode 100755 new mode 100644 index e519f3a..a2501d3 --- a/python_tools/void_python_tools/backend/launchers.py +++ b/python_tools/void_python_tools/backend/launchers.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/backend/launchers.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ # ----------------------------------------------------------------------------- # ----------------------------------------------------------------------------- # routines which communicate with individual data analysis portions - diff --git a/python_tools/void_python_tools/plotting/__init__.py b/python_tools/void_python_tools/plotting/__init__.py index c2750a7..f389009 100644 --- a/python_tools/void_python_tools/plotting/__init__.py +++ b/python_tools/void_python_tools/plotting/__init__.py @@ -1,2 +1,21 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/plotting/__init__.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ from plotTools import * from plotDefs import * diff --git a/python_tools/void_python_tools/plotting/plotDefs.py b/python_tools/void_python_tools/plotting/plotDefs.py index d1da991..7e17025 100644 --- a/python_tools/void_python_tools/plotting/plotDefs.py +++ b/python_tools/void_python_tools/plotting/plotDefs.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/plotting/plotDefs.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ LIGHT_SPEED = 299792.458 colorList = ['r', 'b', 'g', 'y', 'c', 'm', diff --git a/python_tools/void_python_tools/plotting/plotTools.py b/python_tools/void_python_tools/plotting/plotTools.py index 8f51f7d..94b5b13 100644 --- a/python_tools/void_python_tools/plotting/plotTools.py +++ b/python_tools/void_python_tools/plotting/plotTools.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/plotting/plotTools.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ __all__=['plotRedshiftDistribution', 'plotSizeDistribution', 'plot1dProfiles', 'plotMarg1d', 'plotNumberDistribution'] From bce9ac1dd364614f3d9925a419c4605cd3d12f14 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sat, 2 Mar 2013 18:33:33 -0500 Subject: [PATCH 14/16] Removed the possibility of a later version. The patent mess is unclear. --- build_tools/gather_sources.py | 26 ++++++++++++++++--- c_tools/analysis/voidOverlap.cpp | 4 +-- c_tools/libzobov/contour_pixels.cpp | 4 +-- c_tools/libzobov/contour_pixels.hpp | 4 +-- c_tools/libzobov/gslIntegrate.hpp | 4 +-- c_tools/libzobov/loadZobov.cpp | 4 +-- c_tools/libzobov/loadZobov.hpp | 4 +-- c_tools/libzobov/particleInfo.cpp | 4 +-- c_tools/libzobov/particleInfo.hpp | 4 +-- c_tools/libzobov/voidTree.hpp | 4 +-- c_tools/mock/generateFromCatalog.cpp | 4 +-- c_tools/mock/generateMock.cpp | 4 +-- c_tools/mock/generateTestMock.cpp | 4 +-- c_tools/mock/loaders/basic_loader.cpp | 4 +-- c_tools/mock/loaders/flash_loader.cpp | 4 +-- c_tools/mock/loaders/gadget_loader.cpp | 4 +-- c_tools/mock/loaders/multidark_loader.cpp | 4 +-- c_tools/mock/loaders/ramses_loader.cpp | 4 +-- c_tools/mock/loaders/sdf_loader.cpp | 4 +-- c_tools/mock/loaders/sdfloader_internal.hpp | 4 +-- c_tools/mock/loaders/simulation_loader.cpp | 4 +-- c_tools/mock/loaders/simulation_loader.hpp | 4 +-- c_tools/stacking/pruneVoids.cpp | 4 +-- crossCompare/analysis/datasetsToAnalyze.py | 4 +-- crossCompare/analysis/mergerTree.py | 4 +-- crossCompare/plotting/datasetsToPlot.py | 4 +-- crossCompare/plotting/plotCompareDensCon.py | 4 +-- crossCompare/plotting/plotDensConVsR.py | 4 +-- crossCompare/plotting/plotNumberFunc.py | 4 +-- pipeline/datasets/mock_dr9mid.py | 4 +-- pipeline/datasets/multidark.py | 4 +-- pipeline/generateCatalog.py | 4 +-- .../pipeline_source/prepareCatalogs.in.py | 4 +-- python_tools/setup.py | 4 +-- python_tools/void_python_tools/__init__.py | 4 +-- .../void_python_tools/apTools/__init__.py | 4 +-- .../apTools/chi2/__init__.py | 4 +-- .../apTools/chi2/cosmologyTools.py | 4 +-- .../apTools/profiles/__init__.py | 4 +-- .../apTools/profiles/getSurveyProps.py | 4 +-- .../void_python_tools/backend/__init__.py | 4 +-- .../void_python_tools/backend/classes.py | 4 +-- .../void_python_tools/backend/launchers.py | 4 +-- .../void_python_tools/plotting/__init__.py | 4 +-- .../void_python_tools/plotting/plotDefs.py | 4 +-- .../void_python_tools/plotting/plotTools.py | 4 +-- 46 files changed, 112 insertions(+), 94 deletions(-) diff --git a/build_tools/gather_sources.py b/build_tools/gather_sources.py index 44c18be..2b8b4c5 100644 --- a/build_tools/gather_sources.py +++ b/build_tools/gather_sources.py @@ -1,3 +1,22 @@ +#+ +# VIDE -- Void IDEntification pipeline -- ./build_tools/gather_sources.py +# Copyright (C) 2010-2013 Guilhem Lavaux +# Copyright (C) 2011-2013 Paul M. Sutter +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; version 2 of the License. +# +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +#+ import shutil import tempfile import re @@ -27,8 +46,8 @@ def apply_python_license(filename): # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -54,8 +73,7 @@ def apply_cpp_license(filename): This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/c_tools/analysis/voidOverlap.cpp b/c_tools/analysis/voidOverlap.cpp index 5662bf3..cb0c416 100644 --- a/c_tools/analysis/voidOverlap.cpp +++ b/c_tools/analysis/voidOverlap.cpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + // ============================================================================= // // Program: voidOverlap diff --git a/c_tools/libzobov/contour_pixels.cpp b/c_tools/libzobov/contour_pixels.cpp index a43f921..f522863 100644 --- a/c_tools/libzobov/contour_pixels.cpp +++ b/c_tools/libzobov/contour_pixels.cpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #include #include #include diff --git a/c_tools/libzobov/contour_pixels.hpp b/c_tools/libzobov/contour_pixels.hpp index 637a29b..821722f 100644 --- a/c_tools/libzobov/contour_pixels.hpp +++ b/c_tools/libzobov/contour_pixels.hpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #ifndef __CONTOUR_PIXELS_HPP #define __CONTOUR_PIXELS_HPP diff --git a/c_tools/libzobov/gslIntegrate.hpp b/c_tools/libzobov/gslIntegrate.hpp index 8c3f03f..d28560b 100644 --- a/c_tools/libzobov/gslIntegrate.hpp +++ b/c_tools/libzobov/gslIntegrate.hpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #ifndef __MYGSL_INTEGRATE_HPP #define __MYGSL_INTEGRATE_HPP diff --git a/c_tools/libzobov/loadZobov.cpp b/c_tools/libzobov/loadZobov.cpp index 490ec03..4f924b6 100644 --- a/c_tools/libzobov/loadZobov.cpp +++ b/c_tools/libzobov/loadZobov.cpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #include #include #include diff --git a/c_tools/libzobov/loadZobov.hpp b/c_tools/libzobov/loadZobov.hpp index 9da5f3f..95f0bd7 100644 --- a/c_tools/libzobov/loadZobov.hpp +++ b/c_tools/libzobov/loadZobov.hpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #ifndef __LOAD_ZOBOV_HPP #define __LOAD_ZOBOV_HPP diff --git a/c_tools/libzobov/particleInfo.cpp b/c_tools/libzobov/particleInfo.cpp index d7ba09e..4301469 100644 --- a/c_tools/libzobov/particleInfo.cpp +++ b/c_tools/libzobov/particleInfo.cpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #include #include #include diff --git a/c_tools/libzobov/particleInfo.hpp b/c_tools/libzobov/particleInfo.hpp index f1b42e5..ccb87e7 100644 --- a/c_tools/libzobov/particleInfo.hpp +++ b/c_tools/libzobov/particleInfo.hpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #ifndef _PARTICLE_INFO_HEADER_HPP #define _PARTICLE_INFO_HEADER_HPP diff --git a/c_tools/libzobov/voidTree.hpp b/c_tools/libzobov/voidTree.hpp index 14013ba..c46309c 100644 --- a/c_tools/libzobov/voidTree.hpp +++ b/c_tools/libzobov/voidTree.hpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #ifndef _VOID_TREE_HPP #define _VOID_TREE_HPP diff --git a/c_tools/mock/generateFromCatalog.cpp b/c_tools/mock/generateFromCatalog.cpp index f66e22b..8fc33b8 100644 --- a/c_tools/mock/generateFromCatalog.cpp +++ b/c_tools/mock/generateFromCatalog.cpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #include #include #include diff --git a/c_tools/mock/generateMock.cpp b/c_tools/mock/generateMock.cpp index 8d12f56..1a1c9a1 100644 --- a/c_tools/mock/generateMock.cpp +++ b/c_tools/mock/generateMock.cpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #include #include #include diff --git a/c_tools/mock/generateTestMock.cpp b/c_tools/mock/generateTestMock.cpp index 62126d0..a2645de 100644 --- a/c_tools/mock/generateTestMock.cpp +++ b/c_tools/mock/generateTestMock.cpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #include #include #include diff --git a/c_tools/mock/loaders/basic_loader.cpp b/c_tools/mock/loaders/basic_loader.cpp index 2e22151..336e2ec 100644 --- a/c_tools/mock/loaders/basic_loader.cpp +++ b/c_tools/mock/loaders/basic_loader.cpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #include #include #include diff --git a/c_tools/mock/loaders/flash_loader.cpp b/c_tools/mock/loaders/flash_loader.cpp index 16ebcd5..e59b923 100644 --- a/c_tools/mock/loaders/flash_loader.cpp +++ b/c_tools/mock/loaders/flash_loader.cpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #include #include #include diff --git a/c_tools/mock/loaders/gadget_loader.cpp b/c_tools/mock/loaders/gadget_loader.cpp index 5a5230a..c7a9d59 100644 --- a/c_tools/mock/loaders/gadget_loader.cpp +++ b/c_tools/mock/loaders/gadget_loader.cpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #include #include #include diff --git a/c_tools/mock/loaders/multidark_loader.cpp b/c_tools/mock/loaders/multidark_loader.cpp index 8e2a154..583786c 100644 --- a/c_tools/mock/loaders/multidark_loader.cpp +++ b/c_tools/mock/loaders/multidark_loader.cpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #include #include #include diff --git a/c_tools/mock/loaders/ramses_loader.cpp b/c_tools/mock/loaders/ramses_loader.cpp index b70783a..ac19e77 100644 --- a/c_tools/mock/loaders/ramses_loader.cpp +++ b/c_tools/mock/loaders/ramses_loader.cpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #include #include #include diff --git a/c_tools/mock/loaders/sdf_loader.cpp b/c_tools/mock/loaders/sdf_loader.cpp index a836971..32a0ebb 100644 --- a/c_tools/mock/loaders/sdf_loader.cpp +++ b/c_tools/mock/loaders/sdf_loader.cpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #include #include #include diff --git a/c_tools/mock/loaders/sdfloader_internal.hpp b/c_tools/mock/loaders/sdfloader_internal.hpp index 3e356db..215d943 100644 --- a/c_tools/mock/loaders/sdfloader_internal.hpp +++ b/c_tools/mock/loaders/sdfloader_internal.hpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #ifndef __VOID_SDF_LOADER_INTERNAL_HPP #define __VOID_SDF_LOADER_INTERNAL_HPP diff --git a/c_tools/mock/loaders/simulation_loader.cpp b/c_tools/mock/loaders/simulation_loader.cpp index e95531d..f5f3262 100644 --- a/c_tools/mock/loaders/simulation_loader.cpp +++ b/c_tools/mock/loaders/simulation_loader.cpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #include #include #include "simulation_loader.hpp" diff --git a/c_tools/mock/loaders/simulation_loader.hpp b/c_tools/mock/loaders/simulation_loader.hpp index 82c8251..19ac1f5 100644 --- a/c_tools/mock/loaders/simulation_loader.hpp +++ b/c_tools/mock/loaders/simulation_loader.hpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + #ifndef _MOCK_SIMULATION_LOADER_HPP #define _MOCK_SIMULATION_LOADER_HPP diff --git a/c_tools/stacking/pruneVoids.cpp b/c_tools/stacking/pruneVoids.cpp index 0d38ef9..3bb055a 100644 --- a/c_tools/stacking/pruneVoids.cpp +++ b/c_tools/stacking/pruneVoids.cpp @@ -5,8 +5,7 @@ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. + the Free Software Foundation; version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of @@ -18,6 +17,7 @@ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + // Reads in the void catalog and removes any void that could potentially // be affected by a mock particle. It does this by computing the longest // particle distance within each void and comparing it to the distance diff --git a/crossCompare/analysis/datasetsToAnalyze.py b/crossCompare/analysis/datasetsToAnalyze.py index 90c0f1e..1bbad51 100644 --- a/crossCompare/analysis/datasetsToAnalyze.py +++ b/crossCompare/analysis/datasetsToAnalyze.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/crossCompare/analysis/mergerTree.py b/crossCompare/analysis/mergerTree.py index b3421bb..b0fb783 100644 --- a/crossCompare/analysis/mergerTree.py +++ b/crossCompare/analysis/mergerTree.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/crossCompare/plotting/datasetsToPlot.py b/crossCompare/plotting/datasetsToPlot.py index d5a8db7..0b17b2f 100644 --- a/crossCompare/plotting/datasetsToPlot.py +++ b/crossCompare/plotting/datasetsToPlot.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/crossCompare/plotting/plotCompareDensCon.py b/crossCompare/plotting/plotCompareDensCon.py index 172b48a..f8779e9 100644 --- a/crossCompare/plotting/plotCompareDensCon.py +++ b/crossCompare/plotting/plotCompareDensCon.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/crossCompare/plotting/plotDensConVsR.py b/crossCompare/plotting/plotDensConVsR.py index 0788a2f..b20c7ab 100644 --- a/crossCompare/plotting/plotDensConVsR.py +++ b/crossCompare/plotting/plotDensConVsR.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/crossCompare/plotting/plotNumberFunc.py b/crossCompare/plotting/plotNumberFunc.py index 53e7837..e7af48d 100644 --- a/crossCompare/plotting/plotNumberFunc.py +++ b/crossCompare/plotting/plotNumberFunc.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/pipeline/datasets/mock_dr9mid.py b/pipeline/datasets/mock_dr9mid.py index e0ce29a..093cb74 100644 --- a/pipeline/datasets/mock_dr9mid.py +++ b/pipeline/datasets/mock_dr9mid.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/pipeline/datasets/multidark.py b/pipeline/datasets/multidark.py index 2811e3c..bf8c97b 100644 --- a/pipeline/datasets/multidark.py +++ b/pipeline/datasets/multidark.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/pipeline/generateCatalog.py b/pipeline/generateCatalog.py index 4ee7a60..1fc9f5a 100644 --- a/pipeline/generateCatalog.py +++ b/pipeline/generateCatalog.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/python_tools/pipeline_source/prepareCatalogs.in.py b/python_tools/pipeline_source/prepareCatalogs.in.py index 60d2c21..ca42343 100644 --- a/python_tools/pipeline_source/prepareCatalogs.in.py +++ b/python_tools/pipeline_source/prepareCatalogs.in.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/python_tools/setup.py b/python_tools/setup.py index 61a377c..506fbb3 100644 --- a/python_tools/setup.py +++ b/python_tools/setup.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/python_tools/void_python_tools/__init__.py b/python_tools/void_python_tools/__init__.py index 3254e46..de3c0f5 100644 --- a/python_tools/void_python_tools/__init__.py +++ b/python_tools/void_python_tools/__init__.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/python_tools/void_python_tools/apTools/__init__.py b/python_tools/void_python_tools/apTools/__init__.py index 9fc13ce..8a51885 100644 --- a/python_tools/void_python_tools/apTools/__init__.py +++ b/python_tools/void_python_tools/apTools/__init__.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/python_tools/void_python_tools/apTools/chi2/__init__.py b/python_tools/void_python_tools/apTools/chi2/__init__.py index 4ca64f2..16f6bd6 100644 --- a/python_tools/void_python_tools/apTools/chi2/__init__.py +++ b/python_tools/void_python_tools/apTools/chi2/__init__.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/python_tools/void_python_tools/apTools/chi2/cosmologyTools.py b/python_tools/void_python_tools/apTools/chi2/cosmologyTools.py index b2de95c..7456828 100644 --- a/python_tools/void_python_tools/apTools/chi2/cosmologyTools.py +++ b/python_tools/void_python_tools/apTools/chi2/cosmologyTools.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/python_tools/void_python_tools/apTools/profiles/__init__.py b/python_tools/void_python_tools/apTools/profiles/__init__.py index b73f4f0..2a4efd8 100644 --- a/python_tools/void_python_tools/apTools/profiles/__init__.py +++ b/python_tools/void_python_tools/apTools/profiles/__init__.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/python_tools/void_python_tools/apTools/profiles/getSurveyProps.py b/python_tools/void_python_tools/apTools/profiles/getSurveyProps.py index f4e93ab..cc3539e 100644 --- a/python_tools/void_python_tools/apTools/profiles/getSurveyProps.py +++ b/python_tools/void_python_tools/apTools/profiles/getSurveyProps.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/python_tools/void_python_tools/backend/__init__.py b/python_tools/void_python_tools/backend/__init__.py index e11599a..9532a0c 100644 --- a/python_tools/void_python_tools/backend/__init__.py +++ b/python_tools/void_python_tools/backend/__init__.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/python_tools/void_python_tools/backend/classes.py b/python_tools/void_python_tools/backend/classes.py index 6e164ec..55cef30 100644 --- a/python_tools/void_python_tools/backend/classes.py +++ b/python_tools/void_python_tools/backend/classes.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/python_tools/void_python_tools/backend/launchers.py b/python_tools/void_python_tools/backend/launchers.py index a2501d3..85295ab 100644 --- a/python_tools/void_python_tools/backend/launchers.py +++ b/python_tools/void_python_tools/backend/launchers.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/python_tools/void_python_tools/plotting/__init__.py b/python_tools/void_python_tools/plotting/__init__.py index f389009..aa825f8 100644 --- a/python_tools/void_python_tools/plotting/__init__.py +++ b/python_tools/void_python_tools/plotting/__init__.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/python_tools/void_python_tools/plotting/plotDefs.py b/python_tools/void_python_tools/plotting/plotDefs.py index 7e17025..f8c3154 100644 --- a/python_tools/void_python_tools/plotting/plotDefs.py +++ b/python_tools/void_python_tools/plotting/plotDefs.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of diff --git a/python_tools/void_python_tools/plotting/plotTools.py b/python_tools/void_python_tools/plotting/plotTools.py index 94b5b13..0498797 100644 --- a/python_tools/void_python_tools/plotting/plotTools.py +++ b/python_tools/void_python_tools/plotting/plotTools.py @@ -5,8 +5,8 @@ # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# the Free Software Foundation; version 2 of the License. +# # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of From 5d9dad143969a583d4c727ded4382288d8447322 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sat, 2 Mar 2013 20:23:33 -0500 Subject: [PATCH 15/16] Updated Copyright/License --- build_tools/gather_sources.py | 6 +++--- c_tools/analysis/voidOverlap.cpp | 3 ++- c_tools/libzobov/contour_pixels.cpp | 3 ++- c_tools/libzobov/contour_pixels.hpp | 3 ++- c_tools/libzobov/gslIntegrate.hpp | 3 ++- c_tools/libzobov/loadZobov.cpp | 3 ++- c_tools/libzobov/loadZobov.hpp | 3 ++- c_tools/libzobov/particleInfo.cpp | 3 ++- c_tools/libzobov/particleInfo.hpp | 3 ++- c_tools/libzobov/voidTree.hpp | 3 ++- c_tools/mock/generateFromCatalog.cpp | 3 ++- c_tools/mock/generateMock.cpp | 3 ++- c_tools/mock/generateTestMock.cpp | 3 ++- c_tools/mock/loaders/basic_loader.cpp | 3 ++- c_tools/mock/loaders/flash_loader.cpp | 3 ++- c_tools/mock/loaders/gadget_loader.cpp | 3 ++- c_tools/mock/loaders/multidark_loader.cpp | 3 ++- c_tools/mock/loaders/ramses_loader.cpp | 3 ++- c_tools/mock/loaders/sdf_loader.cpp | 3 ++- c_tools/mock/loaders/sdfloader_internal.hpp | 3 ++- c_tools/mock/loaders/simulation_loader.cpp | 3 ++- c_tools/mock/loaders/simulation_loader.hpp | 3 ++- c_tools/stacking/pruneVoids.cpp | 3 ++- crossCompare/analysis/datasetsToAnalyze.py | 2 +- crossCompare/analysis/mergerTree.py | 2 +- crossCompare/plotting/datasetsToPlot.py | 2 +- crossCompare/plotting/plotCompareDensCon.py | 2 +- crossCompare/plotting/plotDensConVsR.py | 2 +- crossCompare/plotting/plotNumberFunc.py | 2 +- pipeline/datasets/mock_dr9mid.py | 2 +- pipeline/datasets/multidark.py | 2 +- pipeline/generateCatalog.py | 2 +- python_tools/pipeline_source/prepareCatalogs.in.py | 2 +- python_tools/setup.py | 2 +- python_tools/void_python_tools/__init__.py | 2 +- python_tools/void_python_tools/apTools/__init__.py | 2 +- python_tools/void_python_tools/apTools/chi2/__init__.py | 2 +- .../void_python_tools/apTools/chi2/cosmologyTools.py | 2 +- python_tools/void_python_tools/apTools/profiles/__init__.py | 2 +- .../void_python_tools/apTools/profiles/getSurveyProps.py | 2 +- python_tools/void_python_tools/backend/__init__.py | 2 +- python_tools/void_python_tools/backend/classes.py | 2 +- python_tools/void_python_tools/backend/launchers.py | 2 +- python_tools/void_python_tools/plotting/__init__.py | 2 +- python_tools/void_python_tools/plotting/plotDefs.py | 2 +- python_tools/void_python_tools/plotting/plotTools.py | 2 +- 46 files changed, 70 insertions(+), 48 deletions(-) diff --git a/build_tools/gather_sources.py b/build_tools/gather_sources.py index 2b8b4c5..bb30185 100644 --- a/build_tools/gather_sources.py +++ b/build_tools/gather_sources.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./build_tools/gather_sources.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -42,7 +42,7 @@ def apply_python_license(filename): license="""#+ # VIDE -- Void IDEntification pipeline -- @FILENAME@ # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -69,7 +69,7 @@ def apply_cpp_license(filename): license="""/*+ VIDE -- Void IDEntification pipeline -- @FILENAME@ Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by diff --git a/c_tools/analysis/voidOverlap.cpp b/c_tools/analysis/voidOverlap.cpp index cb0c416..f62409c 100644 --- a/c_tools/analysis/voidOverlap.cpp +++ b/c_tools/analysis/voidOverlap.cpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/analysis/voidOverlap.cpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + // ============================================================================= // // Program: voidOverlap diff --git a/c_tools/libzobov/contour_pixels.cpp b/c_tools/libzobov/contour_pixels.cpp index f522863..c2f8447 100644 --- a/c_tools/libzobov/contour_pixels.cpp +++ b/c_tools/libzobov/contour_pixels.cpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/contour_pixels.cpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #include #include #include diff --git a/c_tools/libzobov/contour_pixels.hpp b/c_tools/libzobov/contour_pixels.hpp index 821722f..8095024 100644 --- a/c_tools/libzobov/contour_pixels.hpp +++ b/c_tools/libzobov/contour_pixels.hpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/contour_pixels.hpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #ifndef __CONTOUR_PIXELS_HPP #define __CONTOUR_PIXELS_HPP diff --git a/c_tools/libzobov/gslIntegrate.hpp b/c_tools/libzobov/gslIntegrate.hpp index d28560b..140ec81 100644 --- a/c_tools/libzobov/gslIntegrate.hpp +++ b/c_tools/libzobov/gslIntegrate.hpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/gslIntegrate.hpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #ifndef __MYGSL_INTEGRATE_HPP #define __MYGSL_INTEGRATE_HPP diff --git a/c_tools/libzobov/loadZobov.cpp b/c_tools/libzobov/loadZobov.cpp index 4f924b6..a1a6cbb 100644 --- a/c_tools/libzobov/loadZobov.cpp +++ b/c_tools/libzobov/loadZobov.cpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/loadZobov.cpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #include #include #include diff --git a/c_tools/libzobov/loadZobov.hpp b/c_tools/libzobov/loadZobov.hpp index 95f0bd7..0bcf70a 100644 --- a/c_tools/libzobov/loadZobov.hpp +++ b/c_tools/libzobov/loadZobov.hpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/loadZobov.hpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #ifndef __LOAD_ZOBOV_HPP #define __LOAD_ZOBOV_HPP diff --git a/c_tools/libzobov/particleInfo.cpp b/c_tools/libzobov/particleInfo.cpp index 4301469..e368eec 100644 --- a/c_tools/libzobov/particleInfo.cpp +++ b/c_tools/libzobov/particleInfo.cpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/particleInfo.cpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #include #include #include diff --git a/c_tools/libzobov/particleInfo.hpp b/c_tools/libzobov/particleInfo.hpp index ccb87e7..325be23 100644 --- a/c_tools/libzobov/particleInfo.hpp +++ b/c_tools/libzobov/particleInfo.hpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/particleInfo.hpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #ifndef _PARTICLE_INFO_HEADER_HPP #define _PARTICLE_INFO_HEADER_HPP diff --git a/c_tools/libzobov/voidTree.hpp b/c_tools/libzobov/voidTree.hpp index c46309c..f958547 100644 --- a/c_tools/libzobov/voidTree.hpp +++ b/c_tools/libzobov/voidTree.hpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/voidTree.hpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #ifndef _VOID_TREE_HPP #define _VOID_TREE_HPP diff --git a/c_tools/mock/generateFromCatalog.cpp b/c_tools/mock/generateFromCatalog.cpp index 8fc33b8..669a850 100644 --- a/c_tools/mock/generateFromCatalog.cpp +++ b/c_tools/mock/generateFromCatalog.cpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/mock/generateFromCatalog.cpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #include #include #include diff --git a/c_tools/mock/generateMock.cpp b/c_tools/mock/generateMock.cpp index 1a1c9a1..c015749 100644 --- a/c_tools/mock/generateMock.cpp +++ b/c_tools/mock/generateMock.cpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/mock/generateMock.cpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #include #include #include diff --git a/c_tools/mock/generateTestMock.cpp b/c_tools/mock/generateTestMock.cpp index a2645de..4ab3467 100644 --- a/c_tools/mock/generateTestMock.cpp +++ b/c_tools/mock/generateTestMock.cpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/mock/generateTestMock.cpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #include #include #include diff --git a/c_tools/mock/loaders/basic_loader.cpp b/c_tools/mock/loaders/basic_loader.cpp index 336e2ec..0e346d6 100644 --- a/c_tools/mock/loaders/basic_loader.cpp +++ b/c_tools/mock/loaders/basic_loader.cpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/basic_loader.cpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #include #include #include diff --git a/c_tools/mock/loaders/flash_loader.cpp b/c_tools/mock/loaders/flash_loader.cpp index e59b923..b8b6439 100644 --- a/c_tools/mock/loaders/flash_loader.cpp +++ b/c_tools/mock/loaders/flash_loader.cpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/flash_loader.cpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #include #include #include diff --git a/c_tools/mock/loaders/gadget_loader.cpp b/c_tools/mock/loaders/gadget_loader.cpp index c7a9d59..a0562d1 100644 --- a/c_tools/mock/loaders/gadget_loader.cpp +++ b/c_tools/mock/loaders/gadget_loader.cpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/gadget_loader.cpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #include #include #include diff --git a/c_tools/mock/loaders/multidark_loader.cpp b/c_tools/mock/loaders/multidark_loader.cpp index 583786c..bd43748 100644 --- a/c_tools/mock/loaders/multidark_loader.cpp +++ b/c_tools/mock/loaders/multidark_loader.cpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/multidark_loader.cpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #include #include #include diff --git a/c_tools/mock/loaders/ramses_loader.cpp b/c_tools/mock/loaders/ramses_loader.cpp index ac19e77..a7e3a95 100644 --- a/c_tools/mock/loaders/ramses_loader.cpp +++ b/c_tools/mock/loaders/ramses_loader.cpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/ramses_loader.cpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #include #include #include diff --git a/c_tools/mock/loaders/sdf_loader.cpp b/c_tools/mock/loaders/sdf_loader.cpp index 32a0ebb..0c734b8 100644 --- a/c_tools/mock/loaders/sdf_loader.cpp +++ b/c_tools/mock/loaders/sdf_loader.cpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/sdf_loader.cpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #include #include #include diff --git a/c_tools/mock/loaders/sdfloader_internal.hpp b/c_tools/mock/loaders/sdfloader_internal.hpp index 215d943..fb00537 100644 --- a/c_tools/mock/loaders/sdfloader_internal.hpp +++ b/c_tools/mock/loaders/sdfloader_internal.hpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/sdfloader_internal.hpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #ifndef __VOID_SDF_LOADER_INTERNAL_HPP #define __VOID_SDF_LOADER_INTERNAL_HPP diff --git a/c_tools/mock/loaders/simulation_loader.cpp b/c_tools/mock/loaders/simulation_loader.cpp index f5f3262..014ebd2 100644 --- a/c_tools/mock/loaders/simulation_loader.cpp +++ b/c_tools/mock/loaders/simulation_loader.cpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/simulation_loader.cpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #include #include #include "simulation_loader.hpp" diff --git a/c_tools/mock/loaders/simulation_loader.hpp b/c_tools/mock/loaders/simulation_loader.hpp index 19ac1f5..ba8b2da 100644 --- a/c_tools/mock/loaders/simulation_loader.hpp +++ b/c_tools/mock/loaders/simulation_loader.hpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/simulation_loader.hpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + #ifndef _MOCK_SIMULATION_LOADER_HPP #define _MOCK_SIMULATION_LOADER_HPP diff --git a/c_tools/stacking/pruneVoids.cpp b/c_tools/stacking/pruneVoids.cpp index 3bb055a..26c2abd 100644 --- a/c_tools/stacking/pruneVoids.cpp +++ b/c_tools/stacking/pruneVoids.cpp @@ -1,7 +1,7 @@ /*+ VIDE -- Void IDEntification pipeline -- ./c_tools/stacking/pruneVoids.cpp Copyright (C) 2010-2013 Guilhem Lavaux - Copyright (C) 2011-2013 Paul M. Sutter + Copyright (C) 2011-2013 P. M. Sutter This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -18,6 +18,7 @@ +*/ + // Reads in the void catalog and removes any void that could potentially // be affected by a mock particle. It does this by computing the longest // particle distance within each void and comparing it to the distance diff --git a/crossCompare/analysis/datasetsToAnalyze.py b/crossCompare/analysis/datasetsToAnalyze.py index 1bbad51..9c8e5d2 100644 --- a/crossCompare/analysis/datasetsToAnalyze.py +++ b/crossCompare/analysis/datasetsToAnalyze.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./crossCompare/analysis/datasetsToAnalyze.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/crossCompare/analysis/mergerTree.py b/crossCompare/analysis/mergerTree.py index b0fb783..ec70217 100644 --- a/crossCompare/analysis/mergerTree.py +++ b/crossCompare/analysis/mergerTree.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./crossCompare/analysis/mergerTree.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/crossCompare/plotting/datasetsToPlot.py b/crossCompare/plotting/datasetsToPlot.py index 0b17b2f..19002cf 100644 --- a/crossCompare/plotting/datasetsToPlot.py +++ b/crossCompare/plotting/datasetsToPlot.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./crossCompare/plotting/datasetsToPlot.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/crossCompare/plotting/plotCompareDensCon.py b/crossCompare/plotting/plotCompareDensCon.py index f8779e9..5e96dfb 100644 --- a/crossCompare/plotting/plotCompareDensCon.py +++ b/crossCompare/plotting/plotCompareDensCon.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./crossCompare/plotting/plotCompareDensCon.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/crossCompare/plotting/plotDensConVsR.py b/crossCompare/plotting/plotDensConVsR.py index b20c7ab..87a44e8 100644 --- a/crossCompare/plotting/plotDensConVsR.py +++ b/crossCompare/plotting/plotDensConVsR.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./crossCompare/plotting/plotDensConVsR.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/crossCompare/plotting/plotNumberFunc.py b/crossCompare/plotting/plotNumberFunc.py index e7af48d..72a5616 100644 --- a/crossCompare/plotting/plotNumberFunc.py +++ b/crossCompare/plotting/plotNumberFunc.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./crossCompare/plotting/plotNumberFunc.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/pipeline/datasets/mock_dr9mid.py b/pipeline/datasets/mock_dr9mid.py index 093cb74..11fc5b9 100644 --- a/pipeline/datasets/mock_dr9mid.py +++ b/pipeline/datasets/mock_dr9mid.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./pipeline/datasets/mock_dr9mid.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/pipeline/datasets/multidark.py b/pipeline/datasets/multidark.py index bf8c97b..79df229 100644 --- a/pipeline/datasets/multidark.py +++ b/pipeline/datasets/multidark.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./pipeline/datasets/multidark.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/pipeline/generateCatalog.py b/pipeline/generateCatalog.py index 1fc9f5a..f5473f8 100644 --- a/pipeline/generateCatalog.py +++ b/pipeline/generateCatalog.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./pipeline/generateCatalog.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/python_tools/pipeline_source/prepareCatalogs.in.py b/python_tools/pipeline_source/prepareCatalogs.in.py index ca42343..612629b 100644 --- a/python_tools/pipeline_source/prepareCatalogs.in.py +++ b/python_tools/pipeline_source/prepareCatalogs.in.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./python_tools/pipeline_source/prepareCatalogs.in.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/python_tools/setup.py b/python_tools/setup.py index 506fbb3..b0bc165 100644 --- a/python_tools/setup.py +++ b/python_tools/setup.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./python_tools/setup.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/python_tools/void_python_tools/__init__.py b/python_tools/void_python_tools/__init__.py index de3c0f5..5f07ae6 100644 --- a/python_tools/void_python_tools/__init__.py +++ b/python_tools/void_python_tools/__init__.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/__init__.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/python_tools/void_python_tools/apTools/__init__.py b/python_tools/void_python_tools/apTools/__init__.py index 8a51885..8b6353c 100644 --- a/python_tools/void_python_tools/apTools/__init__.py +++ b/python_tools/void_python_tools/apTools/__init__.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/__init__.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/python_tools/void_python_tools/apTools/chi2/__init__.py b/python_tools/void_python_tools/apTools/chi2/__init__.py index 16f6bd6..f4956d6 100644 --- a/python_tools/void_python_tools/apTools/chi2/__init__.py +++ b/python_tools/void_python_tools/apTools/chi2/__init__.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/chi2/__init__.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/python_tools/void_python_tools/apTools/chi2/cosmologyTools.py b/python_tools/void_python_tools/apTools/chi2/cosmologyTools.py index 7456828..4b9b35d 100644 --- a/python_tools/void_python_tools/apTools/chi2/cosmologyTools.py +++ b/python_tools/void_python_tools/apTools/chi2/cosmologyTools.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/chi2/cosmologyTools.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/python_tools/void_python_tools/apTools/profiles/__init__.py b/python_tools/void_python_tools/apTools/profiles/__init__.py index 2a4efd8..d4b802c 100644 --- a/python_tools/void_python_tools/apTools/profiles/__init__.py +++ b/python_tools/void_python_tools/apTools/profiles/__init__.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/profiles/__init__.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/python_tools/void_python_tools/apTools/profiles/getSurveyProps.py b/python_tools/void_python_tools/apTools/profiles/getSurveyProps.py index cc3539e..c4fcb35 100644 --- a/python_tools/void_python_tools/apTools/profiles/getSurveyProps.py +++ b/python_tools/void_python_tools/apTools/profiles/getSurveyProps.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/profiles/getSurveyProps.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/python_tools/void_python_tools/backend/__init__.py b/python_tools/void_python_tools/backend/__init__.py index 9532a0c..43a9c88 100644 --- a/python_tools/void_python_tools/backend/__init__.py +++ b/python_tools/void_python_tools/backend/__init__.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/backend/__init__.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/python_tools/void_python_tools/backend/classes.py b/python_tools/void_python_tools/backend/classes.py index 55cef30..0170199 100644 --- a/python_tools/void_python_tools/backend/classes.py +++ b/python_tools/void_python_tools/backend/classes.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/backend/classes.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/python_tools/void_python_tools/backend/launchers.py b/python_tools/void_python_tools/backend/launchers.py index 85295ab..b619601 100644 --- a/python_tools/void_python_tools/backend/launchers.py +++ b/python_tools/void_python_tools/backend/launchers.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/backend/launchers.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/python_tools/void_python_tools/plotting/__init__.py b/python_tools/void_python_tools/plotting/__init__.py index aa825f8..ff0bc67 100644 --- a/python_tools/void_python_tools/plotting/__init__.py +++ b/python_tools/void_python_tools/plotting/__init__.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/plotting/__init__.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/python_tools/void_python_tools/plotting/plotDefs.py b/python_tools/void_python_tools/plotting/plotDefs.py index f8c3154..9872fc8 100644 --- a/python_tools/void_python_tools/plotting/plotDefs.py +++ b/python_tools/void_python_tools/plotting/plotDefs.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/plotting/plotDefs.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/python_tools/void_python_tools/plotting/plotTools.py b/python_tools/void_python_tools/plotting/plotTools.py index 0498797..5bc617c 100644 --- a/python_tools/void_python_tools/plotting/plotTools.py +++ b/python_tools/void_python_tools/plotting/plotTools.py @@ -1,7 +1,7 @@ #+ # VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/plotting/plotTools.py # Copyright (C) 2010-2013 Guilhem Lavaux -# Copyright (C) 2011-2013 Paul M. Sutter +# Copyright (C) 2011-2013 P. M. Sutter # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by From c385a9a11a0a7b6d32532a6277a18765eafffcd6 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sat, 2 Mar 2013 21:41:07 -0500 Subject: [PATCH 16/16] Added SDFcvt to the build --- external/external_build.cmake | 5 +- external/install_sdf.cmake | 4 + external/libsdf/GNUmakefile | 2 +- external/libsdf/apps/SDFcvt/GNUmakefile | 15 + external/libsdf/apps/SDFcvt/SDFcvt.c | 461 ++++++++++++++++++++++++ 5 files changed, 484 insertions(+), 3 deletions(-) create mode 100644 external/install_sdf.cmake create mode 100644 external/libsdf/apps/SDFcvt/GNUmakefile create mode 100644 external/libsdf/apps/SDFcvt/SDFcvt.c diff --git a/external/external_build.cmake b/external/external_build.cmake index e6b19ac..0cb3d43 100644 --- a/external/external_build.cmake +++ b/external/external_build.cmake @@ -321,7 +321,8 @@ SET(QHULL_LIBRARIES ${QHULL_CPP_LIBRARY} ${QHULL_LIBRARY} ) # Build libSDF ############### IF(SDF_SUPPORT) - SET(LIBSDF_ARCH x86_64) + SET(LIBSDF_ARCH x86_64 CACHE STRING "SDF architecture to activate") + mark_as_advanced(LIBSDF_ARCH) SET(LIBSDF_PATH ${CMAKE_SOURCE_DIR}/external/libsdf) ExternalProject_Add(libSDF @@ -329,7 +330,7 @@ IF(SDF_SUPPORT) SOURCE_DIR ${LIBSDF_PATH} CONFIGURE_COMMAND echo No configure BUILD_COMMAND ${CMAKE_MAKE_PROGRAM} ARCH=${LIBSDF_ARCH} - INSTALL_COMMAND echo No install + INSTALL_COMMAND ${CMAKE_COMMAND} -DDEST_DIR=${CMAKE_BINARY_DIR}/ext_build/sdf -DLIBSDF_ARCH=${LIBSDF_ARCH} -DLIBSDF_PATH=${LIBSDF_PATH} -P ${CMAKE_SOURCE_DIR}/external/install_sdf.cmake BUILD_IN_SOURCE 1 ) SET(LIBSDF_INCLUDE_PATH ${LIBSDF_PATH}/include) diff --git a/external/install_sdf.cmake b/external/install_sdf.cmake new file mode 100644 index 0000000..81cb790 --- /dev/null +++ b/external/install_sdf.cmake @@ -0,0 +1,4 @@ +file(MAKE_DIRECTORY ${DEST_DIR}) +file(MAKE_DIRECTORY ${DEST_DIR}/bin) +file(INSTALL ${LIBSDF_PATH}/apps/SDFcvt/SDFcvt.${LIBSDF_ARCH} DESTINATION ${DEST_DIR}/bin PERMISSIONS OWNER_EXECUTE OWNER_READ OWNER_WRITE GROUP_EXECUTE GROUP_READ) +file(RENAME ${DEST_DIR}/bin/SDFcvt.${LIBSDF_ARCH} ${DEST_DIR}/bin/SDFcvt) diff --git a/external/libsdf/GNUmakefile b/external/libsdf/GNUmakefile index 5ade09d..45309fd 100644 --- a/external/libsdf/GNUmakefile +++ b/external/libsdf/GNUmakefile @@ -20,7 +20,7 @@ all: All # spell them a little differently in this file... include Make-common/Make.generic -subdirs:= libSDF libmpmy libsw +subdirs:= libSDF libmpmy libsw apps/SDFcvt All: for dir in $(subdirs); do (cd $$dir; $(MAKE) ARCH=$(ARCH) all); done diff --git a/external/libsdf/apps/SDFcvt/GNUmakefile b/external/libsdf/apps/SDFcvt/GNUmakefile new file mode 100644 index 0000000..234ff45 --- /dev/null +++ b/external/libsdf/apps/SDFcvt/GNUmakefile @@ -0,0 +1,15 @@ +TREEHOME=../.. +##### Application-specific stuff goes here + +treedir=$(TREEHOME) +programname=SDFcvt +src=SDFcvt.c + +#### end of application-specific stuff +include $(treedir)/Make-common/Make.$(ARCH) + +include $(treedir)/Make-common/Make.generic + +# DO NOT DELETE THIS LINE -- make depend depends on it. + + diff --git a/external/libsdf/apps/SDFcvt/SDFcvt.c b/external/libsdf/apps/SDFcvt/SDFcvt.c new file mode 100644 index 0000000..f236cc1 --- /dev/null +++ b/external/libsdf/apps/SDFcvt/SDFcvt.c @@ -0,0 +1,461 @@ +/* Convert SDF to ascii + Usage: + SDFcvt [-s skip][-n nrecout][-h hdrfile] [-bfv] sdffile name ... + + Not too fancy, but it should handle most SDF files, including + non-unit arrcnt. By using -s and -n is is possible to skip + to a place in the file and examine pieces of files + that would otherwise be too big to handle. We do NOT read the + whole file into memory. We process output lines one at a time, + reading one value of each of the names into memory at a time. + Thrashing is possible. We do nothing to prevent it. + + With -v it prints a potentially useful pair of header lines + starting with '#'. + + CHANGELOG: + 6/28/94: Added the FORMAT_NATIVE option, and made it the default. + This will write SDF_INTS as ints, SDF_SHORTS as shorts, etc. It's + useful for post-processing by programs that can handle mixed types, + e.g., perl, but not AVS. + + 10/18/93: Added the -S (Swapping) flag to write binary data swapped. + Use limits.h/INT_MAX instead of SunOS values.h/MAXINT. + + 8/1/93: add the AT_A_TIME construction. We no longer process lines + one at a time. Instead, we read up to AT_A_TIME to beat the + excessive overhead in each SDFrdvecs call. One of these days + I'll add a hash table to SDF's symbol-lookup functions. Until + then, reading one element at a time will be extremely slow. + + 8/20/93: added the option to produce output in binary. This is MUCH + faster. With a little luck, perl (and presumably other programs) + can read it MUCH faster too (perl uses read and unpack). + +*/ +#define AT_A_TIME 512 /* read this many values at a time */ +#include +#include +#include +#include +#include "SDF.h" +#include "protos.h" +#include "byteswap.h" +#include "error.h" +#include "Malloc.h" + +#ifndef __SUN5__ +extern int getopt(int, char**, const char *); +extern char *optarg; +extern int optind, opterr; +#endif + +#define FORMAT_FLOAT 1 +#define FORMAT_DOUBLE 2 +#define FORMAT_INT 3 +#define FORMAT_NATIVE 4 + +int binary = 0; +int format = FORMAT_NATIVE; +int swap_out = 0; + +int fwrite_maybe_swap(void *p, size_t sz, size_t n, FILE *fp){ + if( swap_out ) + Byteswap(sz, n, p, p); + return fwrite(p, sz, n, fp); +} + +void output_char(short c){ + float f; + double d; + int i; + + if( binary ){ + switch(format){ + case FORMAT_DOUBLE: + d = c; + fwrite_maybe_swap(&d, sizeof(d), 1, stdout); + break; + case FORMAT_FLOAT: + f = c; + fwrite_maybe_swap(&f, sizeof(f), 1, stdout); + break; + case FORMAT_INT: + i = c; + fwrite_maybe_swap(&i, sizeof(i), 1, stdout); + break; + case FORMAT_NATIVE: + fwrite_maybe_swap(&c, sizeof(c), 1, stdout); + break; + } + }else{ + printf("%d", c); + } +} + +void output_short(short s){ + float f; + double d; + int i; + + if( binary ){ + switch(format){ + case FORMAT_DOUBLE: + d = s; + fwrite_maybe_swap(&d, sizeof(d), 1, stdout); + break; + case FORMAT_FLOAT: + f = s; + fwrite_maybe_swap(&f, sizeof(f), 1, stdout); + break; + case FORMAT_INT: + i = s; + fwrite_maybe_swap(&i, sizeof(i), 1, stdout); + break; + case FORMAT_NATIVE: + fwrite_maybe_swap(&s, sizeof(s), 1, stdout); + break; + } + }else{ + printf("%d", s); + } +} + +void output_int(int i){ + float f; + double d; + + if( binary ){ + switch(format){ + case FORMAT_DOUBLE: + d = i; + fwrite_maybe_swap(&d, sizeof(d), 1, stdout); + break; + case FORMAT_FLOAT: + f = i; + fwrite_maybe_swap(&f, sizeof(f), 1, stdout); + break; + case FORMAT_NATIVE: + case FORMAT_INT: + fwrite_maybe_swap(&i, sizeof(i), 1, stdout); + break; + } + }else{ + printf("%d", i); + } +} + +void output_long(long l){ + float f; + double d; + + if( binary ){ + switch(format){ + case FORMAT_DOUBLE: + d = l; + fwrite_maybe_swap(&d, sizeof(d), 1, stdout); + break; + case FORMAT_FLOAT: + f = l; + fwrite_maybe_swap(&f, sizeof(f), 1, stdout); + break; + case FORMAT_NATIVE: + case FORMAT_INT: + fwrite_maybe_swap(&l, sizeof(l), 1, stdout); + break; + } + }else{ + printf("%ld", l); + } +} + +void output_int64(int64_t i64){ + float f; + double d; + + if( binary ){ + switch(format){ + case FORMAT_DOUBLE: + d = i64; + fwrite_maybe_swap(&d, sizeof(d), 1, stdout); + break; + case FORMAT_FLOAT: + f = i64; + fwrite_maybe_swap(&f, sizeof(f), 1, stdout); + break; + case FORMAT_NATIVE: + case FORMAT_INT: + fwrite_maybe_swap(&i64, sizeof(i64), 1, stdout); + break; + } + }else{ +#if __WORDSIZE==64 + printf("%ld", i64); +#else + printf("%lld", i64); +#endif + } +} + + + +void output_float(float f){ + double d; + int i; + + if( binary ){ + switch(format){ + case FORMAT_DOUBLE: + d = f; + fwrite_maybe_swap(&d, sizeof(d), 1, stdout); + break; + case FORMAT_FLOAT: + case FORMAT_NATIVE: + fwrite_maybe_swap(&f, sizeof(f), 1, stdout); + break; + case FORMAT_INT: + i = f; + fwrite_maybe_swap(&i, sizeof(i), 1, stdout); + break; + } + }else{ + switch(format){ + case FORMAT_DOUBLE: + printf("%.15e", f); + break; + case FORMAT_FLOAT: + case FORMAT_NATIVE: + printf("%.6e", f); + break; + case FORMAT_INT: + printf("%.0f", f); + break; + } + } +} + +void output_double(double d){ + float f; + int i; + + if( binary ){ + switch(format){ + case FORMAT_NATIVE: + case FORMAT_DOUBLE: + fwrite_maybe_swap(&d, sizeof(d), 1, stdout); + break; + case FORMAT_FLOAT: + f = d; + fwrite_maybe_swap(&f, sizeof(f), 1, stdout); + break; + case FORMAT_INT: + i = d; + fwrite_maybe_swap(&i, sizeof(i), 1, stdout); + break; + } + }else{ + switch(format){ + case FORMAT_DOUBLE: + case FORMAT_NATIVE: + printf("%.15e", d); + break; + case FORMAT_FLOAT: + printf("%.6e", d); + break; + case FORMAT_INT: + printf("%.0f", d); + break; + } + } +} + +void output_string(const char *s){ + fwrite(s, strlen(s), 1, stdout); +} + +void output_separator(void){ + if( !binary ) + putchar(' '); +} + +void output_record_terminator(void){ + if( !binary ) + putchar('\n'); +} + +int main(int argc, char **argv){ + int c; + char *fname, *hdr; + SDF *sdfp; + int64_t n, start; + int nnames, nn, i, j, k, kk; + int at_a_time; + int64_t nrecs, minnrecs, maxnrecs; + char *newname; + char **names; + void **addrs; + int *nread; + int *acnt; + int *strides; + enum SDF_type_enum *types, t; + int verbose; + + hdr = NULL; + start = 0; + n = 0; + verbose = 0; + at_a_time = 0; + while((c=getopt(argc, argv, "a:h:s:n:vbfdiS")) != -1) + switch(c){ + case 'h': + hdr = optarg; + break; + case 's': + start = atoll(optarg); + break; + case 'n': + n = atoll(optarg); + break; + case 'a': + at_a_time = atoi(optarg); + break; + case 'v': + verbose = 1; + break; + case 'b': + binary = 1; + break; + case 'f': + format = FORMAT_FLOAT; + break; + case 'S': + swap_out = 1; + break; + case 'd': + format = FORMAT_DOUBLE; + break; + case 'i': + format = FORMAT_INT; + break; + case '?': + fprintf(stderr, "Usage: %s [-s start][-n number][-a at-a-time][-v][-h hdrfile][-b][-f][-d][-i][-S] sdffile name ...\n", argv[0]); + } + + fname = argv[optind]; + optind++; + sdfp = SDFopen(hdr, fname); + if( sdfp == NULL ){ + Error("Could not SDFopen(%s, %s): %s\n", + hdr?hdr:"", + fname?fname:"", + SDFerrstring); + } + if( at_a_time == 0 ) + at_a_time = AT_A_TIME; + + nnames = argc - optind; + names = Malloc(nnames*sizeof(char*)); + addrs = Malloc(nnames*sizeof(void*)); + nread = Malloc(nnames*sizeof(int)); + types = Malloc(nnames*sizeof(enum SDF_type_enum)); + strides = Malloc(nnames*sizeof(int)); + acnt = Malloc(nnames*sizeof(int)); + + nn = 0; + minnrecs = INT64_MAX; + maxnrecs = 0; + for(; optind < argc; optind++){ + newname = argv[optind]; + if( !SDFhasname(newname, sdfp) ){ + Error("%s not in %s\n", newname, fname); + } + t = SDFtype(newname, sdfp); + acnt[nn] = SDFarrcnt(newname, sdfp); + addrs[nn] = Malloc(SDFtype_sizes[t] * acnt[nn] * at_a_time); + strides[nn] = SDFtype_sizes[t]*acnt[nn]; + names[nn] = newname; + types[nn] = t; + nrecs = SDFnrecs(newname, sdfp); + if( nrecs < minnrecs ) + minnrecs = nrecs; + if( nrecs > maxnrecs ) + maxnrecs = nrecs; + nread[nn] = at_a_time; + nn++; + } + if( n==0 ){ + n = maxnrecs - start; + } + if( start+n > minnrecs ){ + Error("Not enough records to start at %ld\n", start); + } + + if( start ){ + for(j=0; j0 ){ + if( n < at_a_time ){ + at_a_time = n; + for(j=0; j