/* Measures mean inward and outward attenuation computed over both apical and
* dendritic trees, at a range of frequencies.
*/
objref f // File reference for output
strdef file_name, neuron_name, output_dir, direction, which_secs
objref m, p, sref // matrix
objref imp // Impedance object used to calculate attenuation
objref vec // Vector of impedance results for each segment in the neuron
// Defines voltage_vec and time_vec, vectors that are needed by functions in
// analyticFunctions.hoc.
xopen("actionPotentialPlayer.hoc")
xopen("readcell.hoc")
xopen("analyticFunctions.hoc")
/*
* Opens output file; the specific name of the output file is determined by
* the arguments.
*
* Arguments:
* $1: frequency at which attenuation is measured
* $2: set to 1 if analyzing apical trees, 2 for basal
* $3: set to 1 to correct for spines
* $4: set to 1 for inward attenuaton, 2 for outward
*/
proc openfile() {
output_dir = "/Users/pcoskren-sinai/Subversion/WearneLab/Publications/DoronsPaper/Scripts/Output"
if ($4 == 1) {
direction = "Inward"
} else {
direction = "Outward"
}
f = new File()
if ($2==1 && $3==1) {
sprint(file_name,"%s/%sNormSumAtten%gHzApicSpiny.txt", output_dir, direction, $1)
}
if ($2==1 && $3==2) {
sprint(file_name,"%s/%sNormSumAtten%gHzApic.txt", output_dir, direction, $1)
}
if ($2==2 && $3==1) {
sprint(file_name,"%s/%sNormSumAtten%gHzBasaSpiny.txt", output_dir, direction, $1)
}
if ($2==2 && $3==2) {
sprint(file_name,"%s/%sNormSumAtten%gHzBasa.txt", output_dir, direction, $1)
}
print file_name
f.wopen(file_name)
}
/* meanInwardAttenuationAllFrequencies: calculates the mean inward attenuation over a range of
* frequencies form 0 to 500, over the specified cell.
* Arguments:
* $o1: soma -> A SectionRef referring to the neuron's soma
* For inward attenuation, measurement (imp.loc) is at the soma, and
* voltage clamp (imp.ratio) ranges over the tree.
*/
proc meanInwardAttenuationAllFrequencies() { local freq, i, spine_type,\
real_diam, real_L, ratio \
localobj path, soma, tree_root
soma = $o1
//tree_root = $o2 // cmw 8/26/11: doesn't seem to do anything
access soma.sec
nseg = 1
real_diam = diam(0.5)
real_L = L
diam = 2.0 * STD_SOMA
L = 2.0 * STD_SOMA
for (freq = 0; freq <= 500; freq += 100) {
v_init = E_PAS
finitialize(v_init)
imp = new Impedance() // if no arg then this creates one
soma.sec imp.loc(0.5)
vec = new Vector()
dendriticLength = 0
forsec "dend" {
for (x) {
segmentLength = area(x) / (diam(x) * PI) // area = l*pi*d
if (0 != segmentLength) {
imp.compute(freq)
ratio = imp.ratio(x)
if (ratio > 0) {
logA = log(1 / ratio)
dendriticLength = dendriticLength + segmentLength
scaledLogA = logA * segmentLength
vec.append(scaledLogA)
} else {
printf("Warning: negative voltage ratio\n")
}
}
}
}
sum_norm = vec.sum() / dendriticLength
printf("\tFrequency: %g Inward mean attenuation: %g\n", freq, sum_norm)
}
soma.sec {
diam = real_diam
L = real_L
}
}
/* meanOutwardAttenuationAllFrequencies: calculates the mean outward attenuation
* over a range of frequencies from 0 to 500, for the specified neuron.
* Arguments:
* $o1: soma -> A SectionRef referring to the neuron's soma
*
* For outward attenuation, voltage clamp (imp.ratio) is at the soma, and
* measurement (imp.loc) ranges over the tree.
*/
proc meanOutwardAttenuationAllFrequencies() { local freq, i, spine_type, real_diam, real_L, ratio localobj path, soma, tree_root
soma = $o1
//tree_root = $o2 // cmw 8/26/11: doesn't seem to do anything
soma.sec {
nseg = 1
real_diam = diam(0.5)
real_L = L
diam = 2.0 * STD_SOMA
L = 2.0 * STD_SOMA
}
for (freq = 0; freq <= 500; freq += 100) {
access soma.sec
v_init = E_PAS
finitialize(v_init)
imp = new Impedance() // if no arg then this creates one
vec = new Vector ()
dendriticLength = 0
forsec "dend" {
for(x) {
segmentLength = area(x)/(diam(x) * PI) // area = l * pi * d
dendriticLength=dendriticLength + segmentLength
imp.loc(x)
imp.compute(freq)
soma.sec ratio = imp.ratio(0.5)
if (ratio > 0) {
scaledLogA = log(1/ratio) * segmentLength
vec.append(scaledLogA)
} else {
print "Warning: negative voltage ratio"
}
}
}
sum_norm = vec.sum()/dendriticLength
printf("\tFrequency: %g Outward mean attenuation: %g\n", freq, sum_norm)
}
soma.sec {
diam = real_diam
L = real_L
}
}
/********* same functions as above, except you can just send a SectionList to specify which dendrites
to evaluate
*********/
/* meanInAttenAllFreq_SecList: calculates the mean inward attenuation over a range of
* frequencies form 0 to 500, over the specified cell.
* Arguments:
* $o1: soma -> A SectionRef referring to the neuron's soma
* For inward attenuation, measurement (imp.loc) is at the soma, and
* voltage clamp (imp.ratio) ranges over the tree.
* $o2 SectionList specifying which branches to sum over
*/
proc meanInAttenAllFreqs_SecList() { local freq, i, spine_type,\
real_diam, real_L, ratio, verbose \
localobj path, soma, tree_root
if( numarg() < 3 ) { verbose = 0 } else { verbose = $3 }
soma = $o1
//tree_root = $o2 // cmw 8/26/11: doesn't seem to do anything
access soma.sec
nseg = 1
real_diam = diam(0.5)
real_L = L
diam = 2.0 * STD_SOMA
L = 2.0 * STD_SOMA
for (freq = 0; freq <= 500; freq += 100) {
v_init = E_PAS
finitialize(v_init)
imp = new Impedance() // if no arg then this creates one
soma.sec imp.loc(0.5)
vec = new Vector()
dendriticLength = 0
forsec $o2 { // cmw 8/28/11: this line is the only change.
for (x) {
segmentLength = area(x) / (diam(x) * PI) // area = l*pi*d
if (0 != segmentLength) {
imp.compute(freq)
ratio = imp.ratio(x)
if (ratio > 0) {
logA = log(1 / ratio)
dendriticLength = dendriticLength + segmentLength
scaledLogA = logA * segmentLength
vec.append(scaledLogA)
if( verbose && freq == 0 && scaledLogA > 0 ) {
printf("%s\t%g\t%g\t%g\n",secname(),x,distance(x),scaledLogA)
}
} else {
printf("Warning: negative voltage ratio\n")
}
}
}
}
sum_norm = vec.sum() / dendriticLength
printf("\tFrequency: %g Inward mean attenuation: %g\n", freq, sum_norm)
}
soma.sec {
diam = real_diam
L = real_L
}
}
/* meanOutwardAttenuationAllFrequencies: calculates the mean outward attenuation
* over a range of frequencies from 0 to 500, for the specified neuron.
* Arguments:
* $o1: soma -> A SectionRef referring to the neuron's soma
*
* For outward attenuation, voltage clamp (imp.ratio) is at the soma, and
* measurement (imp.loc) ranges over the tree.
*/
proc meanOutAttenAllFreqs_SecList() { local freq, i, spine_type, real_diam, real_L, ratio, verbose localobj path, soma, tree_root
if( numarg() < 3 ) { verbose = 0 } else { verbose = $3 }
soma = $o1
//tree_root = $o2 // cmw 8/26/11: doesn't seem to do anything
soma.sec {
nseg = 1
real_diam = diam(0.5)
real_L = L
diam = 2.0 * STD_SOMA
L = 2.0 * STD_SOMA
}
for (freq = 0; freq <= 500; freq += 100) {
access soma.sec
v_init = E_PAS
finitialize(v_init)
imp = new Impedance() // if no arg then this creates one
vec = new Vector ()
dendriticLength = 0
forsec $o2 { // cmw 8/28/11: this line is the only change.
for(x) {
segmentLength = area(x)/(diam(x) * PI) // area = l * pi * d
dendriticLength=dendriticLength + segmentLength
imp.loc(x)
imp.compute(freq)
soma.sec ratio = imp.ratio(0.5)
if (ratio > 0) {
scaledLogA = log(1/ratio) * segmentLength
vec.append(scaledLogA)
if( verbose && freq == 0 && scaledLogA > 0) {
printf("%s\t%g\t%g\t%g\n",secname(),x,distance(x),scaledLogA)
}
} else {
print "Warning: negative voltage ratio"
}
}
}
sum_norm = vec.sum()/dendriticLength
printf("\tFrequency: %g Outward mean attenuation: %g\n", freq, sum_norm)
}
soma.sec {
diam = real_diam
L = real_L
}
}
/* meanInAtten_SecListWithLoc: calculates the mean inward attenuation at DC for
* specific SectionList/x location pairs.
*
* Arguments:
* $o1: soma -> A SectionRef referring to the neuron's soma
* For inward attenuation, measurement (imp.loc) is at the soma, and
* voltage clamp (imp.ratio) ranges over the tree.
* $o2 SectionList specifying which branches to sum over
* $o3 vector of locations associated with each branch in the SectionList
* $s4 filename
*/
proc meanInAtten_SecListWithLoc() { local freq, i, spine_type,\
real_diam, real_L, ratio, verbose, cnt, xloc \
localobj path, soma, tree_root
verbose = 1
soma = $o1
print "Filename ",$s4
f = new File()
f.wopen($s4)
access soma.sec
nseg = 1
real_diam = diam(0.5)
real_L = L
diam = 2.0 * STD_SOMA
L = 2.0 * STD_SOMA
freq = 0
print "OK 1"
v_init = E_PAS
print v_init
finitialize(v_init)
imp = new Impedance() // if no arg then this creates one
soma.sec imp.loc(0.5)
print "more"
vec = new Vector()
print "stuff"
dendriticLength = 0
cnt = 0
print "OK 2"
forsec $o2 {
printf("Now: %s",secname())
xloc = $o3.x[cnt]
printf("[%g], %d\t",xloc,cnt)
segmentLength = area(xloc) / (diam(xloc) * PI) // area = l*pi*d
if (0 != segmentLength) {
imp.compute(freq)
ratio = imp.ratio(xloc)
if (ratio > 0) {
logA = log(1 / ratio)
dendriticLength = dendriticLength + segmentLength
scaledLogA = logA * segmentLength
vec.append(scaledLogA)
f.printf("%d\t%g\t%g\t%g\t%g\n",cnt,xloc,segmentLength,logA,imp.transfer(xloc))
printf("%g\n",scaledLogA)
} else { f.printf("%d\t%g\t%g\t-1\t%g\n",cnt,xloc,segmentLength,logA,imp.transfer(xloc)) }
} else { f.printf("%d\t%g\t%g\t-1\t-1\n",cnt,xloc,segmentLength) }
cnt += 1
}
soma.sec {
diam = real_diam
L = real_L
}
f.close
}
/************** end cmw modification of MeasureMeanAtten files **************/
/*
flag_spines=1 // Spine correction
apic=1 // Apical tree
meanInwardAttenuationAllFrequencies()
meanOutwardAttenuationAllFrequencies()
flag_spines=1 // Spine correction
apic=2 // Basal tree
meanInwardAttenuationAllFrequencies()
meanOutwardAttenuationAllFrequencies()
flag_spines=2 // No spine correction
apic=1 // Apical tree
meanInwardAttenuationAllFrequencies()
meanOutwardAttenuationAllFrequencies()
flag_spines=2 // No spine correction
apic=2 // Basal tree
meanInwardAttenuationAllFrequencies()
meanOutwardAttenuationAllFrequencies()
*/
