def to_report_lab(cls, alphabeta_chl, reportlabconfig, make_graphs):
from reportlab.platypus import Paragraph, Table
local_elements = []
local_elements.append(Paragraph("Overview", reportlabconfig.styles['Heading3']))
# Summary:
overview_table_data = [
["Max Conductance (gBar)", alphabeta_chl.conductance.rescale("mS/cm2")],
["Reversal Potential", alphabeta_chl.reversalpotential.rescale("mV")],
["Conductance Equation", "gBar * " + alphabeta_chl.eqn],
]
local_elements.append(Table(overview_table_data, style=reportlabconfig.listTableStyle))
# Plot out the States:
for state, params in alphabeta_chl.statevars.iteritems():
local_elements.append(Paragraph("State: %s" % state, reportlabconfig.styles['Heading3']))
#Equations:
eqns = [
"alpha(V) = (A+BV)/(C+exp((V+D)/E))",
"beta(V) = (A+BV)/(C+exp((V+D)/E))",
]
for eqn in eqns:
local_elements.append(Paragraph(eqn, reportlabconfig.styles['Normal']))
# Alpha Beta
ReportLabTools.build_alpha_beta_table(elements=local_elements,
reportlabconfig=reportlabconfig,
title="Alpha", params=params[0])
ReportLabTools.build_alpha_beta_table(elements=local_elements,
reportlabconfig=reportlabconfig,
title="Beta1", params=params[1])
if make_graphs:
# Figures:
fig = cls.plot_state_curve_summary(alphabeta_chl, state, figsize=(5, 5))
local_elements.append(reportlabconfig.save_mpl_to_rl_image(fig, "somestate"))
import pylab
pylab.close(fig.fig)
return local_elements
def to_report_lab(cls, calciumAlphaBetaBetaChannel, reportlabconfig, make_graphs):
chl = calciumAlphaBetaBetaChannel
localElements = []
localElements.append(Paragraph("Overview", reportlabconfig.styles['Heading3']))
# Summary:
overviewTableData = [
["permeability", chl.permeability],
["intracellular_concentration", chl.intracellular_concentration],
["extracellular_concentration", chl.extracellular_concentration],
["Equation EXPLAIN", chl.eqn],
["beta2threshold", chl.beta2threshold],
["Temperature ", chl.T],
["F", chl.F],
["R", chl.R],
["CaZ", chl.CaZ],
]
localElements.append(Table(overviewTableData, style=reportlabconfig.listTableStyle))
#GHK Max Current Flow
localElements.append(Paragraph("MaxCurrentFlow From GHK", reportlabconfig.styles['Heading3']))
fig = cls.PlotGHKMaxCurrentFlow(calciumAlphaBetaBetaChannel, figsize=(4, 4))
localElements.append(reportlabconfig.save_mpl_to_rl_image(fig, "ghk"))
# Plot out the States:
for state, params in calciumAlphaBetaBetaChannel.statevars.iteritems():
localElements.append(Paragraph("State: %s" % state, reportlabconfig.styles['Heading3']))
if make_graphs:
fig = cls.plot_state_curve_summary(chl, state, figsize=(5, 5))
localElements.append(reportlabconfig.save_mpl_to_rl_image(fig, "somestate"))
fig.close()
#Equations:
eqns = [
"beta2Threshold = %s" % calciumAlphaBetaBetaChannel.beta2threshold,
"beta = beta1 if V less than beta2Threshold otherwise beta2",
"alpha(V) = (A+BV)/(C+exp((V+D)/E))",
"beta(V) = (A+BV)/(C+exp((V+D)/E))",
]
for eqn in eqns:
localElements.append(Paragraph(eqn, reportlabconfig.styles['Normal']))
# Alpha Beta
ReportLabTools.build_alpha_beta_table(elements=localElements,
reportlabconfig=reportlabconfig,
title="Alpha", params=params[0])
ReportLabTools.build_alpha_beta_table(elements=localElements,
reportlabconfig=reportlabconfig,
title="Beta1", params=params[1])
ReportLabTools.build_alpha_beta_table(elements=localElements,
reportlabconfig=reportlabconfig,
title="Beta2", params=params[2])
return localElements
def to_report_lab(cls, alphabeta_beta_chl, reportlabconfig, make_graphs):
from reportlab.platypus import Paragraph, Table
local_elements = []
local_elements.append(Paragraph("Overview", reportlabconfig.styles['Heading3']))
# Summary:
overview_table_data = [
["Channel Type", "AlphaBetaBetaChl"],
["Max Conductance (gBar)", alphabeta_beta_chl.conductance],
["Reversal Potential", alphabeta_beta_chl.reversalpotential],
["Conductance Equation", "gBar * " + alphabeta_beta_chl.eqn],
]
local_elements.append(Table(overview_table_data, style=reportlabconfig.listTableStyle))
# Plot out the States:
for state, params in alphabeta_beta_chl.statevars.iteritems():
local_elements.append(Paragraph("State: %s" % state, reportlabconfig.styles['Heading3']))
if make_graphs:
fig = Summarise_MM_AlphaBetaChannel.plot_state_curve_summary(alphabeta_beta_chl, state, figsize=(5, 5))
local_elements.append(reportlabconfig.save_mpl_to_rl_image(fig, "somestate"))
local_elements.append(Paragraph("Equations", reportlabconfig.styles['Heading4']))
#Equations:
eqns = [
"beta2Threshold = %s" % alphabeta_beta_chl.beta2threshold,
"beta = beta1 if V less than beta2Threshold otherwise beta2",
"alpha(V) = (A+BV)/(C+exp((V+D)/E))",
"beta(V) = (A+BV)/(C+exp((V+D)/E))",
]
for eqn in eqns:
local_elements.append(Paragraph(eqn, reportlabconfig.styles['Normal']))
# Alpha Beta
ReportLabTools.build_alpha_beta_table(elements=local_elements,
reportlabconfig=reportlabconfig,
title="Alpha", params=params[0])
ReportLabTools.build_alpha_beta_table(elements=local_elements,
reportlabconfig=reportlabconfig,
title="Beta1", params=params[1])
ReportLabTools.build_alpha_beta_table(elements=local_elements,
reportlabconfig=reportlabconfig,
title="Beta2", params=params[2])
return local_elements
def toReportLab(cls, alphaBetaBetaChl, reportlabconfig, make_graphs):
from reportlab.platypus import Paragraph, Table
localElements = []
localElements.append( Paragraph("Overview",reportlabconfig.styles['Heading3']) )
# Summary:
overviewTableData = [
["Channel Type", "AlphaBetaBetaChl"],
["Max Conductance (gBar)", alphaBetaBetaChl.conductance],
["Reversal Potential", alphaBetaBetaChl.reversalpotential],
["Conductance Equation", "gBar * " + alphaBetaBetaChl.eqn],
]
localElements.append( Table(overviewTableData, style=reportlabconfig.listTableStyle) )
# Plot out the States:
for state,params in alphaBetaBetaChl.statevars.iteritems():
localElements.append( Paragraph("State: %s"%state,reportlabconfig.styles['Heading3']) )
if make_graphs:
fig = Summarise_MM_AlphaBetaChannel.PlotStateCurveSummary(alphaBetaBetaChl, state, figsize=(5,5))
localElements.append( reportlabconfig.saveMPLToRLImage(fig, "somestate") )
localElements.append( Paragraph("Equations",reportlabconfig.styles['Heading4']) )
#Equations:
eqns = [
"beta2Threshold = %s"%alphaBetaBetaChl.beta2threshold,
"beta = beta1 if V less than beta2Threshold otherwise beta2",
"alpha(V) = (A+BV)/(C+exp( (V+D)/E) )",
"beta(V) = (A+BV)/(C+exp( (V+D)/E) )",
]
for eqn in eqns:
localElements.append( Paragraph(eqn,reportlabconfig.styles['Normal']) )
# Alpha Beta
ReportLabTools.buildAlphaBetaTable( elements=localElements,
reportlabconfig=reportlabconfig,
title="Alpha", params=params[0] )
ReportLabTools.buildAlphaBetaTable( elements=localElements,
reportlabconfig=reportlabconfig,
title="Beta1", params=params[1] )
ReportLabTools.buildAlphaBetaTable( elements=localElements,
reportlabconfig=reportlabconfig,
title="Beta2", params=params[2] )
return localElements
def to_report_lab(cls, calciumAlphaBetaBetaChannel, reportlabconfig,
make_graphs):
chl = calciumAlphaBetaBetaChannel
localElements = []
localElements.append(
Paragraph("Overview", reportlabconfig.styles['Heading3']))
# Summary:
overviewTableData = [
["permeability", chl.permeability],
["intracellular_concentration", chl.intracellular_concentration],
["extracellular_concentration", chl.extracellular_concentration],
["Equation EXPLAIN", chl.eqn],
["beta2threshold", chl.beta2threshold],
["Temperature ", chl.T],
["F", chl.F],
["R", chl.R],
["CaZ", chl.CaZ],
]
localElements.append(
Table(overviewTableData, style=reportlabconfig.listTableStyle))
#GHK Max Current Flow
localElements.append(
Paragraph("MaxCurrentFlow From GHK",
reportlabconfig.styles['Heading3']))
fig = cls.PlotGHKMaxCurrentFlow(calciumAlphaBetaBetaChannel,
figsize=(4, 4))
localElements.append(reportlabconfig.save_mpl_to_rl_image(fig, "ghk"))
# Plot out the States:
for state, params in calciumAlphaBetaBetaChannel.statevars.iteritems():
localElements.append(
Paragraph("State: %s" % state,
reportlabconfig.styles['Heading3']))
if make_graphs:
fig = cls.plot_state_curve_summary(chl, state, figsize=(5, 5))
localElements.append(
reportlabconfig.save_mpl_to_rl_image(fig, "somestate"))
fig.close()
#Equations:
eqns = [
"beta2Threshold = %s" %
calciumAlphaBetaBetaChannel.beta2threshold,
"beta = beta1 if V less than beta2Threshold otherwise beta2",
"alpha(V) = (A+BV)/(C+exp((V+D)/E))",
"beta(V) = (A+BV)/(C+exp((V+D)/E))",
]
for eqn in eqns:
localElements.append(
Paragraph(eqn, reportlabconfig.styles['Normal']))
# Alpha Beta
ReportLabTools.build_alpha_beta_table(
elements=localElements,
reportlabconfig=reportlabconfig,
title="Alpha",
params=params[0])
ReportLabTools.build_alpha_beta_table(
elements=localElements,
reportlabconfig=reportlabconfig,
title="Beta1",
params=params[1])
ReportLabTools.build_alpha_beta_table(
elements=localElements,
reportlabconfig=reportlabconfig,
title="Beta2",
params=params[2])
return localElements
