def load_neuroml():
redocs = []
for i, xmlfile in enumerate(
NeuroMLDataLibrary.get_channelMLV1FilesWithSingleChannel()):
try:
print "XMLFILE:", xmlfile
eqnset, chl_info, default_filename = ChannelMLReader.BuildEqnset(
xmlfile)
# Build the pdf for the channel:
eqnset_redoc = MRedocWriterVisitor.build(eqnset)
#Build the NModl for the channel:
txt, buildparameters = nmodl.WriteToNMODL(eqnset)
section = SectionNewPage(
"Import from: %s" % "/".join(xmlfile.split('/')[-3:]),
Section("Original XML:", VerbatimBlock(open(xmlfile).read())),
eqnset_redoc, Section("Generated Modfile", VerbatimBlock(txt)))
redocs.append(section)
except NeuroUnitsImportNeuroMLNotImplementedException, e:
pass
if i > 1:
break
def main():
# Clear out the old directory:
if os.path.exists(html_output_dir):
shutil.rmtree(html_output_dir)
LocMgr.ensure_dir_exists(html_output_dir)
root_html = Join(html_output_dir, "index.html")
data = []
for xmlfile in NeuroMLDataLibrary.get_channelMLV1FilesWithSingleChannel():
#class NeuroMLDataLibrary(object):
#
# def get_channelMLV1Files(self):
#if xmlfile != "/home/michael/hw_to_come/morphforge/src/test_data/NeuroML/V1/example_simulations/GranCellLayer_NeuroML/Golgi_NaF_CML.xml":
# continue
#if xmlfile != "/home/michael/hw_to_come/morphforge/src/test_data/NeuroML/V1/example_simulations/MainenEtAl_PyramidalCell_NeuroML/K_ChannelML.xml":
# continue
#if xmlfile != "/home/michael/hw_to_come/morphforge/src/test_data/NeuroML/V1/example_simulations/CA1PyramidalCell_NeuroML/kdr.xml":
# continue
# Compare:
data.append(compareNeuroMLChl(xmlfile))
# Re-update the html:
with open(root_html, "w") as f:
f.write(Template(root_html_tmpl, {'data': data}).respond())
def load_neuroml():
redocs = []
for i, xmlfile in enumerate(NeuroMLDataLibrary.get_channelMLV1FilesWithSingleChannel()):
try:
print "XMLFILE:", xmlfile
eqnset, chl_info, default_filename = ChannelMLReader.BuildEqnset(xmlfile)
# Build the pdf for the channel:
eqnset_redoc = MRedocWriterVisitor.build(eqnset)
# Build the NModl for the channel:
txt, buildparameters = nmodl.WriteToNMODL(eqnset)
section = SectionNewPage(
"Import from: %s" % "/".join(xmlfile.split("/")[-3:]),
Section("Original XML:", VerbatimBlock(open(xmlfile).read())),
eqnset_redoc,
Section("Generated Modfile", VerbatimBlock(txt)),
)
redocs.append(section)
except NeuroUnitsImportNeuroMLNotImplementedException, e:
pass
if i > 1:
break
def main():
# Clear out the old directory:
if os.path.exists(html_output_dir):
shutil.rmtree(html_output_dir)
LocMgr.ensure_dir_exists(html_output_dir)
root_html = Join(html_output_dir, "index.html")
data = []
for xmlfile in NeuroMLDataLibrary.get_channelMLV1FilesWithSingleChannel():
# Compare:
data.append(compareNeuroMLChl(xmlfile))
# Re-update the html:
with open(root_html, "w") as f:
f.write(Template(root_html_tmpl, {'data': data}).respond())
#break
print 'Done'
from neurounits.writers.writer_ast_to_mredoc import MRedocWriterVisitor
from neurounits.tools import nmodl
from util_test_locations import TestLocations
from os.path import join as Join
def load_neuroml():
from mredoc.objects.core import Document, TableOfContents, SectionNewPage, Section, VerbatimBlock
redocs = []
for (i, xmlfile) in enumerate(NeuroMLDataLibrary.get_channelMLV1FilesWithSingleChannel()):
try:
print 'XMLFILE:', xmlfile
(eqnset, chl_info, default_filename) = ChannelMLReader.BuildEqnset(xmlfile)
# Build the pdf for the channel:
eqnset_redoc = MRedocWriterVisitor.build(eqnset)
# Build the NModl for the channel:
(txt, buildparameters) = nmodl.WriteToNMODL(eqnset)
section = SectionNewPage("Import from: %s"% "/".join(xmlfile.split('/')[-3:]),
Section("Original XML:", VerbatimBlock(open(xmlfile).read() ) ),
eqnset_redoc,
Section("Generated Modfile",VerbatimBlock(txt) ) )
i=0
ok = []
fail1 = []
fail2 = []
fail3 = []
for xmlfile in NeuroMLDataLibrary.get_channelMLV1FilesWithSingleChannel():
#print i, xmlfile
if xmlfile in [
# has a suffix: pas, which neuron chokes on:
"/home/michael/hw/morphforge/src/test_data/NeuroML/V1/example_simulations/CA1PyramidalCell_NeuroML/pas.xml",
"/home/michael/hw/morphforge/src/test_data/NeuroML/V1/example_simulations/Thalamocortical_NeuroML/pas.xml",
# Choked on build for some reason:
"/home/michael/hw/morphforge/src/test_data/NeuroML/V1/example_simulations/SolinasEtAl_GolgiCell_NeuroML/KAHP_CML.xml",
"/home/michael/hw/morphforge/src/test_data/NeuroML/V1/example_simulations/VervaekeEtAl-GolgiCellNetwork_NeuroML/KAHP_CML.xml",
"/home/michael/hw/morphforge/src/test_data/NeuroML/V1/example_simulations/CA1PyramidalCell_NeuroML/na3.xml",
"/home/michael/hw/morphforge/src/test_data/NeuroML/V1/example_simulations/Thalamocortical_NeuroML/ar.xml",
simtype="_NeuroUnit")
return {
SimMode.XSL: resA,
SimMode.NeuroUnit: resB,
}
i = 0
ok = []
fail1 = []
fail2 = []
fail3 = []
for xmlfile in NeuroMLDataLibrary.get_channelMLV1FilesWithSingleChannel():
#print i, xmlfile
if xmlfile in [
# has a suffix: pas, which neuron chokes on:
"/home/michael/hw/morphforge/src/test_data/NeuroML/V1/example_simulations/CA1PyramidalCell_NeuroML/pas.xml",
"/home/michael/hw/morphforge/src/test_data/NeuroML/V1/example_simulations/Thalamocortical_NeuroML/pas.xml",
# Choked on build for some reason:
"/home/michael/hw/morphforge/src/test_data/NeuroML/V1/example_simulations/SolinasEtAl_GolgiCell_NeuroML/KAHP_CML.xml",
"/home/michael/hw/morphforge/src/test_data/NeuroML/V1/example_simulations/VervaekeEtAl-GolgiCellNetwork_NeuroML/KAHP_CML.xml",
"/home/michael/hw/morphforge/src/test_data/NeuroML/V1/example_simulations/CA1PyramidalCell_NeuroML/na3.xml",
"/home/michael/hw/morphforge/src/test_data/NeuroML/V1/example_simulations/Thalamocortical_NeuroML/ar.xml",
# Funny alpha term that I don't get:
"/home/michael/hw/morphforge/src/test_data/NeuroML/V1/example_simulations/Thalamocortical_NeuroML/kc_fast.xml",
"/home/michael/hw/morphforge/src/test_data/NeuroML/V1/example_simulations/Thalamocortical_NeuroML/kc.xml",