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 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'
def _write_to_file(self, bundlefilename=None):
bundleloc = LocMgr.get_simulation_tmp_dir()
bundlesuffix = '.bundle'
if bundlefilename is None:
bundle_dir = bundleloc + '/' + self.get_sim_md5sum()[0:2] + '/'
bundle_dir = LocMgr.ensure_dir_exists(bundle_dir)
bundle_fname = self.get_sim_md5sum() + bundlesuffix
bundlefilename = os.path.join(bundle_dir, bundle_fname)
FileIO.write_to_file(txt=cPickle.dumps(self), filename=bundlefilename)
# print 'bundlefilename', bundlefilename
return bundlefilename
def prepare_sim_bundle(cls, sim):
simstring = cPickle.dumps(sim)
simmd5sum = StrUtils.get_hash_md5(simstring)
simloc = LocMgr.get_simulation_tmp_dir() + simmd5sum[0:2]
simloc = LocMgr.ensure_dir_exists(simloc)
simfilename = Join(simloc, simmd5sum + cls.simsuffix)
FileIO.write_to_file(txt=simstring, filename=simfilename)
bundle = SimMetaDataBundle(sim)
return bundle
def prepare_sim_bundle(cls, sim):
simstring = cPickle.dumps(sim)
simmd5sum = StrUtils.get_hash_md5(simstring)
simloc = LocMgr.get_simulation_tmp_dir() + simmd5sum[0:2]
simloc = LocMgr.ensure_dir_exists(simloc)
simfilename = Join(simloc, simmd5sum + cls.simsuffix)
FileIO.write_to_file(txt=simstring, filename=simfilename)
bundle = SimMetaDataBundle(sim)
return bundle
def _write_to_file(self, bundlefilename=None):
bundleloc = LocMgr.get_simulation_tmp_dir()
bundlesuffix = '.bundle'
if bundlefilename is None:
bundle_dir = bundleloc + '/' + self.get_sim_md5sum()[0:2] + '/'
bundle_dir = LocMgr.ensure_dir_exists(bundle_dir)
bundle_fname = self.get_sim_md5sum() + bundlesuffix
bundlefilename = os.path.join(bundle_dir, bundle_fname)
FileIO.write_to_file(txt=cPickle.dumps(self),
filename=bundlefilename)
# print 'bundlefilename', bundlefilename
return bundlefilename
def _trace_from_string(cls, srcstr):
parser = ply.yacc.yacc(tabmodule='tracestring_parsetab',
outputdir=LocMgr.ensure_dir_exists('/tmp/parsetabs/'),
debug=SettingsMgr.get_ply_yacc_debug_flag())
(unit, trace_prototypes) = parser.parse(srcstr, lexer=l)
# Copy accross the start values:
start_value = 0
for prototype in trace_prototypes:
prototype.start_value = start_value
piece = prototype.toTracePiece()
start_value = piece.get_end_value()
# Convert to pieces
pieces = [trace_prototype.toTracePiece() for trace_prototype in trace_prototypes]
trace = TracePiecewise(pieces=pieces, comment='Src: %s' % srcstr)
trace = trace * (1.0 * unit)
return trace
def _trace_from_string(cls, srcstr):
parser = ply.yacc.yacc(
tabmodule='tracestring_parsetab',
outputdir=LocMgr.ensure_dir_exists('/tmp/parsetabs/'),
debug=SettingsMgr.get_ply_yacc_debug_flag())
(unit, trace_prototypes) = parser.parse(srcstr, lexer=l)
# Copy accross the start values:
start_value = 0
for prototype in trace_prototypes:
prototype.start_value = start_value
piece = prototype.toTracePiece()
start_value = piece.get_end_value()
# Convert to pieces
pieces = [
trace_prototype.toTracePiece()
for trace_prototype in trace_prototypes
]
trace = TracePiecewise(pieces=pieces, comment='Src: %s' % srcstr)
trace = trace * (1.0 * unit)
return trace
def compareNeuroMLChl(xmlFile):
model, chl_type = os.path.splitext(xmlFile)[0].split("/")[-2:]
print model, chl_type
op_dir = LocMgr.ensure_dir_exists(Join(html_output_dir, model, chl_type))
op_html = Join(op_dir, "index.html")
c = ComparisonResult(xmlfile=xmlFile, op_file = op_html, same_chl=True, exception=None)
try:
# Make the NeuroUnits channel:
chl_neuro = NeuroML_Via_NeuroUnits_ChannelNEURON(xml_filename=xmlFile, )
c.chl_neurounits = chl_neuro
op_pdf_file = Join(op_dir, 'Op1.pdf')
#WriteToPDF(eqnset = chl_neuro.eqnset, filename = op_pdf_file)
c.chl_neurounits_pdf = op_pdf_file
# Make the NeuroML channel:
xsl_file = "/home/michael/srcs/neuroml/CommandLineUtils/ChannelMLConverter/ChannelML_v1.8.1_NEURONmod.xsl"
chl_xsl = NeuroML_Via_XSL_ChannelNEURON(xml_filename=xmlFile, xsl_filename=xsl_file, )
c.chl_xsl = chl_xsl
c.chl_xsl_hoc = []
chl_neuro_res = simulate_chl_all(chl_neuro)
chl_xsl_res = simulate_chl_all(chl_xsl)
c.chl_neurounit_hoc = []
for i, (rN, rX) in enumerate(zip(chl_neuro_res, chl_xsl_res)):
c.chl_neurounit_hoc.append(rN.hocfilename )
c.chl_xsl_hoc.append(rX.hocfilename )
tN = rN.get_trace("CurrentClamp").convert_to_fixed(dt=unit("1.01:ms"))
tX = rX.get_trace("CurrentClamp").convert_to_fixed(dt=unit("1.01:ms"))
# Compare current traces:
tN._data[np.fabs(tN.time_pts_ms - 0) <0.05] *=0
tX._data[np.fabs(tX.time_pts_ms - 0) <0.05] *=0
tN._data[np.fabs(tN.time_pts_ms - 200) <0.05] *=0
tX._data[np.fabs(tX.time_pts_ms - 200) <0.05] *=0
tN._data[np.fabs(tN.time_pts_ms - 700) <0.05] *=0
tX._data[np.fabs(tX.time_pts_ms - 700) <0.05] *=0
print "TR1"
f = QuantitiesFigure()
ax1 = f.add_subplot(4, 1, 1)
ax2 = f.add_subplot(4, 1, 2)
ax3 = f.add_subplot(4, 1, 3)
ax4 = f.add_subplot(4, 1, 4)
ax1.plotTrace(tN, color='b')
ax1.plotTrace(tX, color='g', linewidth=20, alpha=0.2)
ax2.plotTrace(tN.window((200, 250)*pq.ms), color='b')
ax2.plotTrace(tX.window((200, 250)*pq.ms), color='g', linewidth=20, alpha=0.2)
num = (tN-tX)
denom = (tN+tX)
diff = num/denom
ax3.plotTrace(diff, color='r')
ax4.plotTrace(rN.get_trace('SomaVoltage'), color='m')
ax4.plotTrace(rX.get_trace('SomaVoltage'), color='m', linewidth=20, alpha=0.2)
if num.max()[1] > unit("0.1:pA"):
c.same_chl = False
out_im = Join(op_dir, "out_im%03d" % i)
pylab.savefig(out_im+".png")
pylab.savefig(out_im+".pdf")
c.output_image_files.append(out_im)
pylab.close()
c.finished_ok=True
except NeuroUnitsImportNeuroMLNotImplementedException, e:
print 'Exception caught:', e
s = StringIO.StringIO()
traceback.print_exc(file=s)
c.exception_long=s.getvalue()
c.exception="%s (%s)"%(str(e), str(type(e)))
c.same_chl = False
c.finished_ok=False
def buildsectionsurface(cls, s):
import gts
from morphforge.core import LocMgr
from os.path import join as Join
print 'Building Mesh'
working_dir = LocMgr.ensure_dir_exists('/tmp/mf/mesh/')
fTemp1 = Join(working_dir, 'pts.txt')
fTemp2 = Join(working_dir, 'pts.off')
fTemp3 = Join(working_dir, 'pts.stl')
fTemp2b = Join(working_dir, 'pts_postSub.off')
fTemp4 = Join(working_dir, 'pts.gts')
nstep = 5
print 'Building Spheres'
distal_offset = np.array((0.05, 0.05, 0.05))
ptsP = GeomTools.produce_sphere(centre=s.get_proximal_npa3(),
radius=s.p_r, n_steps=nstep)
ptsD = GeomTools.produce_sphere(centre=s.get_distal_npa3()
+ distal_offset, radius=s.d_r, n_steps=nstep)
print 'Removing Close Points'
pts = cls.only_pts_at_min_dist(ptsP + ptsD, min_dist=0.01)
print 'Writing:', fTemp2
with open(fTemp1, 'w') as f:
f.write('3 %d\n' % len(pts))
np.savetxt(f, np.array(pts))
if os.path.exists(fTemp2):
os.unlink(fTemp2)
os.system('qhull T1 QJ o < %s > %s' % (fTemp1, fTemp2))
# Don't do the subdivision, just copy the files:
os.system('cp %s %s' % (fTemp2, fTemp2b))
# fTemp2 = fTemp2b
f = open(fTemp2b).read().split()
(nVertex, nFace, nEdge) = [int(i) for i in f[1:4]]
assert nVertex > 5
vertices = np.array([float(t) for t in f[4:4 + nVertex
* 3]]).reshape(nVertex, 3)
triangles = np.array([int(t) for t in f[4 + nVertex * 3:]])
triangles = triangles.reshape((nFace, 4))
triangles = triangles[:, (1, 2, 3)]
print 'Writing STL'
with open(fTemp3, 'w') as fSTL:
fSTL.write('solid name\n')
for i in range(triangles.shape[0]):
(a, b, c) = triangles[i, :]
fSTL.write('facet normal 0 0 0\n')
fSTL.write('outer loop \n')
fSTL.write('vertex %f %f %f\n' % (vertices[a, 0], vertices[a, 1], vertices[a, 2]))
fSTL.write('vertex %f %f %f\n' % (vertices[b, 0], vertices[b, 1], vertices[b, 2]))
fSTL.write('vertex %f %f %f\n' % (vertices[c, 0], vertices[c, 1], vertices[c, 2]))
fSTL.write('endloop \n')
fSTL.write('endfacet\n')
fSTL.write('solid end')
print 'Running stl2gts...'
if os.path.exists(fTemp4):
os.unlink(fTemp4)
os.system('stl2gts < %s > %s' % (fTemp3, fTemp4))
assert os.path.exists(fTemp4)
import gts
f = open(fTemp4)
s = gts.Surface()
s = gts.read(f)
s.cleanup()
assert s.is_closed()
assert s.is_orientable()
# s.tessellate()
return s
def buildsectionsurface(cls, s):
import gts
from morphforge.core import LocMgr
from os.path import join as Join
print 'Building Mesh'
working_dir = LocMgr.ensure_dir_exists('/tmp/mf/mesh/')
fTemp1 = Join(working_dir, 'pts.txt')
fTemp2 = Join(working_dir, 'pts.off')
fTemp3 = Join(working_dir, 'pts.stl')
fTemp2b = Join(working_dir, 'pts_postSub.off')
fTemp4 = Join(working_dir, 'pts.gts')
nstep = 5
print 'Building Spheres'
distal_offset = np.array((0.05, 0.05, 0.05))
ptsP = GeomTools.produce_sphere(centre=s.get_proximal_npa3(),
radius=s.p_r,
n_steps=nstep)
ptsD = GeomTools.produce_sphere(centre=s.get_distal_npa3() +
distal_offset,
radius=s.d_r,
n_steps=nstep)
print 'Removing Close Points'
pts = cls.only_pts_at_min_dist(ptsP + ptsD, min_dist=0.01)
print 'Writing:', fTemp2
with open(fTemp1, 'w') as f:
f.write('3 %d\n' % len(pts))
np.savetxt(f, np.array(pts))
if os.path.exists(fTemp2):
os.unlink(fTemp2)
os.system('qhull T1 QJ o < %s > %s' % (fTemp1, fTemp2))
# Don't do the subdivision, just copy the files:
os.system('cp %s %s' % (fTemp2, fTemp2b))
# fTemp2 = fTemp2b
f = open(fTemp2b).read().split()
(nVertex, nFace, nEdge) = [int(i) for i in f[1:4]]
assert nVertex > 5
vertices = np.array([float(t) for t in f[4:4 + nVertex * 3]
]).reshape(nVertex, 3)
triangles = np.array([int(t) for t in f[4 + nVertex * 3:]])
triangles = triangles.reshape((nFace, 4))
triangles = triangles[:, (1, 2, 3)]
print 'Writing STL'
with open(fTemp3, 'w') as fSTL:
fSTL.write('solid name\n')
for i in range(triangles.shape[0]):
(a, b, c) = triangles[i, :]
fSTL.write('facet normal 0 0 0\n')
fSTL.write('outer loop \n')
fSTL.write('vertex %f %f %f\n' %
(vertices[a, 0], vertices[a, 1], vertices[a, 2]))
fSTL.write('vertex %f %f %f\n' %
(vertices[b, 0], vertices[b, 1], vertices[b, 2]))
fSTL.write('vertex %f %f %f\n' %
(vertices[c, 0], vertices[c, 1], vertices[c, 2]))
fSTL.write('endloop \n')
fSTL.write('endfacet\n')
fSTL.write('solid end')
print 'Running stl2gts...'
if os.path.exists(fTemp4):
os.unlink(fTemp4)
os.system('stl2gts < %s > %s' % (fTemp3, fTemp4))
assert os.path.exists(fTemp4)
import gts
f = open(fTemp4)
s = gts.Surface()
s = gts.read(f)
s.cleanup()
assert s.is_closed()
assert s.is_orientable()
# s.tessellate()
return s
