def summarise_all(cls):
from morphforge.stdimports import PostSynapticTemplateLibrary, CellLibrary, ChannelLibrary, MorphologyLibrary
types = mrd.SectionNewPage(
"Available class types",
cls.summarise_channeltypes(),
cls.summarise_currentclamptypes(),
cls.summarise_voltageclamptypes(),
cls.summarise_presynaptictriggertypes(),
cls.summarise_postsynaptictemplatetypes(),
cls.summarise_tracemethods(),
)
libraries = mrd.SectionNewPage(
"Library Contents",
ChannelLibrary.summary_table(),
MorphologyLibrary.summary_table(),
PostSynapticTemplateLibrary.summary_table(),
CellLibrary.summary_table(),
)
return mrd.SectionNewPage("Morphforge Configuration", types, libraries)
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# ----------------------------------------------------------------------
""" Summarise the cells and channels that are registered to an environment
"""
import mredoc
from morphforge.stdimports import PluginMgr, CellLibrary, ChannelLibrary, MorphologyLibrary
import morphforgecontrib.stdimports as mfc
from modelling import *
fname = '~/Desktop/morphforge_channels.pdf'
mredoc.Section('Summary',
CellLibrary.summary_table(),
ChannelLibrary.summary_table(),
MorphologyLibrary.summary_table(),
).to_pdf(fname)
print 'Cell & Channel summary stored at: %s'%fname
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# ----------------------------------------------------------------------
import os
from morphforge.stdimports import ChannelLibrary, LocMgr
from morphforgecontrib.stdimports import NeuroML_Via_NeuroUnits_Channel
xsl_filename = os.path.join(LocMgr.get_test_srcs_path(), "neuroml/channelml/ChannelML_v1.8.1_NEURONmod.xsl")
def apply_hh_chls_neuroml_neurounits_na(env):
return env.Channel(NeuroML_Via_NeuroUnits_Channel,
xml_filename = os.path.join(LocMgr.get_test_srcs_path(), "neuroml/channelml/NaChannel_HH.xml"),
)
def apply_hh_chls_neuroml_neurounits_k(env):
return env.Channel(NeuroML_Via_NeuroUnits_Channel,
xml_filename = os.path.join(LocMgr.get_test_srcs_path(), "neuroml/channelml/KChannel_HH.xml"),
)
ChannelLibrary.register_channel(modelsrc="_test_neuroml_via_neurounits_HH52", channeltype='Na', chl_functor=apply_hh_chls_neuroml_neurounits_na)
ChannelLibrary.register_channel(modelsrc="_test_neuroml_via_neurounits_HH52", channeltype='K', chl_functor=apply_hh_chls_neuroml_neurounits_k)
@cached_functor
def get_hh_na(env):
return env.Channel(
NeuroUnitEqnsetMechanism,
name="_neurounits_hh_na",
eqnset=eqnset_txt_na,
default_parameters={"g":qty("120:mS/cm2")}
)
@cached_functor
def get_hh_k(env):
return env.Channel(
NeuroUnitEqnsetMechanism,
name="_neurounits_hh_k",
eqnset=eqnset_txt_k,
)
@cached_functor
def get_hh_lk(env):
return env.Channel(
NeuroUnitEqnsetMechanism,
name="_neurounits_hh_lk",
eqnset=eqnset_txt_lk,
)
ChannelLibrary.register_channel(modelsrc="_test_neurounits_HH52", channeltype='Na', chl_functor=get_hh_na)
ChannelLibrary.register_channel(modelsrc="_test_neurounits_HH52", channeltype='K', chl_functor=get_hh_k)
ChannelLibrary.register_channel(modelsrc="_test_neurounits_HH52", channeltype='Lk', chl_functor=get_hh_lk)