From cef0d1d4681c3e38d2b35d69b305f5c724cbb3ba Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Thu, 20 Oct 2022 15:18:15 +0200
Subject: [PATCH] Make decor mandatory and labels optional. (#1978)
* Make decor mandatory and labels optional.
* Sort morphology, decor, labels
* No more optional decor.
---
arbor/cable_cell.cpp | 2 +-
arbor/include/arbor/cable_cell.hpp | 5 +--
arborio/cableio.cpp | 2 +-
doc/concepts/decor.rst | 2 +-
doc/cpp/cable_cell.rst | 23 ++++++++------
doc/cpp/morphology.rst | 5 +--
doc/dev/debug.rst | 2 +-
doc/python/cable_cell.rst | 6 ++--
doc/python/morphology.rst | 3 +-
doc/python/probe_sample.rst | 2 +-
doc/scripts/gen-labels.py | 6 ++--
example/diffusion/diffusion.cpp | 2 +-
example/dryrun/branch_cell.hpp | 2 +-
example/gap_junctions/gap_junctions.cpp | 2 +-
example/generators/generators.cpp | 2 +-
example/lfp/lfp.cpp | 2 +-
example/plasticity/plasticity.cpp | 2 +-
example/probe-demo/probe-demo.cpp | 2 +-
example/ring/branch_cell.hpp | 2 +-
example/single/single.cpp | 2 +-
lmorpho/lmorpho.cpp | 2 +-
python/cells.cpp | 22 ++++++++-----
python/example/diffusion.py | 2 +-
python/example/dynamic-catalogue.py | 2 +-
python/example/gap_junctions.py | 2 +-
python/example/network_ring.py | 2 +-
python/example/network_ring_gpu.py | 2 +-
python/example/network_ring_mpi.py | 2 +-
.../network_two_cells_gap_junctions.py | 2 +-
python/example/plasticity.py | 2 +-
python/example/probe_lfpykit.py | 2 +-
python/example/single_cell_allen.py | 2 +-
python/example/single_cell_cable.py | 2 +-
python/example/single_cell_detailed.py | 2 +-
python/example/single_cell_detailed_recipe.py | 2 +-
python/example/single_cell_model.py | 2 +-
python/example/single_cell_nml.py | 2 +-
python/example/single_cell_recipe.py | 2 +-
python/example/single_cell_stdp.py | 2 +-
python/example/single_cell_swc.py | 2 +-
python/test/fixtures.py | 2 +-
python/test/unit/test_cable_probes.py | 2 +-
python/test/unit/test_catalogues.py | 2 +-
python/test/unit/test_multiple_connections.py | 4 +--
.../test_domain_decompositions.py | 4 +--
test/common_cells.hpp | 2 +-
test/unit-distributed/test_communicator.cpp | 6 ++--
test/unit/test_cable_cell.cpp | 2 +-
test/unit/test_cv_geom.cpp | 22 ++++++-------
test/unit/test_cv_layout.cpp | 10 +++---
test/unit/test_cv_policy.cpp | 31 ++++++++++---------
test/unit/test_diffusion.cpp | 2 +-
test/unit/test_event_delivery.cpp | 2 +-
test/unit/test_fvm_layout.cpp | 10 +++---
test/unit/test_fvm_lowered.cpp | 8 ++---
test/unit/test_probe.cpp | 24 +++++++-------
test/unit/test_recipe.cpp | 4 +--
test/unit/test_sde.cpp | 22 ++++++-------
test/unit/test_spikes.cpp | 2 +-
59 files changed, 152 insertions(+), 145 deletions(-)
diff --git a/arbor/cable_cell.cpp b/arbor/cable_cell.cpp
index 9f6a523f..8b7d0382 100644
--- a/arbor/cable_cell.cpp
+++ b/arbor/cable_cell.cpp
@@ -222,7 +222,7 @@ void cable_cell_impl::init(const decor& d) {
}
}
-cable_cell::cable_cell(const arb::morphology& m, const label_dict& dictionary, const decor& decorations):
+cable_cell::cable_cell(const arb::morphology& m, const decor& decorations, const label_dict& dictionary):
impl_(make_impl(new cable_cell_impl(m, dictionary, decorations)))
{}
diff --git a/arbor/include/arbor/cable_cell.hpp b/arbor/include/arbor/cable_cell.hpp
index 6556deb0..cb0570bc 100644
--- a/arbor/include/arbor/cable_cell.hpp
+++ b/arbor/include/arbor/cable_cell.hpp
@@ -266,10 +266,7 @@ public:
}
/// Construct from morphology, label and decoration descriptions.
- cable_cell(const class morphology&, const label_dict&, const decor&);
- cable_cell(const class morphology& m):
- cable_cell(m, {}, {})
- {}
+ cable_cell(const class morphology& m, const decor& d, const label_dict& l={});
/// Access to labels
const label_dict& labels() const;
diff --git a/arborio/cableio.cpp b/arborio/cableio.cpp
index 103246eb..8be039c6 100644
--- a/arborio/cableio.cpp
+++ b/arborio/cableio.cpp
@@ -352,7 +352,7 @@ cable_cell make_cable_cell(const std::vector<std::variant<morphology, label_dict
[&](const decor & p){ dec = p; });
std::visit(cable_cell_visitor, a);
}
- return cable_cell(morpho, dict, dec);
+ return cable_cell(morpho, dec, dict);
}
version_tuple make_version(const std::string& v) {
return version_tuple{v};
diff --git a/doc/concepts/decor.rst b/doc/concepts/decor.rst
index 62f2690e..d1b7f9fa 100644
--- a/doc/concepts/decor.rst
+++ b/doc/concepts/decor.rst
@@ -265,7 +265,7 @@ ion at the cell level using the Python interface:
# Method 2: set directly using a string description.
decor.set_ion(ion='ca', method='nernst/x=ca')
- cell = arbor.cable_cell(morph, labels, decor)
+ cell = arbor.cable_cell(morph, decor)
The NMODL code for the
diff --git a/doc/cpp/cable_cell.rst b/doc/cpp/cable_cell.rst
index b44e36dc..9013db7d 100644
--- a/doc/cpp/cable_cell.rst
+++ b/doc/cpp/cable_cell.rst
@@ -27,6 +27,8 @@ Properties shared by all cable cells, as returned by the recipe
object of type :cpp:type:`cable_cell_global_properties`.
+
+
The :cpp:type:`cable_cell` object
---------------------------------
@@ -55,14 +57,15 @@ are specified via the ``place`` method. See :ref:`cppcablecell-dynamics`, below.
Cell dynamics
-------------
-Each segment in a cell may have attached to it one or more density *mechanisms*,
-which describe biophysical processes. These are processes
-that are distributed in space, but whose behaviour is defined purely
-by the state of the cell and the process at any given point.
+Dynamics are imbued onto the cell by setting a :cpp:type:`decor` object during
+construction. Each segment in a cell may have attached to it one or more density
+*mechanisms*, which describe biophysical processes. These are processes that are
+distributed in space, but whose behaviour is defined purely by the state of the
+cell and the process at any given point.
-Cells may also have *point* mechanisms, describing the dynamics
-at post-synaptic sites. And *junction* mechanisms, describing the
-dynamics at each site of the two sites of a gap-junction connection.
+Cells may also have *point* mechanisms, describing the dynamics at post-synaptic
+sites. And *junction* mechanisms, describing the dynamics at each site of the
+two sites of a gap-junction connection.
A fourth type of mechanism, which describes ionic reversal potential
behaviour, can be specified for cells or the whole model via cell parameter
@@ -121,14 +124,14 @@ Relevant methods:
Density mechanisms are associated with a cable cell object with:
-.. cpp:function:: void cable_cell::paint(const region&, density)
+.. cpp:function:: void decor::paint(const region&, density)
Point mechanisms, which are associated with connection end points on a
cable cell, are placed on a set of locations given by a locset. The group
of generated items are given a label which can be used to create connections
in the recipe. Point mechanisms are attached to a cell with:
-.. cpp:function:: void cable_cell::place(const locset&, synapse, cell_tag_type label)
+.. cpp:function:: void decor::place(const locset&, synapse, cell_tag_type label)
Gap-junction mechanisms, which are associated with gap-junction connection
end points on a cable cell, are placed on a single location given by a locset
@@ -136,7 +139,7 @@ end points on a cable cell, are placed on a single location given by a locset
is given a label which can be used to create gap-junction connections in the
recipe. Gap-junction mechanisms are attached to a cell with:
-.. cpp:function:: void cable_cell::place(const locset&, junction, cell_tag_type label)
+.. cpp:function:: void decor::place(const locset&, junction, cell_tag_type label)
.. todo::
diff --git a/doc/cpp/morphology.rst b/doc/cpp/morphology.rst
index 9a21ea24..ba0c2473 100644
--- a/doc/cpp/morphology.rst
+++ b/doc/cpp/morphology.rst
@@ -190,9 +190,10 @@ by two stitches:
builder.add({"dend", dend_end, 4}, "soma", 0.5);
stitched_morphology stitched(std::move(builder));
- cable_cell cell(stitched.morphology(), stitched.labels());
- cell.paint("\"soma\"", density("hh"));
+ auto dec = decor{}.paint("\"soma\"", density("hh"));
+
+ cable_cell cell(stitched.morphology(), dec, stitched.labels());
.. _locsets-and-regions:
diff --git a/doc/dev/debug.rst b/doc/dev/debug.rst
index e3ae77e5..a9705c4c 100644
--- a/doc/dev/debug.rst
+++ b/doc/dev/debug.rst
@@ -39,7 +39,7 @@ LLDB.
# [...]
decor = (arbor.decor()
.place('"synapse_site"', arbor.synapse("expsyn"), "syn"))
- return arbor.cable_cell(tree, labels, decor)
+ return arbor.cable_cell(tree, decor, labels)
rec = Recipe() # "Ok"
sim = arb.simulation(rec) # ERROR here
diff --git a/doc/python/cable_cell.rst b/doc/python/cable_cell.rst
index 03603b98..7eb028b6 100644
--- a/doc/python/cable_cell.rst
+++ b/doc/python/cable_cell.rst
@@ -52,14 +52,14 @@ Cable cells
decor.paint('"soma"', arbor.density('hh'))
# Construct a cable cell.
- cell = arbor.cable_cell(morph, labels, decor)
+ cell = arbor.cable_cell(morph, decor, labels)
- .. method:: __init__(morphology, labels, decorations)
+ .. method:: __init__(morphology, decorations, labels)
Constructor.
:param morphology: the morphology of the cell
- :type morphology: :py:class:`morphology`
+ :type morphology: :py:class:`morphology` or :py:class:`segment_tree`
:param labels: dictionary of labeled regions and locsets
:type labels: :py:class:`label_dict`
:param decorations: the decorations on the cell
diff --git a/doc/python/morphology.rst b/doc/python/morphology.rst
index f72fb781..f0ee2045 100644
--- a/doc/python/morphology.rst
+++ b/doc/python/morphology.rst
@@ -761,8 +761,7 @@ Neurolucida
asc = arbor.load_asc('granule.asc')
# Construct a cable cell.
- decor = arbor.decor()
- cell = arbor.cable_cell(asc.morphology, asc.labels, decor)
+ cell = arbor.cable_cell(asc.morphology, arbor.decor(), asc.labels)
:param str filename: the name of the input file.
diff --git a/doc/python/probe_sample.rst b/doc/python/probe_sample.rst
index 3ac24a0c..a6625298 100644
--- a/doc/python/probe_sample.rst
+++ b/doc/python/probe_sample.rst
@@ -79,7 +79,7 @@ Example
.paint('"soma"', arbor.density("hh"))
.place('"midpoint"', arbor.iclamp(10, 2, 0.8), "iclamp"))
- cell = arbor.cable_cell(tree, labels, decor)
+ cell = arbor.cable_cell(tree, decor)
class single_recipe(arbor.recipe):
def __init__(self):
diff --git a/doc/scripts/gen-labels.py b/doc/scripts/gen-labels.py
index 69dd8e36..caab422f 100644
--- a/doc/scripts/gen-labels.py
+++ b/doc/scripts/gen-labels.py
@@ -223,7 +223,7 @@ labels = {**regions, **locsets}
d = arbor.label_dict(labels)
# Create a cell to concretise the region and locset definitions
-cell = arbor.cable_cell(label_morph, d, arbor.decor())
+cell = arbor.cable_cell(label_morph, None, d)
###############################################################################
# Tutorial Example: single_cell_detailed
@@ -263,7 +263,7 @@ tutorial_labels = {**tutorial_regions, **tutorial_locsets}
tutorial_dict = arbor.label_dict(tutorial_labels)
# Create a cell to concretise the region and locset definitions
-tutorial_cell = arbor.cable_cell(tutorial_morph, tutorial_dict, arbor.decor())
+tutorial_cell = arbor.cable_cell(tutorial_morph, None, tutorial_dict)
###############################################################################
# Tutorial Example: network_ring
@@ -298,7 +298,7 @@ tutorial_network_ring_dict = arbor.label_dict(tutorial_network_ring_labels)
# Create a cell to concretise the region and locset definitions
tutorial_network_ring_cell = arbor.cable_cell(
- tutorial_network_ring_morph, tutorial_network_ring_dict, arbor.decor()
+ tutorial_network_ring_morph, None, tutorial_network_ring_dict
)
################################################################################
diff --git a/example/diffusion/diffusion.cpp b/example/diffusion/diffusion.cpp
index 991a351d..6b0bb382 100644
--- a/example/diffusion/diffusion.cpp
+++ b/example/diffusion/diffusion.cpp
@@ -43,7 +43,7 @@ struct linear: public recipe {
decor.set_default(ion_diffusivity{"na", b});
decor.place("(location 0 0.5)"_ls, synapse("inject/x=na", {{"alpha", 200.0*l}}), "Zap");
decor.paint("(all)"_reg, density("decay/x=na"));
- return cable_cell({tree}, {}, decor);
+ return cable_cell({tree}, decor);
}
cable_cell_global_properties gprop;
diff --git a/example/dryrun/branch_cell.hpp b/example/dryrun/branch_cell.hpp
index cf208d6d..6b930d5d 100644
--- a/example/dryrun/branch_cell.hpp
+++ b/example/dryrun/branch_cell.hpp
@@ -121,5 +121,5 @@ arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& param
for (unsigned i=1u; i<params.synapses; ++i) {
decor.place(arb::mlocation{1, 0.5}, arb::synapse("expsyn"), "dummy_synapses");
}
- return arb::cable_cell{arb::morphology(tree), labels, decor};
+ return arb::cable_cell{arb::morphology(tree), decor, labels};
}
diff --git a/example/gap_junctions/gap_junctions.cpp b/example/gap_junctions/gap_junctions.cpp
index 5d5d8c12..937cda15 100644
--- a/example/gap_junctions/gap_junctions.cpp
+++ b/example/gap_junctions/gap_junctions.cpp
@@ -298,7 +298,7 @@ arb::cable_cell gj_cell(cell_gid_type gid, unsigned ncell, double stim_duration)
}
// Create the cell and set its electrical properties.
- return arb::cable_cell(tree, {}, decor);
+ return arb::cable_cell(tree, decor);
}
gap_params read_options(int argc, char** argv) {
diff --git a/example/generators/generators.cpp b/example/generators/generators.cpp
index c0b32d37..6ab8d905 100644
--- a/example/generators/generators.cpp
+++ b/example/generators/generators.cpp
@@ -66,7 +66,7 @@ public:
// event_generators.
.place(arb::mlocation{0, 0.5}, arb::synapse("expsyn"), "syn");
- return arb::cable_cell(tree, labels, decor);
+ return arb::cable_cell(tree, decor, labels);
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
diff --git a/example/lfp/lfp.cpp b/example/lfp/lfp.cpp
index 95ead2c1..96c0f358 100644
--- a/example/lfp/lfp.cpp
+++ b/example/lfp/lfp.cpp
@@ -94,7 +94,7 @@ private:
.paint("(tag 4)"_reg, density("pas/e=-70.0"))
// Add exponential synapse at centre of soma.
.place(synapse_location_, synapse("expsyn", {{"e", 0}, {"tau", 2}}), "syn");
- cell_ = cable_cell(tree, {}, dec);
+ cell_ = cable_cell(tree, dec);
}
};
diff --git a/example/plasticity/plasticity.cpp b/example/plasticity/plasticity.cpp
index 37748caf..d72f24c4 100644
--- a/example/plasticity/plasticity.cpp
+++ b/example/plasticity/plasticity.cpp
@@ -67,7 +67,7 @@ struct recipe: public arb::recipe {
.place(center, arb::synapse("expsyn"), syn)
.place(center, arb::threshold_detector{-10.0}, det)
.set_default(arb::cv_policy_every_segment());
- return arb::cable_cell({tree}, {}, decor);
+ return arb::cable_cell({tree}, decor);
}
};
diff --git a/example/probe-demo/probe-demo.cpp b/example/probe-demo/probe-demo.cpp
index 16bcef34..d7f21181 100644
--- a/example/probe-demo/probe-demo.cpp
+++ b/example/probe-demo/probe-demo.cpp
@@ -125,7 +125,7 @@ struct cable_recipe: public arb::recipe {
.place(arb::mlocation{0, 0.}, arb::i_clamp{1.}, "iclamp") // Inject a 1 nA current indefinitely.
.place(arb::mlocation{0, 0.}, arb::synapse("expsyn"), "synapse1") // a synapse
.place(arb::mlocation{0, 0.5}, arb::synapse("expsyn"), "synapse2"); // another synapse
- return arb::cable_cell(tree, {}, decor);
+ return arb::cable_cell(tree, decor);
}
virtual std::vector<arb::event_generator> event_generators(arb::cell_gid_type) const override {
diff --git a/example/ring/branch_cell.hpp b/example/ring/branch_cell.hpp
index 503827c0..61740a99 100644
--- a/example/ring/branch_cell.hpp
+++ b/example/ring/branch_cell.hpp
@@ -124,7 +124,7 @@ arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& param
// Make a CV between every sample in the sample tree.
decor.set_default(arb::cv_policy_every_segment());
- arb::cable_cell cell(arb::morphology(tree), labels, decor);
+ arb::cable_cell cell(arb::morphology(tree), decor, labels);
return cell;
}
diff --git a/example/single/single.cpp b/example/single/single.cpp
index 26afc366..94131025 100644
--- a/example/single/single.cpp
+++ b/example/single/single.cpp
@@ -72,7 +72,7 @@ struct single_recipe: public arb::recipe {
// Add synapse to last branch.
.place(arb::mlocation{ morpho.num_branches()-1, 1. }, arb::synapse("exp2syn"), "synapse");
- return arb::cable_cell(morpho, dict, decor);
+ return arb::cable_cell(morpho, decor, dict);
}
arb::morphology morpho;
diff --git a/lmorpho/lmorpho.cpp b/lmorpho/lmorpho.cpp
index d6ed240f..cbcba1a3 100644
--- a/lmorpho/lmorpho.cpp
+++ b/lmorpho/lmorpho.cpp
@@ -87,7 +87,7 @@ int main(int argc, char** argv) {
labels.set("apical", "(tag 4)"_reg);
arb::decor decor;
- arb::cable_cell cell(morph, labels, decor);
+ arb::cable_cell cell(morph, decor, labels);
if(acc_file) {
std::string filename = acc_file.value();
diff --git a/python/cells.cpp b/python/cells.cpp
index d79059cf..7d9159e5 100644
--- a/python/cells.cpp
+++ b/python/cells.cpp
@@ -923,17 +923,23 @@ void register_cells(pybind11::module& m) {
"tree of one-dimensional cable segments.");
cable_cell
.def(pybind11::init(
- [](const arb::morphology& m, const label_dict_proxy& labels, const arb::decor& d) {
- return arb::cable_cell(m, labels.dict, d);
+ [](const arb::morphology& m, const arb::decor& d, const std::optional<label_dict_proxy>& l) {
+ if (l) return arb::cable_cell(m, d, l->dict);
+ return arb::cable_cell(m, d);
}),
- "morphology"_a, "labels"_a, "decor"_a,
- "Construct with a morphology, label dictionary and decor.")
+ "morphology"_a,
+ "decor"_a,
+ pybind11::arg_v("labels", pybind11::none(), "Labels"),
+ "Construct with a morphology, decor, and label dictionary.")
.def(pybind11::init(
- [](const arb::segment_tree& t, const label_dict_proxy& labels, const arb::decor& d) {
- return arb::cable_cell(arb::morphology(t), labels.dict, d);
+ [](const arb::segment_tree& t, const arb::decor& d, const std::optional<label_dict_proxy>& l) {
+ if (l) return arb::cable_cell({t}, d, l->dict);
+ return arb::cable_cell({t}, d);
}),
- "segment_tree"_a, "labels"_a, "decor"_a,
- "Construct with a morphology derived from a segment tree, label dictionary and decor.")
+ "segment_tree"_a,
+ "decor"_a,
+ pybind11::arg_v("labels", pybind11::none(), "Labels"),
+ "Construct with a morphology derived from a segment tree, decor, and label dictionary.")
.def_property_readonly("num_branches",
[](const arb::cable_cell& c) {return c.morphology().num_branches();},
"The number of unbranched cable sections in the morphology.")
diff --git a/python/example/diffusion.py b/python/example/diffusion.py
index 438ae0d5..7ef2d210 100644
--- a/python/example/diffusion.py
+++ b/python/example/diffusion.py
@@ -49,7 +49,7 @@ dec.paint("(tag 1)", ion_name="na", int_con=100.0, diff=0.01)
prb = [
A.cable_probe_ion_diff_concentration_cell("na"),
]
-cel = A.cable_cell(tree, A.label_dict(), dec)
+cel = A.cable_cell(tree, dec)
rec = recipe(cel, prb)
sim = A.simulation(rec)
hdl = (sim.sample((0, 0), A.regular_schedule(0.1)),)
diff --git a/python/example/dynamic-catalogue.py b/python/example/dynamic-catalogue.py
index 64c74cc9..6ed1a83f 100644
--- a/python/example/dynamic-catalogue.py
+++ b/python/example/dynamic-catalogue.py
@@ -15,7 +15,7 @@ class recipe(arb.recipe):
self.props = arb.neuron_cable_properties()
self.props.catalogue = arb.load_catalogue(cat)
d = arb.decor().paint("(all)", "dummy").set_property(Vm=0.0)
- self.cell = arb.cable_cell(self.tree, arb.label_dict(), d)
+ self.cell = arb.cable_cell(self.tree, d)
def global_properties(self, _):
return self.props
diff --git a/python/example/gap_junctions.py b/python/example/gap_junctions.py
index dcdbbfa5..a06bc8de 100644
--- a/python/example/gap_junctions.py
+++ b/python/example/gap_junctions.py
@@ -55,7 +55,7 @@ def make_cable_cell(gid):
.place('"root"', arbor.threshold_detector(-10), "detector")
)
- return arbor.cable_cell(tree, labels, decor)
+ return arbor.cable_cell(tree, decor, labels)
# Create a recipe that generates connected chains of cells
diff --git a/python/example/network_ring.py b/python/example/network_ring.py
index 3e0f3de6..d30e83a4 100755
--- a/python/example/network_ring.py
+++ b/python/example/network_ring.py
@@ -68,7 +68,7 @@ def make_cable_cell(gid):
.place('"root"', arbor.threshold_detector(-10), "detector")
)
- return arbor.cable_cell(tree, labels, decor)
+ return arbor.cable_cell(tree, decor, labels)
# (5) Create a recipe that generates a network of connected cells.
diff --git a/python/example/network_ring_gpu.py b/python/example/network_ring_gpu.py
index 61b7be3e..22a9b43d 100644
--- a/python/example/network_ring_gpu.py
+++ b/python/example/network_ring_gpu.py
@@ -69,7 +69,7 @@ def make_cable_cell(gid):
# Attach a detector with threshold of -10 mV.
decor.place('"root"', arbor.threshold_detector(-10), "detector")
- cell = arbor.cable_cell(tree, labels, decor)
+ cell = arbor.cable_cell(tree, decor, labels)
return cell
diff --git a/python/example/network_ring_mpi.py b/python/example/network_ring_mpi.py
index dc1b0d2c..73621685 100644
--- a/python/example/network_ring_mpi.py
+++ b/python/example/network_ring_mpi.py
@@ -70,7 +70,7 @@ def make_cable_cell(gid):
.place('"root"', arbor.threshold_detector(-10), "detector")
)
- return arbor.cable_cell(tree, labels, decor)
+ return arbor.cable_cell(tree, decor, labels)
# (5) Create a recipe that generates a network of connected cells.
diff --git a/python/example/network_two_cells_gap_junctions.py b/python/example/network_two_cells_gap_junctions.py
index 95fd830e..1eeec49f 100755
--- a/python/example/network_two_cells_gap_junctions.py
+++ b/python/example/network_two_cells_gap_junctions.py
@@ -98,7 +98,7 @@ class TwoCellsWithGapJunction(arbor.recipe):
else:
decor.discretization(arbor.cv_policy_single())
- return arbor.cable_cell(tree, labels, decor)
+ return arbor.cable_cell(tree, decor, labels)
def gap_junctions_on(self, gid):
# create a bidirectional gap junction from cell 0 at label "gj_label" to cell 1 at label "gj_label" and back.
diff --git a/python/example/plasticity.py b/python/example/plasticity.py
index cd8b8a2b..ab57d099 100644
--- a/python/example/plasticity.py
+++ b/python/example/plasticity.py
@@ -56,7 +56,7 @@ class recipe(A.recipe):
# - detector for reporting spikes on the cable cells.
decor.place("(location 0 0.5)", A.threshold_detector(-10.0), "detector")
# return the cable cell description
- return A.cable_cell(tree, A.label_dict(), decor)
+ return A.cable_cell(tree, decor)
def connections_on(self, gid):
# If we have added a connection to this cell, return it, else nothing.
diff --git a/python/example/probe_lfpykit.py b/python/example/probe_lfpykit.py
index 8519b933..0db4733f 100644
--- a/python/example/probe_lfpykit.py
+++ b/python/example/probe_lfpykit.py
@@ -109,7 +109,7 @@ def make_cable_cell(morphology, clamp_location):
p = arbor.place_pwlin(morphology)
# create cell and set properties
- cell = arbor.cable_cell(morphology, labels, decor)
+ cell = arbor.cable_cell(morphology, decor, labels)
return p, cell
diff --git a/python/example/single_cell_allen.py b/python/example/single_cell_allen.py
index 1296a29b..dade963a 100644
--- a/python/example/single_cell_allen.py
+++ b/python/example/single_cell_allen.py
@@ -114,7 +114,7 @@ def make_cell(swc, fit):
decor.discretization(arbor.cv_policy_max_extent(20))
# (11) Create cell
- return arbor.cable_cell(morphology, labels, decor), offset
+ return arbor.cable_cell(morphology, decor, labels), offset
# (12) Create cell, model
diff --git a/python/example/single_cell_cable.py b/python/example/single_cell_cable.py
index 8cb5d4cf..25f6aa14 100755
--- a/python/example/single_cell_cable.py
+++ b/python/example/single_cell_cable.py
@@ -108,7 +108,7 @@ class Cable(arbor.recipe):
policy = arbor.cv_policy_max_extent(self.cv_policy_max_extent)
decor.discretization(policy)
- return arbor.cable_cell(tree, labels, decor)
+ return arbor.cable_cell(tree, decor, labels)
def get_rm(g):
diff --git a/python/example/single_cell_detailed.py b/python/example/single_cell_detailed.py
index 37873eba..25495c51 100755
--- a/python/example/single_cell_detailed.py
+++ b/python/example/single_cell_detailed.py
@@ -67,7 +67,7 @@ decor.discretization('(replace (single (region "soma")) (max-extent 1.0))')
# (4) Create the cell.
-cell = arbor.cable_cell(morph, labels, decor)
+cell = arbor.cable_cell(morph, decor, labels)
# (5) Construct the model
diff --git a/python/example/single_cell_detailed_recipe.py b/python/example/single_cell_detailed_recipe.py
index ac01e73a..b5056254 100644
--- a/python/example/single_cell_detailed_recipe.py
+++ b/python/example/single_cell_detailed_recipe.py
@@ -68,7 +68,7 @@ decor = (
# (4) Create the cell.
-cell = arbor.cable_cell(morph, labels, decor)
+cell = arbor.cable_cell(morph, decor, labels)
# (5) Create a class that inherits from arbor.recipe
diff --git a/python/example/single_cell_model.py b/python/example/single_cell_model.py
index 229862ab..0737983f 100755
--- a/python/example/single_cell_model.py
+++ b/python/example/single_cell_model.py
@@ -23,7 +23,7 @@ decor = (
)
# (4) Create cell and the single cell model based on it
-cell = arbor.cable_cell(tree, labels, decor)
+cell = arbor.cable_cell(tree, decor, labels)
# (5) Make single cell model.
m = arbor.single_cell_model(cell)
diff --git a/python/example/single_cell_nml.py b/python/example/single_cell_nml.py
index 0061e72b..f69b195f 100755
--- a/python/example/single_cell_nml.py
+++ b/python/example/single_cell_nml.py
@@ -69,7 +69,7 @@ decor = (
)
# Combine morphology with region and locset definitions to make a cable cell.
-cell = arbor.cable_cell(morpho, labels, decor)
+cell = arbor.cable_cell(morpho, decor, labels)
print(cell.locations('"axon_end"'))
diff --git a/python/example/single_cell_recipe.py b/python/example/single_cell_recipe.py
index 6b780009..447266e5 100644
--- a/python/example/single_cell_recipe.py
+++ b/python/example/single_cell_recipe.py
@@ -26,7 +26,7 @@ decor = (
.place('"midpoint"', arbor.threshold_detector(-10), "detector")
)
-cell = arbor.cable_cell(tree, labels, decor)
+cell = arbor.cable_cell(tree, decor, labels)
# (4) Define a recipe for a single cell and set of probes upon it.
# This constitutes the corresponding generic recipe version of
diff --git a/python/example/single_cell_stdp.py b/python/example/single_cell_stdp.py
index a2079748..9799d69f 100755
--- a/python/example/single_cell_stdp.py
+++ b/python/example/single_cell_stdp.py
@@ -41,7 +41,7 @@ class single_recipe(arbor.recipe):
)
)
- return arbor.cable_cell(tree, labels, decor)
+ return arbor.cable_cell(tree, decor, labels)
def event_generators(self, gid):
"""two stimuli: one that makes the cell spike, the other to monitor STDP"""
diff --git a/python/example/single_cell_swc.py b/python/example/single_cell_swc.py
index 43e76cdb..4edaec7b 100755
--- a/python/example/single_cell_swc.py
+++ b/python/example/single_cell_swc.py
@@ -59,7 +59,7 @@ decor = (
)
# Combine morphology with region and locset definitions to make a cable cell.
-cell = arbor.cable_cell(morpho, labels, decor)
+cell = arbor.cable_cell(morpho, decor, labels)
print(cell.locations('"axon_end"'))
diff --git a/python/test/fixtures.py b/python/test/fixtures.py
index 72633215..19f88ae9 100644
--- a/python/test/fixtures.py
+++ b/python/test/fixtures.py
@@ -218,7 +218,7 @@ class art_spiker_recipe(arbor.recipe):
)
else:
tree, labels, decor = self._cable_cell_elements()
- return arbor.cable_cell(tree, labels, decor)
+ return arbor.cable_cell(tree, decor, labels)
@_fixture
diff --git a/python/test/unit/test_cable_probes.py b/python/test/unit/test_cable_probes.py
index e49b3930..daa0ffd2 100644
--- a/python/test/unit/test_cable_probes.py
+++ b/python/test/unit/test_cable_probes.py
@@ -24,7 +24,7 @@ class cc_recipe(A.recipe):
dec.place("(location 0 0.1)", A.iclamp(20.0), "iclamp")
dec.paint("(all)", A.density("hh"))
- self.cell = A.cable_cell(st, A.label_dict(), dec)
+ self.cell = A.cable_cell(st, dec)
self.props = A.neuron_cable_properties()
self.props.catalogue = A.default_catalogue()
diff --git a/python/test/unit/test_catalogues.py b/python/test/unit/test_catalogues.py
index 7e9608df..38175fda 100644
--- a/python/test/unit/test_catalogues.py
+++ b/python/test/unit/test_catalogues.py
@@ -23,7 +23,7 @@ class recipe(arb.recipe):
d = arb.decor()
d.paint("(all)", arb.density("pas"))
d.set_property(Vm=0.0)
- self.cell = arb.cable_cell(self.tree, arb.label_dict(), d)
+ self.cell = arb.cable_cell(self.tree, d)
def global_properties(self, _):
return self.props
diff --git a/python/test/unit/test_multiple_connections.py b/python/test/unit/test_multiple_connections.py
index b23326c4..1f7dab5a 100644
--- a/python/test/unit/test_multiple_connections.py
+++ b/python/test/unit/test_multiple_connections.py
@@ -111,7 +111,7 @@ class TestMultipleConnections(unittest.TestCase):
"postsyn_target",
) # place synapse for input from another presynaptic neuron at the center of the soma
# (using the same label as above!)
- return arb.cable_cell(tree, labels, decor)
+ return arb.cable_cell(tree, decor, labels)
art_spiker_recipe.cell_description = types.MethodType(
cell_description, art_spiker_recipe
@@ -352,7 +352,7 @@ class TestMultipleConnections(unittest.TestCase):
) # place synapse for input from another presynaptic neuron at the center of the soma
# (using another label as above!)
- return arb.cable_cell(tree, labels, decor)
+ return arb.cable_cell(tree, decor, labels)
art_spiker_recipe.cell_description = types.MethodType(
cell_description, art_spiker_recipe
diff --git a/python/test/unit_distributed/test_domain_decompositions.py b/python/test/unit_distributed/test_domain_decompositions.py
index e19bd55c..b8fbbfb8 100644
--- a/python/test/unit_distributed/test_domain_decompositions.py
+++ b/python/test/unit_distributed/test_domain_decompositions.py
@@ -47,7 +47,7 @@ class hetero_recipe(arb.recipe):
tree.append(arb.mnpos, arb.mpoint(-3, 0, 0, 3), arb.mpoint(3, 0, 0, 3), tag=1)
decor = arb.decor()
decor.place("(location 0 0.5)", arb.gap_junction_site(), "gj")
- return arb.cable_cell(tree, arb.label_dict(), decor)
+ return arb.cable_cell(tree, decor)
def cell_kind(self, gid):
if gid % 2:
@@ -132,7 +132,7 @@ class gj_non_symmetric(arb.recipe):
tree.append(arb.mnpos, arb.mpoint(-3, 0, 0, 3), arb.mpoint(3, 0, 0, 3), tag=1)
decor = arb.decor()
decor.place("(location 0 0.5)", arb.gap_junction_site(), "gj")
- return arb.cable_cell(tree, arb.label_dict(), decor)
+ return arb.cable_cell(tree, decor)
def cell_kind(self, gid):
return arb.cell_kind.cable
diff --git a/test/common_cells.hpp b/test/common_cells.hpp
index 44212794..9b22af70 100644
--- a/test/common_cells.hpp
+++ b/test/common_cells.hpp
@@ -18,7 +18,7 @@ struct cable_cell_description {
decor decorations;
operator cable_cell() const {
- return cable_cell(morph, labels, decorations);
+ return cable_cell(morph, decorations, labels);
}
};
diff --git a/test/unit-distributed/test_communicator.cpp b/test/unit-distributed/test_communicator.cpp
index 7836fc54..5884a311 100644
--- a/test/unit-distributed/test_communicator.cpp
+++ b/test/unit-distributed/test_communicator.cpp
@@ -201,7 +201,7 @@ namespace {
decor.set_default(arb::cv_policy_fixed_per_branch(10));
decor.place(arb::mlocation{0, 0.5}, arb::threshold_detector{10}, "src");
decor.place(arb::mlocation{0, 0.5}, arb::synapse("expsyn"), "tgt");
- return arb::cable_cell(arb::morphology(tree), {}, decor);
+ return arb::cable_cell(arb::morphology(tree), decor);
}
return arb::lif_cell("src", "tgt");
}
@@ -274,7 +274,7 @@ namespace {
decor.set_default(arb::cv_policy_fixed_per_branch(10));
decor.place(arb::mlocation{0, 0.5}, arb::threshold_detector{10}, "src");
decor.place(arb::ls::uniform(arb::reg::all(), 0, size_, gid), arb::synapse("expsyn"), "tgt");
- return arb::cable_cell(arb::morphology(tree), {}, decor);
+ return arb::cable_cell(arb::morphology(tree), decor);
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
return cell_kind::cable;
@@ -352,7 +352,7 @@ namespace {
decor.place(arb::ls::uniform(arb::reg::all(), 0, 2, gid), arb::threshold_detector{10}, "detectors_0");
decor.place(arb::ls::uniform(arb::reg::all(), 3, 3, gid), arb::threshold_detector{10}, "detectors_1");
}
- return arb::cable_cell(arb::morphology(tree), {}, decor);
+ return arb::cable_cell(arb::morphology(tree), decor);
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
diff --git a/test/unit/test_cable_cell.cpp b/test/unit/test_cable_cell.cpp
index 2898a617..1e59691b 100644
--- a/test/unit/test_cable_cell.cpp
+++ b/test/unit/test_cable_cell.cpp
@@ -39,7 +39,7 @@ TEST(cable_cell, lid_ranges) {
decorations.place(three_sites, synapse("expsyn"), "t3");
decorations.place("term"_lab, synapse("exp2syn"), "t3");
- cable_cell cell(morph, dict, decorations);
+ cable_cell cell(morph, decorations, dict);
// Get the assigned lid ranges for each placement
const auto& src_ranges = cell.detector_ranges();
diff --git a/test/unit/test_cv_geom.cpp b/test/unit/test_cv_geom.cpp
index cfca8a58..7d49151b 100644
--- a/test/unit/test_cv_geom.cpp
+++ b/test/unit/test_cv_geom.cpp
@@ -73,7 +73,7 @@ std::ostream& operator<<(std::ostream& out, ::arb::cv_prefer::type p) {
TEST(cv_geom, empty) {
using namespace common_morphology;
- cable_cell empty_cell{m_empty};
+ cable_cell empty_cell{m_empty, {}};
cv_geometry geom(empty_cell, ls::nil());
EXPECT_TRUE(verify_cv_children(geom));
@@ -96,7 +96,7 @@ TEST(cv_geom, trivial) {
if (p.second.empty()) continue;
SCOPED_TRACE(p.first);
- cable_cell cell{p.second};
+ cable_cell cell{p.second, {}};
auto& m = cell.morphology();
// Equivalent ways of specifying one CV comprising whole cell:
@@ -137,7 +137,7 @@ TEST(cv_geom, one_cv_per_branch) {
if (p.second.empty()) continue;
SCOPED_TRACE(p.first);
- cable_cell cell{p.second};
+ cable_cell cell{p.second, {}};
auto& m = cell.morphology();
auto cell_cv_geom = cv_geometry(cell, sum(ls::on_branches(0), ls::on_branches(1)));
@@ -192,7 +192,7 @@ TEST(cv_geom, midpoints) {
if (p.second.empty()) continue;
SCOPED_TRACE(p.first);
- cable_cell cell{p.second};
+ cable_cell cell{p.second, {}};
auto& m = cell.morphology();
cv_geometry geom(cell, ls::on_branches(0.5));
@@ -285,7 +285,7 @@ TEST(cv_geom, weird) {
using C = mcable;
using testing::seq_eq;
- cable_cell cell{common_morphology::m_reg_b6};
+ cable_cell cell{common_morphology::m_reg_b6, {}};
cv_geometry geom(cell, mlocation_list{{1, 0}, {4,0}});
EXPECT_TRUE(verify_cv_children(geom));
@@ -304,7 +304,7 @@ TEST(cv_geom, weird) {
TEST(cv_geom, location_cv) {
using namespace common_morphology;
- cable_cell cell{m_reg_b6};
+ cable_cell cell{m_reg_b6, {}};
auto& m = cell.morphology();
auto cv_extent = [](const cv_geometry& geom, auto cv) {
@@ -451,7 +451,7 @@ TEST(cv_geom, multicell) {
using namespace common_morphology;
using index_type = cv_geometry::index_type;
- cable_cell cell = cable_cell(m_reg_b6);
+ cable_cell cell = cable_cell(m_reg_b6, {});
cv_geometry geom(cell, ls::on_branches(0.5));
unsigned n_cv = geom.size();
@@ -489,7 +489,7 @@ TEST(cv_geom, multicell) {
TEST(region_cv, empty) {
using namespace common_morphology;
- cable_cell empty_cell{m_empty};
+ cable_cell empty_cell{m_empty, {}};
cell_cv_data cv_data(empty_cell, ls::nil());
auto all_cv = intersect_region(reg::all(), cv_data);
@@ -506,7 +506,7 @@ TEST(region_cv, trivial) {
if (p.second.empty()) continue;
SCOPED_TRACE(p.first);
- cable_cell cell{p.second};
+ cable_cell cell{p.second, {}};
// One CV comprising whole cell:
cell_cv_data cell_geom1(cell, ls::nil());
@@ -585,7 +585,7 @@ TEST(region_cv, custom_geometry) {
decor d;
// Discretize by segment
d.set_default(cv_policy_every_segment());
- auto cell = cable_cell(m, l, d);
+ auto cell = cable_cell(m, d, l);
auto geom = cv_data(cell);
EXPECT_TRUE(geom);
@@ -643,7 +643,7 @@ TEST(region_cv, custom_geometry) {
{2, 1}
});
d.set_default(cv_policy_explicit(ls));
- auto cell = cable_cell(m, l, d);
+ auto cell = cable_cell(m, d, l);
auto geom = cv_data(cell);
EXPECT_TRUE(geom);
diff --git a/test/unit/test_cv_layout.cpp b/test/unit/test_cv_layout.cpp
index d4fbe24d..8852f61a 100644
--- a/test/unit/test_cv_layout.cpp
+++ b/test/unit/test_cv_layout.cpp
@@ -19,7 +19,7 @@ using util::make_span;
TEST(cv_layout, empty) {
using namespace common_morphology;
- cable_cell empty_cell{m_empty, {}, {}};
+ cable_cell empty_cell{m_empty, {}};
fvm_cv_discretization D = fvm_cv_discretize(empty_cell, neuron_parameter_defaults);
EXPECT_TRUE(D.empty());
@@ -50,7 +50,7 @@ TEST(cv_layout, trivial) {
// they are not 'connected', and will generate multiple CVs.
if (p.second.branch_children(mnpos).size()>1u) continue;
- cells.emplace_back(p.second, label_dict{}, decor{});
+ cells.emplace_back(p.second, decor{});
n_cv += !p.second.empty(); // one cv per non-empty cell
}
@@ -95,7 +95,7 @@ TEST(cv_layout, cable) {
decs.paint(reg::cable(0, 0.0, 0.2), init_membrane_potential{10});
decs.paint(reg::cable(0, 0.2, 0.7), init_membrane_potential{20});
decs.paint(reg::cable(0, 0.7, 1.0), init_membrane_potential{30});
- cable_cell c(morph, {}, decs);
+ cable_cell c(morph, decs);
params.discretization = cv_policy_explicit(ls::nil());
fvm_cv_discretization D = fvm_cv_discretize(c, params);
@@ -118,7 +118,7 @@ TEST(cv_layout, cable_conductance) {
auto params = neuron_parameter_defaults;
params.axial_resistivity = rho;
- cable_cell c(morph, {}, {});
+ cable_cell c(morph, {});
double radius = c.embedding().radius(mlocation{0, 0.5});
double length = c.embedding().branch_length(0);
@@ -140,7 +140,7 @@ TEST(cv_layout, zero_size_cv) {
// Six branches; branches 0, 1 and 2 meet at (0, 1); branches
// 2, 3, 4, and 5 meet at (2, 1). Terminal branches are 1, 3, 4, and 5.
auto morph = common_morphology::m_reg_b6;
- cable_cell cell(morph, {}, {});
+ cable_cell cell(morph, {});
auto params = neuron_parameter_defaults;
const double rho = 5.; // [Ω·cm]
diff --git a/test/unit/test_cv_policy.cpp b/test/unit/test_cv_policy.cpp
index 89279ffc..95f22597 100644
--- a/test/unit/test_cv_policy.cpp
+++ b/test/unit/test_cv_policy.cpp
@@ -38,7 +38,8 @@ TEST(cv_policy, single) {
// the extremal points of the completions of the components of the
// supplied region.
- cable_cell cell(m_mlt_b6);
+
+ cable_cell cell(m_mlt_b6, {});
for (region reg:
{reg::all(), reg::branch(2), reg::cable(3, 0.25, 1.),
join(reg::cable(1, 0.75, 1), reg::branch(3), reg::cable(2, 0, 0.5)),
@@ -57,7 +58,7 @@ TEST(cv_policy, explicit_policy) {
cv_policy pol = cv_policy_explicit(lset);
for (auto& m: {m_reg_b6, m_mlt_b6}) {
- cable_cell cell(m);
+ cable_cell cell(m, {});
locset result = pol.cv_boundary_points(cell);
locset expected = join(ls::boundary(reg::all()), lset);
@@ -71,7 +72,7 @@ TEST(cv_policy, explicit_policy) {
region b12 = join(reg::branch(1), reg::branch(2));
pol = cv_policy_explicit(lset, b12);
for (auto& m: {m_reg_b6, m_mlt_b6}) {
- cable_cell cell(m);
+ cable_cell cell(m, {});
locset result = pol.cv_boundary_points(cell);
locset expected = as_locset(L{1, 0}, L{1, 0.5}, L{1, 1}, L{2, 0}, L{2, 1});
@@ -83,7 +84,7 @@ TEST(cv_policy, explicit_policy) {
pol = cv_policy_explicit(lset, reg::complete(b12));
for (auto& m: {m_mlt_b6}) {
- cable_cell cell(m);
+ cable_cell cell(m, {});
locset result = pol.cv_boundary_points(cell);
locset expected = as_locset(L{0, 1}, L{1, 0.5}, L{1, 1}, L{2, 1});
@@ -106,7 +107,8 @@ TEST(cv_policy, empty_morphology) {
cv_policy_explicit(ls::location(0, 0))
};
- cable_cell cell(m_empty);
+
+ cable_cell cell(m_empty, {});
for (auto& pol: policies) {
EXPECT_TRUE(locset_eq(cell.provider(), ls::nil(), pol.cv_boundary_points(cell)));
@@ -119,7 +121,7 @@ TEST(cv_policy, fixed_per_branch) {
// Root branch only:
{
- cable_cell cell(m_reg_b1);
+ cable_cell cell(m_reg_b1, {});
{
// boundary fork points
cv_policy pol = cv_policy_fixed_per_branch(4);
@@ -138,8 +140,7 @@ TEST(cv_policy, fixed_per_branch) {
// Multiple top level branches:
// top level branches are 0 and 3, terminal branches are 1, 2, 4 and 5.
{
- cable_cell cell(m_mlt_b6);
-
+ cable_cell cell(m_mlt_b6, {});
{
// With boundary fork points:
cv_policy pol = cv_policy_fixed_per_branch(2);
@@ -167,7 +168,7 @@ TEST(cv_policy, fixed_per_branch) {
// Restrict to an incomplete subtree (distal half of branch 0 and all of branch 2)
// in m_mlt_b6 morphology.
{
- cable_cell cell(m_mlt_b6);
+ cable_cell cell(m_mlt_b6, {});
region reg = mcable_list{{0, 0.5, 1.}, {2, 0., 1.}};
{
// With two per branch and fork points as boundaries, expect to see:
@@ -204,7 +205,7 @@ TEST(cv_policy, max_extent) {
// Root branch only:
{
- cable_cell cell(m_reg_b1);
+ cable_cell cell(m_reg_b1, {});
ASSERT_EQ(1.0, cell.embedding().branch_length(0));
{
@@ -238,7 +239,7 @@ TEST(cv_policy, max_extent) {
// Cell with varying branch lengths; extent not exact fraction:
{
- cable_cell cell(m_mlt_b6);
+ cable_cell cell(m_mlt_b6, {});
ASSERT_EQ(1.0, cell.embedding().branch_length(0));
ASSERT_EQ(1.0, cell.embedding().branch_length(1));
ASSERT_EQ(2.0, cell.embedding().branch_length(2));
@@ -285,7 +286,7 @@ TEST(cv_policy, every_segment) {
// Including all samples:
{
- cable_cell cell(m);
+ cable_cell cell(m, {});
cv_policy pol = cv_policy_every_segment();
mlocation_list expected = {
@@ -298,7 +299,7 @@ TEST(cv_policy, every_segment) {
}
// Restricting to the two child branches (disconnected):
{
- cable_cell cell(m);
+ cable_cell cell(m, {});
region reg = join(reg::branch(1), reg::branch(2));
cv_policy pol = cv_policy_every_segment(reg);
@@ -321,7 +322,7 @@ TEST(cv_policy, domain) {
region reg1 = join(reg::branch(1), reg::cable(2, 0, 0.5));
region reg2 = join(reg::branch(1), reg::cable(2, 0.5, 1), reg::cable(4, 0, 1));
- cable_cell cell(m_mlt_b6);
+ cable_cell cell(m_mlt_b6, {});
EXPECT_TRUE(region_eq(cell.provider(), reg1, cv_policy_single(reg1).domain()));
EXPECT_TRUE(region_eq(cell.provider(), reg1, cv_policy_fixed_per_branch(3, reg1).domain()));
@@ -337,7 +338,7 @@ TEST(cv_policy, domain) {
TEST(cv_policy, combinators) {
auto unique_sum = [](auto... a) { return ls::support(sum(locset(a)...)); };
- cable_cell cell(m_reg_b6);
+ cable_cell cell(m_reg_b6, {});
auto eval_locset_eq = [&cell](const locset& a, const cv_policy& p) {
return locset_eq(cell.provider(), a, p.cv_boundary_points(cell));
};
diff --git a/test/unit/test_diffusion.cpp b/test/unit/test_diffusion.cpp
index f6d89396..de56e11a 100644
--- a/test/unit/test_diffusion.cpp
+++ b/test/unit/test_diffusion.cpp
@@ -50,7 +50,7 @@ struct linear: public recipe {
arb::cell_kind get_cell_kind(arb::cell_gid_type) const override { return arb::cell_kind::cable; }
std::any get_global_properties(arb::cell_kind) const override { return gprop; }
std::vector<arb::probe_info> get_probes(arb::cell_gid_type) const override { return {arb::cable_probe_ion_diff_concentration_cell{"na"}}; }
- util::unique_any get_cell_description(arb::cell_gid_type) const override { return arb::cable_cell(morph, {}, decor); }
+ util::unique_any get_cell_description(arb::cell_gid_type) const override { return arb::cable_cell(morph, decor); }
std::vector<arb::event_generator> event_generators(arb::cell_gid_type gid) const override {
std::vector<arb::event_generator> result;
diff --git a/test/unit/test_event_delivery.cpp b/test/unit/test_event_delivery.cpp
index ecc135e2..89718a19 100644
--- a/test/unit/test_event_delivery.cpp
+++ b/test/unit/test_event_delivery.cpp
@@ -39,7 +39,7 @@ struct test_recipe: public n_cable_cell_recipe {
decorations.place(mlocation{0, 0.5}, synapse("expsyn"), "synapse");
decorations.place(mlocation{0, 0.5}, threshold_detector{-64}, "detector");
decorations.place(mlocation{0, 0.5}, junction("gj"), "gapjunction");
- cable_cell c(st, labels, decorations);
+ cable_cell c(st, decorations, labels);
return c;
}
diff --git a/test/unit/test_fvm_layout.cpp b/test/unit/test_fvm_layout.cpp
index f81c76fd..e937d02d 100644
--- a/test/unit/test_fvm_layout.cpp
+++ b/test/unit/test_fvm_layout.cpp
@@ -1665,7 +1665,7 @@ TEST(fvm_layout, vinterp_cable) {
// CV midpoints at branch pos 0.1, 0.3, 0.5, 0.7, 0.9.
// Expect voltage reference locations to be CV modpoints.
d.set_default(cv_policy_fixed_per_branch(5));
- cable_cell cell{m, {}, d};
+ cable_cell cell{m, d};
fvm_cv_discretization D = fvm_cv_discretize(cell, neuron_parameter_defaults);
// Test locations, either side of CV midpoints plus extrema, CV boundaries.
@@ -1725,7 +1725,7 @@ TEST(fvm_layout, vinterp_forked) {
// and contain branches 1 and 2 respectively, excluding the fork point.
mlocation_list cv_ends{{1, 0.}, {2, 0.}};
d.set_default(cv_policy_explicit(cv_ends));
- cable_cell cell{m, {}, d};
+ cable_cell cell{m, d};
fvm_cv_discretization D = fvm_cv_discretize(cell, neuron_parameter_defaults);
// Points in branch 0 should only get CV 0 for interpolation.
@@ -1778,11 +1778,11 @@ TEST(fvm_layout, iinterp) {
decor d;
d.set_default(cv_policy_fixed_per_branch(3));
- cells.emplace_back(cable_cell{p.second, {}, d});
+ cells.emplace_back(cable_cell{p.second, d});
label.push_back(p.first+": forks-at-end"s);
d.set_default(cv_policy_fixed_per_branch(3, cv_policy_flag::interior_forks));
- cells.emplace_back(cable_cell{p.second, {}, d});
+ cells.emplace_back(cable_cell{p.second, d});
label.push_back(p.first+": interior-forks"s);
}
@@ -1831,7 +1831,7 @@ TEST(fvm_layout, iinterp) {
// and contain branches 1 and 2 respectively, excluding the fork point.
mlocation_list cv_ends{{1, 0.}, {2, 0.}};
d.set_default(cv_policy_explicit(cv_ends));
- cable_cell cell{m, {}, d};
+ cable_cell cell{m, d};
D = fvm_cv_discretize(cell, neuron_parameter_defaults);
// Expect axial current interpolations on branches 1 and 2 to match CV 1 and 2
diff --git a/test/unit/test_fvm_lowered.cpp b/test/unit/test_fvm_lowered.cpp
index 0b2cbcaa..a11be575 100644
--- a/test/unit/test_fvm_lowered.cpp
+++ b/test/unit/test_fvm_lowered.cpp
@@ -367,7 +367,7 @@ TEST(fvm_lowered, ac_stimulus) {
// Envelope is linear ramp from 0 to max_time.
dec.place(mlocation{0, 0}, i_clamp({{0, 0}, {max_time, max_amplitude}, {max_time, 0}}, freq, phase), "clamp");
- std::vector<cable_cell> cells = {cable_cell(tree, {}, dec)};
+ std::vector<cable_cell> cells = {cable_cell(tree, dec)};
cable_cell_global_properties gprop;
gprop.default_parameters = neuron_parameter_defaults;
@@ -877,7 +877,7 @@ TEST(fvm_lowered, post_events_shared_state) {
}
decor.place(arb::mlocation{0, 0.5}, synapse_, "syanpse");
- return arb::cable_cell(arb::morphology(tree), {}, decor);
+ return arb::cable_cell(arb::morphology(tree), decor);
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
@@ -969,7 +969,7 @@ TEST(fvm_lowered, label_data) {
decor.place(uniform(all(), 4, 4, 42), arb::synapse("expsyn"), "1_synapse");
decor.place(uniform(all(), 5, 5, 42), arb::threshold_detector{10}, "1_detector");
- cells_.push_back(arb::cable_cell(arb::morphology(tree), {}, decor));
+ cells_.push_back(arb::cable_cell(arb::morphology(tree), decor));
}
{
arb::decor decor;
@@ -979,7 +979,7 @@ TEST(fvm_lowered, label_data) {
decor.place(uniform(all(), 5, 6, 24), arb::junction("gj"), "2_gap_junctions");
decor.place(uniform(all(), 7, 7, 24), arb::junction("gj"), "1_gap_junction");
- cells_.push_back(arb::cable_cell(arb::morphology(tree), {}, decor));
+ cells_.push_back(arb::cable_cell(arb::morphology(tree), decor));
}
}
diff --git a/test/unit/test_probe.cpp b/test/unit/test_probe.cpp
index a6b3ed6e..6377298d 100644
--- a/test/unit/test_probe.cpp
+++ b/test/unit/test_probe.cpp
@@ -218,7 +218,7 @@ void run_v_cell_probe_test(context ctx) {
decor d;
d.set_default(testcase.second);
- cable_cell cell(m, {}, d);
+ cable_cell cell(m, d);
cable1d_recipe rec(cell, false);
rec.add_probe(0, 0, cable_probe_membrane_voltage_cell{});
@@ -384,7 +384,7 @@ void run_expsyn_g_cell_probe_test(context ctx) {
}
}
- std::vector<cable_cell> cells(2, arb::cable_cell(m, {}, d));
+ std::vector<cable_cell> cells(2, arb::cable_cell(m, d));
auto run_test = [&](bool coalesce_synapses) {
cable1d_recipe rec(cells, coalesce_synapses);
@@ -514,7 +514,7 @@ void run_ion_density_probe_test(context ctx) {
mlocation loc1{0, 0.5};
mlocation loc2{0, 0.9};
- cable1d_recipe rec(cable_cell(m, {}, d));
+ cable1d_recipe rec(cable_cell(m, d));
rec.catalogue() = cat;
// Probe (0, 0): ca internal on CV 0.
@@ -707,8 +707,8 @@ void run_partial_density_probe_test(context ctx) {
d1.paint(mcable{0, 0.7, 0.8}, mk_mech(10));
d1.paint(mcable{0, 0.9, 1.0}, mk_mech(11));
- cells[0] = cable_cell(m, {}, d0);
- cells[1] = cable_cell(m, {}, d1);
+ cells[0] = cable_cell(m, d0);
+ cells[1] = cable_cell(m, d1);
// Place probes in the middle of each 10% interval, i.e. at 0.05, 0.15, etc.
struct test_probe {
@@ -798,10 +798,10 @@ void run_axial_and_ion_current_sampled_probe_test(context ctx) {
d.set_default(membrane_capacitance{0.01}); // [F/m²]
const double tau = 0.1; // [ms]
- cable1d_recipe rec(cable_cell(m, {}, d));
+ cable1d_recipe rec(cable_cell(m, d));
rec.catalogue() = cat;
- cable_cell cell(m, {}, d);
+ cable_cell cell(m, d);
// Place axial current probes at CV boundaries and make cell-wide probes for
// total ionic membrane current and stimulus currents.
@@ -950,7 +950,7 @@ void run_multi_probe_test(context ctx) {
d.paint(reg::branch(2), density("param_as_state", {{"p", 20.}}));
d.paint(reg::branch(5), density("param_as_state", {{"p", 50.}}));
- auto tracev = run_simple_sampler<double, mlocation>(ctx, 0.1, {cable_cell{m, {}, d}}, 0, cable_probe_density_state{ls::terminal(), "param_as_state", "s"}, {0.});
+ auto tracev = run_simple_sampler<double, mlocation>(ctx, 0.1, {cable_cell{m, d}}, 0, cable_probe_density_state{ls::terminal(), "param_as_state", "s"}, {0.});
// Expect to have received a sample on each of the terminals of branches 1, 2, and 5.
ASSERT_EQ(3u, tracev.size());
@@ -989,7 +989,7 @@ void run_v_sampled_probe_test(context ctx) {
d1.place(mlocation{1, 1}, i_clamp::box(0, 1.0, 1.), "clamp1");
mlocation probe_loc{1, 0.2};
- std::vector<cable_cell> cells = {{bs.morph, bs.labels, d0}, {bs.morph, bs.labels, d1}};
+ std::vector<cable_cell> cells = {{bs.morph, d0, bs.labels}, {bs.morph, d1, bs.labels}};
const double t_end = 1.; // [ms]
std::vector<double> when = {0.3, 0.6}; // Sample at 0.3 and 0.6 ms.
@@ -1060,7 +1060,7 @@ void run_total_current_probe_test(context ctx) {
cv_policy policy = cv_policy_fixed_per_branch(n_cv_per_branch, flags);
d0.set_default(policy);
d1.set_default(policy);
- std::vector<cable_cell> cells = {{m, {}, d0}, {m, {}, d1}};
+ std::vector<cable_cell> cells = {{m, d0}, {m, d1}};
for (unsigned i = 0; i<2; ++i) {
@@ -1166,7 +1166,7 @@ void run_stimulus_probe_test(context ctx) {
d1.place(mlocation{0, 1}, i_clamp::box(0., stim_until, -10.), "clamp1");
double expected_stim1 = 20;
- std::vector<cable_cell> cells = {{m, {}, d0}, {m, {}, d1}};
+ std::vector<cable_cell> cells = {{m, d0}, {m, d1}};
// Sample the cells during the stimulus, and after.
@@ -1357,7 +1357,7 @@ TEST(probe, get_probe_metadata) {
d.paint(reg::branch(2), density("param_as_state", {{"p", 20.}}));
d.paint(reg::branch(5), density("param_as_state", {{"p", 50.}}));
- cable1d_recipe rec(cable_cell{m, {}, d}, false);
+ cable1d_recipe rec(cable_cell{m, d}, false);
rec.catalogue() = make_unit_test_catalogue(global_default_catalogue());
rec.add_probe(0, 7, cable_probe_density_state{ls::terminal(), "param_as_state", "s"});
diff --git a/test/unit/test_recipe.cpp b/test/unit/test_recipe.cpp
index ec51e718..27b04cb7 100644
--- a/test/unit/test_recipe.cpp
+++ b/test/unit/test_recipe.cpp
@@ -69,7 +69,7 @@ namespace {
tree.append(arb::mnpos, {0,0,0,10}, {0,0,20,10}, 1); // soma
tree.append(0, {0,0, 20, 2}, {0,0, 320, 2}, 3); // dendrite
- arb::cable_cell cell(tree);
+ arb::cable_cell cell(tree, {});
arb::decor decorations;
@@ -88,7 +88,7 @@ namespace {
decorations.place(arb::mlocation{0,(double)i/num_gj}, arb::junction("gj"), "gapjunction"+std::to_string(i));
}
- return arb::cable_cell(tree, {}, decorations);
+ return arb::cable_cell(tree, decorations);
}
}
diff --git a/test/unit/test_sde.cpp b/test/unit/test_sde.cpp
index b43169ce..da527499 100644
--- a/test/unit/test_sde.cpp
+++ b/test/unit/test_sde.cpp
@@ -264,7 +264,7 @@ public:
segment_tree tree;
tree.append(mnpos, {i*20., 0, 0.0, 4.0}, {i*20., 0, n1*cv_size, 4.0}, 1);
tree.append(0, {i*20., 0, ncvs*cv_size, 4.0}, 2);
- cells_.push_back(cable_cell(morphology(tree), labels, dec));
+ cells_.push_back(cable_cell(morphology(tree), dec, labels));
}
}
@@ -276,7 +276,7 @@ public:
std::any get_global_properties(cell_kind) const override { return cell_gprop_; }
- sde_recipe& add_probe(probe_tag tag, std::any address) {
+ sde_recipe& add_probe_all_gids(probe_tag tag, std::any address) {
for (unsigned i=0; i<cells_.size(); ++i) {
simple_recipe_base::add_probe(i, tag, address);
}
@@ -541,7 +541,7 @@ TEST(sde, solver) {
dec.place(*labels.locset("locs"), synapse(m4), "m4");
// a basic sampler: stores result in a vector
- auto sampler_ = [ncells, nsteps] (std::vector<arb_value_type>& results, unsigned count,
+ auto sampler_ = [nsteps] (std::vector<arb_value_type>& results, unsigned count,
probe_metadata pm, std::size_t n, sample_record const * samples) {
auto* point_info_ptr = arb::util::any_cast<const std::vector<arb::cable_probe_point_info>*>(pm.meta);
@@ -589,10 +589,10 @@ TEST(sde, solver) {
sde_recipe rec(ncells, ncvs, labels, dec, false);
// add probes
- rec.add_probe(1, cable_probe_point_state_cell{m1, "S"});
- rec.add_probe(2, cable_probe_point_state_cell{m2, "S"});
- rec.add_probe(3, cable_probe_point_state_cell{m3, "S"});
- rec.add_probe(4, cable_probe_point_state_cell{m4, "S"});
+ rec.add_probe_all_gids(1, cable_probe_point_state_cell{m1, "S"});
+ rec.add_probe_all_gids(2, cable_probe_point_state_cell{m2, "S"});
+ rec.add_probe_all_gids(3, cable_probe_point_state_cell{m3, "S"});
+ rec.add_probe_all_gids(4, cable_probe_point_state_cell{m4, "S"});
// results are accumulated for each time step
std::vector<accumulator> stats_m1(nsteps);
@@ -694,7 +694,7 @@ TEST(sde, coupled) {
dec.place(*labels.locset("locs"), synapse(m1), "m1");
// a basic sampler: stores result in a vector
- auto sampler_ = [ncells, nsteps] (std::vector<arb_value_type>& results, unsigned count,
+ auto sampler_ = [nsteps] (std::vector<arb_value_type>& results, unsigned count,
probe_metadata pm, std::size_t n, sample_record const * samples) {
auto* point_info_ptr = arb::util::any_cast<const std::vector<arb::cable_probe_point_info>*>(pm.meta);
@@ -732,8 +732,8 @@ TEST(sde, coupled) {
sde_recipe rec(ncells, ncvs, labels, dec, false);
// add probes
- rec.add_probe(1, cable_probe_point_state_cell{m1, "P"});
- rec.add_probe(2, cable_probe_point_state_cell{m1, "sigma"});
+ rec.add_probe_all_gids(1, cable_probe_point_state_cell{m1, "P"});
+ rec.add_probe_all_gids(2, cable_probe_point_state_cell{m1, "sigma"});
// results are accumulated for each time step
std::vector<accumulator> stats_P(nsteps);
@@ -854,7 +854,7 @@ public:
segment_tree tree;
tree.append(mnpos, {i*20., 0, 0.0, 4.0}, {i*20., 0, n1*cv_size, 4.0}, 1);
tree.append(0, {i*20., 0, ncvs*cv_size, 4.0}, 2);
- cells_.push_back(cable_cell(morphology(tree), labels, dec));
+ cells_.push_back(cable_cell(morphology(tree), dec, labels));
}
}
diff --git a/test/unit/test_spikes.cpp b/test/unit/test_spikes.cpp
index 4e923d79..987dd99f 100644
--- a/test/unit/test_spikes.cpp
+++ b/test/unit/test_spikes.cpp
@@ -230,7 +230,7 @@ TEST(SPIKES_TEST_CLASS, threshold_watcher_interpolation) {
decor.place("mid"_lab, arb::i_clamp::box(0.01+i*dt, duration, 0.5), "clamp");
decor.place("mid"_lab, arb::synapse("expsyn"), "synapse");
- arb::cable_cell cell(morpho, dict, decor);
+ arb::cable_cell cell(morpho, decor, dict);
cable1d_recipe rec({cell});
auto decomp = arb::partition_load_balance(rec, context);
--
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