From 7e9d9bd08b228662ded7fef432a23e80a1eedaf0 Mon Sep 17 00:00:00 2001
From: Ben Cumming <bcumming@cscs.ch>
Date: Tue, 12 May 2020 15:07:42 +0200
Subject: [PATCH] restrict locset (#1033)
Add a `restrict` locset expression type that returns all locations in a locset that are in a specified region.
Also allow region and locset names with hyphens.
Fixes #1031
Fixes #1032
---
arbor/include/arbor/morph/locset.hpp | 3 +++
arbor/morph/locset.cpp | 34 +++++++++++++++++++++++++
python/cells.cpp | 2 +-
python/morph_parse.cpp | 2 ++
python/morphology.cpp | 6 ++---
python/s_expr.cpp | 6 +++--
python/test/cpp/s_expr.cpp | 8 +++++-
test/unit/morph_pred.hpp | 8 +++++-
test/unit/test_morph_expr.cpp | 37 ++++++++++++++++++++++++++++
9 files changed, 98 insertions(+), 8 deletions(-)
diff --git a/arbor/include/arbor/morph/locset.hpp b/arbor/include/arbor/morph/locset.hpp
index 24d9217e..a815b67f 100644
--- a/arbor/include/arbor/morph/locset.hpp
+++ b/arbor/include/arbor/morph/locset.hpp
@@ -142,6 +142,9 @@ locset most_distal(region reg);
// Most proximal point of a region.
locset most_proximal(region reg);
+// Returns all locations in a locset that are also in the region.
+locset restrict(locset ls, region reg);
+
// A range `left` to `right` of randomly selected locations with a
// uniform distribution from region `reg` generated using `seed`
locset uniform(region reg, unsigned left, unsigned right, uint64_t seed);
diff --git a/arbor/morph/locset.cpp b/arbor/morph/locset.cpp
index dc9b7617..0e4df9c3 100644
--- a/arbor/morph/locset.cpp
+++ b/arbor/morph/locset.cpp
@@ -348,6 +348,40 @@ std::ostream& operator<<(std::ostream& o, const lsum& x) {
return o << "(sum " << x.lhs << " " << x.rhs << ")";
}
+// Restrict a locset on to a region: returns all locations in the locset that
+// are also in the region.
+
+struct lrestrict_ {
+ locset ls;
+ region reg;
+};
+
+mlocation_list thingify_(const lrestrict_& P, const mprovider& p) {
+ mlocation_list L;
+
+ auto cables = thingify(P.reg, p).cables();
+ auto ends = util::transform_view(cables, [](const auto& c){return mlocation{c.branch, c.dist_pos};});
+
+ for (auto l: thingify(P.ls, p)) {
+ auto it = std::lower_bound(ends.begin(), ends.end(), l);
+ if (it==ends.end()) continue;
+ const auto& c = cables[std::distance(ends.begin(), it)];
+ if (c.branch==l.branch && c.prox_pos<=l.pos) {
+ L.push_back(l);
+ }
+ }
+
+ return L;
+}
+
+locset restrict(locset ls, region reg) {
+ return locset{lrestrict_{std::move(ls), std::move(reg)}};
+}
+
+std::ostream& operator<<(std::ostream& o, const lrestrict_& x) {
+ return o << "(restrict " << x.ls << " " << x.reg << ")";
+}
+
} // namespace ls
// The intersect and join operations in the arb:: namespace with locset so that
diff --git a/python/cells.cpp b/python/cells.cpp
index a74856bd..e0ae99ac 100644
--- a/python/cells.cpp
+++ b/python/cells.cpp
@@ -529,7 +529,7 @@ void register_cells(pybind11::module& m) {
.def("locations",
[](arb::cable_cell& c, const char* label) {return c.concrete_locset(label);},
"label"_a, "The locations of the cell morphology for a locset label.")
- .def("region",
+ .def("cables",
[](arb::cable_cell& c, const char* label) {return c.concrete_region(label).cables();},
"label"_a, "The cable segments of the cell morphology for a region label.")
// Discretization control.
diff --git a/python/morph_parse.cpp b/python/morph_parse.cpp
index 38111045..6c261029 100644
--- a/python/morph_parse.cpp
+++ b/python/morph_parse.cpp
@@ -239,6 +239,8 @@ std::unordered_multimap<std::string, evaluator> eval_map {
"'on_branches' with 1 argument: (pos:double)")},
{"locset", make_call<std::string>(arb::ls::named,
"'locset' with 1 argument: (name:string)")},
+ {"restrict", make_call<arb::locset, arb::region>(arb::ls::restrict,
+ "'restrict' with 2 arguments: (ls:locset, reg:region)")},
{"join", make_fold<arb::locset>(static_cast<arb::locset(*)(arb::locset, arb::locset)>(arb::join),
"'join' with at least 2 arguments: (locset locset [...locset])")},
{"sum", make_fold<arb::locset>(static_cast<arb::locset(*)(arb::locset, arb::locset)>(arb::sum),
diff --git a/python/morphology.cpp b/python/morphology.cpp
index 4c2047d5..443a1642 100644
--- a/python/morphology.cpp
+++ b/python/morphology.cpp
@@ -38,7 +38,7 @@ void register_morphology(pybind11::module& m) {
" position: The relative position (from 0., proximal, to 1., distal) on the branch.\n")
.def_readonly("branch", &arb::mlocation::branch,
"The id of the branch.")
- .def_readonly("position", &arb::mlocation::pos,
+ .def_readonly("pos", &arb::mlocation::pos,
"The relative position on the branch (∈ [0.,1.], where 0. means proximal and 1. distal).")
.def("__str__",
[](arb::mlocation l) { return util::pprintf("(location {} {})", l.branch, l.pos); })
@@ -101,9 +101,9 @@ void register_morphology(pybind11::module& m) {
return c;
}),
"branch_id"_a, "prox"_a, "dist"_a)
- .def_readonly("prox_pos", &arb::mcable::prox_pos,
+ .def_readonly("prox", &arb::mcable::prox_pos,
"The relative position of the proximal end of the cable on its branch ∈ [0,1].")
- .def_readonly("dist_pos", &arb::mcable::dist_pos,
+ .def_readonly("dist", &arb::mcable::dist_pos,
"The relative position of the distal end of the cable on its branch ∈ [0,1].")
.def_readonly("branch", &arb::mcable::branch,
"The id of the branch on which the cable lies.")
diff --git a/python/s_expr.cpp b/python/s_expr.cpp
index a7e40e8a..e879c17d 100644
--- a/python/s_expr.cpp
+++ b/python/s_expr.cpp
@@ -155,15 +155,17 @@ private:
}
// Parse alphanumeric sequence that starts with an alphabet character,
- // and my contain alphabet, numeric or underscor '_' characters.
+ // and my contain alphabet, numeric or underscore '_' characters.
//
// Valid names:
// sub_dendrite
+ // sub-dendrite
// temp_
// branch3
// A
// Invalid names:
// _cat ; can't start with underscore
+ // -cat ; can't start with hyphen
// 2ndvar ; can't start with numeric character
//
// Returns the appropriate token kind if name is a keyword.
@@ -182,7 +184,7 @@ private:
while(1) {
c = *current_;
- if(is_alphanumeric(c) || c=='_') {
+ if(is_alphanumeric(c) || c=='_' || c=='-') {
name += character();
}
else {
diff --git a/python/test/cpp/s_expr.cpp b/python/test/cpp/s_expr.cpp
index 567ec754..772103e5 100644
--- a/python/test/cpp/s_expr.cpp
+++ b/python/test/cpp/s_expr.cpp
@@ -16,15 +16,21 @@ TEST(s_expr, identifier) {
EXPECT_TRUE(test_identifier("f_1__"));
EXPECT_TRUE(test_identifier("A_1__"));
+ EXPECT_TRUE(test_identifier("A-1"));
+ EXPECT_TRUE(test_identifier("hello-world"));
+ EXPECT_TRUE(test_identifier("hello--world"));
+ EXPECT_TRUE(test_identifier("hello--world_"));
+
EXPECT_FALSE(test_identifier("_foobar"));
+ EXPECT_FALSE(test_identifier("-foobar"));
EXPECT_FALSE(test_identifier("2dogs"));
EXPECT_FALSE(test_identifier("1"));
EXPECT_FALSE(test_identifier("_"));
+ EXPECT_FALSE(test_identifier("-"));
EXPECT_FALSE(test_identifier(""));
EXPECT_FALSE(test_identifier(" foo"));
EXPECT_FALSE(test_identifier("foo "));
EXPECT_FALSE(test_identifier("foo bar"));
- EXPECT_FALSE(test_identifier("foo-bar"));
EXPECT_FALSE(test_identifier(""));
}
diff --git a/test/unit/morph_pred.hpp b/test/unit/morph_pred.hpp
index ebe57bd9..c66e85cf 100644
--- a/test/unit/morph_pred.hpp
+++ b/test/unit/morph_pred.hpp
@@ -4,6 +4,7 @@
#include "../gtest.h"
+#include <arbor/morph/locset.hpp>
#include <arbor/morph/morphology.hpp>
#include <arbor/morph/primitives.hpp>
#include <arbor/morph/region.hpp>
@@ -69,7 +70,7 @@ inline ::testing::AssertionResult region_eq(const arb::mprovider& p, arb::region
inline ::testing::AssertionResult mlocationlist_eq(const arb::mlocation_list& as, const arb::mlocation_list& bs) {
if (as.size()!=bs.size()) {
return ::testing::AssertionFailure()
- << "cablelists " << as << " and " << bs << " differ";
+ << "mlocation lists " << as << " and " << bs << " differ";
}
for (auto i: arb::util::count_along(as)) {
@@ -80,5 +81,10 @@ inline ::testing::AssertionResult mlocationlist_eq(const arb::mlocation_list& as
return ::testing::AssertionSuccess();
}
+inline ::testing::AssertionResult locset_eq(const arb::mprovider& p, arb::locset a, arb::locset b) {
+ return mlocationlist_eq(thingify(a, p), thingify(b, p));
+}
+
+
} // namespace testing
diff --git a/test/unit/test_morph_expr.cpp b/test/unit/test_morph_expr.cpp
index 35b0db1c..af9ef3c6 100644
--- a/test/unit/test_morph_expr.cpp
+++ b/test/unit/test_morph_expr.cpp
@@ -20,6 +20,7 @@ using namespace arb;
using embedding = embed_pwlin;
using testing::region_eq;
+using testing::locset_eq;
using testing::cablelist_eq;
using testing::mlocationlist_eq;
@@ -574,6 +575,42 @@ TEST(region, thingify_moderate_morphologies) {
EXPECT_TRUE(region_eq(mp, radius_gt(reg_c_, 2), cl{{0,0.55,0.7},{2,0,0.5},{3,0.1,0.375},{3,0.9,1}}));
EXPECT_TRUE(region_eq(mp, radius_gt(reg_d_, 2), cl{{0,0.55,0.7},{2,0,0.5},{3,0.1,0.375},{3,0.75,0.9}}));
+ // Test restriction
+
+ {
+ using ll = mlocation_list;
+ // two empty inputs -> empty output
+ EXPECT_TRUE(locset_eq(mp, ls::restrict(ll{}, {}), ll{}));
+ // empty locset + non-empty region -> empty output
+ EXPECT_TRUE(locset_eq(mp, ls::restrict(ll{}, reg::all()), ll{}));
+ // non-empty locset + empty region -> empty output
+ EXPECT_TRUE(locset_eq(mp, ls::restrict(ll{{0,0.4}, {3, 0.1}}, {}), ll{}));
+
+ ll locs{{0,0.4}, {3,0.1}};
+ // none of locs in region -> empty output
+ EXPECT_TRUE(locset_eq(mp, ls::restrict(locs, branch(1)), ll{}));
+ // some but not all locs in region -> correct subset
+ EXPECT_TRUE(locset_eq(mp, ls::restrict(locs, branch(0)), ll{{0,0.4}}));
+ // all locs in region -> locs in output
+ EXPECT_TRUE(locset_eq(mp, ls::restrict(locs, join(branch(0), branch(3))), locs));
+ // all locs in region -> locs in output
+ EXPECT_TRUE(locset_eq(mp, ls::restrict(locs, join(branch(0), branch(1), branch(3))), locs));
+ // should also work with non-ordered input locset
+ std::reverse(locs.begin(), locs.end());
+ EXPECT_TRUE(locset_eq(mp, ls::restrict(locs, join(branch(0), branch(3))), locs));
+
+ mlocation loc{1,0.5};
+ // location at end of cable
+ EXPECT_TRUE(locset_eq(mp, ls::restrict(loc, cable(1, 0.2, 0.5)), loc));
+ // location at start of cable
+ EXPECT_TRUE(locset_eq(mp, ls::restrict(loc, cable(1, 0.5, 0.7)), loc));
+ // location in zero-length cable
+ EXPECT_TRUE(locset_eq(mp, ls::restrict(loc, cable(1, 0.5, 0.5)), loc));
+ // location between cable end points
+ EXPECT_TRUE(locset_eq(mp, ls::restrict(loc, cable(1, 0.2, 0.7)), loc));
+ }
+
+
// Test some more interesting intersections and unions.
// 123456789 123456789
--
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