Filter connections also by target when dumping layer connections

nestkernel/conn_builder.cpp

@@ -619,14 +619,14 @@ nest::OneToOneBuilder::connect_()
           Node* target = n->get_node();
 
           const size_t tnode_id = n->get_node_id();
-          const int idx = targets_->find( tnode_id );
-          if ( idx < 0 ) // Is local node in target list?
+          const long lid = targets_->get_lid( tnode_id );
+          if ( lid < 0 ) // Is local node in target list?
           {
             continue;
           }
 
           // one-to-one, thus we can use target idx for source as well
-          const size_t snode_id = ( *sources_ )[ idx ];
+          const size_t snode_id = ( *sources_ )[ lid ];
           if ( not allow_autapses_ and snode_id == tnode_id )
           {
             // no skipping required / possible,
@@ -819,7 +819,7 @@ nest::AllToAllBuilder::connect_()
           const size_t tnode_id = n->get_node_id();
 
           // Is the local node in the targets list?
-          if ( targets_->find( tnode_id ) < 0 )
+          if ( targets_->get_lid( tnode_id ) < 0 )
           {
             continue;
           }
@@ -1102,7 +1102,7 @@ nest::FixedInDegreeBuilder::connect_()
           const size_t tnode_id = n->get_node_id();
 
           // Is the local node in the targets list?
-          if ( targets_->find( tnode_id ) < 0 )
+          if ( targets_->get_lid( tnode_id ) < 0 )
           {
             continue;
           }
@@ -1534,7 +1534,7 @@ nest::BernoulliBuilder::connect_()
           const size_t tnode_id = n->get_node_id();
 
           // Is the local node in the targets list?
-          if ( targets_->find( tnode_id ) < 0 )
+          if ( targets_->get_lid( tnode_id ) < 0 )
           {
             continue;
           }

nestkernel/layer_impl.h

@@ -306,8 +306,9 @@ Layer< D >::dump_connections( std::ostream& out,
   std::vector< std::pair< Position< D >, size_t > >* src_vec = get_global_positions_vector( node_collection );
 
   // Dictionary with parameters for get_connections()
-  DictionaryDatum ncdict( new Dictionary );
-  def( ncdict, names::synapse_model, syn_model );
+  DictionaryDatum conn_filter( new Dictionary );
+  def( conn_filter, names::synapse_model, syn_model );
+  def( conn_filter, names::target, NodeCollectionDatum( target_layer->get_node_collection() ) );
 
   // Avoid setting up new array for each iteration of the loop
   std::vector< size_t > source_array( 1 );
@@ -321,8 +322,8 @@ Layer< D >::dump_connections( std::ostream& out,
     const Position< D > source_pos = src_iter->first;
 
     source_array[ 0 ] = source_node_id;
-    def( ncdict, names::source, NodeCollectionDatum( NodeCollection::create( source_array ) ) );
-    ArrayDatum connectome = kernel().connection_manager.get_connections( ncdict );
+    def( conn_filter, names::source, NodeCollectionDatum( NodeCollection::create( source_array ) ) );
+    ArrayDatum connectome = kernel().connection_manager.get_connections( conn_filter );
 
     // Print information about all local connections for current source
     for ( size_t i = 0; i < connectome.size(); ++i )
@@ -344,8 +345,9 @@ Layer< D >::dump_connections( std::ostream& out,
       Layer< D >* tgt_layer = dynamic_cast< Layer< D >* >( target_layer.get() );
 
       out << ' ';
-      const size_t tnode_id = tgt_layer->node_collection_->find( target_node_id );
-      tgt_layer->compute_displacement( source_pos, tnode_id ).print( out );
+      const long tnode_lid = tgt_layer->node_collection_->get_lid( target_node_id );
+      assert( tnode_lid >= 0 );
+      tgt_layer->compute_displacement( source_pos, tnode_lid ).print( out );
       out << '\n';
     }
   }

nestkernel/nestmodule.cpp

@@ -1072,7 +1072,7 @@ NestModule::Find_g_iFunction::execute( SLIInterpreter* i ) const
   NodeCollectionDatum nodecollection = getValue< NodeCollectionDatum >( i->OStack.pick( 1 ) );
   const long node_id = getValue< long >( i->OStack.pick( 0 ) );
 
-  const auto res = nodecollection->find( node_id );
+  const auto res = nodecollection->get_lid( node_id );
   i->OStack.pop( 2 );
   i->OStack.push( res );
   i->EStack.pop();

nestkernel/node_collection.cpp

@@ -981,11 +981,11 @@ NodeCollectionComposite::merge_parts_( std::vector< NodeCollectionPrimitive >& p
 bool
 NodeCollectionComposite::contains( const size_t node_id ) const
 {
-  return find( node_id ) != -1;
+  return get_lid( node_id ) != -1;
 }
 
 long
-NodeCollectionComposite::find( const size_t node_id ) const
+NodeCollectionComposite::get_lid( const size_t node_id ) const
 {
   const auto add_size_op = []( const long a, const NodeCollectionPrimitive& b ) { return a + b.size(); };
 
@@ -1018,7 +1018,7 @@ NodeCollectionComposite::find( const size_t node_id ) const
         // Need to find number of nodes in previous parts to know if the the step hits the node_id.
         const auto num_prev_nodes =
           std::accumulate( parts_.begin(), parts_.begin() + middle, static_cast< size_t >( 0 ), add_size_op );
-        const auto absolute_pos = num_prev_nodes + parts_[ middle ].find( node_id );
+        const auto absolute_pos = num_prev_nodes + parts_[ middle ].get_lid( node_id );
 
         // The first or the last node can be somewhere in the middle part.
         const auto absolute_part_start = start_part_ == middle ? start_offset_ : 0;
@@ -1041,7 +1041,7 @@ NodeCollectionComposite::find( const size_t node_id ) const
         // Since NC is not sliced, we can just calculate and return the local ID.
         const auto sum_pre =
           std::accumulate( parts_.begin(), parts_.begin() + middle, static_cast< size_t >( 0 ), add_size_op );
-        return sum_pre + parts_[ middle ].find( node_id );
+        return sum_pre + parts_[ middle ].get_lid( node_id );
       }
     }
   }

nestkernel/node_collection.h

@@ -386,7 +386,7 @@ class NodeCollection
    *
    * @return Index of node with given node ID; -1 if node not in NodeCollection.
    */
-  virtual long find( const size_t ) const = 0;
+  virtual long get_lid( const size_t ) const = 0;
 
   /**
    * Returns whether the NodeCollection contains any nodes with proxies or not.
@@ -512,7 +512,7 @@ class NodeCollectionPrimitive : public NodeCollection
   bool is_range() const override;
   bool empty() const override;
 
-  long find( const size_t ) const override;
+  long get_lid( const size_t ) const override;
 
   bool has_proxies() const override;
 
@@ -650,7 +650,7 @@ class NodeCollectionComposite : public NodeCollection
   bool is_range() const override;
   bool empty() const override;
 
-  long find( const size_t ) const override;
+  long get_lid( const size_t ) const override;
 
   bool has_proxies() const override;
 };
@@ -807,7 +807,7 @@ NodeCollectionPrimitive::empty() const
 }
 
 inline long
-NodeCollectionPrimitive::find( const size_t neuron_id ) const
+NodeCollectionPrimitive::get_lid( const size_t neuron_id ) const
 {
   if ( neuron_id > last_ )
   {

pynest/nest/lib/hl_api_helper.py

@@ -24,17 +24,16 @@
 API of the PyNEST wrapper.
 """
 
-import warnings
-import json
 import functools
-import textwrap
+import json
 import os
 import pydoc
-
+import textwrap
+import warnings
 from string import Template
 
-from ..ll_api import sli_func, sps, sr, spp
 from .. import pynestkernel as kernel
+from ..ll_api import sli_func, spp, sps, sr
 
 __all__ = [
     "broadcast",
@@ -52,6 +51,7 @@
     "restructure_data",
     "show_deprecation_warning",
     "show_help_with_pager",
+    "stringify_path",
     "SuppressedDeprecationWarning",
 ]
 
@@ -148,6 +148,31 @@ def new_func(*args, **kwargs):
     return deprecated_decorator
 
 
+def stringify_path(filepath):
+    """
+    Convert path-like object to string form.
+
+    Attempt to convert path-like object to a string by coercing objects
+    supporting the fspath protocol to its ``__fspath__`` method. Anything that
+    is not path-like, which includes bytes and strings, is passed through
+    unchanged.
+
+    Parameters
+    ----------
+    filepath : object
+        Object representing file system path.
+
+    Returns
+    -------
+    filepath : str
+        Stringified filepath.
+    """
+
+    if isinstance(filepath, os.PathLike):
+        filepath = filepath.__fspath__()  # should return str or bytes object
+    return filepath
+
+
 def is_literal(obj):
     """Check whether obj is a "literal": a unicode string or SLI literal
 

pynest/nest/lib/hl_api_spatial.py

@@ -23,19 +23,20 @@
 Functions relating to spatial properties of nodes
 """
 
+import os
 
 import numpy as np
 
 from ..ll_api import sli_func
-from .hl_api_helper import is_iterable
 from .hl_api_connections import GetConnections
+from .hl_api_helper import is_iterable, stringify_path
 from .hl_api_parallel_computing import NumProcesses, Rank
 from .hl_api_types import NodeCollection
 
 try:
     import matplotlib as mpl
-    import matplotlib.path as mpath
     import matplotlib.patches as mpatches
+    import matplotlib.path as mpath
 
     HAVE_MPL = True
 except ImportError:
@@ -530,9 +531,12 @@ def DumpLayerNodes(layer, outname):
             nest.DumpLayerNodes(s_nodes, 'positions.txt')
 
     """
+
     if not isinstance(layer, NodeCollection):
         raise TypeError("layer must be a NodeCollection")
 
+    outname = stringify_path(outname)
+
     sli_func(
         """
              (w) file exch DumpLayerNodes close
@@ -599,11 +603,15 @@ def DumpLayerConnections(source_layer, target_layer, synapse_model, outname):
             # write connectivity information to file
             nest.DumpLayerConnections(s_nodes, s_nodes, 'static_synapse', 'conns.txt')
     """
+
     if not isinstance(source_layer, NodeCollection):
         raise TypeError("source_layer must be a NodeCollection")
+
     if not isinstance(target_layer, NodeCollection):
         raise TypeError("target_layer must be a NodeCollection")
 
+    outname = stringify_path(outname)
+
     sli_func(
         """
              /oname  Set
@@ -1467,8 +1475,8 @@ def _create_mask_patches(mask, periodic, extent, source_pos, face_color="yellow"
 
     # import pyplot here and not at toplevel to avoid preventing users
     # from changing matplotlib backend after importing nest
-    import matplotlib.pyplot as plt
     import matplotlib as mtpl
+    import matplotlib.pyplot as plt
 
     edge_color = "black"
     alpha = 0.2

testsuite/pytests/sli2py_regressions/test_issue_2629.py

@@ -0,0 +1,91 @@
+# -*- coding: utf-8 -*-
+#
+# test_issue_2629.py
+#
+# This file is part of NEST.
+#
+# Copyright (C) 2004 The NEST Initiative
+#
+# NEST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#
+# NEST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with NEST.  If not, see <http://www.gnu.org/licenses/>.
+
+"""
+Regression test for Issue #2629 (GitHub).
+
+The issue was that ``DumpLayerConnections`` failed when a source layer was
+connected to more than one target layer. The test ensures that this is no
+longer the case.
+
+For each connection between the specified source and target layer,
+``DumpLayerConnections`` writes the following to file:
+
+    source_node_id target_node_id weight delay dx dy [dz]
+
+where (dx, dy [, dz]) is the displacement from source to target node.
+
+This test uses the ``tmp_path`` Pytest fixture, which will provide a
+temporary directory unique to the test invocation. ``tmp_path`` is a
+``pathlib.Path`` object. Hence, the test also implicitly verifies that it
+is possible to pass a ``pathlib.Path`` object as filename.
+"""
+
+import pytest
+
+import nest
+
+
+@pytest.fixture(scope="module")
+def network():
+    """Fixture for building network."""
+
+    grid = nest.spatial.grid(shape=[2, 1])
+    src_layer = nest.Create("iaf_psc_alpha", positions=grid)
+    tgt_layer_1 = nest.Create("iaf_psc_alpha", positions=grid)
+    tgt_layer_2 = nest.Create("iaf_psc_alpha", positions=grid)
+
+    nest.Connect(src_layer, tgt_layer_1, "all_to_all")
+    nest.Connect(src_layer, tgt_layer_2, "one_to_one")
+
+    return src_layer, tgt_layer_1, tgt_layer_2
+
+
+def test_dump_layer_connections_target_1(tmp_path, network):
+    """Test that dumping connections with target layer 1 works."""
+
+    src_layer, tgt_layer_1, _ = network
+
+    fname_1 = tmp_path / "conns_1.txt"
+    nest.DumpLayerConnections(src_layer, tgt_layer_1, "static_synapse", fname_1)
+    expected_dump_1 = [
+        "1 3 1 1 0 0",
+        "1 4 1 1 0.5 0",
+        "2 3 1 1 -0.5 0",
+        "2 4 1 1 0 0",
+    ]
+    actual_dump_1 = fname_1.read_text().splitlines()
+    assert actual_dump_1 == expected_dump_1
+
+
+def test_dump_layer_connections_target_2(tmp_path, network):
+    """Test that dumping connections with target layer 2 works."""
+
+    src_layer, _, tgt_layer_2 = network
+
+    fname_2 = tmp_path / "conns_2.txt"
+    nest.DumpLayerConnections(src_layer, tgt_layer_2, "static_synapse", fname_2)
+    expected_dump_2 = [
+        "1 5 1 1 0 0",
+        "2 6 1 1 0 0",
+    ]
+    actual_dump_2 = fname_2.read_text().splitlines()
+    assert actual_dump_2 == expected_dump_2