Merge pull request #773 from pnbabu/vectors_bugs

Fix vector resize

pynestml/codegeneration/printers/nest_reference_converter.py

@@ -165,7 +165,7 @@ def convert_name_reference(self, variable: ASTVariable, prefix: str = '') -> str
             return "((POST_NEURON_TYPE*)(__target))->get_" + _name + "(_tr_t)"
 
         if variable.get_name() == PredefinedVariables.E_CONSTANT:
-            return 'numerics::e'
+            return "numerics::e"
 
         symbol = variable.get_scope().resolve_to_symbol(variable.get_complete_name(), SymbolKind.VARIABLE)
         if symbol is None:
@@ -176,10 +176,14 @@ def convert_name_reference(self, variable: ASTVariable, prefix: str = '') -> str
             code, message = Messages.get_could_not_resolve(variable.get_name())
             Logger.log_message(log_level=LoggingLevel.ERROR, code=code, message=message,
                                error_position=variable.get_source_position())
-            return ''
+            return ""
 
-        if symbol.is_local():
-            return variable.get_name() + ('[' + variable.get_vector_parameter() + ']' if symbol.has_vector_parameter() else '')
+        vector_param = ""
+        if symbol.has_vector_parameter():
+            vector_param = "[" + variable.get_vector_parameter() + "]"
+
+        # if symbol.is_local():
+        #     return variable.get_name() + vector_param
 
         if symbol.is_buffer():
             if isinstance(symbol.get_type_symbol(), UnitTypeSymbol):
@@ -190,33 +194,25 @@ def convert_name_reference(self, variable: ASTVariable, prefix: str = '') -> str
             if not units_conversion_factor == 1:
                 s += "(" + str(units_conversion_factor) + " * "
             s += self.print_origin(symbol, prefix=prefix) + self.buffer_value(symbol)
-            if symbol.has_vector_parameter():
-                s += '[' + variable.get_vector_parameter() + ']'
+            s += vector_param
             if not units_conversion_factor == 1:
                 s += ")"
             return s
 
         if symbol.is_inline_expression:
-            return 'get_' + variable.get_name() + '()' + ('[i]' if symbol.has_vector_parameter() else '')
+            return self.getter(symbol) + "()" + vector_param
 
         assert not symbol.is_kernel(), "NEST reference converter cannot print kernel; kernel should have been converted during code generation"
 
-        if symbol.is_state():
-            temp = ""
-            temp += self.getter(symbol) + "()"
-            temp += ('[' + variable.get_vector_parameter() + ']' if symbol.has_vector_parameter() else '')
-            return temp
+        if symbol.is_state() or symbol.is_inline_expression:
+            return self.getter(symbol) + "()" + vector_param
 
         variable_name = self.convert_to_cpp_name(variable.get_complete_name())
         if symbol.is_local():
-            return variable_name + ('[i]' if symbol.has_vector_parameter() else '')
-
-        if symbol.is_inline_expression:
-            return 'get_' + variable_name + '()' + ('[i]' if symbol.has_vector_parameter() else '')
+            return variable_name + vector_param
 
         return self.print_origin(symbol, prefix=prefix) + \
-            self.name(symbol) + \
-            ('[' + variable.get_vector_parameter() + ']' if symbol.has_vector_parameter() else '')
+            self.name(symbol) + vector_param
 
     def __get_unit_name(self, variable: ASTVariable):
         assert variable.get_scope() is not None, "Undeclared variable: " + variable.get_complete_name()

pynestml/codegeneration/resources_nest/point_neuron/directives/ReadFromDictionaryToTmp.jinja2

@@ -3,9 +3,12 @@
   @param variable VariableSymbol
 #}
 {%- if tracing %}/* generated by {{self._TemplateReference__context.name}} */ {% endif %}
-{%- if not variable.is_inline_expression and not variable.is_state() %}
+
+{%- if not variable.is_inline_expression %}
+{%- if not variable.is_state() %}
 {{declarations.print_variable_type(variable)}} tmp_{{names.name(variable)}} = {{names.getter(variable)}}();
 updateValue<{{declarations.print_variable_type(variable)}}>(__d, nest::{{names_namespace}}::_{{names.name(variable)}}, tmp_{{names.name(variable)}});
+
 {%- if vector_symbols|length > 0 %}
 // Resize vectors
 if (tmp_{{names.name(variable)}} != {{names.getter(variable)}}())
@@ -19,9 +22,29 @@ if (tmp_{{names.name(variable)}} != {{names.getter(variable)}}())
 {%- endfor %}
 }
 {%- endif %}
-{%- elif not variable.is_inline_expression and variable.is_state() %}
+
+{%- else %}
 {{declarations.print_variable_type(variable)}} tmp_{{names.convert_to_cpp_name(variable.get_symbol_name())}} = {{names.getter(variable)}}();
 updateValue<{{declarations.print_variable_type(variable)}}>(__d, nest::{{names_namespace}}::_{{variable.get_symbol_name()}}, tmp_{{names.convert_to_cpp_name(variable.get_symbol_name())}});
+{%- endif %}
+
+{%- if variable.has_vector_parameter() %}
+ {#
+Typecast the vector parameter to an int. If the typecast fails with a return value of 0, the vector parameter is a
+variable
+ #}
+{%- set vector_size = variable.get_vector_parameter() | int %}
+{%- if not vector_size %}
+{%- set vector_size = "tmp_" + variable.get_vector_parameter() %}
+{%- endif %}
+// Check if the new vector size matches its original size
+if ( tmp_{{names.name(variable)}}.size() != {{vector_size}} )
+{
+  std::stringstream msg;
+  msg << "The vector \"{{names.name(variable)}}\" does not match its size: " << {{vector_size}};
+  throw nest::BadProperty(msg.str());
+}
+{%- endif %}
 {%- else %}
   // ignores '{{names.name(variable)}}' {{declarations.print_variable_type(variable)}}' since it is an function and setter isn't defined
 {%- endif %}

tests/nest_tests/nest_vectors_test.py

@@ -19,15 +19,16 @@
 # You should have received a copy of the GNU General Public License
 # along with NEST.  If not, see <http://www.gnu.org/licenses/>.
 import os
-import unittest
 import numpy as np
 
 import nest
+import pytest
+from nest.lib.hl_api_exceptions import NESTErrors
 
 from pynestml.frontend.pynestml_frontend import generate_nest_target
 
 
-class NestVectorsIntegrationTest(unittest.TestCase):
+class TestNestVectorsIntegration:
     r"""
     Tests the code generation and vector operations from NESTML to NEST.
     """
@@ -70,3 +71,26 @@ def test_vectors(self):
         v_m = multimeter.get("events")["V_m"]
         print("V_m: {}".format(v_m))
         np.testing.assert_almost_equal(v_m[-1], -0.3)
+
+    @pytest.mark.xfail(strict=True, raises=NESTErrors.BadProperty)
+    def test_vectors_resize(self):
+        input_path = os.path.join(
+            os.path.realpath(os.path.join(os.path.dirname(__file__), "resources", "VectorsResize.nestml")))
+        target_path = "target"
+        logging_level = "INFO"
+        module_name = "vectorsmodule"
+        suffix = "_nestml"
+
+        generate_nest_target(input_path,
+                             target_path=target_path,
+                             logging_level=logging_level,
+                             module_name=module_name,
+                             suffix=suffix)
+        nest.set_verbosity("M_ALL")
+
+        nest.ResetKernel()
+        nest.Install(module_name)
+
+        neuron = nest.Create("vector_resize_nestml", params={"N": 200})
+        neuron.set(x=[1.0, 1.0, 4.0])
+        nest.Simulate(10)

tests/nest_tests/resources/VectorsResize.nestml

@@ -0,0 +1,52 @@
+"""
+VectorsResize.nestml
+####################
+
+
+Description
++++++++++++
+
+This model is used to test vector operations with NEST.
+
+
+Copyright statement
++++++++++++++++++++
+
+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/>.
+"""
+neuron vector_resize:
+    state:
+      # accumulator for x values
+      y real = 0.
+
+      x[N] real = 1.
+    end
+
+    parameters:
+      N integer = 1  # array size
+    end
+
+    update:
+      j integer = 0
+      y = 0
+      for j in 0 ... N step 1:
+        y += x[j]
+      end
+      print ("y= {y}\n")
+    end
+end