Merge pull request #3093 from HanjiaJiang/rename_ca_astro

Rename the variable "Ca" in astrocyte_lr_1994 to "Ca_astro"

doc/htmldoc/model_details/astrocyte_model_implementation.ipynb

@@ -84,39 +84,39 @@
     "    Parameters\n",
     "    ----------\n",
     "    y : list\n",
-    "        Vector containing the state variables [IP3, Ca, h_IP3R]\n",
+    "        Vector containing the state variables [IP3, Ca_astro, h_IP3R]\n",
     "    _ : unused var\n",
     "    p : Params instance\n",
     "        Object containing the astrocyte parameters.\n",
     "\n",
     "    Returns\n",
     "    -------\n",
-    "    dCa : double\n",
-    "        Derivative of Ca\n",
+    "    dCa_astro : double\n",
+    "        Derivative of Ca_astro\n",
     "    dIP3 : double\n",
     "        Derivative of IP3\n",
     "    dh_IP3R : double\n",
     "        Derivative of h_IP3R\n",
     "    \"\"\"\n",
     "    IP3 = y[0]\n",
-    "    Ca = y[1]\n",
+    "    Ca_astro = y[1]\n",
     "    h_IP3R = y[2]\n",
     "\n",
-    "    Ca = max(0, min(Ca, p.Ca_tot * (1 + p.ratio_ER_cyt)))\n",
+    "    Ca_astro = max(0, min(Ca_astro, p.Ca_tot * (1 + p.ratio_ER_cyt)))\n",
     "    alpha = p.k_IP3R * p.Kd_inh * (IP3 + p.Kd_IP3_1) / (IP3 + p.Kd_IP3_2)\n",
-    "    beta = p.k_IP3R * Ca\n",
-    "    Ca_ER = (p.Ca_tot - Ca) / p.ratio_ER_cyt\n",
+    "    beta = p.k_IP3R * Ca_astro\n",
+    "    Ca_ER = (p.Ca_tot - Ca_astro) / p.ratio_ER_cyt\n",
     "    m_inf = IP3 / (IP3 + p.Kd_IP3_1)\n",
-    "    n_inf = Ca / (Ca + p.Kd_act)\n",
-    "    J_ch = p.ratio_ER_cyt * p.rate_IP3R * ((m_inf * n_inf * h_IP3R) ** 3) * (Ca_ER - Ca)\n",
-    "    J_pump = p.rate_SERCA * (Ca**2) / (p.Km_SERCA**2 + Ca**2)\n",
-    "    J_leak = p.ratio_ER_cyt * p.rate_L * (Ca_ER - Ca)\n",
+    "    n_inf = Ca_astro / (Ca_astro + p.Kd_act)\n",
+    "    J_ch = p.ratio_ER_cyt * p.rate_IP3R * ((m_inf * n_inf * h_IP3R) ** 3) * (Ca_ER - Ca_astro)\n",
+    "    J_pump = p.rate_SERCA * (Ca_astro**2) / (p.Km_SERCA**2 + Ca_astro**2)\n",
+    "    J_leak = p.ratio_ER_cyt * p.rate_L * (Ca_ER - Ca_astro)\n",
     "\n",
-    "    dCa = J_ch - J_pump + J_leak\n",
+    "    dCa_astro = J_ch - J_pump + J_leak\n",
     "    dIP3 = (p.IP3_0 - IP3) / p.tau_IP3\n",
     "    dh_IP3R = alpha * (1 - h_IP3R) - beta * h_IP3R\n",
     "\n",
-    "    return dIP3, dCa, dh_IP3R"
+    "    return dIP3, dCa_astro, dh_IP3R"
    ]
   },
   {
@@ -164,7 +164,7 @@
     "    \"\"\"\n",
     "    t = np.arange(0, simtime, dt)  # time axis\n",
     "    n = len(t)\n",
-    "    y = np.zeros((n, 3))  # state variables: IP3, Ca, h_IP3R\n",
+    "    y = np.zeros((n, 3))  # state variables: IP3, Ca_astro, h_IP3R\n",
     "    # for the state variables, assign the same initial values as in test_astrocyte.py\n",
     "    y[0, 0] = 1.0\n",
     "    y[0, 1] = 1.0\n",
@@ -282,7 +282,7 @@
     "implementation detailed in\n",
     "``doc/htmldoc/model_details/astrocyte_model_implementation.ipynb``.\n",
     "This data is used as reference for the tests in ``test_astrocyte.py``.\\n\n",
-    "       Times                     IP3                       Ca                     h_IP3R         \"\"\",\n",
+    "       Times                     IP3                    Ca_astro                  h_IP3R\"\"\",\n",
     ")"
    ]
   },

models/astrocyte_lr_1994.cpp

@@ -61,7 +61,7 @@ RecordablesMap< astrocyte_lr_1994 >::create()
 {
   // use standard names whereever you can for consistency!
   insert_( names::IP3, &astrocyte_lr_1994::get_y_elem_< astrocyte_lr_1994::State_::IP3 > );
-  insert_( names::Ca, &astrocyte_lr_1994::get_y_elem_< astrocyte_lr_1994::State_::Ca > );
+  insert_( names::Ca_astro, &astrocyte_lr_1994::get_y_elem_< astrocyte_lr_1994::State_::Ca_astro > );
   insert_( names::h_IP3R, &astrocyte_lr_1994::get_y_elem_< astrocyte_lr_1994::State_::h_IP3R > );
 }
 
@@ -85,7 +85,7 @@ astrocyte_lr_1994_dynamics( double time, const double y[], double f[], void* pno
   const double& ip3 = y[ S::IP3 ];
   // Ca_tot_ corresponds to the c_0 (total [Ca++] in terms of cytosolic vol)
   // in De Young & Keizer (1992) and Li & Rinzel (1994)
-  const double& calc = std::max( 0.0, std::min( y[ S::Ca ], node.P_.Ca_tot_ ) ); // keep calcium within limits
+  const double& calc = std::max( 0.0, std::min( y[ S::Ca_astro ], node.P_.Ca_tot_ ) ); // keep calcium within limits
   const double& h_ip3r = y[ S::h_IP3R ];
 
   const double alpha_h_ip3r =
@@ -101,7 +101,7 @@ astrocyte_lr_1994_dynamics( double time, const double y[], double f[], void* pno
     * std::pow( h_ip3r, 3 ) * ( calc_ER - calc );
 
   f[ S::IP3 ] = ( node.P_.IP3_0_ - ip3 ) / node.P_.tau_IP3_;
-  f[ S::Ca ] = J_channel - J_pump + J_leak + node.B_.J_noise_;
+  f[ S::Ca_astro ] = J_channel - J_pump + J_leak + node.B_.J_noise_;
   f[ S::h_IP3R ] = alpha_h_ip3r * ( 1.0 - h_ip3r ) - beta_h_ip3r * h_ip3r;
 
   return GSL_SUCCESS;
@@ -137,7 +137,7 @@ nest::astrocyte_lr_1994::State_::State_( const Parameters_& p )
 {
   // initial values based on Li & Rinzel (1994) and Nadkarni & Jung (2003)
   y_[ IP3 ] = p.IP3_0_;
-  y_[ Ca ] = 0.073;
+  y_[ Ca_astro ] = 0.073;
   y_[ h_IP3R ] = 0.793;
 }
 
@@ -278,22 +278,22 @@ void
 nest::astrocyte_lr_1994::State_::get( DictionaryDatum& d ) const
 {
   def< double >( d, names::IP3, y_[ IP3 ] );
-  def< double >( d, names::Ca, y_[ Ca ] );
+  def< double >( d, names::Ca_astro, y_[ Ca_astro ] );
   def< double >( d, names::h_IP3R, y_[ h_IP3R ] );
 }
 
 void
 nest::astrocyte_lr_1994::State_::set( const DictionaryDatum& d, const Parameters_&, Node* node )
 {
   updateValueParam< double >( d, names::IP3, y_[ IP3 ], node );
-  updateValueParam< double >( d, names::Ca, y_[ Ca ], node );
+  updateValueParam< double >( d, names::Ca_astro, y_[ Ca_astro ], node );
   updateValueParam< double >( d, names::h_IP3R, y_[ h_IP3R ], node );
 
   if ( y_[ IP3 ] < 0 )
   {
     throw BadProperty( "IP3 concentration must be non-negative." );
   }
-  if ( y_[ Ca ] < 0 )
+  if ( y_[ Ca_astro ] < 0 )
   {
     throw BadProperty( "Calcium concentration must be non-negative." );
   }
@@ -465,15 +465,15 @@ nest::astrocyte_lr_1994::update( Time const& origin, const long from, const long
     }
 
     // keep calcium within limits
-    S_.y_[ State_::Ca ] = std::max( 0.0, std::min( S_.y_[ State_::Ca ], P_.Ca_tot_ ) );
+    S_.y_[ State_::Ca_astro ] = std::max( 0.0, std::min( S_.y_[ State_::Ca_astro ], P_.Ca_tot_ ) );
 
     // this is to add the incoming spikes to IP3
     S_.y_[ State_::IP3 ] += P_.delta_IP3_ * B_.spike_exc_.get_value( lag );
 
     // SIC generation according to Nadkarni & Jung, 2003
     //   Suprathreshold log of calcium concentration determines SIC generation
     //   1000.0: change unit to nM as in the original paper
-    const double calc_thr = ( S_.y_[ State_::Ca ] - P_.SIC_th_ ) * 1000.0;
+    const double calc_thr = ( S_.y_[ State_::Ca_astro ] - P_.SIC_th_ ) * 1000.0;
     const double sic_value = calc_thr > 1.0 ? std::log( calc_thr ) * P_.SIC_scale_ : 0.0;
     B_.sic_values[ lag ] = sic_value;
 

models/astrocyte_lr_1994.h

@@ -164,15 +164,15 @@ Parameters
 
 The following parameters can be set in the status dictionary.
 
-======  ========= =============================================================
+======== ========= =============================================================
 **Dynamic state variables**
--------------------------------------------------------------------------------
-IP3     µM        Inositol 1,4,5-trisphosphate concentration in the astrocytic
-                  cytosol
-Ca      µM        Calcium concentration in the astrocytic cytosol
-h_IP3R  unitless  Fraction of IP3 receptors on the astrocytic ER that are not
-                  yet inactivated by calcium
-======  ========= =============================================================
+--------------------------------------------------------------------------------
+IP3      µM        Inositol 1,4,5-trisphosphate concentration in the astrocytic
+                   cytosol
+Ca_astro µM        Calcium concentration in the astrocytic cytosol
+h_IP3R   unitless  Fraction of IP3 receptors on the astrocytic ER that are not
+                   yet inactivated by calcium
+======== ========= =============================================================
 
 =============== ========= =====================================================
 **Parameters**
@@ -354,8 +354,8 @@ class astrocyte_lr_1994 : public StructuralPlasticityNode
     enum StateVecElems
     {
       IP3 = 0,
-      Ca,     // 1
-      h_IP3R, // 2
+      Ca_astro, // 1
+      h_IP3R,   // 2
       STATE_VEC_SIZE
     };
 

nestkernel/nest_names.cpp

@@ -84,6 +84,7 @@ const Name buffer_size_target_data( "buffer_size_target_data" );
 
 const Name C_m( "C_m" );
 const Name Ca( "Ca" );
+const Name Ca_astro( "Ca_astro" );
 const Name Ca_tot( "Ca_tot" );
 const Name c( "c" );
 const Name c_1( "c_1" );

nestkernel/nest_names.h

@@ -110,6 +110,7 @@ extern const Name buffer_size_target_data;
 
 extern const Name C_m;
 extern const Name Ca;
+extern const Name Ca_astro;
 extern const Name Ca_tot;
 extern const Name c;
 extern const Name c_1;

pynest/examples/astrocytes/astrocyte_brunel.py

@@ -256,7 +256,7 @@ def plot_dynamics(astro_data, neuron_data, start):
     # astrocyte data
     astro_mask = astro_data["times"] > start
     astro_ip3 = astro_data["IP3"][astro_mask]
-    astro_cal = astro_data["Ca"][astro_mask]
+    astro_cal = astro_data["Ca_astro"][astro_mask]
     astro_times = astro_data["times"][astro_mask]
     astro_times_set = list(set(astro_times))
     ip3_means = np.array([np.mean(astro_ip3[astro_times == t]) for t in astro_times_set])
@@ -329,7 +329,7 @@ def run_simulation():
     # create and connect recorders (multimeter default resolution = 1 ms)
     sr_neuron = nest.Create("spike_recorder")
     mm_neuron = nest.Create("multimeter", params={"record_from": ["I_SIC"]})
-    mm_astro = nest.Create("multimeter", params={"record_from": ["IP3", "Ca"]})
+    mm_astro = nest.Create("multimeter", params={"record_from": ["IP3", "Ca_astro"]})
 
     # select nodes randomly and connect them with recorders
     print("Connecting recorders ...")

pynest/examples/astrocytes/astrocyte_interaction.py

@@ -95,7 +95,7 @@
 # Create and connect the astrocyte and its devices.
 
 astrocyte = nest.Create("astrocyte_lr_1994", params=params_astro)
-mm_astro = nest.Create("multimeter", params={"record_from": ["IP3", "Ca"]})
+mm_astro = nest.Create("multimeter", params={"record_from": ["IP3", "Ca_astro"]})
 nest.Connect(mm_astro, astrocyte)
 
 ###############################################################################
@@ -133,7 +133,7 @@
 axes[0].plot(data_pre["times"], data_pre["V_m"])
 axes[1].plot(data_astro["times"], data_astro["IP3"])
 axes[2].plot(data_post["times"], data_post["I_SIC"])
-axes[3].plot(data_astro["times"], data_astro["Ca"])
+axes[3].plot(data_astro["times"], data_astro["Ca_astro"])
 axes[0].set_title(f"Presynaptic neuron\n(Poisson rate = {poisson_rate_neuro} Hz)")
 axes[0].set_ylabel("Membrane potential (mV)")
 axes[2].set_title("Postsynaptic neuron")

pynest/examples/astrocytes/astrocyte_single.py

@@ -78,7 +78,7 @@
 
 astrocyte = nest.Create("astrocyte_lr_1994", params=params_astro)
 ps_astro = nest.Create("poisson_generator", params={"rate": poisson_rate})
-mm_astro = nest.Create("multimeter", params={"record_from": ["IP3", "Ca"]})
+mm_astro = nest.Create("multimeter", params={"record_from": ["IP3", "Ca_astro"]})
 nest.Connect(ps_astro, astrocyte, syn_spec={"weight": poisson_weight})
 nest.Connect(mm_astro, astrocyte)
 
@@ -93,7 +93,7 @@
 
 fig, axes = plt.subplots(2, 1, sharex=True, figsize=(6.4, 4.8), dpi=100)
 axes[0].plot(data["times"], data["IP3"])
-axes[1].plot(data["times"], data["Ca"])
+axes[1].plot(data["times"], data["Ca_astro"])
 axes[0].set_ylabel(r"[IP$_{3}$] ($\mu$M)")
 axes[1].set_ylabel(r"[Ca$^{2+}$] ($\mu$M)")
 axes[1].set_xlabel("Time (ms)")

pynest/examples/astrocytes/astrocyte_small_network.py

@@ -342,7 +342,7 @@ def plot_dynamics(astro_data, neuron_data, start):
     print("Plotting dynamics ...")
     # get astrocyte data
     astro_times, astro_ip3_mean, astro_ip3_sd = get_plot_data(astro_data, "IP3")
-    astro_times, astro_ca_mean, astro_ca_sd = get_plot_data(astro_data, "Ca")
+    astro_times, astro_ca_mean, astro_ca_sd = get_plot_data(astro_data, "Ca_astro")
     # get neuron data
     neuron_times, neuron_sic_mean, neuron_sic_sd = get_plot_data(neuron_data, "I_SIC")
     # set plots
@@ -413,7 +413,7 @@ def plot_dynamics(astro_data, neuron_data, start):
 )
 mm_pre_neurons = nest.Create("multimeter", params={"record_from": ["V_m"]})
 mm_post_neurons = nest.Create("multimeter", params={"record_from": ["V_m", "I_SIC"]})
-mm_astrocytes = nest.Create("multimeter", params={"record_from": ["IP3", "Ca"]})
+mm_astrocytes = nest.Create("multimeter", params={"record_from": ["IP3", "Ca_astro"]})
 nest.Connect(mm_pre_neurons, pre_neurons)
 nest.Connect(mm_post_neurons, post_neurons)
 nest.Connect(mm_astrocytes, astrocytes)

testsuite/pytests/test_astrocyte.dat

@@ -9,7 +9,7 @@
 # ``doc/htmldoc/model_details/astrocyte_model_implementation.ipynb``.
 # This data is used as reference for the tests in ``test_astrocyte.py``.
 # 
-#        Times                     IP3                       Ca                     h_IP3R         
+#        Times                     IP3                    Ca_astro                  h_IP3R
 1.000000000000000056e-01 9.999882386709698645e-01 1.000187105302611235e+00 9.999799984511013040e-01
 2.000000000000000111e-01 9.999764775066160016e-01 1.000374129429669079e+00 9.999599938057039950e-01
 3.000000000000000444e-01 9.999647165069364130e-01 1.000561072405474095e+00 9.999399860656773553e-01

testsuite/pytests/test_astrocyte.py

@@ -58,10 +58,10 @@ def test_closeness_nest_odeint():
 
     # create astrocyte and devices
     # initial values of the state variables as in the reference solution
-    astrocyte = nest.Create("astrocyte_lr_1994", params={"IP3": 1.0, "Ca": 1.0, "h_IP3R": 1.0})
+    astrocyte = nest.Create("astrocyte_lr_1994", params={"IP3": 1.0, "Ca_astro": 1.0, "h_IP3R": 1.0})
     mm = nest.Create(
         "multimeter",
-        {"interval": nest.resolution, "record_from": ["IP3", "Ca", "h_IP3R"]},
+        {"interval": nest.resolution, "record_from": ["IP3", "Ca_astro", "h_IP3R"]},
     )
     spk_ge = nest.Create("spike_generator", {"spike_times": spike_times, "spike_weights": spike_weights})
 
@@ -74,5 +74,5 @@ def test_closeness_nest_odeint():
 
     # compare results with reference data
     assert mm.events["IP3"] == pytest.approx(ref_ip3)
-    assert mm.events["Ca"] == pytest.approx(ref_ca)
+    assert mm.events["Ca_astro"] == pytest.approx(ref_ca)
     assert mm.events["h_IP3R"] == pytest.approx(ref_h_ip3r)

testsuite/pytests/test_sic_connection.py

@@ -63,11 +63,11 @@ def test_SynapseFunctionWithAeifModel():
     resol = nest.resolution
 
     # Create neurons and devices
-    astrocyte = nest.Create("astrocyte_lr_1994", {"Ca": 0.2})  # a calcium value which produces SIC
+    astrocyte = nest.Create("astrocyte_lr_1994", {"Ca_astro": 0.2})  # a calcium value which produces SIC
     neuron = nest.Create("aeif_cond_alpha_astro")
 
     mm_neuron = nest.Create("multimeter", params={"record_from": ["I_SIC"], "interval": resol})
-    mm_astro = nest.Create("multimeter", params={"record_from": ["Ca"], "interval": resol})
+    mm_astro = nest.Create("multimeter", params={"record_from": ["Ca_astro"], "interval": resol})
 
     nest.Connect(astrocyte, neuron, syn_spec={"synapse_model": "sic_connection"})
     nest.Connect(mm_neuron, neuron)
@@ -80,7 +80,7 @@ def test_SynapseFunctionWithAeifModel():
     # The expected SIC values are calculated based on the astrocyte dynamics
     # implemented in astrocyte_lr_1994.cpp.
     actual_sic_values = mm_neuron.events["I_SIC"]
-    Ca = mm_astro.events["Ca"]
+    Ca = mm_astro.events["Ca_astro"]
     f_v = np.vectorize(lambda x: np.log(x * 1000.0 - 196.69) if x * 1000.0 - 196.69 > 1.0 else 0.0)
     expected_sic_values = f_v(Ca)