New LFPy logo, some docstring fixes (#421)

* compartment->segment

* code-generated LFPy logo

* logo in docs

LFPy/alias_method.pyx

@@ -27,16 +27,16 @@ cpdef np.ndarray[long, ndim=1, negative_indices=False] alias_method(
     Parameters
     ----------
     idx: np.ndarray
-        compartment indices as array of ints
+        segment indices as array of ints
     probs: np.ndarray
-        compartment areas as array of floats
+        segment areas as array of floats
     nsyn: int
-        number of randomized compartment indices
+        number of randomized segment indices
 
     Returns
     -------
     out: np.ndarray
-        integer array of randomly drawn compartment indices
+        integer array of randomly drawn segment indices
 
     """
     assert idx.size == probs.size, 'length of idx and probs arrays must be equal'
@@ -77,7 +77,7 @@ cpdef alias_setup(np.ndarray[DTYPE_t, ndim=1, negative_indices=False] probs):
     Parameters
     ----------
     probs: np.ndarray
-        float array of compartment areas
+        float array of segment areas
 
     Returns
     -------

LFPy/cell.py

@@ -70,7 +70,7 @@ class Cell(object):
     tstop: float
         Stop time for simulation > 0 ms. Defaults to 100 ms.
     nsegs_method: 'lambda100' or 'lambda_f' or 'fixed_length' or None
-        nseg rule, used by NEURON to determine number of compartments.
+        nseg rule, used by NEURON to determine number of segments.
         Defaults to 'lambda100'
     max_nsegs_length: float or None
         Maximum segment length for method 'fixed_length'. Defaults to None
@@ -529,7 +529,7 @@ def set_synapse(self, idx, syntype,
         Parameters
         ----------
         idx: int
-            Index of compartment where synapse is inserted
+            Index of segment where synapse is inserted
         syntype: str
             Type of synapse. Built-in types in NEURON: ExpSyn, Exp2Syn
         record_current: bool
@@ -607,7 +607,7 @@ def set_point_process(self, idx, pptype, record_current=False,
         Parameters
         ----------
         idx: int
-            Index of compartment where point process is inserted
+            Index of segment where point process is inserted
         pptype: str
             Type of pointprocess. Examples: SEClamp, VClamp,
             IClamp, SinIClamp, ChirpIClamp
@@ -708,7 +708,7 @@ def _collect_geometry(self):
 
     def get_idx(self, section='allsec', z_min=-np.inf, z_max=np.inf):
         """
-        Returns compartment idx of segments from sections with names that match
+        Returns segment idx of segments from sections with names that match
         the pattern defined in input section on interval [z_min, z_max].
 
         Parameters
@@ -908,7 +908,7 @@ def enable_extracellular_stimulation(
         mechanism. Extracellular potentials are computed from electrode
         currents using the point-source approximation.
         If ``model`` is ``'inf'`` (default), potentials are computed as
-        (:math:`r_i` is the position of a compartment :math:`i`,
+        (:math:`r_i` is the position of a segment :math:`i`,
         :math:`r_n` is the position of an electrode :math:`n`,
         :math:`\\sigma` is the conductivity of the medium):
 
@@ -1006,7 +1006,7 @@ def simulate(self, probes=None,
         probes: list of :obj:, optional
             None or list of LFPykit.RecExtElectrode like object instances that
             each have a public method `get_transformation_matrix` returning
-            a matrix that linearly maps each compartments' transmembrane
+            a matrix that linearly maps each segments' transmembrane
             current to corresponding measurement as
 
             .. math:: \\mathbf{P} = \\mathbf{M} \\mathbf{I}
@@ -1845,7 +1845,7 @@ def get_intersegment_distance(self, idx0=0, idx1=0):
             raise ValueError(ERRMSG)
 
     def get_idx_children(self, parent="soma[0]"):
-        """Get the idx of parent's children sections, i.e. compartments ids
+        """Get the idx of parent's children sections, i.e. segments ids
         of sections connected to parent-argument
 
         Parameters
@@ -1952,7 +1952,7 @@ def get_idx_name(self, idx=np.array([0], dtype=int)):
         # ensure all idx are valid
         if np.any(idx >= self.totnsegs):
             wrongidx = idx[np.where(idx >= self.totnsegs)]
-            raise Exception('idx %s >= number of compartments' % str(wrongidx))
+            raise Exception('idx %s >= number of segments' % str(wrongidx))
 
         # create list of seg names:
         allsegnames = []
@@ -2306,13 +2306,13 @@ def get_idx_polygons(self, projection=('x', 'z')):
     def insert_v_ext(self, v_ext, t_ext):
         """Set external extracellular potential around cell.
         Playback of some extracellular potential v_ext on each cell.totnseg
-        compartments. Assumes that the "extracellular"-mechanism is inserted
-        on each compartment.
+        segments. Assumes that the "extracellular"-mechanism is inserted
+        on each segment.
         Can be used to study ephaptic effects and similar
         The inputs will be copied and attached to the cell object as
         cell.v_ext, cell.t_ext, and converted
         to (list of) neuron.h.Vector types, to allow playback into each
-        compartment e_extracellular reference.
+        segment e_extracellular reference.
         Can not be deleted prior to running cell.simulate()
 
         Parameters
@@ -2531,7 +2531,7 @@ def get_axial_currents_from_vmem(self, timepoints=None):
 
     def get_axial_resistance(self):
         """
-        Return NEURON axial resistance for all cell compartments.
+        Return NEURON axial resistance for all cell segments.
 
         Returns
         -------
@@ -2692,7 +2692,7 @@ def distort_geometry(self, factor=0., axis='z', nu=0.0):
         the neuron geometry along each axis.
         This method does not affect the underlying cable properties of the
         cell, only predictions of extracellular measurements (by affecting the
-        relative locations of sources representing the compartments).
+        relative locations of sources representing the segments).
 
         Parameters
         ----------

LFPy/eegmegcalc.py

@@ -108,7 +108,7 @@ def get_dipole_potential_from_multi_dipoles(self, cell, timepoints=None):
 
         By multiple current dipoles we mean the dipoles computed from all
         axial currents in a neuron simulation, typically two
-        axial currents per compartment, except for the root compartment.
+        axial currents per segment, except for the root segment.
 
         Parameters
         ----------
@@ -215,7 +215,7 @@ def get_multi_dipole_potential(self, cell,
 
         The multiple current dipoles corresponds to dipoles computed from all
         axial currents in a neuron simulation, typically two
-        axial currents per compartment, excluding the root compartment.
+        axial currents per segment, excluding the root segment.
 
         Parameters
         ----------

LFPy/network.py

@@ -84,7 +84,7 @@ class NetworkCell(TemplateCell):
     tstop: float
         stop time for simulation > 0 ms. Defaults to 100.
     nsegs_method: 'lambda100' or 'lambda_f' or 'fixed_length' or None
-        nseg rule, used by NEURON to determine number of compartments.
+        nseg rule, used by NEURON to determine number of segments.
         Defaults to 'lambda100'
     max_nsegs_length: float or None
         max segment length for method 'fixed_length'. Defaults to None
@@ -773,7 +773,7 @@ def connect(self, pre, post, connectivity,
             ``weight`` connection weight, ``delay`` connection delay,
             ``sec`` section name, ``sec.x`` relative location on section,
             and ``x``, ``y``, ``z`` the corresponding
-            midpoint coordinates of the target compartment.
+            midpoint coordinates of the target segment.
 
         Returns
         -------
@@ -1012,7 +1012,7 @@ def enable_extracellular_stimulation(self, electrode, t_ext=None, n=1,
         mechanism. Extracellular potentials are computed from electrode
         currents using the point-source approximation.
         If ``model`` is ``'inf'`` (default), potentials are computed as
-        (:math:`r_i` is the position of a compartment :math:`i`,
+        (:math:`r_i` is the position of a segment :math:`i`,
         :math:`r_n` is the position of an electrode :math:`n`,
         :math:`\\sigma` is the conductivity of the medium):
 
@@ -1076,7 +1076,7 @@ def simulate(self, probes=None,
         probes: list of :obj:, optional
             None or list of LFPykit.RecExtElectrode like object instances that
             each have a public method `get_transformation_matrix` returning
-            a matrix that linearly maps each compartments' transmembrane
+            a matrix that linearly maps each segments' transmembrane
             current to corresponding measurement as
 
             .. math:: \\mathbf{P} = \\mathbf{M} \\mathbf{I}
@@ -1394,7 +1394,7 @@ def __run_simulation_with_probes(self, cvode,
         probes: list of :obj:, optional
             None or list of LFPykit.RecExtElectrode like object instances that
             each have a public method `get_transformation_matrix` returning
-            a matrix that linearly maps each compartments' transmembrane
+            a matrix that linearly maps each segments' transmembrane
             current to corresponding measurement as
 
             .. math:: \\mathbf{P} = \\mathbf{M} \\mathbf{I}

LFPy/pointprocess.py

@@ -226,9 +226,9 @@ class StimIntElectrode(PointProcess):
     such as VClamp, SEClamp and ICLamp.
 
     Membrane currents will no longer sum to zero if these mechanisms are used,
-    as the equivalent circuit is akin to a current input to the compartment
+    as the equivalent circuit is akin to a current input to the segment
     from a far away extracellular location ("ground"), not immediately from
-    the surface to the inside of the compartment as with transmembrane
+    the surface to the inside of the segment as with transmembrane
     currents.
 
     Refer to NEURON documentation @ neuron.yale.edu for keyword arguments or

LFPy/templatecell.py

@@ -62,7 +62,7 @@ class TemplateCell(Cell):
     tstop : float
         stop time for simulation > 0 ms. Defaults to 100.
     nsegs_method : 'lambda100' or 'lambda_f' or 'fixed_length' or None
-        nseg rule, used by NEURON to determine number of compartments.
+        nseg rule, used by NEURON to determine number of segments.
         Defaults to 'lambda100'
     max_nsegs_length : float or None
         max segment length for method 'fixed_length'. Defaults to None

README.md

@@ -87,7 +87,7 @@ Information
 
 LFPy provides a set of easy-to-use Python classes for setting up your model, running your simulations and calculating the extracellular potentials arising from activity in your model neuron. If you have a model working in NEURON (www.neuron.yale.edu) already, it is likely that it can be adapted to work with LFPy.
 
-The extracellular potentials are calculated from transmembrane currents in multi-compartment neuron models using the line-source method (Holt & Koch, J Comp Neurosci 1999),
+The extracellular potentials are calculated from transmembrane currents in multicompartment neuron models using the line-source method (Holt & Koch, J Comp Neurosci 1999),
 but a simpler point-source method is also available. The calculations assume that the neuron are surrounded by an infinite extracellular medium with homogeneous and frequency
 independent conductivity, and compartments are assumed to be at least at a minimal distance from the electrode (which can be specified by the user). For more information on
 the biophysics underlying the numerical framework used see this coming book chapter: