Updated folder structure of downloaded patdemo folder

torbjone · May 20, 2016 · c06f262 · c06f262
1 parent 0e735c6
commit c06f262
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Showing 4 changed files with 19 additions and 16 deletions.
diff --git a/examples/example1.py b/examples/example1.py
@@ -19,15 +19,15 @@
 
 
 #Fetch Mainen&Sejnowski 1996 model files
-if not os.path.isfile(join('patdemo', 'cells', 'cells', 'j4a.hoc')):
+if not os.path.isfile(join('cells', 'cells', 'j4a.hoc')):
     #get the model files:
     u = urlopen('http://senselab.med.yale.edu/ModelDB/eavBinDown.asp?o=2488&a=23&mime=application/zip')
     localFile = open('patdemo.zip', 'w')
     localFile.write(u.read())
     localFile.close()
     #unzip:
     myzip = zipfile.ZipFile('patdemo.zip', 'r')
-    myzip.extractall('patdemo')
+    myzip.extractall('.')
     myzip.close()
 
 
@@ -38,7 +38,7 @@
 
 # Define cell parameters
 cell_parameters = {          # various cell parameters,
-    'morphology' : join('patdemo', 'cells', 'cells', 'j4a.hoc'), # Mainen&Sejnowski, 1996
+    'morphology' : join('cells', 'cells', 'j4a.hoc'), # Mainen&Sejnowski, 1996
     'rm' : 30000.,      # membrane resistance
     'cm' : 1.0,         # membrane capacitance
     'Ra' : 150,        # axial resistance

diff --git a/examples/example3.py b/examples/example3.py
@@ -2,10 +2,12 @@
 '''
 LFPs from a population of cells relying on MPI
 '''
+
 import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib.collections import PolyCollection, LineCollection
 import os
+from os.path import join
 import sys
 if sys.version < '3':
     from urllib2 import urlopen
@@ -16,7 +18,6 @@
 import neuron
 from mpi4py import MPI
 
-
 #initialize the MPI interface
 COMM = MPI.COMM_WORLD
 SIZE = COMM.Get_size()
@@ -40,7 +41,7 @@ def stationary_poisson(nsyn,lambd,tstart,tstop):
 
 
 #Fetch Mainen&Sejnowski 1996 model files
-if not os.path.isfile('patdemo/cells/j4a.hoc') and RANK==0:
+if not os.path.isfile(join('cells', 'cells', 'j4a.hoc')) and RANK==0:
     #get the model files:
     u = urlopen('http://senselab.med.yale.edu/ModelDB/eavBinDown.asp?o=2488&a=23&mime=application/zip')
     localFile = open('patdemo.zip', 'w')
@@ -56,7 +57,7 @@ def stationary_poisson(nsyn,lambd,tstart,tstop):
 
 # Define cell parameters
 cell_parameters = {          # various cell parameters,
-    'morphology' : 'patdemo/cells/j4a.hoc', # Mainen&Sejnowski, 1996
+    'morphology' : join('cells', 'cells', 'j4a.hoc'), # Mainen&Sejnowski, 1996
     'rm' : 30000.,      # membrane resistance
     'cm' : 1.0,         # membrane capacitance
     'Ra' : 150,         # axial resistance
@@ -162,7 +163,7 @@ def stationary_poisson(nsyn,lambd,tstart,tstop):
     plt.axis('off')
 
     for i_cell in range(n_cells):
-        cell = LFPy.Cell('patdemo/cells/j4a.hoc',
+        cell = LFPy.Cell(join('cells', 'cells', 'j4a.hoc'),
                          nsegs_method='lambda_f',
                          lambda_f=5)
         cell.set_rotation(x=4.99, y=-4.33, z=z_rotation[i_cell])
@@ -188,8 +189,8 @@ def stationary_poisson(nsyn,lambd,tstart,tstop):
     ax.plot(point_electrode.x, point_electrode.z, 'o',
             markeredgecolor='none', markerfacecolor='b', markersize=3,
             zorder=10, clip_on=False)
-    plt.annotate("Electrode",\
-            xy=(0., 0.), xycoords='data',\
+    plt.annotate("Electrode",
+            xy=(0., 0.), xycoords='data',
             xytext=(-100., 1000.),
             arrowprops=dict(arrowstyle='wedge',
                             shrinkA=1,

diff --git a/examples/example5.py b/examples/example5.py
@@ -22,6 +22,7 @@
 
 #import some plotting stuff and the LFPy-module
 import os
+from os.path import join
 import sys
 if sys.version < '3':
     from urllib2 import urlopen
@@ -33,7 +34,7 @@
 import matplotlib.pyplot as plt
 
 #Fetch Mainen&Sejnowski 1996 model files
-if not os.path.isfile('patdemo/cells/j4a.hoc'):
+if not os.path.isfile(join('cells', 'cells', 'j4a.hoc')):
     #get the model files:
     u = urlopen('http://senselab.med.yale.edu/ModelDB/eavBinDown.asp?o=2488&a=23&mime=application/zip')
     localFile = open('patdemo.zip', 'w')
@@ -46,11 +47,11 @@
 
 #compile mod files every time, because of incompatibility with Hay2011 files:
 os.system('''
-          cd patdemo
+          cd cells
           nrnivmodl
           ''')
 #os.system('nrnivmodl')
-LFPy.cell.neuron.load_mechanisms('patdemo')
+LFPy.cell.neuron.load_mechanisms('cells')
 
 ################################################################################
 # Define parameters, using dictionaries

diff --git a/examples/example6.py b/examples/example6.py
@@ -23,6 +23,7 @@
 # importing some modules, including LFPy
 import LFPy
 import os
+from os.path import join
 import sys
 if sys.version < '3':
     from urllib2 import urlopen
@@ -41,7 +42,7 @@
 np.random.seed(1234)
 
 #Fetch Mainen&Sejnowski 1996 model files
-if not os.path.isfile('patdemo/cells/j4a.hoc'):
+if not os.path.isfile(join('cells', 'cells', 'j4a.hoc')):
     #get the model files:
     u = urlopen('http://senselab.med.yale.edu/ModelDB/eavBinDown.asp?o=2488&a=23&mime=application/zip')
     localFile = open('patdemo.zip', 'w')
@@ -54,11 +55,11 @@
 
 #compile mod files every time, because of incompatibility with Hay2011 files:
 os.system('''
-          cd patdemo
+          cd cells
           nrnivmodl
           ''')
 #os.system('nrnivmodl')
-LFPy.cell.neuron.load_mechanisms('patdemo')
+LFPy.cell.neuron.load_mechanisms('cells')
 
 ################################################################################
 # A couple of function declarations
@@ -219,7 +220,7 @@ def insert_synapses(synparams, section, n, spTimesFun, args):
 
 #define cell parameters used as input to cell-class
 cellParameters = {
-    'morphology' : 'morphologies/L5_Mainen96_wAxon_LFPy.hoc',
+    'morphology' : join('morphologies', 'L5_Mainen96_wAxon_LFPy.hoc'),
     'rm' : 30000,               # membrane resistance
     'cm' : 1.0,                 # membrane capacitance
     'Ra' : 150,                 # axial resistance