Merge pull request LFPy#3 from torbjone/master

Bug in example cell model folder structure?
torbjone · May 20, 2016 · 7222165 · 7222165
2 parents 471838c + fad2bf2
commit 7222165
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diff --git a/README.md b/README.md
@@ -22,8 +22,8 @@ The article can be found at http://dx.doi.org/10.3389%2Ffninf.2013.00041
 Citation:
 Linden H, Hagen E, Leski S, Norheim ES, Pettersen KH and Einevoll GT (2013). LFPy: A tool for biophysical simulation of extracellular potentials generated by detailed model neurons. Front. Neuroinform. 7:41. doi: 10.3389/fninf.2013.00041
 
-LFPy was developed in the Computational Neuroscience Group (http://compneuro.umb.no), Department of Mathemathical Sciences and Technology (http://www.nmbu.no/imt),
-at the Norwegian University of Life Sciences (http://www.nmbu.no) ,
+LFPy was developed in the Computational Neuroscience Group, Department of Mathemathical Sciences and Technology (http://www.nmbu.no/imt),
+at the Norwegian University of Life Sciences (http://www.nmbu.no),
 in collaboration with the Laboratory of Neuroinformatics (http://www.nencki.gov.pl/en/laboratory-of-neuroinformatics), 
 Nencki Institute of Experimental Biology (http://www.nencki.gov.pl), Warsaw, Poland. The effort was supported by 
 International Neuroinformatics Coordinating Facility (http://incf.org), the Research Council of Norway (http://www.forskningsradet.no/english) (eScience, NevroNor) and EU-FP7 (BrainScaleS, http://www.brainscales.org).
@@ -82,10 +82,10 @@ There are few options to install LFPy:
         cd LFPy-x.x
         (sudo) python setup.py install (--user)
 
-4.  Development version from subversion repository:
+4.  Development version from the GitHub repository:
     ::
-    
-        svn checkout http://bebiservice.umb.no/svn-public/LFPy-release/trunk LFPy
+
+        git clone https://github.com/LFPy/LFPy.git
         cd LFPy
         (sudo) python setup.py install (--user)
 

diff --git a/examples/example1.py b/examples/example1.py
@@ -13,13 +13,13 @@
 import zipfile
 import matplotlib.pyplot as plt
 from matplotlib.collections import PolyCollection
-
+from os.path import join
 plt.interactive(1)
 plt.close('all')
 
 
 #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')
@@ -38,7 +38,7 @@
 
 # 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

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

diff --git a/examples/example_mpi.py b/examples/example_mpi.py
@@ -8,7 +8,9 @@
 # The example uses mpi4py with openmpi, and do not rely on NEURON's MPI.
 ################################################################################
 '''
+
 import os
+from os.path import join
 import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib.collections import PolyCollection
@@ -27,31 +29,30 @@
 RANK = COMM.Get_rank()
 
 #Fetch Mainen&Sejnowski 1996 model files
-if not os.path.isfile('patdemo/cells/j4a.hoc'):
-    if 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')
-        localFile.write(u.read())
-        localFile.close()
-        #unzip:
-        myzip = zipfile.ZipFile('patdemo.zip', 'r')
-        myzip.extractall('.')
-        myzip.close()
+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')
+    localFile.write(u.read())
+    localFile.close()
+    #unzip:
+    myzip = zipfile.ZipFile('patdemo.zip', 'r')
+    myzip.extractall('.')
+    myzip.close()
+
+if RANK == 0:
+    #compile mod files
+    os.system('''
+              cd cells
+              nrnivmodl
+              ''')
 
-        #compile mod files
-        os.system('''
-                  cd patdemo
-                  nrnivmodl
-                  ''')
-    else:
-        pass
-
     #sync threads
-    COMM.Barrier()
+COMM.Barrier()
 
 #os.system('nrnivmodl')
-LFPy.cell.neuron.load_mechanisms('patdemo')
+LFPy.cell.neuron.load_mechanisms('cells')
 
 #set one global seed, ensure all randomizations are set on RANK 0 in script!
 np.random.seed(12345)
@@ -252,7 +253,7 @@ def plotstuff(self):
     ########### PARAMETERS ##################
     #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