gin commit from gb-laptop

Modified files: 9

figs/fig2.py

@@ -8,6 +8,7 @@ import pandas
 from scipy import stats
 from importlib import reload
 import spatint_utils
+import os
 
 # reload
 reload(spatint_utils)
@@ -23,8 +24,10 @@ class Fig2:
         """Init class"""
 
         # read lgn size tuning dataframe
+        parentdir = os. path. dirname(os. getcwd())
+        filename = parentdir + '/data/lgn_sztun_df.pkl'
         self.lgn_sztun_df = pandas.read_pickle(
-            filepath_or_buffer='./to_publish/data/lgn_sztun_df.pkl')
+            filepath_or_buffer=filename)
 
     def ex_sztun_curve(self, figsize=(2.5, 2.5), ax=None):
         """Plot example dLGN size-tuning curve (Fig. 2h)

figs/fig4.py

@@ -11,6 +11,7 @@ from scipy import stats
 from importlib import reload
 import pickle
 import spatint_utils
+import os
 
 # reload modules
 reload(spatint_utils)
@@ -26,17 +27,20 @@ class Fig4:
     def __init__(self):
         """Init class"""
 
+        parentdir = os. path. dirname(os. getcwd())
+        filename = parentdir + '/data/params_mouse.yaml'
+
         # read trn size tuning dataframe
         self.trn_sztun_df = pandas.read_pickle(
-            filepath_or_buffer='./to_publish/data/trn_sztun_df.pkl')
+            filepath_or_buffer= parentdir + '/data/trn_sztun_df.pkl')
 
         # read dict for trn_sztun_ex
-        with open('./to_publish/data/trn_sztun_ex_dict.pkl', 'rb') as f:
+        with open(parentdir + '/data/trn_sztun_ex_dict.pkl', 'rb') as f:
             self.trn_sztun_ex_dict = pickle.load(f)
 
         # read trn retinotopy dataframe
         self.trn_retino_df = pandas.read_pickle(
-            filepath_or_buffer='./to_publish/data/trn_retino_df.pkl')
+            filepath_or_buffer=parentdir + '/data/trn_retino_df.pkl')
 
         # get data for trn retinotopy example series
         self.trn_retino_ex = self.trn_retino_df[(self.trn_retino_df.m == 'BL6_2018_0003') &
@@ -44,11 +48,11 @@ class Fig4:
 
         # read trn/lgn rf area dataframe
         self.rf_area_df = pandas.read_pickle(
-            filepath_or_buffer='./to_publish/data/rf_area_df.pkl')
+            filepath_or_buffer=parentdir + '/data/rf_area_df.pkl')
 
         # read lgn size tuning dataframe
         self.lgn_sztun_df = pandas.read_pickle(
-            filepath_or_buffer='./to_publish/data/lgn_sztun_df.pkl')
+            filepath_or_buffer=parentdir + '/data/lgn_sztun_df.pkl')
 
     def exrfs(self):
         """Plot example receptive fields (Fig. 4d,h)

figs/fig5.py

@@ -9,7 +9,7 @@ from importlib import reload
 import pickle
 from scipy.optimize import curve_fit
 import spatint_utils
-
+import os
 
 # reload module
 reload(spatint_utils)
@@ -24,12 +24,14 @@ class Fig5:
     def __init__(self):
         """Init class"""
 
+        parentdir = os. path. dirname(os. getcwd())
+
         # read trn size tuning dataframe
         self.trn_sztun_opto_df = pandas.read_pickle(
-            filepath_or_buffer='./to_publish/data/trn_sztun_opto_df.pkl')
+            filepath_or_buffer=parentdir + '/data/trn_sztun_opto_df.pkl')
 
         # read dict for trn sz tuning example
-        with open('./to_publish/data/trn_sztun_opto_ex_dict.pkl', 'rb') as f:
+        with open(parentdir + '/data/trn_sztun_opto_ex_dict.pkl', 'rb') as f:
             self.trn_sztun_opto_ex_dict = pickle.load(f)
 
     def ex_sztun_curve(self, figsize=(5, 2.5), ax=None):

figs/figS10.py

@@ -7,6 +7,7 @@ import pandas
 from scipy import stats
 from importlib import reload
 import spatint_utils
+import os
 
 # reload modules
 reload(spatint_utils)
@@ -20,17 +21,19 @@ class FigS10:
     def __init__(self):
         """Init class"""
 
+        parentdir = os. path. dirname(os. getcwd())
+
         # read lgn size tuning dataframe
         self.lgn_sztun_df = pandas.read_pickle(
-            filepath_or_buffer='./to_publish/data/lgn_sztun_df.pkl')
+            filepath_or_buffer=parentdir + '/data/lgn_sztun_df.pkl')
 
         # read trn size tuning dataframe
         self.trn_sztun_df = pandas.read_pickle(
-            filepath_or_buffer='./to_publish/data/trn_sztun_df.pkl')
+            filepath_or_buffer=parentdir + '/data/trn_sztun_df.pkl')
 
         # read trn/lgn rf area dataframe
         self.rf_area_df = pandas.read_pickle(
-            filepath_or_buffer='./to_publish/data/rf_area_df.pkl')
+            filepath_or_buffer=parentdir + '/data/rf_area_df.pkl')
 
     def drfstim_x_si(self, figsize=(2.5, 2.5), ax=None, ms=15, fs=6, lw=0.5):
         """Plots for each unit normalized distance between stimulus center and

figs/figS4.py

@@ -2,9 +2,10 @@
 
 # import
 import matplotlib.pyplot as plt
-import scipy
+import scipy.io
 import numpy as np
 import spatint_utils
+import os
 
 # load plot params
 spatint_utils.plot_params()
@@ -16,8 +17,10 @@ class FigS4:
     def __init__(self):
         """Init class"""
 
+        parentdir = os. path. dirname(os. getcwd())
+
         # load data from matfile
-        data = scipy.io.loadmat('./to_publish/data/v1_spat_int.mat')
+        data = scipy.io.loadmat(parentdir + '/data/v1_spat_int.mat')
 
         # unfold data
         self.layerDepth = data['layerDepth'][0]

figs/figS6.py

@@ -5,6 +5,7 @@ import matplotlib.pyplot as plt
 from importlib import reload
 import pandas
 import spatint_utils
+import os
 
 # reload modules
 reload(spatint_utils)
@@ -19,9 +20,11 @@ class FigS6:
     def __init__(self):
         """Init class"""
 
+        parentdir = os. path. dirname(os. getcwd())
+
         # read lgn size tuning dataframe
         self.lgn_sztun_df = pandas.read_pickle(
-            filepath_or_buffer='./to_publish/data/lgn_sztun_df.pkl')
+            filepath_or_buffer=parentdir + '/data/lgn_sztun_df.pkl')
 
     def ex_curves(self, figsize=(5, 2), axs=None):
         """Plot example dLGN size tuning curves (Fig. S6 a-j)

figs/figS8.py

@@ -6,6 +6,7 @@ from importlib import reload
 import pandas
 import spatint_utils
 import numpy as np
+import os
 
 # reload modules
 reload(spatint_utils)
@@ -21,9 +22,11 @@ class FigS8:
     def __init__(self):
         """Init class"""
 
+        parentdir = os. path. dirname(os. getcwd())
+
         # read lgn size tuning dataframe
         self.trn_sztun_opto_df = pandas.read_pickle(
-            filepath_or_buffer='./to_publish/data/trn_sztun_opto_df.pkl')
+            filepath_or_buffer=parentdir + '/data/trn_sztun_opto_df.pkl')
 
     def ex_curves(self, axs=None, figsize=(5, 2)):
         """Plot example dLGN size tuning curves (Fig. S6 a-j)

figs/figS9.py

@@ -7,6 +7,7 @@ import pandas
 from scipy import stats
 from importlib import reload
 import spatint_utils
+import os
 
 # reload modules
 reload(spatint_utils)
@@ -20,13 +21,15 @@ class FigS9:
     def __init__(self):
         """Init class"""
 
+        parentdir = os. path. dirname(os. getcwd())
+
         # read lgn size tuning dataframe
         self.trn_sztun_opto_df = pandas.read_pickle(
-            filepath_or_buffer='./to_publish/data/trn_sztun_opto_df.pkl')
+            filepath_or_buffer=parentdir + '/data/trn_sztun_opto_df.pkl')
 
         # read trn/lgn rf area dataframe
         self.rf_area_df = pandas.read_pickle(
-            filepath_or_buffer='./to_publish/data/rf_area_df.pkl')
+            filepath_or_buffer=parentdir + '/data/rf_area_df.pkl')
 
     def trnchange_x_props(self, figsize=(8, 2.7), axs=None):
         """Plot example dLGN size tuning curves (Fig. S6 a-j)

data/sim_edog.py

@@ -6,6 +6,7 @@ from operator import itemgetter
 from edog.tools import*
 import spatint_utils
 from importlib import reload
+import os
 
 # reload modules
 reload(spatint_utils)
@@ -157,7 +158,8 @@ class SimEdog:
         """
 
         # get parameters
-        filename = "./to_publish/data/params_mouse.yaml"
+        parentdir = os. path. dirname(os. getcwd())
+        filename = parentdir + '/data/params_mouse.yaml'
         params = parse_parameters(filename)
 
         nt, nr, dt, dr = itemgetter("nt", "nr", "dt", "dr")(params["grid"])

figs/wrap.py

@@ -1,14 +1,10 @@
-import fig2
-import fig3
-import sim_edog
-import fig4
-import fig5
-import figS4
-import figS6
-import figS8
-import figS9
-import figS10
+from importlib import reload
 
+figs = ['fig2', 'fig3', 'sim_edog', 'fig4', 'fig5', 'figS4', 'figS6', 'figS8', 'figS9', 'figS10']
+
+for fig in figs:
+    exec ('import ' + fig)
+    reload(eval(fig))
 
 # panels for figure 2
 f2 = fig2.Fig2()