Merge pull request #226 from mingujo/min-test_re

fixed all of my scripts

code/utils/scripts/convolution_high_res_script.py

@@ -19,15 +19,13 @@
 
 from __future__ import absolute_import, division, print_function
 import sys, os
-#TODO : i'm gonna fix the location when i finish the test for stimuli.py
-sys.path.append(os.path.join(os.path.dirname(__file__), "../"))
+sys.path.append(os.path.join(os.path.dirname(__file__), "../functions/"))
 import numpy as np
 import matplotlib.pyplot as plt
 import nibabel as nib
 from stimuli import *
 from scipy.stats import gamma
 from organize_behavior_data import *
-from load_BOLD import *
 
 # Create the necessary directories if they do not exist
 dirs = ['../../../txt_output', '../../../txt_output/conv_high_res',\

code/utils/scripts/convolution_normal_script.py

@@ -18,15 +18,13 @@
 
 from __future__ import absolute_import, division, print_function
 import sys, os
-#TODO : i'm gonna fix the location when i finish the test for stimuli.py
-sys.path.append(os.path.join(os.path.dirname(__file__), "../"))
+sys.path.append(os.path.join(os.path.dirname(__file__), "../functions/"))
 import numpy as np
 import matplotlib.pyplot as plt
 import nibabel as nib
 from stimuli import *
 from scipy.stats import gamma
 from organize_behavior_data import *
-from load_BOLD import *
 
 # Create the necessary directories if they do not exist
 dirs = ['../../../txt_output', '../../../txt_output/conv_normal',\

code/utils/scripts/log_regression_script.py

@@ -12,7 +12,7 @@
 from __future__ import absolute_import, division, print_function
 import sys, os
 #TODO : later change this
-sys.path.append(os.path.join(os.path.dirname(__file__), "../"))
+sys.path.append(os.path.join(os.path.dirname(__file__), "../functions/"))
 import numpy as np
 import matplotlib.pyplot as plt
 import nibabel as nib
@@ -22,7 +22,7 @@
 
 
 # Create the necessary directories if they do not exist
-dirs = ['../../fig','../../fig/log_reg_behav']
+dirs = ['../../../fig','../../../fig/log_reg_behav']
 for d in dirs:
     if not os.path.exists(d):
             os.makedirs(d)

code/utils/tests/test_logistic_reg.py

@@ -0,0 +1,83 @@
+"""test_diagnostics.py
+Tests for the functions in logistic_reg.py module 
+
+Run with:
+
+    nosetests test_logistic_reg.py
+"""
+
+
+import os, sys
+sys.path.append(os.path.join(os.path.dirname(__file__), "../functions/"))
+from logistic_reg import *
+from organize_behavior_data import *
+from nose.tools import assert_equal
+from numpy.testing import assert_almost_equal, assert_array_equal
+import pandas as pd
+import statsmodels.api as sm
+import pylab as pl
+import numpy as np
+from scipy import stats
+from statsmodels.formula.api import logit, ols
+
+def test_add_gainlossratio():
+	"""Tests whether the gain/loss ratio is properly added in the data frame
+
+	"""
+
+	#load the subject 2's combined runs on the dataframe (use organize_behav_data.py)
+	run = load_in_dataframe(2)
+	gain = run.ix[:,1]
+	loss = run.ix[:,2]
+	#add the column for gain/loss ratio
+	run['ratio'] = gain/loss
+	run_mat=run.as_matrix()
+	run_ratio=run_mat[:,7]
+	#compare with the output from the actual output
+	test_run = load_in_dataframe(2)
+	test_run_added = add_gainlossratio(test_run).as_matrix()
+	test_run_added_ratio = test_run_added[:,7]
+	assert_array_equal(run_ratio,test_run_added_ratio)
+
+
+def test_organize_columns():
+	"""Tests whether columns in the data frame are organized or not for logistic regression
+
+	"""
+
+	run = load_in_dataframe(2)
+	run_added = add_gainlossratio(run)
+	a = run_added.drop('onset', 1) 
+	# drop PTval column
+	run_organized = a.drop('PTval', 1) 
+	# get the column names
+	cols = run_organized.columns.tolist() 
+	# put respcat column into front
+	cols.insert(0, cols.pop(cols.index('respcat'))) 
+	cols.insert(3, cols.pop(cols.index('ratio')))
+	# reorganize
+	run_organized = run_organized.reindex(columns= cols) 
+	# drop error(rescap=-1) in experiment
+	run_final = run_organized.drop(run_organized[run_organized.respcat == -1].index) 
+	test_run_final = organize_columns(run).as_matrix()
+	assert_array_equal(run_final.as_matrix(),test_run_final)
+
+
+
+def test_log_regression():
+	"""Tests the results of logistic regression.
+	Explore on the beta coefficient
+
+	"""
+	run = load_in_dataframe(2)
+	run_added = add_gainlossratio(run)
+	run_final = organize_columns(run_added)
+
+	#fit the logistic regression line
+	fitted = logit("respcat ~ gain + loss", run_final).fit()
+	#get the parameters
+	fitted_params = fitted.params.as_matrix()
+	test_fitted_params = log_regression(run_final).as_matrix()
+	assert_array_equal(fitted_params,test_fitted_params)
+
+