adding more tests to improve coverage

Author: ccluri

README.rst

@@ -42,6 +42,10 @@ Also included here are installation instructions, authors and their
 contributions, citation policy, contacts etc.,
 
 
+Also included are `Tutorials!`_
+
+.. _Tutorials!: /docs/source/TUTORIALS.rst
+
 .. include:: ./docs/source/TUTORIALS.rst
 
 

figures/kCSD_properties/sources_electrodes.odg

@@ -11,7 +11,7 @@
 import unittest
 import numpy as np
 from kcsd import ValidateKCSD1D, ValidateKCSD2D, ValidateKCSD3D
-from kcsd import csd_profile as CSD
+from kcsd import csd_profile as CSDp
 from kcsd import KCSD1D, KCSD2D, MoIKCSD, KCSD3D, oKCSD2D, oKCSD3D
 
 
@@ -21,7 +21,7 @@ def setUp(self):
         utils = ValidateKCSD1D(csd_seed=42)
         self.ele_pos = utils.generate_electrodes(total_ele=10,
                                                  ele_lims=[0.1, 0.9])
-        self.csd_profile = CSD.gauss_1d_mono
+        self.csd_profile = CSDp.gauss_1d_mono
         self.csd_at, self.csd = utils.generate_csd(self.csd_profile,
                                                    csd_seed=42)
         pots = utils.calculate_potential(self.csd, self.csd_at, self.ele_pos,
@@ -42,6 +42,25 @@ def test_kcsd1d_estimate(self, cv_params={}):
         rms /= np.linalg.norm(true_csd)
         self.assertLess(rms, 0.5, msg='RMS between trueCSD and estimate > 0.5')
 
+    def test_lcurve(self):
+        result = KCSD1D(self.ele_pos, self.pots,
+                        **self.test_params)
+        result.L_curve()
+        vals = result.values()
+        pvals = result.values('POT')
+        true_csd = self.csd_profile(result.estm_x, 42)
+        rms = np.linalg.norm(np.array(vals[:, 0]) - true_csd)
+        rms /= np.linalg.norm(true_csd)
+        self.assertLess(rms, 0.5, msg='RMS between trueCSD and estimate > 0.5')
+        
+    # def test_method_generic_lim(self):
+    #     self.test_params.update({'src_type': 'gauss_lim'})
+    #     self.test_kcsd1d_estimate()
+
+    # def test_method_generic_step(self):
+    #     self.test_params.update({'src_type': 'step'})
+    #     self.test_kcsd1d_estimate()
+        
     def test_valid_inputs(self):
         self.test_method = 'KCSD1D'
         self.test_params = {'src_type': 22}
@@ -51,15 +70,15 @@ def test_valid_inputs(self):
         self.assertRaises(TypeError, self.test_kcsd1d_estimate)
         cv_params = {'InvalidCVArg': np.array((0.1, 0.25, 0.5))}
         self.assertRaises(TypeError, self.test_kcsd1d_estimate, cv_params)
-
+        
 
 class KCSD2D_TestCase(unittest.TestCase):
     def setUp(self):
         dim = 2
         utils = ValidateKCSD2D(csd_seed=43)
         self.ele_pos = utils.generate_electrodes(total_ele=49,
                                                  ele_lims=[0.1, 0.9])
-        self.csd_profile = CSD.gauss_2d_large
+        self.csd_profile = CSDp.gauss_2d_large
         self.csd_at, self.csd = utils.generate_csd(self.csd_profile,
                                                    csd_seed=43)
         pots = utils.calculate_potential(self.csd, self.csd_at, self.ele_pos,
@@ -95,6 +114,26 @@ def test_moi_estimate(self):
         self.assertLess(rms, 2.5, msg='RMS ' + str(rms) +
                         'between trueCSD and estimate > 2.5')
 
+    def test_lcurve(self):
+        result = KCSD2D(self.ele_pos, self.pots,
+                        **self.test_params)
+        result.L_curve()
+        vals = result.values()
+        pvals = result.values('POT')
+        true_csd = self.csd_profile(result.estm_pos, 43)
+        rms = np.linalg.norm(np.array(vals[:, :, 0]) - true_csd)
+        rms /= np.linalg.norm(true_csd)
+        self.assertLess(rms, 0.5, msg='RMS ' + str(rms) +
+                        'between trueCSD and estimate > 0.5')
+
+    def test_method_generic_lim(self):
+        self.test_params.update({'src_type': 'gauss_lim'})
+        self.test_kcsd2d_estimate()
+
+    # def test_method_generic_step(self):
+    #     self.test_params.update({'src_type': 'step'})
+    #     self.test_kcsd2d_estimate()
+        
     def test_valid_inputs(self):
         self.test_method = 'KCSD2D'
         self.test_params = {'src_type': 22}
@@ -111,7 +150,7 @@ def setUp(self):
         utils = ValidateKCSD3D(csd_seed=44)
         self.ele_pos = utils.generate_electrodes(total_ele=64,
                                                  ele_lims=[0.1, 0.9])
-        self.csd_profile = CSD.gauss_3d_large
+        self.csd_profile = CSDp.gauss_3d_large
         self.csd_at, self.csd = utils.generate_csd(self.csd_profile,
                                                    csd_seed=44)
         pots = utils.calculate_potential(self.csd, self.csd_at, self.ele_pos,
@@ -130,13 +169,22 @@ def test_kcsd3d_estimate(self, cv_params={}):
                         **self.test_params)
         result.cross_validate()
         vals = result.values()
+        pvals = result.values('POT')
         true_csd = self.csd_profile(result.estm_pos, 44)
-        print(true_csd.shape, vals.shape)  # Meh here!
+        # print(true_csd.shape, vals.shape)  # Meh here!
         rms = np.linalg.norm(np.array(vals[:, :, :, 0]) - true_csd)
         rms /= np.linalg.norm(true_csd)
         self.assertLess(rms, 0.5, msg='RMS ' + str(rms) +
                         'between trueCSD and estimate > 0.5')
 
+    def test_method_generic_lim(self):
+        self.test_params.update({'src_type': 'gauss_lim'})
+        self.test_kcsd3d_estimate()
+    
+    # def test_method_generic_step(self):
+    #     self.test_params.update({'src_type': 'step'})
+    #     self.test_kcsd3d_estimate()
+        
     def test_valid_inputs(self):
         self.test_method = 'KCSD3D'
         self.test_params = {'src_type': 22}