[ENH] Integrate trials object with Unitary Event Analysis (UE) #643
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Comment on lines
-330
to
-372
| win_size = 100 * pq.ms | ||
| bin_size = 5 * pq.ms | ||
| win_step = 20 * pq.ms | ||
| pattern_hash = [3] | ||
| UE_dic = ue.jointJ_window_analysis(spiketrains=data, | ||
| pattern_hash=pattern_hash, | ||
| bin_size=bin_size, | ||
| win_size=win_size, | ||
| win_step=win_step) | ||
| expected_Js = np.array( | ||
| [0.57953708, 0.47348757, 0.1729669, | ||
| 0.01883295, -0.21934742, -0.80608759]) | ||
| expected_n_emp = np.array( | ||
| [9., 9., 7., 7., 6., 6.]) | ||
| expected_n_exp = np.array( | ||
| [6.5, 6.85, 6.05, 6.6, 6.45, 8.7]) | ||
| expected_rate = np.array( | ||
| [[0.02166667, 0.01861111], | ||
| [0.02277778, 0.01777778], | ||
| [0.02111111, 0.01777778], | ||
| [0.02277778, 0.01888889], | ||
| [0.02305556, 0.01722222], | ||
| [0.02388889, 0.02055556]]) * pq.kHz | ||
| expected_indecis_tril26 = [4., 4.] | ||
| expected_indecis_tril4 = [1.] | ||
| assert_array_almost_equal(UE_dic['Js'].squeeze(), expected_Js) | ||
| assert_array_almost_equal(UE_dic['n_emp'].squeeze(), expected_n_emp) | ||
| assert_array_almost_equal(UE_dic['n_exp'].squeeze(), expected_n_exp) | ||
| assert_array_almost_equal(UE_dic['rate_avg'].squeeze(), expected_rate) | ||
| assert_array_almost_equal(UE_dic['indices']['trial26'], | ||
| expected_indecis_tril26) | ||
| assert_array_almost_equal(UE_dic['indices']['trial4'], | ||
| expected_indecis_tril4) | ||
|
|
||
| # check the input parameters | ||
| input_params = UE_dic['input_parameters'] | ||
| self.assertEqual(input_params['pattern_hash'], pattern_hash) | ||
| self.assertEqual(input_params['bin_size'], bin_size) | ||
| self.assertEqual(input_params['win_size'], win_size) | ||
| self.assertEqual(input_params['win_step'], win_step) | ||
| self.assertEqual(input_params['method'], 'analytic_TrialByTrial') | ||
| self.assertEqual(input_params['t_start'], 0 * pq.s) | ||
| self.assertEqual(input_params['t_stop'], 200 * pq.ms) |
There was a problem hiding this comment.
Only indentation level changed.
Comment on lines
-510
to
-566
| UE_dic = ue.jointJ_window_analysis(spiketrains, bin_size=5 * pq.ms, | ||
| win_size=300 * pq.ms, | ||
| win_step=100 * pq.ms) | ||
|
|
||
| js_expected = [[0.3978179], | ||
| [0.08131966], | ||
| [-1.4239882], | ||
| [-0.9377029], | ||
| [-0.3374434], | ||
| [-0.2043383], | ||
| [-1.001536], | ||
| [-np.inf]] | ||
| indices_expected = \ | ||
| {'trial3': [12, 27, 31, 34, 27, 31, 34, 136, 136, 136], | ||
| 'trial4': [4, 60, 60, 60, 117, 117, 117]} | ||
| n_emp_expected = [[5.], | ||
| [4.], | ||
| [1.], | ||
| [2.], | ||
| [2.], | ||
| [2.], | ||
| [1.], | ||
| [0.]] | ||
| n_exp_expected = [[3.5591667], | ||
| [3.4536111], | ||
| [3.3158333], | ||
| [3.8466666], | ||
| [2.370278], | ||
| [2.0811112], | ||
| [2.4011111], | ||
| [3.0533333]] | ||
| rate_expected = [[[0.042, 0.03933334, 0.048]], | ||
| [[0.04533333, 0.038, 0.05]], | ||
| [[0.046, 0.04, 0.04666667]], | ||
| [[0.05066667, 0.042, 0.046]], | ||
| [[0.04466667, 0.03666667, 0.04066667]], | ||
| [[0.04066667, 0.03533333, 0.04333333]], | ||
| [[0.03933334, 0.038, 0.038]], | ||
| [[0.04066667, 0.04866667, 0.03666667]]] * (1. / pq.ms) | ||
| input_parameters_expected = {'pattern_hash': [7], | ||
| 'bin_size': 5 * pq.ms, | ||
| 'win_size': 300 * pq.ms, | ||
| 'win_step': 100 * pq.ms, | ||
| 'method': 'analytic_TrialByTrial', | ||
| 't_start': 0 * pq.s, | ||
| 't_stop': 1 * pq.s, 'n_surrogates': 100} | ||
|
|
||
| assert_array_almost_equal(UE_dic['Js'], js_expected) | ||
| assert_array_almost_equal(UE_dic['n_emp'], n_emp_expected) | ||
| assert_array_almost_equal(UE_dic['n_exp'], n_exp_expected) | ||
| assert_array_almost_equal(UE_dic['rate_avg'], rate_expected) | ||
| self.assertEqual(sorted(UE_dic['indices'].keys()), | ||
| sorted(indices_expected.keys())) | ||
| for trial_key in indices_expected.keys(): | ||
| assert_array_equal(indices_expected[trial_key], | ||
| UE_dic['indices'][trial_key]) | ||
| self.assertEqual(UE_dic['input_parameters'], input_parameters_expected) |
There was a problem hiding this comment.
Only indentation level changed.
| @@ -117,7 +119,7 @@ | |||
| " 'suptitle': None,\n", | |||
| "}\n", | |||
| "\n", | |||
| "\n", | |||
| "@trials_to_list_of_spiketrainlist\n", | |||
There was a problem hiding this comment.
- use Viziphant function here (later)
plot_ueshould accept trial object (-> later in Viziphant)- update
plot_uefunction in Viziphant - copy updated code into this notebook for now
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This pull request introduces an enhancement to Unitary Event Analysis (UE) using the the
elephant.trialsmodule to represent trials. This change is part of a greater effort to provide a more structured and unified approach for handling trial data in Elephant.Trial representations
trial object: The new trial_object is now used as the primary input structure for representing trials. This object handles trial data, see https://elephant.readthedocs.io/en/latest/reference/trials.html .
list of lists: The previous implementation relied on a nested structure of lists to represent trials.
Changes
jointJ_window_analysisno handles trial object