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0.1.99
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Final release 0.2.0?
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@DominiqueMakowski
DominiqueMakowski committed Aug 14, 2017
1 parent 61bbaef commit 92c2878
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Showing 5 changed files with 124 additions and 73 deletions.
2 changes: 1 addition & 1 deletion neurokit/__init__.py
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@@ -1,7 +1,7 @@
"""
neurokit module.
"""
__version__ = "0.1.94"
__version__ = "0.1.99"

from .miscellaneous import *
from .statistics import *
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4 changes: 2 additions & 2 deletions neurokit/bio/bio_ecg.py
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Expand Up @@ -906,9 +906,9 @@ def compute_features(variable, prefix, response):
keys = [s.replace('_Baseline', '') for s in keys] # Remove baseline part
for key in keys:
try:
ECG_Response["ECG_HRV_" + key + "_Diff"] = ECG_Response[key] - ECG_Response[key + "_Baseline"]
ECG_Response[key + "_Diff"] = ECG_Response[key] - ECG_Response[key + "_Baseline"]
except KeyError:
ECG_Response["ECG_HRV_" + key + "_Diff"] = np.nan
ECG_Response[key + "_Diff"] = np.nan



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17 changes: 17 additions & 0 deletions neurokit/eeg/eeg_complexity.py
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Expand Up @@ -8,6 +8,23 @@
import re


# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
#def eeg_complexity(epochs):
# """
# """
# df = epochs.to_data_frame(index=["epoch", "time", "condition"])
#
# for index, epoch in enumerate(epochs):
# df = epoch



# ==============================================================================
# ==============================================================================
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105 changes: 104 additions & 1 deletion neurokit/eeg/eeg_data.py
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Expand Up @@ -314,18 +314,24 @@ def eeg_create_events(onsets, conditions=None):
"""
event_id = {}

# Sanity check
if len(conditions) != len(onsets):
print("NeuroKit Warning: eeg_create_events(): conditions parameter of different length than onsets. Aborting.")
return()

if conditions is None:
conditions = ["Event"] * len(onsets)



event_names = list(set(conditions))
# event_index = [1, 2, 3, 4, 5, 32, 64, 128]
event_index = list(range(len(event_names)))
for i in enumerate(event_names):
conditions = [event_index[i[0]] if x==i[1] else x for x in conditions]
event_id[i[1]] = event_index[i[0]]

events = np.array([onsets, [0]*len(onsets), conditions]).T
events = np.array([onsets, [0]*len(onsets), conditions])
return(events, event_id)


Expand Down Expand Up @@ -421,8 +427,105 @@ def eeg_add_events(raw, events_channel, conditions=None, treshold="auto", cut="h



# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
def eeg_epochs_to_dict(epochs, include="all", exclude=None, hemisphere="both", include_central=True):
"""
Convert mne.Epochs object to Python dict.
"""
data = {}
for index, epoch in enumerate(epochs.get_data()):
epoch = pd.DataFrame(epoch.T)
epoch.columns = epochs.ch_names

selection = eeg_select_sensor_area(include=include, exclude=exclude, hemisphere=hemisphere, include_central=include_central)

data[index] = epoch[selection]
return()


# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
def eeg_select_sensor_area(include="all", exclude=None, hemisphere="both", include_central=True):
"""
Returns list of electrodes names (according to a 10-20 EEG montage). This function is probably not very flexibile. Looking for help to improve it.
Parameters
----------
include : str
Sensor area to include.
exclude : str or None
Sensor area to exclude.
hemisphere : str
Select both hemispheres? "both", "left" or "right".
include_central : bool
if `hemisphere != "both"`, select the central line?
Returns
----------
sensors : list
List of sensors corresponding to the selected area.
Example
----------
>>> import neurokit as nk
>>> nk.eeg_select_sensor_area(include="F", exclude="C")
Notes
----------
*Authors*
- Dominique Makowski (https://github.com/DominiqueMakowski)
References
------------
- None
"""
sensors = ['AF3', 'AF4', 'AF7', 'AF8', 'C1', 'C2', 'C3', 'C4', 'C5', 'C6', 'CP1', 'CP2', 'CP3', 'CP4', 'CP5', 'CP6', 'CPz', 'Cz', 'F1', 'F2', 'F3', 'F4', 'F5', 'F6', 'F7', 'F8', 'FC1', 'FC2', 'FC3', 'FC4', 'FC5', 'FC6', 'Fp1', 'Fp2', 'FT10', 'FT7', 'FT8', 'FT9', 'O1', 'O2', 'Oz', 'P1', 'P2', 'P3', 'P4', 'P5', 'P6', 'P7', 'P8', 'PO3', 'PO4', 'PO7', 'PO8', 'POz', 'Pz', 'FCz', 'T7', 'T8', 'TP10', 'TP7', 'TP8', 'TP9', 'AFz']

if include != "all":
sensors = [s for s in sensors if include in s]

if exclude != None:
if isinstance(exclude, str):
exclude = [exclude]
for to_exclude in exclude:
sensors = [s for s in sensors if to_exclude not in s]

if hemisphere != "both":
if include_central == False:
if hemisphere == "left":
sensors = [s for s in sensors if "1" in s or "3" in s or "5" in s or "7" in s or "9" in s]
if hemisphere == "right":
sensors = [s for s in sensors if "2" in s or "4" in s or "6" in s or "8" in s or "10" in s]
else:
if hemisphere == "left":
sensors = [s for s in sensors if "1" in s or "3" in s or "5" in s or "7" in s or "9" in s or "z" in s]
if hemisphere == "right":
sensors = [s for s in sensors if "2" in s or "4" in s or "6" in s or "8" in s or "10" in s or "z" in s]


return(sensors)



#==============================================================================
#==============================================================================
#==============================================================================
#==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
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69 changes: 0 additions & 69 deletions neurokit/eeg/eeg_preprocessing.py
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Expand Up @@ -315,72 +315,3 @@ def eeg_epoching(raw, events, event_id, tmin=-0.2, tmax=1, eog_reject=600e-6, pr
epochs.pick_types(meg=False, eeg=True)
return(epochs)

# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
# ==============================================================================
def eeg_select_sensor_area(include="all", exclude=None, hemisphere="both", include_central=True):
"""
Returns list of electrodes names (according to a 10-20 EEG montage). This function is probably not very flexibile. Looking for help to improve it.
Parameters
----------
include : str
Sensor area to include.
exclude : str or None
Sensor area to exclude.
hemisphere : str
Select both hemispheres? "both", "left" or "right".
include_central : bool
if `hemisphere != "both"`, select the central line?
Returns
----------
sensors : list
List of sensors corresponding to the selected area.
Example
----------
>>> import neurokit as nk
>>> nk.eeg_select_sensor_area(include="F", exclude="C")
Notes
----------
*Authors*
- Dominique Makowski (https://github.com/DominiqueMakowski)
References
------------
- None
"""
sensors = ['AF3', 'AF4', 'AF7', 'AF8', 'C1', 'C2', 'C3', 'C4', 'C5', 'C6', 'CP1', 'CP2', 'CP3', 'CP4', 'CP5', 'CP6', 'CPz', 'Cz', 'F1', 'F2', 'F3', 'F4', 'F5', 'F6', 'F7', 'F8', 'FC1', 'FC2', 'FC3', 'FC4', 'FC5', 'FC6', 'Fp1', 'Fp2', 'FT10', 'FT7', 'FT8', 'FT9', 'O1', 'O2', 'Oz', 'P1', 'P2', 'P3', 'P4', 'P5', 'P6', 'P7', 'P8', 'PO3', 'PO4', 'PO7', 'PO8', 'POz', 'Pz', 'FCz', 'T7', 'T8', 'TP10', 'TP7', 'TP8', 'TP9', 'AFz']

if include != "all":
sensors = [s for s in sensors if include in s]

if exclude != None:
if isinstance(exclude, str):
exclude = [exclude]
for to_exclude in exclude:
sensors = [s for s in sensors if to_exclude not in s]

if hemisphere != "both":
if include_central == False:
if hemisphere == "left":
sensors = [s for s in sensors if "1" in s or "3" in s or "5" in s or "7" in s or "9" in s]
if hemisphere == "right":
sensors = [s for s in sensors if "2" in s or "4" in s or "6" in s or "8" in s or "10" in s]
else:
if hemisphere == "left":
sensors = [s for s in sensors if "1" in s or "3" in s or "5" in s or "7" in s or "9" in s or "z" in s]
if hemisphere == "right":
sensors = [s for s in sensors if "2" in s or "4" in s or "6" in s or "8" in s or "10" in s or "z" in s]


return(sensors)

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