Merge pull request #926 from neuropsychology/dev

0.2.8

.gitignore

@@ -215,3 +215,4 @@ studies/complexity_structure/README_cache/
 studies/complexity_structure/manuscript_cache/
 studies/complexity_eeg/data_attractor.csv
 studies/complexity_eeg/data_delay.csv
+testing.ipynb

MANIFEST.in

@@ -4,8 +4,9 @@ include NEWS.rst
 include LICENSE
 include README.rst
 
-recursive-include tests *
+recursive-exclude tests *
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 
 recursive-include docs *.rst conf.py *.jpg *.png *.gif
+

NEWS.rst

@@ -1,6 +1,17 @@
 News
 =====
 
+0.2.8
+-------------------
+New Features
++++++++++++++
+
+* New feature `events_find()`: is now able to combine multiple digital input channels,
+  retrieve events from the combined events channel and differentiate between the inputs that
+  occur simultaneously.
+
+
+
 0.2.4
 -------------------
 Fixes

docs/examples/ecg_hrv/ecg_hrv.ipynb

@@ -4,7 +4,7 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "# Heart Rate Varability (HRV)"
+                "# Heart Rate Variability (HRV)"
             ]
         },
         {

neurokit2/__init__.py

@@ -1,4 +1,5 @@
 """Top-level package for NeuroKit."""
+
 import datetime
 import platform
 
@@ -32,12 +33,12 @@
 from .video import *
 
 # Info
-__version__ = "0.2.7"
+__version__ = "0.2.8"
 
 
 # Maintainer info
 __author__ = "The NeuroKit development team"
-__email__ = "[email protected]"
+__email__ = "[email protected]"
 
 
 # Citation

neurokit2/complexity/utils_complexity_symbolize.py

@@ -184,8 +184,8 @@ def complexity_symbolize(signal, method="mean", c=3, random_state=None, show=Fal
             symbolic = (signal > np.nanmean(signal)).astype(int)
             if show is True:
                 df = pd.DataFrame({"A": signal, "B": signal})
-                df["A"][df["A"] > np.nanmean(signal)] = np.nan
-                df["B"][df["B"] <= np.nanmean(signal)] = np.nan
+                df.loc[df["A"] > np.nanmean(signal), "A"] = np.nan
+                df.loc[df["B"] <= np.nanmean(signal), "B"] = np.nan
                 df.plot()
                 plt.axhline(y=np.nanmean(signal), color="r", linestyle="dotted")
                 plt.title("Method A")
@@ -194,8 +194,8 @@ def complexity_symbolize(signal, method="mean", c=3, random_state=None, show=Fal
             symbolic = (signal > np.nanmedian(signal)).astype(int)
             if show is True:
                 df = pd.DataFrame({"A": signal, "B": signal})
-                df["A"][df["A"] > np.nanmedian(signal)] = np.nan
-                df["B"][df["B"] <= np.nanmedian(signal)] = np.nan
+                df.loc[df["A"] > np.nanmedian(signal), "A"] = np.nan
+                df.loc[df["B"] <= np.nanmedian(signal), "B"] = np.nan
                 df.plot()
                 plt.axhline(y=np.nanmean(signal), color="r", linestyle="dotted")
                 plt.title("Binarization by median")
@@ -206,8 +206,9 @@ def complexity_symbolize(signal, method="mean", c=3, random_state=None, show=Fal
             symbolic = np.logical_or(signal < m - sd, signal > m + sd).astype(int)
             if show is True:
                 df = pd.DataFrame({"A": signal, "B": signal})
-                df["A"][np.logical_or(signal < m - sd, signal > m + sd)] = np.nan
-                df["B"][~np.isnan(df["A"])] = np.nan
+                condition = np.logical_or(signal < m - sd, signal > m + sd)
+                df.loc[condition, "A"] = np.nan
+                df.loc[~np.isnan(df["A"]), "B"] = np.nan
                 df.plot()
                 plt.axhline(y=m - sd, color="r", linestyle="dotted")
                 plt.axhline(y=m + sd, color="r", linestyle="dotted")
@@ -217,8 +218,8 @@ def complexity_symbolize(signal, method="mean", c=3, random_state=None, show=Fal
             symbolic = np.signbit(np.diff(signal)).astype(int)
             if show is True:
                 df = pd.DataFrame({"A": signal, "B": signal})
-                df["A"][np.insert(symbolic, 0, False)] = np.nan
-                df["B"][~np.isnan(df["A"])] = np.nan
+                df.loc[np.insert(symbolic, 0, False), "A"] = np.nan
+                df.loc[~np.isnan(df["A"]), "B"] = np.nan
                 df.plot()
                 plt.title("Method C")
 

neurokit2/data/database.py

@@ -1,9 +1,7 @@
 import pathlib
-import urllib.parse
+import urllib
 import zipfile
 
-import requests
-
 
 def download_from_url(url, destination_path=None):
     """**Download Files from URLs**
@@ -26,7 +24,7 @@ def download_from_url(url, destination_path=None):
     destination_path = _download_path_sanitize(url, destination_path)
 
     # Download the file
-    response = requests.get(url)
+    response = urllib.request.urlopen(url)
 
     if response.status_code == 200:
         with destination_path.open("wb") as file:

neurokit2/data/read_acqknowledge.py

@@ -1,15 +1,15 @@
 # -*- coding: utf-8 -*-
 import os
 
+from collections import Counter
+
 import numpy as np
 import pandas as pd
 
 from ..signal import signal_resample
 
 
-def read_acqknowledge(
-    filename, sampling_rate="max", resample_method="interpolation", impute_missing=True
-):
+def read_acqknowledge(filename, sampling_rate="max", resample_method="interpolation", impute_missing=True):
     """**Read and format a BIOPAC's AcqKnowledge file into a pandas' dataframe**
 
     The function outputs both the dataframe and the sampling rate (retrieved from the
@@ -69,10 +69,7 @@ def read_acqknowledge(
         filename += ".acq"
 
     if os.path.exists(filename) is False:
-        raise ValueError(
-            "NeuroKit error: read_acqknowledge(): couldn't"
-            " find the following file: " + filename
-        )
+        raise ValueError("NeuroKit error: read_acqknowledge(): couldn't" " find the following file: " + filename)
 
     # Read file
     file = bioread.read(filename)
@@ -84,24 +81,34 @@ def read_acqknowledge(
             freq_list.append(file.named_channels[channel].samples_per_second)
         sampling_rate = np.max(freq_list)
 
+    # Counter for checking duplicate channel names
+    channel_counter = Counter()
+
     # Loop through channels
     data = {}
-    for channel in file.named_channels:
-        signal = np.array(file.named_channels[channel].data)
+    for channel_num, channel in enumerate(file.channels):
+        signal = np.array(file.channels[channel_num].data)
 
         # Fill signal interruptions
         if impute_missing is True and np.isnan(np.sum(signal)):
             signal = pd.Series(signal).fillna(method="pad").values
 
         # Resample if necessary
-        if file.named_channels[channel].samples_per_second != sampling_rate:
+        if file.channels[channel_num].samples_per_second != sampling_rate:
             signal = signal_resample(
                 signal,
-                sampling_rate=file.named_channels[channel].samples_per_second,
+                sampling_rate=file.channels[channel_num].samples_per_second,
                 desired_sampling_rate=sampling_rate,
                 method=resample_method,
             )
-        data[channel] = signal
+
+        # If there is a duplicate channel name, append a number
+        if channel_counter[channel.name] == 0:
+            data[channel.name] = signal
+        else:
+            data[f"{channel.name} ({channel_counter[channel.name]})"] = signal
+
+        channel_counter[channel.name] += 1
 
     # Sanitize lengths
     lengths = []

neurokit2/data/read_xdf.py

@@ -79,10 +79,16 @@ def read_xdf(filename, upsample=2, fillmissing=None):
 
         # Special treatment for some devices
         if stream["info"]["name"][0] == "Muse":
-            # Rename GYRO channels and add ACCelerometer
+            # Rename GYRO channels
             if stream["info"]["type"][0] == "GYRO":
                 dat = dat.rename(columns={"X": "GYRO_X", "Y": "GYRO_Y", "Z": "GYRO_Z"})
-                dat["ACC"] = np.sqrt(dat["GYRO_X"] ** 2 + dat["GYRO_Y"] ** 2 + dat["GYRO_Z"] ** 2)
+                # Compute movement
+                dat["GYRO"] = np.sqrt(dat["GYRO_X"] ** 2 + dat["GYRO_Y"] ** 2 + dat["GYRO_Z"] ** 2)
+
+            if stream["info"]["type"][0] == "ACC":
+                dat = dat.rename(columns={"X": "ACC_X", "Y": "ACC_Y", "Z": "ACC_Z"})
+                # Compute acceleration
+                dat["ACC"] = np.sqrt(dat["ACC_X"] ** 2 + dat["ACC_Y"] ** 2 + dat["ACC_Z"] ** 2)
 
             # Muse - PPG data has three channels: ambient, infrared, red
             if stream["info"]["type"][0] == "PPG":