Merge pull request #109 from Gauravu2/Info_theory_enhancement

[WIP] Multivariate Info Theory

miv/statistics/info_theory.py

@@ -1,12 +1,16 @@
 __all__ = [
+    "probability_distribution",
     "shannon_entropy",
     "block_entropy",
     "entropy_rate",
     "active_information",
     "mutual_information",
+    "joint_entropy",
     "relative_entropy",
     "conditional_entropy",
+    "cross_entropy",
     "transfer_entropy",
+    "pid",
 ]
 
 
@@ -27,6 +31,50 @@
 from miv.typing import SpikestampsType
 
 
+def probability_distribution(
+    spiketrains: SpikestampsType,
+    channel: float,
+    t_start: float,
+    t_end: float,
+    bin_size: float,
+):
+
+    """
+    Forms the probability distribution required to compute the information theory measures. Probability is computed based on the binned spiketrain generated for the specified bin size.
+
+    Parameters
+    ----------
+    spiketrains : SpikestampsType
+        Single spike-stamps
+    channel : float
+        electrode/channel
+    t_start : float
+        Binning start time
+    t_end : float
+        Binning end time
+    bin_size : float
+        bin size in seconds
+
+    Returns
+    -------
+        probability_distribution: np.ndarray
+        probability distribution for the provided spiketrain
+
+    """
+
+    assert t_start < t_end, "start time cannot be equal or greater than end time"
+    assert bin_size > 0, "bin_size should be a finite positive value"
+
+    bin_spike = binned_spiketrain(spiketrains, channel, t_start, t_end, bin_size)
+    prob_spike = np.sum(bin_spike) / np.size(bin_spike)
+    prob_no_spike = 1 - prob_spike
+    probability_distribution = bin_spike.copy()
+    probability_distribution[probability_distribution == 1] = prob_spike
+    probability_distribution[probability_distribution == 0] = prob_no_spike
+
+    return probability_distribution
+
+
 def shannon_entropy(
     spiketrains: SpikestampsType,
     channel: float,
@@ -35,7 +83,7 @@ def shannon_entropy(
     bin_size: float,
 ):
     """
-    Estimates the shannon entropy for a single channel recording using the binned spiketrain
+    Estimates the shannon entropy for a single channel recording using the binned spiketrain.
 
     Parameters
     ----------
@@ -56,10 +104,14 @@ def shannon_entropy(
         Shannon entropy for the given channel
 
     """
-
+    assert t_start < t_end, "start time cannot be equal or greater than end time"
+    assert bin_size > 0, "bin_size should be a finite positive value"
     bin_spike = binned_spiketrain(spiketrains, channel, t_start, t_end, bin_size)
-    spike_dist = pyinform.dist.Dist(bin_spike)
-    shannon_entropy = pyinform.shannon.entropy(spike_dist)
+    prob_spike = np.sum(bin_spike) / np.size(bin_spike)
+    prob_no_spike = 1 - prob_spike
+    shannon_entropy = -(
+        prob_spike * np.log2(prob_spike) + prob_no_spike * np.log2(prob_no_spike)
+    )
     return shannon_entropy
 
 
@@ -95,7 +147,9 @@ def block_entropy(
         Block entropy for the given channel
 
     """
-
+    assert t_start < t_end, "start time cannot be equal or greater than end time"
+    assert bin_size > 0, "bin_size should be a finite positive value"
+    assert his > 0, "history length should be a finite positive value"
     bin_spike = binned_spiketrain(spiketrains, channel, t_start, t_end, bin_size)
     block_entropy = pyinform.blockentropy.block_entropy(bin_spike, his)
     return block_entropy
@@ -133,7 +187,9 @@ def entropy_rate(
         entropy rate for the given channel
 
     """
-
+    assert t_start < t_end, "start time cannot be equal or greater than end time"
+    assert bin_size > 0, "bin_size should be a finite positive value"
+    assert his > 0, "history length should be a finite positive value"
     bin_spike = binned_spiketrain(spiketrains, channel, t_start, t_end, bin_size)
     entropy_rate = pyinform.entropyrate.entropy_rate(bin_spike, k=his)
     return entropy_rate
@@ -171,7 +227,9 @@ def active_information(
         Active information for the given channel
 
     """
-
+    assert t_start < t_end, "start time cannot be equal or greater than end time"
+    assert bin_size > 0, "bin_size should be a finite positive value"
+    assert his > 0, "history length should be a finite positive value"
     bin_spike = binned_spiketrain(spiketrains, channel, t_start, t_end, bin_size)
     active_information = pyinform.activeinfo.active_info(bin_spike, his)
     return active_information
@@ -209,13 +267,60 @@ def mutual_information(
         Mutual information for the given pair of electrodes
 
     """
-
+    assert t_start < t_end, "start time cannot be equal or greater than end time"
+    assert bin_size > 0, "bin_size should be a finite positive value"
     bin_spike_x = binned_spiketrain(spiketrains, channelx, t_start, t_end, bin_size)
     bin_spike_y = binned_spiketrain(spiketrains, channely, t_start, t_end, bin_size)
     mutual_information = pyinform.mutualinfo.mutual_info(bin_spike_x, bin_spike_y)
     return mutual_information
 
 
+def joint_entropy(
+    spiketrains: SpikestampsType,
+    channelx: float,
+    channely: float,
+    t_start: float,
+    t_end: float,
+    bin_size: float,
+):
+    """
+    Estimates the joint entropy for the pair of electorde recordings (X & Y) using the binned spiketrains
+
+    Parameters
+    ----------
+    spiketrains : SpikestampsType
+        Single spike-stamps
+    channelx : float
+        electrode/channel X
+    channely : float
+        electrode/channel Y
+    t_start : float
+        Binning start time
+    t_end : float
+        Binning end time
+    bin_size : float
+        bin size in seconds
+
+    Returns
+    -------
+    joint_entropy: float
+        joint entropy for the given pair of electrodes
+
+    """
+    assert t_start < t_end, "start time cannot be equal or greater than end time"
+    assert bin_size > 0, "bin_size should be a finite positive value"
+
+    spike_dist_x = probability_distribution(
+        spiketrains, channelx, t_start, t_end, bin_size
+    )
+    spike_dist_y = probability_distribution(
+        spiketrains, channely, t_start, t_end, bin_size
+    )
+    spike_dist_xy = np.logical_and(spike_dist_x, spike_dist_y)
+    joint_entropy = -np.sum(spike_dist_xy * np.log2(spike_dist_xy))
+    return joint_entropy
+
+
 def relative_entropy(
     spiketrains: SpikestampsType,
     channelx: float,
@@ -248,6 +353,8 @@ def relative_entropy(
         Relative_entropy for the given pair of electrodes
 
     """
+    assert t_start < t_end, "start time cannot be equal or greater than end time"
+    assert bin_size > 0, "bin_size should be a finite positive value"
 
     bin_spike_x = binned_spiketrain(spiketrains, channelx, t_start, t_end, bin_size)
     bin_spike_y = binned_spiketrain(spiketrains, channely, t_start, t_end, bin_size)
@@ -289,6 +396,8 @@ def conditional_entropy(
         conditional entropy for the given pair of electrodes
 
     """
+    assert t_start < t_end, "start time cannot be equal or greater than end time"
+    assert bin_size > 0, "bin_size should be a finite positive value"
 
     bin_spike_x = binned_spiketrain(spiketrains, channelx, t_start, t_end, bin_size)
     bin_spike_y = binned_spiketrain(spiketrains, channely, t_start, t_end, bin_size)
@@ -298,6 +407,51 @@ def conditional_entropy(
     return conditional_entropy
 
 
+def cross_entropy(
+    spiketrains: SpikestampsType,
+    channelx: float,
+    channely: float,
+    t_start: float,
+    t_end: float,
+    bin_size: float,
+):
+    """
+    Estimates the cross entropy for the pair of electorde recordings (X & Y) using the binned spiketrains
+
+    Parameters
+    ----------
+    spiketrains : SpikestampsType
+        Single spike-stamps
+    channelx : float
+        electrode/channel X
+    channely : float
+        electrode/channel Y
+    t_start : float
+        Binning start time
+    t_end : float
+        Binning end time
+    bin_size : float
+        bin size in seconds
+
+    Returns
+    -------
+    cross_entropy: float
+        cross entropy for the given pair of electrodes
+
+    """
+    assert t_start < t_end, "start time cannot be equal or greater than end time"
+    assert bin_size > 0, "bin_size should be a finite positive value"
+
+    spike_dist_x = probability_distribution(
+        spiketrains, channelx, t_start, t_end, bin_size
+    )
+    spike_dist_y = probability_distribution(
+        spiketrains, channely, t_start, t_end, bin_size
+    )
+    cross_entropy = -np.sum(spike_dist_x * np.log2(spike_dist_y))
+    return cross_entropy
+
+
 def transfer_entropy(
     spiketrains: SpikestampsType,
     channelx: float,
@@ -333,10 +487,95 @@ def transfer_entropy(
         Transfer_entropy for the given pair of electrodes
 
     """
+    assert t_start < t_end, "start time cannot be equal or greater than end time"
+    assert bin_size > 0, "bin_size should be a finite positive value"
+    assert his > 0, "history length should be a finite positive value"
 
     bin_spike_x = binned_spiketrain(spiketrains, channelx, t_start, t_end, bin_size)
     bin_spike_y = binned_spiketrain(spiketrains, channely, t_start, t_end, bin_size)
     transfer_entropy = pyinform.transferentropy.transfer_entropy(
         bin_spike_x, bin_spike_y, k=his
     )
     return transfer_entropy
+
+
+def pid(
+    spiketrains: SpikestampsType,
+    channelx: float,
+    channely: float,
+    channelz: float,
+    t_start: float,
+    t_end: float,
+    bin_size: float,
+):
+    """
+    Decomposes the information provided by channel x and y about channel z in redundancy, unique information, and synergy.
+
+    Parameters
+    ----------
+    spiketrains : SpikestampsType
+        Single spike-stamps
+    channelx : float
+        electrode/channel X
+    channely : float
+        electrode/channel Y
+    channelz : float
+        electrode/channel Y
+    t_start : float
+        Binning start time
+    t_end : float
+        Binning end time
+    bin_size : float
+        bin size in seconds
+
+    Returns
+    -------
+    redundancy: float
+        redundant information provided by both x and y about z
+    unique_information_x: float
+        information uniquely provided by x about z
+    unique_information_y: float
+        information uniquely provided by y about z
+    synergy: float
+        synergetic information provided by both x and y about z
+    total_information: float
+        total information provided by both x and y about z
+    """
+    assert t_start < t_end, "start time cannot be equal or greater than end time"
+    assert bin_size > 0, "bin_size should be a finite positive value"
+
+    spike_dist_x = probability_distribution(
+        spiketrains, channelx, t_start, t_end, bin_size
+    )
+    spike_dist_y = probability_distribution(
+        spiketrains, channely, t_start, t_end, bin_size
+    )
+    spike_dist_z = probability_distribution(
+        spiketrains, channely, t_start, t_end, bin_size
+    )
+    spike_dist_xz = np.logical_and(spike_dist_x, spike_dist_z)
+    spike_dist_yz = np.logical_and(spike_dist_y, spike_dist_z)
+    spike_dist_xy = np.logical_and(spike_dist_x, spike_dist_y)
+    spike_dist_xyz = np.logical_and(spike_dist_x, spike_dist_y, spike_dist_z)
+    I_x_z = np.sum(
+        spike_dist_xz * np.log2(spike_dist_xz / (spike_dist_x * spike_dist_z))
+    )
+    I_y_z = np.sum(
+        spike_dist_yz * np.log2(spike_dist_yz / (spike_dist_y * spike_dist_z))
+    )
+    redundancy = np.min(I_x_z, I_y_z)
+    unique_information_x = I_x_z - redundancy
+    unique_information_y = I_y_z - redundancy
+    total_information = np.sum(
+        spike_dist_xyz * np.log2(spike_dist_xyz / (spike_dist_xy * spike_dist_z))
+    )
+    synergy = (
+        total_information - redundancy - unique_information_x - unique_information_y
+    )
+    return (
+        redundancy,
+        unique_information_x,
+        unique_information_y,
+        synergy,
+        total_information,
+    )