Merge pull request #89 from GazzolaLab/update-0.2.0

Update 0.2.0

.coveragerc

@@ -3,6 +3,7 @@
 exclude_lines =
     # Enable pragma
     pragma: no cover
+    TODO
 
     # Don't complain if non-runnable code isn't run:
     if 0:

.github/workflows/ci-sphinx.yml

@@ -23,19 +23,20 @@ jobs:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v3
       - name: Setup Poetry
-        uses: Gr1N/setup-poetry@v7
-        with:
-          poetry-preview: false
+        uses: snok/install-poetry@v1
       - name: Poetry install docs dependencies
         run: |
             poetry --version
-            poetry config virtualenvs.in-project false
-            poetry config virtualenvs.create false
+            poetry config virtualenvs.in-project true
+            #poetry config virtualenvs.create false
             poetry install -E docs
-
       - name: Sphinx Build Check
         run: |
+            source .venv/bin/activate
             cd docs
+            python --version
+            which python
+            sphinx-build --version
             make clean
             if ! (make html SPHINXOPTS="-W --keep-going") ; then
                 echo Please resolve the warnings/errors
@@ -44,9 +45,9 @@ jobs:
                 echo Doc build success
                 exit 0
             fi
-
       - name: Sphinx Link Check
         run: |
+            source .venv/bin/activate
             cd docs
             make clean
             make linkcheck

.gitignore

@@ -6,6 +6,7 @@ __pycache__/
 
 # C extensions
 *.so
+*.o
 
 # Distribution / packaging
 .Python

Makefile

@@ -1,5 +1,5 @@
 #* Variables
-PYTHON := python
+PYTHON := python3
 PYTHONPATH := `pwd`
 
 #* Poetry

docs/api/_toctree/VisualizationAPI/miv.visualization.connectivity.plot_connectivity.rst

@@ -0,0 +1,6 @@
+miv.visualization.connectivity.plot\_connectivity
+=================================================
+
+.. currentmodule:: miv.visualization.connectivity
+
+.. autofunction:: plot_connectivity

docs/api/_toctree/VisualizationAPI/miv.visualization.connectivity.plot_connectivity_interactive.rst

@@ -0,0 +1,6 @@
+miv.visualization.connectivity.plot\_connectivity\_interactive
+==============================================================
+
+.. currentmodule:: miv.visualization.connectivity
+
+.. autofunction:: plot_connectivity_interactive

docs/api/coding.rst

@@ -0,0 +1,13 @@
+*************
+Neural Coding
+*************
+
+Temporal Encoding/Decoding
+==========================
+
+.. automodule:: miv.coding.temporal
+
+Spatial Encoding/Decoding
+=========================
+
+.. automodule:: miv.coding.spatial

docs/api/visualization.rst

@@ -60,6 +60,20 @@ Burst Analysis
 
       plot_burst
 
+Connectivity Plots
+------------------
+
+.. currentmodule:: miv.visualization
+
+.. automodule:: miv.visualization.connectivity
+
+   .. autosummary::
+      :nosignatures:
+      :toctree: _toctree/VisualizationAPI
+
+      plot_connectivity
+      plot_connectivity_interactive
+
 
 Useful External Packages
 ========================

docs/guide/connectivity_network.md

@@ -0,0 +1,104 @@
+---
+jupytext:
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.13.8
+kernelspec:
+  display_name: Python 3 (ipykernel)
+  language: python
+  name: python3
+---
+
+# Channel-wise Signal Correlation
+
+Here is the example script of cross-correlation analysis using `Elephant` package.
+
+```{code-cell} ipython3
+:tags: [hide-cell]
+
+import os
+import sys
+
+import matplotlib.pyplot as plt
+import numpy as np
+import scipy.signal as ss
+
+import miv
+from miv.datasets import optogenetic
+from miv.io import DataManager
+from miv.signal.filter import ButterBandpass, FilterCollection, MedianFilter
+from miv.signal.spike import ThresholdCutoff
+from miv.visualization.connectivity import plot_connectivity
+
+```
+
+## Pre-processing
+
+```{code-cell} ipython3
+# Experiment name
+experiment_query = "experiment0"
+
+# Data call
+signal_filter = (
+    FilterCollection()
+        .append(ButterBandpass(600, 2400, order=4))
+        .append(MedianFilter(threshold=60, k=30))
+)
+spike_detection = ThresholdCutoff(cutoff=5)
+
+# Spike Detection
+data_collection = optogenetic.load_data()
+data = data_collection.query_path_name(experiment_query)[0]
+#false_channels = [12,15,36,41,42,43,45,47,53,57,55,58,61,62]
+#data.set_channel_mask(false_channels)
+with data.load() as (signal, timestamps, sampling_rate):
+    # Preprocess
+    signal = signal_filter(signal, sampling_rate)
+    spiketrains = spike_detection(signal, timestamps, sampling_rate)
+```
+
+## Provide MEA mao
+
+```{code-cell} ipython3
+#Matrix containing electrode numbers according to their spatial location
+mea_map = np.array([[25  , 10 , 12 , 14 , 31 , 28 , 26 , 40],
+                         [18 , 17 , 11 , 13 , 32 , 27 , 38 , 37],
+                         [20 , 19 , 9  , 15 , 30 , 39 , 36 , 35],
+                         [23 , 22 , 21 , 16 , 29 , 34 , 33 , 56],
+                         [24 , 1  , 2  , 61 , 44 , 53 , 54 , 55],
+                         [3  , 4  , 7  , 62 , 43 , 48 , 51 , 52],
+                         [5  , 6  , 59 , 64 , 41 , 46 , 49 , 50],
+                         [57 , 58 , 60 , 63 , 42 , 45 , 47 , 8]])
+
+```
+
+## Forming Connectivity Matrix
+
+```{code-cell} ipython3
+#Correlation using Elephant
+import elephant.statistics
+import quantities as pq
+from elephant.spike_train_correlation import correlation_coefficient
+
+rates = elephant.statistics.BinnedSpikeTrain(spiketrains, bin_size=2*pq.ms)
+corrcoef_matrix = correlation_coefficient(rates)
+
+```
+
+## Plot Connectivity
+
+Plots connectivity using the provided MEA map and connectivity matrix. Documentation is available [here](miv.visualization.connectivity.plot_connectivity)
+
+```{code-cell} ipython3
+#Non-interactive connectivity plot using correlation
+plot_connectivity(mea_map, corrcoef_matrix, False)
+
+```
+
+```{code-cell} ipython3
+#Interactive connectivity plot using correlation
+plot_connectivity_interactive(mea_map, corrcoef_matrix, False)
+
+```

docs/guide/lyon_ear_model.md

@@ -0,0 +1,176 @@
+---
+jupytext:
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.13.8
+kernelspec:
+  display_name: Python 3 (ipykernel)
+  language: python
+  name: python3
+---
+
+# Temporal Encoding: Lyon Ear Model
+
+- Schroeder, M. R. (1973). An integrable model for the basilar membrane. The Journal of the Acoustical Society of America, 53(2), 429–434. doi:10.1121/1.1913339
+- Zweig, G., Lipes, R., & Pierce, J. R. (1976). The cochlear compromise. Journal of the Acoustical Society of America, 59(4), 975–982. doi:10.1121/1.380956
+- Lyon, R. F. (1982). A Computational Model of Filtering, Detection, and Compreion in the Cochlea. IEEE Artificial IntelligenceArtificial Intelligence, 3–6.
+- Lyon, R. F., & Lauritzen, N. (1985). Processing Speech With the Multi-Serial Signal Processor. ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings, 981–984. doi:10.1109/icassp.1985.1168158
+- Slaney, M. (1988). Lyon’s Cochlear Model. 1–79.
+- Van, L. M. (1992). Pitch and voiced/unvoiced determination with an auditory model. Journal of the Acoustical Society of America, 91(6), 3511–3526. doi:10.1121/1.402840
+- Gabbiani, Fabrizio. (1996). Coding of time-varying signals in spike trains of linear and half-wave rectifying neurons. Network: Computation in Neural Systems, 7(1), 61–85. doi:10.1080/0954898x.1996.11978655
+- Reich, D. S., Victor, J. D., & Knight, B. W. (1998). The power ratio and the interval map: Spiking models and extracellular recordings. Journal of Neuroscience, 18(23), 10090–10104. doi:10.1523/jneurosci.18-23-10090.1998
+- Gabbiani, F., & Metzner, W. (1999). Encoding and processing of sensory information in neuronal spike trains. Journal of Experimental Biology, 202(10), 1267–1279. doi:10.1242/jeb.202.10.1267
+- Schrauwen, B., & Van Campenhout, J. (2003). BSA, a Fast and Accurate Spike Train Encoding Scheme. Proceedings of the International Joint Conference on Neural Networks, 4, 2825–2830. doi:10.1109/ijcnn.2003.1224019
+- Cosi, P., & Zovato, E. (2012). Lyon ’ s Auditory Model Inversion : a Tool for Sound Separation and Speech Enhancement. 3–6.
+- Swanson, B. A. (2015). Pitch Perception with Cochlear Implants. (August 2008).
+- Zai, A. T., Bhargava, S., Mesgarani, N., & Liu, S. C. (2015). Reconstruction of audio waveforms from spike trains of artificial cochlea models. Frontiers in Neuroscience, 9(OCT), 1–13. doi:10.3389/fnins.2015.00347
+- Jin, Y., & Li, P. (2017). Performance and robustness of bio-inspired digital liquid state machines: A case study of speech recognition. Neurocomputing, 226(September 2015), 145–160. doi:10.1016/j.neucom.2016.11.045
+- Huang, N., Slaney, M., & Elhilali, M. (2018). Connecting deep neural networks to physical, perceptual, and electrophysiological auditory signals. Frontiers in Neuroscience, 12(AUG), 1–14. doi:10.3389/fnins.2018.00532
+- Petro, B., Kasabov, N., & Kiss, R. M. (2020). Selection and Optimization of Temporal Spike Encoding Methods for Spiking Neural Networks. IEEE Transactions on Neural Networks and Learning Systems, 31(2), 358–370. doi:10.1109/TNNLS.2019.2906158
+
+- Xu, Y., Thakur, C. S., Singh, R. K., Hamilton, T. J., Wang, R. M., & van Schaik, A. (2018). A FPGA implementation of the CAR-FAC cochlear model. Frontiers in Neuroscience, 12(APR), 1–14. doi:10.3389/fnins.2018.00198
+
++++
+
+## Quick Demo
+
+```{code-cell} ipython3
+:tags: [hide-cell]
+
+import IPython
+import numpy as np
+import matplotlib.pyplot as plt
+from scipy.io import wavfile
+```
+
+```{code-cell} ipython3
+from miv.converter.temporal import LyonEarModel, BensSpikerAlgorithm
+```
+
+```{code-cell} ipython3
+filepath = "Cochlear-Implant-Processor/Samples/Birds.wav"
+IPython.display.Audio(filepath)
+```
+
+```{code-cell} ipython3
+sampling_rate, waveform = wavfile.read(filepath)
+waveform = waveform.astype(np.float_)
+print(f"{sampling_rate=}, {waveform.shape=}")
+
+left_wave = np.ascontiguousarray(waveform[:,0])
+right_wave = np.ascontiguousarray(waveform[:,1])
+```
+
+### Lyon Ear Model
+
+```{code-cell} ipython3
+decimation_factor = 64
+ear_model = LyonEarModel(sampling_rate=sampling_rate, decimation_factor=decimation_factor)
+```
+
+```{code-cell} ipython3
+decimation_factor = 64
+cochlear_left = ear_model(left_wave)
+cochlear_right = ear_model(right_wave)
+print(cochlear_right.shape)
+```
+
+```{code-cell} ipython3
+fig = plt.figure(figsize=(16,8))
+ax1 = fig.add_subplot(211)
+img1 = ax1.imshow(cochlear_right.T)
+ax1.set_aspect('auto')
+plt.colorbar(img1)
+ax2 = fig.add_subplot(212)
+img2 = ax2.imshow(cochlear_right.T)
+ax2.set_aspect('auto')
+plt.colorbar(img2)
+```
+
+## BSA
+
+```{code-cell} ipython3
+out = np.stack([cochlear_left, cochlear_right])
+```
+
+```{code-cell} ipython3
+bsa = BensSpikerAlgorithm(out)
+spiketrain = bsa.get_spikes()[0]
+```
+
+```{code-cell} ipython3
+# Binning
+spiketime = [[] for _ in range(spiketrain.shape[1])]
+spikestamp = np.where(spiketrain)
+for i, j in zip(spikestamp[0], spikestamp[1]):
+    spiketime[j].append(i)
+```
+
+### Replay
+
+```{code-cell} ipython3
+from matplotlib import animation
+plt.rcParams["animation.html"] = "jshtml"
+plt.rcParams["figure.dpi"] = 150
+plt.ioff()
+```
+
+```{code-cell} ipython3
+fig, ax = plt.subplots()
+
+window = 0.15
+tfinal = 10.0
+dps = int(spiketrain.shape[0] / tfinal)
+fps = 60.0
+def animate(frame):
+    t = frame / fps
+    plt.cla()
+    low = t * dps
+    high = (t + window) * dps
+    plt.eventplot([np.array(list(filter(lambda x: x >= low and x <= high, sp)))/dps for sp in spiketime])
+    plt.xlim(t,t+window)
+    plt.xlabel('time (sec)')
+    plt.ylabel('channel')
+    plt.title(f'{t=:.02f} {frame=}')
+    ax.set_aspect('auto')
+animation.FuncAnimation(fig, animate, frames=int(tfinal * fps))
+```
+
+## Testing (Sinusoidal)
+
+```{code-cell} ipython3
+raise Exception # Do not proceed beyond
+```
+
+```{code-cell} ipython3
+out = calc.lyon_passive_ear(data[:,0], samplerate)
+print('Out:')
+print(out.shape)
+```
+
+```{code-cell} ipython3
+data2 = np.sin(np.arange(2041)/20000*2*np.pi*1000)
+out = calc.lyon_passive_ear(data2, 20000, 20)
+```
+
+```{code-cell} ipython3
+plt.imshow(out, aspect='auto')
+plt.colorbar()
+```
+
+```{code-cell} ipython3
+data3 = np.zeros(256); data3[0] = 1
+out = calc.lyon_passive_ear(data3, 16000, 1)
+out = np.fmin(out, 0.0004)
+```
+
+```{code-cell} ipython3
+plt.imshow(out, aspect='auto')
+plt.colorbar()
+```
+
+```{code-cell} ipython3
+
+```