Merge branch 'master' of https://github.com/zekearneodo/swissknife

zekearneodo · Nov 7, 2018 · 5717df4 · 5717df4
2 parents 85494cb + fd06f25
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diff --git a/.idea/swissknife.iml b/.idea/swissknife.iml
diff --git a/README.md b/README.md
@@ -0,0 +1,11 @@
+# swissknife
+Multiple tools to:
+
+- post-process neural data recorded in singing/anesthetized with the Intan RHD2000 system using both Intan and OpenEphys software.
+- convert it to the Klusta-team's Kwik format.
+- sort spikes using klusta/kilosort/mountainsort, or simply detect supra-threshold events.
+- align the neural data with the stimuli played/bouts detected
+- fit parameters and create synthetic vocalizations by integrating the Mindlin model for the vocal organ of the zebra finch.
+- Use a FFNN/LSTM/Linear decoder to produce synthetic vocalizations driven by neural activity.
+
+(Documentation and splitting into more reasonably sized, stand-alone packages is in progress).
diff --git a/nohup.out b/nohup.out
diff --git a/setup.py b/setup.py
@@ -8,5 +8,15 @@
       author_email='[email protected]',
       license='MIT',
       packages=['swissknife'],
-      requires=['numpy', 'scipy', 'matplotlib'],
+      install_requires=['numpy',
+                        'pandas>=0.23',
+                        'more_itertools',
+                        'peakutils>=1.3',
+                        'scipy',
+                        'matplotlib',
+                        'librosa',
+                        'tqdm',
+                        'joblib',
+                        'h5py',
+                        'yml'],
       zip_safe=False)
diff --git a/swissknife.egg-info/PKG-INFO b/swissknife.egg-info/PKG-INFO
diff --git a/swissknife.egg-info/SOURCES.txt b/swissknife.egg-info/SOURCES.txt
diff --git a/swissknife.egg-info/dependency_links.txt b/swissknife.egg-info/dependency_links.txt
diff --git a/swissknife.egg-info/not-zip-safe b/swissknife.egg-info/not-zip-safe
diff --git a/swissknife.egg-info/top_level.txt b/swissknife.egg-info/top_level.txt