Saravanan666/pypi-org huggingface dataset:
Package: ephypype
.. _readme:.. image::https://travis-ci.org/neuropycon/ephypype.svg?branch=master:target:https://travis-ci.org/neuropycon/ephypype.. image::https://codecov.io/gh/neuropycon/ephypype/branch/master/graph/badge.svg:target:https://codecov.io/gh/neuropycon/ephypype.. image::https://circleci.com/gh/neuropycon/ephypype.svg?style=svg:target:https://circleci.com/gh/neuropycon/ephypype.. image::https://zenodo.org/badge/92522975.svg:target:https://zenodo.org/badge/latestdoi/92522975READMEDescriptionNeuropycon package of functions for electrophysiology analysis, can be used from
graphpype and nipypeDocumentationhttps://neuropycon.github.io/ephypypeInstallationRequirementsephypype works withpython3The dependencies (mne, nipype) are automatically installed during ephypype installation (see :ref:ephy_install).We also recommend to install MNE python by following theinstallation instructions <http://martinos.org/mne/dev/install_mne_python.html#check-your-installation>_.. _ephy_install:Install ephypypeTo install ephypype, use the following command:.. code-block:: bash$ pip install ephypypeor alternatively, you can download from github the last version and install it:.. code-block:: bash$ git clone https://github.com/neuropycon/ephypype.git
$ cd ephypype
$ python setup.py develop.. comment:
.. _conda_install:Install dependencies with conda
+++++++++++++++++++++++++++++++

.. code-block:: bash 

    conda install pandas
    conda install matplotlibSoftwareFreesurfer
++++++++++Download Freesurfer software:https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstallFollow the Installation instructionshttps://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall.. comment:
MNE
+++1. Download MNE software:

http://martinos.org/mne/dev/install_mne_c.html
Package: ephyra
ContentsIntroductionUsageLicenseIntroductionEphyra is a library to help with mouse input configuration; includes both Python and native C
(CPython, tested with Windows 10 and Visual Studio 2019 tools) implementations. It supports full rotation and same screen
ratio/distance approaches.UsageThis code shows how to get sensitivity coefficients and values for a new application or a different view within same
application as well as characteristic of a particular setup. See tests for more examples.from fractions import Fraction
from math import radians

from ephyra import DataHelper, FT_HORIZONTAL, FS_HORIZONTAL_PLUS, FS_VERTICAL_MINUS, RT_AZIMUTHAL, \
    FullRotationCalculator, ScreenRatioCalculator, DetailsCalculator
from ephyra.formula import horizontal_4_to_3_fov_coefficient, horizontal_fov_to_80_coefficient

dh1 = DataHelper(screen_aspect_ratio=Fraction(16, 10), fov=radians(90), fov_aspect_ratio=Fraction(4, 3),
                 fov_type=FT_HORIZONTAL, fov_scaling=FS_HORIZONTAL_PLUS, rt=RT_AZIMUTHAL,
                 ltr_coefficient_transformation_formula=horizontal_4_to_3_fov_coefficient,
                 radians_per_count=radians(0.022), counts_per_unit=800, screen_diagonal=24)

dh2 = DataHelper(screen_aspect_ratio=Fraction(16, 10), fov=radians(100), fov_aspect_ratio=Fraction(16, 10),
                 fov_type=FT_HORIZONTAL, fov_scaling=FS_VERTICAL_MINUS, rt=RT_AZIMUTHAL,
                 ltr_coefficient_transformation_formula=horizontal_fov_to_80_coefficient,
                 radians_per_count=radians(2.2278481012658227), counts_per_unit=800, screen_diagonal=24)

frc = FullRotationCalculator(dh1.primary_state, dh1.parameters, dh2.parameters)

fr_c, fr_sens = frc.sensitivity_for(s1_sens=2, s2=dh2.primary_state)

print(f'Full rotation & different applications, coefficient: {fr_c:.4f}, sensitivity: {fr_sens:.4f}')

src = ScreenRatioCalculator(ratio1=.10, s1=dh2.primary_state, p1=dh2.parameters)

dh2_s2 = dh2.get_state_for_fov(radians(40))

src_c, src_sens = src.sensitivity_for(s1_sens=.0158, s2=dh2_s2)

print(f'Screen ratio & same application, coefficient: {src_c:.4f}, sensitivity: {src_sens:.4f}')

dc = DetailsCalculator(dh1.primary_state, dh1.parameters)

print(f'Details, full rotation distance: {dc.full_rotation_units(sens=2):.4f}')LicenseEphyra is released under version 2.0 of theApache License.
Package: ephys-anonymizer
EPHYS-ANONYMIZERUse this to anonymize faces and electrophysiology data. Please cite the github repository if you do.There is absolutely no warrenty that this will correctly remove faces from all video frames or all data from files. You must check all the videos and data to be sure they are anonymized.INSTALLATIONInstall Python (using Condahttps://docs.conda.io/en/latest/or nothttps://www.python.org/)
In a terminal typepip installephys-anonymizer.
You’re ready to go! Try it out usingvideo_anonymize path/to/my/video.Alex Rockhill
Eugene, OR 2020
Package: ephysio
ephysioPython code for reading ephys filesopenEphysIOThis module provides convenient access to continuous and event data saved by OpenEphys. For instance:from ephysio import openEphysIO
import matplotlib.pyplot as plt

ldr = openEphysIO.Loader("/path/to/data")

# first probe
strm = ldr.spikestreams()[0] 

# time x channel map of the data
dat = ldr.data(strm) 

# sampling rate in Hz
fs_Hz = ldr.samplingrate(strm) 
STIMMARKERCHANNEL = 2

# time stamps of events in channel 2 on the NIDAQ, translated to neuropixel time
evts = ldr.nidaqevents()[STIMMARKERCHANNEL] 
CHANNEL = 100
STIMNO = 10

# Start time of event #10
s0 = evts[STIMNO, 0] 

# prepare to receive 100 ms of data
ds = np.arange(int(.1*fs_Hz)) 

# 100 ms of data following the stimulus 
response = dat[s0:s0+ds, CHANNEL] 

# plot data with time in ms on x-axis
plt.plot(ds*1000/fs_Hz, response)Much more documentation is included in the module itself. Most users will want to use the Loader class rather than the various other functions.CreditsDeveloped and tested by DAW and Frank Lanfranchi.
Package: ephysiopy
[![Python package](https://github.com/rhayman/ephysiopy/actions/workflows/python-package.yml/badge.svg)](https://github.com/rhayman/ephysiopy/actions/workflows/python-package.yml)SynopsisTools for the analysis of electrophysiological data collected with the Axona or openephys recording systems.Installationephysiopy requires python3.7 or greater. The easiest way to install is using pip:python3-mpip install ephysiopyor,pip3 install ephysiopyOr similar.Code ExampleNeuropixels / openephys tetrode recordingsFor openephys-type analysis there are two main entry classes depending on whether you are doing
OpenEphys- or Axona-based analysis. Both classes inherit from the same abstract base
class (TrialInterface) and so share a high degree of overlap in what they can do. Because
of the inheritance structure, the methods you call on each concrete class are the same`python from ephysiopy.io.recording import OpenEphysBase trial =OpenEphysBase("/path/to/top_level")`The “/path/to/top_level” bit here means that if your directory hierarchy looks like this:├── 2020-03-20_12-40-15
├── Record Node 101
|    └── settings.xml
         experiment1
|        └── recording1
|            ├── structure.oebin
|            ├── sync_messages.txt
|            ├── continuous
|            |   └── Neuropix-PXI-107.0
|            |       └── continuous.dat
|            └── events
├── Record Node 102Then the “/path/to/top_level” is the folder “2020-03-20_12-40-15”On insantiation of an OpenEphysBase object the directory structure containing the recording
is traversed and various file locations are noted for later processing of the data in them.The pos data is loaded by calling the load_pos_data() method:`python npx.load_pos_data(ppm=300, jumpmax=100, cm=True) `Note
ppm = pixels per metre, used to convert pixel coords to cms.
jumpmax = maximum “jump” in cms for point to be considered “bad” and smoothed overThe same principles apply to the other classes that inherit from TrialInterface (AxonaTrial and OpenEphysNWB)Plotting dataA mixin class called FigureMaker allows consistent plots, regardless of recording technique. All plotting functions
there begin with “make” e.g “makeRateMap” and return an instance of a matplotlib axis
Package: ephys-link
Electrophysiology Manipulator LinkTheElectrophysiology Manipulator Link(or Ephys Link for short) is a PythonSocket.IOserver that allows any
Socket.IO-compliant application (such
asPinpoint)
to communicate with manipulators used in electrophysiology experiments.Supported Manipulators:ManufacturerModelSensapexuMp-4uMp-3New ScalePathfinder MPM Control v2.8+M3-USB-3:1-EPEphys Link is an open and extensible platform. It is designed to easily support integration with other manipulators.For more information regarding the server's implementation and how the code is organized, see
thepackage's development documentation.For detailed descriptions of the server's API, see
theAPI reference.InstallationPrerequisitesAnx86 Windows PC is requiredto run the server.For Sensapex devices, the controller unit must be connected via an ethernet
cable and powered. A USB-to-ethernet adapter is acceptable. For New Scale manipulators,
the controller unit must be connected via USB and be powered by a 6V power
supply.To use the emergency stop feature, ensure an Arduino with
theStopSignalsketch is
connected to the computer. Follow the instructions on that repo for how to
set up the Arduino.NOTE:Ephys Link is an HTTP server without cross-origin support. The server
is currently designed to interface with local/desktop instances of Pinpoint. It
will not work with the web browser versions of Pinpoint at this time.Install as Standalone ExecutableDownload the latest executable from
thereleases page.Double-click the executable file to launch the configuration window.Take note of the IP address and port.Copy this information into Pinpoint to connect.Select the desired configuration and click "Launch Server".The configuration window will close and the server will launch. Your configurations will be saved for future use.To connect to the server from Pinpoint, provide the IP address and port. For example, if the server is running on the
same computer that Pinpoint is, useServer:localhostPort:8081If the server is running on a different (local) computer, use the IP address of that computer as shown in the startup
window instead oflocalhost.Install as a Python packagepipinstallephys-linkImport the modules you need and launch the server.fromephys_link.serverimportServerserver=Server()server.launch("sensapex",8081)Install for DevelopmentClone the repository.InstallHatchInstall the latest Microsoft Visual C++ (MSVC v143+ x86/64) and the Windows SDK (10/11)
viaVisual Studio Build Tools Installer.In a terminal, navigate to the repository's root directory and runhatchshellThis will create a virtual environment, install Python 12 (if not found), and install the package in editable mode.Documentation and More InformationComplete documentation including API usage and development installation can be
found on theVirtual Brain Lab Documentation pagefor Ephys Link.CitingIf this project is used as part of a research project you should cite
thePinpoint repository. Please email
Dan (dbirman@uw.edu) if you have questions.Please reach out to Kenneth (kjy5@uw.edu) for questions
about the Electrophysiology Manipulator Link server. Bugs may be reported
through the issues tab.
Package: ephyspy
EphysPyPackage to extract electrophysiological features from current clamp experiments.This package provies an API to extract a multitude of features from voltage clamp recordings with the help of theAllenSDK.InstallationThe package can be installed viapip install ephyspy.
Alternatively, clone the package withhttps://github.com/berenslab/ephyspy.gitand install using pip viapip install -e ./ephyspy.Getting startedTo get started seeexample.ipynb.
Package: ephysvibe
EphysVibeImplementing pipeline analyses for electrophysiology data.
Spiking and LFP activity of 32 channels linear probes from LIP; 64 Utah Arrays channels from PFC; 64 Utah Arrays channels from V4?
Animals perform a delay conjunction matching task, controlled by MonkeyLogic (Matlab):https://monkeylogic.nimh.nih.gov/Raw electrophysiology data are acquired with OpenEphys:https://github.com/open-ephys
Package: ephyviewer
Simple viewers for ephys signals, events, video and moreDistributions:Source Code:Tests Status:Documentation|Release Notes|Issue Trackerephyvieweris a Python library based onpyqtgraphfor building custom
viewers for electrophysiological signals, video, events, epochs, spike trains,
data tables, and time-frequency representations of signals. It also provides an
epoch encoder for creating annotations.ephyviewercan be used at two levels: standalone app and library.For an example of an application that utilizesephyviewer’s capabilities as
a library, see theneuroticapp and this paper:Gill, J. P., Garcia, S., Ting, L. H., Wu, M., & Chiel, H. J. (2020).neurotic: Neuroscience Tool for Interactive Characterization. eNeuro,
7(3).https://doi.org/10.1523/ENEURO.0085-20.2020Standalone applicationThe standalone app works with file types supported byNeo’s RawIO interface
(Axograph, Axon, Blackrock, BrainVision, Neuralynx, NeuroExplorer, Plexon,
Spike2, Tdt, etc.; see the documentation forneo.rawiofor the full list).Launch it from the console and use the menu to select a data file:ephyviewerAlternatively, launch it from the console with a filename (and optionally the
format):ephyviewer File_axon_1.abf
ephyviewer File_axon_1.abf -f AxonLibrary for designing custom viewers for ephys datasetsBuild viewers using code like this:importephyviewerimportnumpyasnpapp=ephyviewer.mkQApp()#signalssigs=np.random.rand(100000,16)sample_rate=1000.t_start=0.view1=ephyviewer.TraceViewer.from_numpy(sigs,sample_rate,t_start,'Signals')win=ephyviewer.MainViewer(debug=True,show_auto_scale=True)win.add_view(view1)win.show()app.exec_()Check the docs for moreexamples.
Package: epi2melabs
epi2melabsTheepi2melabspython package provides utility functions and scripts for
running in notebook environments.Installationepi2melabsis easily installed in the standard python tradition:git clone --recursive https://github.com/epi2me-labs/epi2melabs.git
cd epi2melabs
pip install -r requirements.txt
python setup.py installor via pip:pip install epi2melabs.
Package: epi2melabs-splash
epi2melabs_splashA JupyterLab splash extension.RequirementsJupyterLab >= 3.0InstallTo install the extension, execute:pipinstallepi2melabs_splashUninstallTo remove the extension, execute:pipuninstallepi2melabs_splashContributingDevelopment installNote: You will need NodeJS to build the extension package.Thejlpmcommand is JupyterLab's pinned version ofyarnthat is installed with JupyterLab. You may useyarnornpmin lieu ofjlpmbelow.# Clone the repo to your local environment# Change directory to the epi2melabs_splash directory# Install package in development modepipinstall-e.# Link your development version of the extension with JupyterLabjupyterlabextensiondevelop.--overwrite# Rebuild extension Typescript source after making changesjlpmrunbuildYou can watch the source directory and run JupyterLab at the same time in different terminals to watch for changes in the extension's source and automatically rebuild the extension.# Watch the source directory in one terminal, automatically rebuilding when neededjlpmrunwatch# Run JupyterLab in another terminaljupyterlabWith the watch command running, every saved change will immediately be built locally and available in your running JupyterLab. Refresh JupyterLab to load the change in your browser (you may need to wait several seconds for the extension to be rebuilt).By default, thejlpm run buildcommand generates the source maps for this extension to make it easier to debug using the browser dev tools. To also generate source maps for the JupyterLab core extensions, you can run the following command:jupyterlabbuild--minimize=FalseDevelopment uninstallpipuninstallepi2melabs_splashIn development mode, you will also need to remove the symlink created byjupyter labextension developcommand. To find its location, you can runjupyter labextension listto figure out where thelabextensionsfolder is located. Then you can remove the symlink named@epi2melabs/epi2melabs-splashwithin that folder.
Package: epi2melabs-splashpage
epi2melabs_splashpageLaunch our tutorials the easy way!Accompanies the EPI2ME labs experience. Not for general use.RequirementsJupyterLab >= 3.0InstallTo install the extension, execute:pipinstallepi2melabs_splashpageUninstallTo remove the extension, execute:pipuninstallepi2melabs_splashpageContributingDevelopment installNote: You will need NodeJS to build the extension package.Thejlpmcommand is JupyterLab's pinned version ofyarnthat is installed with JupyterLab. You may useyarnornpmin lieu ofjlpmbelow.# Clone the repo to your local environment# Change directory to the epi2melabs_splashpage directory# Install package in development modepipinstall-e.# Link your development version of the extension with JupyterLabjupyterlabextensiondevelop.--overwrite# Rebuild extension Typescript source after making changesjlpmrunbuildYou can watch the source directory and run JupyterLab at the same time in different terminals to watch for changes in the extension's source and automatically rebuild the extension.# Watch the source directory in one terminal, automatically rebuilding when neededjlpmrunwatch# Run JupyterLab in another terminaljupyterlabWith the watch command running, every saved change will immediately be built locally and available in your running JupyterLab. Refresh JupyterLab to load the change in your browser (you may need to wait several seconds for the extension to be rebuilt).By default, thejlpm run buildcommand generates the source maps for this extension to make it easier to debug using the browser dev tools. To also generate source maps for the JupyterLab core extensions, you can run the following command:jupyterlabbuild--minimize=FalseDevelopment uninstallpipuninstallepi2melabs_splashpageIn development mode, you will also need to remove the symlink created byjupyter labextension developcommand. To find its location, you can runjupyter labextension listto figure out where thelabextensionsfolder is located. Then you can remove the symlink named@epi2melabs/epi2melabs-splashpagewithin that folder.
Package: epi2melabs-theme
epi2melabs_themeA JupyterLab theme extension.RequirementsJupyterLab >= 3.0InstallTo install the extension, execute:pipinstallepi2melabs_themeUninstallTo remove the extension, execute:pipuninstallepi2melabs_themeContributingDevelopment installNote: You will need NodeJS to build the extension package.Thejlpmcommand is JupyterLab's pinned version ofyarnthat is installed with JupyterLab. You may useyarnornpmin lieu ofjlpmbelow.# Clone the repo to your local environment# Change directory to the epi2melabs_theme directory# Install package in development modepipinstall-e.# Link your development version of the extension with JupyterLabjupyterlabextensiondevelop.--overwrite# Rebuild extension Typescript source after making changesjlpmrunbuildYou can watch the source directory and run JupyterLab at the same time in different terminals to watch for changes in the extension's source and automatically rebuild the extension.# Watch the source directory in one terminal, automatically rebuilding when neededjlpmrunwatch# Run JupyterLab in another terminaljupyterlabWith the watch command running, every saved change will immediately be built locally and available in your running JupyterLab. Refresh JupyterLab to load the change in your browser (you may need to wait several seconds for the extension to be rebuilt).By default, thejlpm run buildcommand generates the source maps for this extension to make it easier to debug using the browser dev tools. To also generate source maps for the JupyterLab core extensions, you can run the following command:jupyterlabbuild--minimize=FalseDevelopment uninstallpipuninstallepi2melabs_themeIn development mode, you will also need to remove the symlink created byjupyter labextension developcommand. To find its location, you can runjupyter labextension listto figure out where thelabextensionsfolder is located. Then you can remove the symlink named@epi2melabs/epi2melabs-themewithin that folder.
Package: epi2melabs-wfpage
epi2melabs_wfpageThis extension is composed of a Python package namedepi2melabs_wfpagefor the server extension and a NPM package namedepi2melabs-wfpagefor the frontend extension.RequirementsJupyterLab >= 3.0InstallTo install the extension, execute:pipinstallepi2melabs_wfpageUninstallTo remove the extension, execute:pipuninstallepi2melabs_wfpageTroubleshootIf you are seeing the frontend extension, but it is not working, check
that the server extension is enabled:jupyterserverextensionlistIf the server extension is installed and enabled, but you are not seeing
the frontend extension, check the frontend extension is installed:jupyterlabextensionlistContributingDevelopment installNote: You will need NodeJS to build the extension package.Thejlpmcommand is JupyterLab's pinned version ofyarnthat is installed with JupyterLab. You may useyarnornpmin lieu ofjlpmbelow.# Clone the repo to your local environment# Change directory to the epi2melabs_wfpage directory# Install package in development modepipinstall-e.# Link your development version of the extension with JupyterLabjupyterlabextensiondevelop.--overwrite# Server extension must be manually installed in develop modejupyterserverextensionenableepi2melabs_wfpage# Rebuild extension Typescript source after making changesjlpmrunbuildYou can watch the source directory and run JupyterLab at the same time in different terminals to watch for changes in the extension's source and automatically rebuild the extension.# Watch the source directory in one terminal, automatically rebuilding when neededjlpmrunwatch# Run JupyterLab in another terminaljupyterlabWith the watch command running, every saved change will immediately be built locally and available in your running JupyterLab. Refresh JupyterLab to load the change in your browser (you may need to wait several seconds for the extension to be rebuilt).By default, thejlpm run buildcommand generates the source maps for this extension to make it easier to debug using the browser dev tools. To also generate source maps for the JupyterLab core extensions, you can run the following command:jupyterlabbuild--minimize=FalseDevelopment uninstall# Server extension must be manually disabled in develop modejupyterserverextensiondisableepi2melabs_wfpage
pipuninstallepi2melabs_wfpageIn development mode, you will also need to remove the symlink created byjupyter labextension developcommand. To find its location, you can runjupyter labextension listto figure out where thelabextensionsfolder is located. Then you can remove the symlink namedepi2melabs-wfpagewithin that folder.Packaging the extensionSeeRELEASE