Saravanan666/pypi-org huggingface dataset:
Package: niolithic
NiolithicA simple Matrix client library wrapped aroundmatrix-nio.It's meant to ressemble the very easy to work with design ofdiscord.py. The intention is to make it quicker and simpler to set up a bot regardless of your skill level. But if you want to make a full-blown application or intricate bot, you should usematrix-nioas it is.ExamplefromniolithicimportSimpleClientclassMyBot(SimpleClient):asyncdefon_ready(self):print('Bot is live!')asyncdefon_message(self,room:MatrixRoom,event:RoomMessageText):print(f"Message received in room{room.display_name}\n"f"{room.user_name(event.sender)}|{event.body}")command,*args=event.body.split()ifcommand=='!clear':# Remove the last N messagesiflen(args)<1:awaitself.send_text(room.room_id,'You need to provide the number of messages to clear out. Ex. `!clear 10`')returnlimit=int(args[0])+1# Plus 1 to include the commandasyncformessageinself.get_messages(room.room_id,(RoomMessageText,),limit=limit):awaitself.redact_event(message,reason='Mass deletion by `!clear`')print(f'{limit}messages redacted.')client=MyBot('https://matrix.org',# Homeserver'@username123:matrix.org',# User ID'MyBot',# Device name)client.run()
Package: nionctl
nionctlAn abbreviation of common linux command-line utilities into one ctlInstallationInstallnionctlwith pip:pipinstallnionctlThe PyPi page is availiblehere.Current commands (WIP):Basic WiFi controlling (usesnmcli)Basic Bluetooth controlling (usesbluetoothctl)git clonefrom url to default directoryBasic archiving utilities (supports.zip,.tar,.tar.gz,.tar.bz2)Simple image editing (converting, rotating, resizing, negating etc)ContributingAny kinds of contributions are very welcome!
Currently the main goals are to bring more utilities and make the ctl cross-platform. Any tests on other linux distros are also welcome!
Package: nionswift
Nion Swift: Scientific Image ProcessingNion Swift is open source scientific image processing software integrating hardware control, data acquisition,
visualization, processing, and analysis using Python. Nion Swift is easily extended using Python. It runs on Windows,
Linux, and macOS.Nion Swift is developed for the operation of Nion electron microscope instruments. It is also useful as an offline tool
to visualize, process, and analyze data from the Nion instruments. It is being developed with the intention of
supporting additional instrumentation and fields.GitHub testsTravis testsPyPIPyPI DownloadsTwitterUser’s GuideNion Swift User’s GuideMore InformationChangelog
Package: nionswift-eels-analysis
Nion Swift EELS AnalysisA Nion Swift library for EELS analysis (used in Nion Swift)Nion Swift EELS analysis is comprised of libraries and UI’s useful for EELS
analysis.testspackageMore InformationChangelogChangelog (nionswift-eels-analysis)0.6.5 (2023-09-28):Fix a bug in temperature calculation.0.6.4 (2023-08-17):Add Python 3.11 support. Drop 3.8.Update titles for new auto-title system in nionswift.Fix thermometry issues.0.6.3 (2022-09-14):Fix regression in elemental mapping radio buttons for picked edge.0.6.2 (2022-07-26):Introduce power law (uniform) background model, uses uniform background shape.0.6.1 (2022-05-28):Minor changes for improved nionui compatibility.0.6.0 (2021-11-12):Nion Swift 0.16 compatibility.Add measure temperature computation.0.5.4 (2021-05-26):Maintenance to reduce dependency on new/unstable niondata features.Improve colors for better visibility in align ZLP, live ZLP, live thickness.Vectorize thickness mapping for significant speed-up.Add calibrate spectrum tool.0.5.3 (2021-03-12):Fix issue with Align ZLP (COM) when using it on empty data.Fix issue with Align ZLP (COM) that caused a bias towards half-integer shifts.Allow Align ZLP to be used on single spectra. Useful for bringing the ZLP to calibrated zero.0.5.2 (2020-11-13):Fix issue with single channel zero loss peaks in thickness calculation.Ensure default background is power law.Improve wording in background menu.0.5.1 (2020-10-06):Add exponential functions for two-area method.Add two-area background fitting class.Improve speed of polynomial background and fix power law.0.5.0 (2020-08-31):Rework background models to allow for plug-in models.Made Align ZLP output the measured shifts in addition to the aligned spectra.Allow graphics to select the ROI for aligning spectra in Align ZLP.Allow 2D images in Align ZLP and interpret y-axis as sequence axis.Reworked Align ZLP to eliminate duplicate code.0.4.4 (2019-10-24)Changed shift method in ZLP subpixel align to scipy.ndimage.shift with linear interpolation to get rid of artifacts.0.4.3 (2019-04-29)Added checks to avoid applying live ZLP and thickness to 2D data items.Moved ZLP analysis functions to nion.eels_analysis module for better reuse.0.4.2 (2019-03-27)Make Align ZLP support sequences AND 1D collections.Added menu items for center-of-mass and gaussian fit for ZLP alignment (both do sub-pixel alignment but much faster than cross-correlation)0.4.1 (2019-01-07)Improve data type handling (do not auto-promote to float64).Improve menu item layout.0.4.0 (2018-12-21)Add menu items for live thickness, thickness mapping, align zlp.0.3.0 (2018-12-12)Nion Swift 0.14 compatibility.Use composite line plot display for display again.0.2.1 (2018-10-14)Update original background subtraction to not use deprecated composite library item.0.2.0 (2018-09-28)Add simplified background subtraction.Add live ZLP tracking.0.1.1 (2018-05-12)Initial version online.
Package: nionswift-experimental
Nion Swift ExperimentalA Nion Swift package for experimental menu items and scripts and other items.This is a public repository maintained primarily by Nion.packageMore InformationChangelogChangelog (nionswift-experimental)0.7.12 (2023-08-17)Add typing support.0.7.10 (2023-08-17)Add Python 3.11 support. Drop Python 3.8.Add crop to valid area functionality.Remove measure ZLP; functionality moved to eels-analysis.Add find local maxima computation.Use multi-d processing base functions from nion.data.0.7.9 (2022-07-26)Add I vs E square plot computation.Fix multi-dimensional crop computation axis choice.0.7.8 (2022-05-28)Change defaults for SI align.Add image sequence align computation.Add align SI sequence computation.Fix threading problem in measure shifts.0.7.7 (2022-04-20)Add drift corrector to experimental.Use multithreading for measure shifts.Minor error improvements during measure shifts.0.7.6 (2022-02-18)Clean up computations and associated UI.0.7.5 (2021-12-13)Add option for relative shifts and limited shift range to Multi-D measure shifts.Python 3.10 compatibility.0.7.4 (2021-10-24)Add wizard base classes.Add computation for visualizing tableau data.Add more fine-grained axis control for multi-dimensional integrate.0.7.3 (2021-10-20)Release skipped.0.7.2 (2021-06-16)Fix problem with some axis + shape combinations in MultiDimensionalProcessing.Add computations for aligning virtual detector images and combining COM data into a color image.Rework DoubleGaussian to use new-style computations and and improved UI.Add affine transformation computation.Add computation for making an iDPC image out of DPC data.0.7.1 (2020-11-13)Make join/split preserve display layers.Utilize improved tracking of 4D back-graphics.0.7.0 (2020-08-31)Fix issue with “Select map graphics” buttons in 4D tools.Reconnect 4D tools pick graphics after a Swift restart.0.6.0 (2019-10-24)Add 4D tools (menu items and panel).Use eels_analysis library for ZLP amplitude position.0.5.2 (2019-04-29)Fix issue with mark 0eV being allowed to operate on 2D data.0.5.1 (2019-01-14)Fix issue with measure ZLP being allowed to operate on 2D data.0.5.0 (2018-12-12)Nion Swift 0.14 compatibility.Align ZLP script.Find interface script.0.4.0 (2018-10-03)Add Multi EELS script.0.3.1 (2018-05-14)Initial version online.
Package: nionswift-io
Nion Swift I/OThe Nion Swift I/O library (used in Nion Swift)Nion Swift I/O is the I/O library for Nion Swift, providing additional commonly used file formats.testspackageMore InformationChangelogChangelog (nionswift-io)15.2.1 (2023-10-23)Update requirements.15.2.0 (2023-08-17)Update requirements, version.Add Python 3.11 support; drop Python 3.8 support.0.15.1 (2022-05-28)Update dependencies for Swift 0.16.3 compatibility.0.15.0 (2021-11-12)Fix handling of spectrum image export in DM format (now recognized in DM).Drop support for Python 3.7.Compatible with Swift 0.160.14.3 (2021-01-16)Partially fix issue storing tuple-of-tuple as rectangle in dm3 import/export.0.14.2 (2020-11-04)Write out high tension tag with no units.Improve writing SI data (always mark 1D datum as a spectrum).0.14.1 (2020-11-04)Skipped.0.14.0 (2019-11-12)Add support for writing DM4 files. Contributed by Marcel Tencé.0.13.9 (2019-04-17)Handle large format data items (HDF5 backed) when exporting to TIFF.Improve support for multi-dimensional data as available in latest TIFF library.0.13.8 (2019-01-31)Improve treatment of 1D collections/sequences of spectra/images when exporting/import to DM file.0.13.7 (2018-12-11)Improve treatment of spectrum images when exporting/import to DM file.0.13.6 (2018-06-18)Improve support for exporting large format (HDF5) data items to DM file format.0.13.5 (2018-05-21)Add support for timestamp/timezone when exporting/importing to DM file.0.13.4 (2018-05-20)Fix bug with large integers (showing up in timestamp).0.13.2 (2018-05-17)Improve recognition of 1d data (spectrum) during import. Also sequences.0.13.0 (2018-05-10)Initial version online.
Package: nionswift-segmentation
Installingvia pip:
pip install nionswift-segmentationUsageAfter this package is installed successfully,
a new menu item “Segmentation” will be added into
the GUI of nionswift. Currently there is only
one option “Real-space segmentation” in this
menu. Click it to perform a segmentation for
the image.Image segmentationtestspackageMore InformationChangelog
Package: nionswift-video-capture
# Nion Swift Video CaptureA video capture package for Nion Swift.## Installation` conda install opencv conda installnionswift-video-capture`## LicenseThis project is licensed under [GPLv3](https://www.gnu.org/licenses/gpl-3.0.en.html).Changelog (nionswift-video-capture)2.6.0 (2023-09-14)Update compatibility requirement for nionswift-instrumentation kit, nionswift.0.2.5 (2022-12-08)Update compatibility requirement for instrumentation kit.0.2.4 (2022-09-14)Make opencv an optional package.0.2.3 (2021-11-12)nionswift-instrumentation 0.20 compatibility.0.1.0 (INITIAL VERSION)Initial version.
Package: niota
NIOTAMake IOTA to be an integrity chain.Niota registers Asset history records to the integrity chain.Installationpython3-mpipinstallniotaUnit TestingmaketestUsageIota ClientTheIotaClientclass is a client to interact withIOTA REST API.Below is a minimal example for connecting to an IOTA hornet node with JWT authentication enabled, and create a message.fromniotaimportIotaClientiota=IotaClient(base_url='https://example.iota.hornet.node',jwt_token='enter JWT token here')create_message_resp=iota.create_message('example-index','example-data')message_id=create_message_resp.data.messageIdNiota clientTheNiotaclass can be used as a client to interact with IOTA Tangle messages with Numbers Protocol integrity record format.example_integrity_info={'raw_cid':'bafkreihdwdcefgh4dqkjv67uzcmw7ojee6xedzdetojuzjevtenxquvyku','ida_cid':'bafkreihdwdcefgh4dqkjv67uzcmw7ojee6xedzdetojuzjevtenxquvyku','ida_mid':'c7dfa6e5-346d-4b4d-a663-a421e7f9171f','ida_sha256sum':'e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855','metadata_cid':'bafkreidgkmzpzvot7a5r2iy44tmcojuvoyjgbwi5udldfisbvn4lnfrmoq','service_message':'Create test data',}niota=Niota(base_url='https://example.iota.hornet.node',jwt_token='enter JWT token here'private_key=private_key,public_key=public_key,)message_id,index=niota.create_message(**message_data_fixture)
Package: nipals
A module for calculation of PCA and PLS with the NIPALS algorithm. Based on the R packagesnipalsandpcaMethodsas well as the
statistical appendixes to “Introduction to Multi- and Megavariate Data Analysis
using Projection Methods (PCA & PLS)” by Eriksson et. al.
Tested to give same results as the above packages and Simca, with some rounding errors.Free software: MIT licenseInstallationpip install nipalsDocumentationSeehttps://github.com/fredrikw/python-nipals/blob/master/docs/nipals_demo_iris.ipynbfor an example and the tests athttps://github.com/fredrikw/python-nipals/tree/master/tests.DevelopmentTo run the all tests run:toxNote, to combine the coverage data from all the tox environments run:Windowsset PYTEST_ADDOPTS=--cov-append
toxOtherPYTEST_ADDOPTS=--cov-append toxChangelog0.5.6 (2023-10-20)Updated supported Python versions0.5.5 (2022-09-28)Added check for X-matrix with row full of NAs0.5.4 (2021-05-07)Fixed Packaging error (0.5.3 was never released)0.5.3 (2021-05-06)Fixed error on numpy version >= 1.19Updated supported versionsMoved CI to Github Action (pt 1)0.5.2 (2019-06-04)Added compatibility with Nipals objects saved from pre-0.5 versions0.5.1 (2019-05-23)Added checks for, and optional removal of, zero variance in variablesAdded support for Python 3.7(0.5.0 was never released due to failing CI tests)0.4.3 (2018-04-24)Fixed test that failed after last bug fix0.4.2 (2018-04-24)Fixed bug with selection of starting column for cross validation of PCA0.4.1 (2018-04-09)Fixed bug with cross validation of PCA0.4.0 (2018-04-09)Added cross validationsAdded calculation of distance to model with plotsAdded model overview plots0.3.0 (2018-04-05)Added R2X and R2Y to the PLS classMade plot color selectable also for scoreplots without classes0.2.0 (2018-03-29)Added a PLS classImproved plottingFixed some problems with missing/infinite values0.1.0 (2018-03-14)First release on PyPI.
Package: niphlem
# niphlemniphlemis a toolbox that extracts physiological recordings during MRI scanning and estimates the signal phases so that they can be used as a covariate in your general linear model (GLM) with fMRI data.niphlemcan generate multiple models of physiological noise to include as regressors in your GLM model from either ECG, pneumatic breathing belt or pulse-oximetry data.  These are described in Verstynen and Deshpande (2011).Briefly, niphlem implements two physiological models for regressors generation:RETROICOR:  A phasic decomposition method that isolates the fourier series that best describes the spectral properties of the input signal.  This was first described by Glover and colleagues.Variation Models:  For low frequency signals (like the pneumatic belt and low-pass filtered pulse-oximetry) this does the combined respiration variance and response function described by Birn and colleagues (2008).  For high frequency signals (i.e., ECG or high-pass filtered pulse-oximetry), this generates the heart-rate variance and cardiac response function described by Chang and colleagues (2009).niphlemcan also extract cardiac and respiratory signals from the pulse-oximitry data stream itself, as described in Verstynen and Deshpande (2011).## DependenciesPython 3.6 or greater is required. Any of the below dependencies compatible wth such versions of Python should be OK:numpymatplotlibpandasscipyscikit_learnoutlier_utils## Installpip install niphlem## References:
- Verstynen TD, Deshpande V. Using pulse oximetry to account for high and low frequency physiological artifacts in the BOLD signal. Neuroimage. 2011 Apr 15;55(4):1633-44.
- Chang C, Cunningham JP, Glover GH. Influence of heart rate on the BOLD signal: the cardiac response function. Neuroimage. 2009 Feb 1;44(3):857-69.
- Birn RM, Smith MA, Jones TB, Bandettini PA. The respiration response function: the temporal dynamics of fMRI signal fluctuations related to changes in respiration. Neuroimage. 2008;40(2):644-654.
Package: nipiezojenapy
Control of PiezoSystemJena NV40/3CLE via NI DAQmxControl of the Jena's piezo accuators via their multi-channel amplifier.https://www.piezosystem.com/products/amplifiers/multi-channel/40ma-multi-channel-amplifiers/Uses NIDAQ device to read and write analog voltages between 0 and 10 to
three input and output voltage channels connected to a Jena NV40/3CLE
amplifier. Each input/output channel controls one of three axis (x, y, or z).When using this software, one must at least provide three analog channels on
the NIDAQ that are connected to the NV40/3CLE amplifier that control (write)
the location of the piezo stage.This program does notneedto read voltages from the amplifier. If no read
channels are provided, this program will report the last written values when
reporting the current location.This controller doesNOTlock out usage of analog input and output channels
on the NI-DAQ card. It writes or reads to the analog channels and then releases
the resource. This would allow external programs to access those channels, so
long as the access is not simultaneous.InstallationRequirementsThis python package depends upon National Instruments driver and NI DAQ card
that contains three analog input and output channels.You must first install the NI DAQmx driver.http://www.ni.com/downloads/.PIP should install the rest of the dependencies.Local Installationpip install nipiezojenapyUsageGUI ApplicationFrom the shell prompt, launch> qt3piezoFor help on hardware configuration use the help option (qt3piezo -h)Programmaticallyimport nipiezojenapy
pcon = nipiezojenapy.PiezoControl(device_name = 'Dev1',
                                  write_channels = ['ao0','ao1','ao2'],
                                  read_channels = ['ai0','ai1','ai2'])Read Positionprint(pcon.get_current_position())
[39.953595487425225, 40.047631567251806, 39.9510191567554]Go To Positionpcon.go_to_position(x = 20, y = 20, z = 20)
pcon.get_current_position()
[19.935887437291537, 19.94876864898489, 19.872769502734947]Note that each axis can be set independently. That is, one may move along
a single axis without specifying the other axis values.pcon.go_to_position(z = 40)
pcon.get_current_position()
[19.913989377848296, 19.988700406441584, 39.91623869419529]LICENSELICENCE
Package: nipistaa
NipistaaA pincer library that provides templates commands for thePincerAPI wrapper.Usage exampleimportnipistaafromnipistaa.templatesimportpingfrompincerimportClient@nipistaa.hook(ping,guild=1234567890)classBot(Client):@Client.eventasyncdefon_ready(self):print('Logged in as',self.bot)if__name__=='__main__':Bot('...').run()fileor even make it with bare python Client!importnipistaafrompincerimportClientBot=nipistaa.hook('ping',guild=1234567890)(Client)Bot('...').run()filewant  to use nipistaa withing a Cog? No problem.frompincerimportcommandfrompincer.objectsimportEmbed,MessageContextimportnipistaafromnipistaa.templatesimportping@nipistaa.hook(ping,guild=134567890)classMyBeautifulCog:# your own commands@commandasyncdefsay(self,ctx:MessageContext,message:str):returnEmbed(description=f"{ctx.author.user.mention}said:\n{message}")setup=MyBeautifulCogfile
Package: nippe
NiPPE -NibePowerPerformanceEnhancementPrerequisitesVSCodeRemote Containers ExtensionOpen in ContainerClone the repository to your local machineOpen the repository in VSCodeA window will pop up in the lower left corner, asking if you want to open the repository in a container. Click "Reopen in Container"
(ORpressF1and type "Remote-Containers: Reopen in Container")FormattingFormatting is strictly done byBlackand the project is setup to automatically format on save.VersioningVersioning follows SemVer and is handled automatically bysetuptools-git-versioningtogether with tags.To get the current version you can runsetuptools-git-versioningin a terminal inside of the repo.TestingWe encourage you to provide unit tests for your code contributions.The tests should be added in thetests/folder and can be run by executingpytestin a terminal.Tests can also be run through VSCodesCommand Palette or Test Explorer.Building code for ESP deviceInstallESP-IDFextension in VSCodeInstallESPHomelocallyChange ssid and password to match your wifi in the nippegw.yaml file in the root of the projectRunesphome -v compile nippegw.yamlin the root of the project which will probably fail with the following messageCopy the argument from the last 3 rows in the above picture i.e.--chipesp32c3merge_bin-oC:\reps\git\nippe\.esphome\build\nippegw\.pioenvs\nippegw/firmware-factory.bin--flash_size4MB0x0000C:\Users\bt6259\.platformio\packages\framework-arduinoespressif32\tools\sdk\esp32c3\bin\bootloader__40m.bin0x8000C:\reps\git\nippe\.esphome\build\nippegw\.pioenvs\nippegw\partitions.bin0xe000C:\Users\bt6259\.platformio\packages\framework-arduinoespressif32\tools\partitions\boot_app0.bin0x10000C:\reps\git\nippe\.esphome\build\nippegw\.pioenvs\nippegw/firmware.binMake the following change to the copied text (above = before, below = after)Run the followingesptool.exe <Your copied text>in the root of the project, this will generate a binary for you to upload to the esp device.Hold the "EN" button on the esp device and connect it to your computer via USBOpen device manager to find the COM port that the device is connected to (in our case COM9)Run the following command in the root of the project to flash the deviceesptool.exe --port <Your COM port> write_flash --flash_mode dio --flash_freq 80m --flash_size 4MB 0x0 .\.esphome\build\nippegw\.pioenvs\nippegw\firmware-factory.binPress the "BOOT" button on the esp device to load the new firmware, the device will show up as a wifi called "nippegw" in your wifi list
Package: nipreps-versions
Nipreps version schemesThis package provides asetuptools_scmplugin for version schemes used
by the Nipreps family of projects.UsageAddnipreps_versionsto yourbuild-system.requireslist, e.g.,[build-system]requires=["flit_scm","nipreps_versions",]build-backend="flit_scm:buildapi"or[build-system]requires=["setuptools","setuptools_scm","nipreps_versions",]build-backend="setuptools.build_meta"Then request a nipreps version scheme:[tool.setuptools_scm]version_scheme="nipreps-calver"SchemesCurrently, only one versioning scheme is implemented:nipreps-calverAs described inReleases - Principles,The basic release form isYY.MINOR.PATCH, so the first minor release of 2020 is 20.0.0, and the first minor release of 2021 will be 21.0.0, whatever the final minor release of 2020 is. A series of releases share aYY.MINOR. prefix, which we refer to as theYY.MINOR.xseries. For example, the 20.0.x series contains version 20.0.0, 20.0.1, and any other releases needed.If the last tag was 22.1.0 and the year remains 2022, the development version is22.2.0.devN. When the year changes to 2023, the development version will become23.0.0.devN.
If the branch ismaint/22.1.x, then the computed version will be22.1.1.devN.
If the branch isrel/22.0.3(and the last tag for that branch is 22.0.2), then
the computed version will be22.0.3.devN.
Package: niprov
provenance for neuroimaging dataEver encountered a file of which you weren’t sure what analysis steps it
had gone through? Ever wanted to know what types of data you have
available for a subject in one overview? Automatically document an
analysis pipeline?Provenance is meta-data that tracks the ‘history’ of a file, and niprov
is a python program to create, store and publish provenance for brain
imaging files.A list with all provenance attributes collected can be foundhere.
Read more in thefull online
documentation(orpdf).
For additional detailed information on image files, installnibabel,mneand/orpydicom.Commandline UsageInstall niprov:pipinstallniprovLook for existing image files in your data directory:provenancediscover/my/data/directoryRun a transformation command and log it as provenance for the new file:provenancerecordmcflirt-int1flip_all_orig-outt1all_reg-refvol0Store provenance of known MEG files as an xml file:provenanceexport--modality"MEG"--xmlPython APIimportniprovprovenance=niprov.ProvenanceContext()# Log an analysis step:someAnalysisPackage.correctmotion(input='JD-fmri.nii',output='JD-fmri-3dmc.nii')provenance.log('JD-fmri.nii','motion correction',['JD-fmri-3dmc.nii'])# Loop over images of John Smith and display a preview:forimageinprovenance.get().bySubject('John Smith'):image.viewSnapshot()# Make sure two files were acquired with the same parameters:img1.compare(img2).assertEqualProtocol()Web browserBy running the commandprovenance serveyou can start a mini
webserver in the background, and browse images in your webbrowser: