Saravanan666/pypi-org huggingface dataset:
Package: wsinfer
WSInfer: deep learning inference on whole slide imagesOriginal H&EHeatmap of Tumor Probability🔥 🚀 Blazingly fast pipeline to run patch-based classification models on whole slide images.Seehttps://wsinfer.readthedocs.iofor documentation.The main feature of WSInfer is a minimal command-line interface for running deep learning inference
on whole slide images. Here is an example:wsinfer run \
   --wsi-dir slides/ \
   --results-dir results/ \
   --model breast-tumor-resnet34.tcga-brcaInstallationWSInfer can be installed usingpiporconda. WSInfer will install PyTorch automatically
if it is not installed, but this may not install GPU-enabled PyTorch even if a GPU is available.
For this reason,install PyTorch before installing WSInfer.Install PyTorch firstPlease seePyTorch's installation instructionsfor help installing PyTorch. The installation instructions differ based on your operating system
and choice ofpiporconda. Thankfully, the instructions provided
by PyTorch also install the appropriate version of CUDA. We refrain from including code
examples of installation commands because these commands can change over time. Please
refer toPyTorch's installation instructionsfor the most up-to-date instructions.You will need a new-enough driver for your NVIDIA GPU. Please seethis version compatibility tablefor the minimum versions required for different CUDA versions.To test whether PyTorch can detect your GPU, check that this code snippet printsTrue.python -c 'import torch; print(torch.cuda.is_available())'Install WSInferWSInfer can be installed withpiporconda(fromconda-forge).PipTo install the latest stable version, usepython -m pip install wsinferTo install thebleeding edge(which may have breaking changes), usepython -m pip install git+https://github.com/SBU-BMI/wsinfer.gitCondaTo install the latest stable version, useconda install -c conda-forge wsinferIf you usemamba, simply replaceconda installwithmamba install.DevelopersClone this GitHub repository and install the package (in editable mode with thedevextras).git clone https://github.com/SBU-BMI/wsinfer.git
cd wsinfer
python -m pip install --editable .[dev]
pre-commit installWe usepre-committo automatically run various checks duringgit commit.CitationIf you find our work useful, please citeour paper!Kaczmarzyk, J.R., O’Callaghan, A., Inglis, F. et al. Open and reusable deep learning for pathology with WSInfer and QuPath.npj Precis. Onc.8, 9 (2024).https://doi.org/10.1038/s41698-024-00499-9@article{kaczmarzyk2024open,title={Open and reusable deep learning for pathology with WSInfer and QuPath},author={Kaczmarzyk, Jakub R. and O'Callaghan, Alan and Inglis, Fiona and Gat, Swarad and Kurc, Tahsin and Gupta, Rajarsi and Bremer, Erich and Bankhead, Peter and Saltz, Joel H.},journal={npj Precision Oncology},volume={8},number={1},pages={9},year={2024},month={Jan},day=10,doi={10.1038/s41698-024-00499-9},issn={2397-768X},url={https://doi.org/10.1038/s41698-024-00499-9}}
Package: wsinfo
The wsinfo librarywsinfo (short for website information) is a Python package for getting some
useful information about some website, without the need to write some
complicated hackish Python code.RequirementsThe package is compatible with both Python 2 and 3, so everything you need is
a recent Python installation.InstallationThe wsinfo library is available onPyPI,
so you can install it usingpip:pip install wsinfoUsageThe usage of the wsinfo library is as easy as:>>> import wsinfo
>>> w = wsinfo.Info("https://github.com")
>>> w.ip
'192.30.253.112'
>>> w.http_status_code
200
>>> w.title
'How people build software · GitHub'
>>> w.content
'<!DOCTYPE html>\n<html>\n[...]\n</html>'DocumentationThe latest documentation is always available here:https://wsinfo.readthedocs.io/en/latest/Tested Platforms and Python VersionsThe code was tested on all major platforms using a wide range of Python
versions.If you experience some issues, feel free to contact me oropen an issue on
GitHub.Changes1.3.0Added properties:content_type,http_header_dictandserver_osCorrect handling of HTTP Errors (retrieve error page)Documentation updatesCode cleanupMinor fixes and improvements1.2.0Hosted docs onreadthedocs.ioMinor documentation changes1.1.0Added function to list a websites heading structureDocumentation improvementsCode formattingMinor improvementsAdded/extended project infrastructure:GitHubPyPITravisCILandscape1.0.0Initial release
Package: wsingular
Wasserstein Singular Vectorswsingularis the Python package for the ICML 2022 paper "Unsupervised Ground Metric Learning Using Wasserstein Singular Vectors".Wasserstein Singular Vectorssimultaneously compute a Wasserstein distance betweensamplesand a Wasserstein distance betweenfeaturesof a dataset.
These distance matrices emerge naturally as positive singular vectors of the function mapping ground costs to pairwise Wasserstein distances.Get startedInstall the package:pip install wsingularFollow the documentation:https://wsingular.rtfd.ioCiting usThe conference proceedings will be out soon. In the meantime you can cite our arXiv preprint.@article{huizing2021unsupervised,
  title={Unsupervised Ground Metric Learning using Wasserstein Eigenvectors},
  author={Huizing, Geert-Jan and Cantini, Laura and Peyr{\'e}, Gabriel},
  journal={arXiv preprint arXiv:2102.06278},
  year={2021}
}
Package: wsipc
wsipcAsync Python IPC using WebSocketsServer Example (Simple Broker)fromasyncioimportrunfromwsipcimportWSIPCServerserver=WSIPCServer(heartbeat=45)run(server.start(block=True))Client Examplefromasyncioimportcreate_task,run,sleepfromwsipcimportWSIPCClientclient=WSIPCClient()@client.listener()asyncdefon_message(message):print(message)@client.listener()defsync_listener(message):print(message)asyncdefmain()->None:create_task(client.connect())awaitclient.connected.wait()awaitclient.send("Hello World!")awaitsleep(1)awaitclient.close()run(main())
Package: wsipipe
wsipipeA set of tools for processing pathology whole slide images for deep learning.Free software: MIT licenseDocumentation:https://wsipipe.readthedocs.io.FeaturesTODOCreditsThis package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.History0.1.0 (2022-09-08)First release on PyPI.
Package: wsipre
wsipreWhole-SlideImagePREprocessingwsipreis a small Python package to handle whole-slide images (WSI; also
known as virtual slides) with region-level annotations.wsiprecan be installed from PyPI as shown below. For more detail check out
thedocs.pip install wsipreLicenseThis project is licensed under the terms of the MIT license. SeeLICENSEfile for details.
Package: wsiprocess
Convert Helper for Histopathological / Cytopathological Machine Learning TasksMain FlowScan some WSIs.Make some annotations with WSI annotation tools. (ASAPandSlideRunner v.1.31.0,QuPath v0.2.3are now available. Seewikifor details.)Then wsiprocess helps converting WSI + Annotation data into patches and easy-to-use annotation data.WSIPatcherwill give you GUI.SeeWikiforavailable applications for annotation,speed comparisonbetween patched images and loading from raw WSIs,how to use the other annotatiion files.Installationpip UserInstallopenslideorlibvips. See [wiki] for installation hints.Install wsiprocesspip install wsiprocessAnaconda User# Only for python 3.6 or higher
conda install -c tand826 wsiprocessDocumentationDocumentationExampleAs a python moduleseeexamplesseewsiprocess/cli.pyto check the detailed flow.As a command line toolseeexamples.Available annotation toolsASAPSlideRunner version 1.31.0QuPath v0.2.3NDP.View2and your favorite tools withcustom parserdetails:wikiAvailable WSIsTest ongoingFrom below we tested wsi data.:smile: => worked well.:umbrella: => did not work well.otherwise => did not checkAperioCMU-1-JP2K-33005.svs:smile: CMU-1-Small-Region.svs:smile: CMU-1.svsCMU-2.svsCMU-3.svsJP2K-33003-1.svsJP2K-33003-2.svsGeneric-TIFF:umbrella:CMU-1.tiffCan not set magnification.Hamamatsu-vms:smile:CMU-1.zipCMU-2.zipCMU-3.zipCould not DOWNLOAD fromhttp://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu-vms/Hamamatsu:smile:CMU-1.ndpiCMU-2.ndpiCMU-3.ndpiOS-1.ndpiOS-2.ndpiOS-3.ndpiLeica:smile:Leica-1.scnLeica-2.scnLeica-3.scnLeica-Fluorescence-1.scnMiraxCMU-1-Exported.zipCMU-1-Saved-1_16.zipCMU-1-Saved-1_2.zip:umbrella:CMU-1.zipCan not make the foreground mask.CMU-2.zipCMU-3.zipMirax2-Fluorescence-1.zipMirax2-Fluorescence-2.zipMirax2.2-1.zipMirax2.2-2.zipMirax2.2-3.zipMirax2.2-4-BMP.zipMirax2.2-4-PNG.zipOlympusOS-1.zipOS-2.zipOS-3.zipTrestle:umbrella:CMU-1.zipASAP can not show the image properly, and it's hard to annotate.CMU-2.zipCMU-3.zipVentanaOS-1.bifOS-2.bif:umbrella:Zeiss : Can not load slide - :umbrella:Zeiss-1-Merged.zvi - :umbrella:Zeiss-1-Stacked.zvi - :umbrella:Zeiss-2-Merged.zvi - :umbrella:Zeiss-2-Stacked.zvi - :umbrella:Zeiss-3-Mosaic.zvi - :umbrella:Zeiss-4-Mosaic.zviTestDownload sample WSIcurl -O -C - https://data.cytomine.coop/open/openslide/hamamatsu-ndpi/CMU-1.ndpiMake random annotationInstall ASAP ( Linux / Windows ) -https://github.com/computationalpathologygroup/ASAP/releasesOpen CMU-1.ndpi and make some random annotation. - Save the annotation xml as "CMU-1.xml".Run test.pycd tests
pytest tests.pyCitation@software{takumi_ando_2022_5938308,
  author       = {Takumi Ando},
  title        = {tand826/wsiprocess: version 0.9},
  month        = feb,
  year         = 2022,
  publisher    = {Zenodo},
  version      = {v0.9},
  doi          = {10.5281/zenodo.5938308},
  url          = {https://doi.org/10.5281/zenodo.5938308}
}
Package: wsireg
wsiregMulti-modal or mono-modal whole slide image registration in a graph structure for complex registration tasks usingelastix.Documentation:https://wsireg.readthedocs.io.FeaturesGraph based approach to defining modalities and arbitrary transformation paths between associated imagesUse ofelastix(throughITKElastix) to perform registrationSupport for linear and non-linear transformation modelsTransform associated data (masks, shape data) along the same path as the images.Supports images converted to OME-TIFF usingbioformats2raw->raw2ometiffpipelineAll registered images exported as pyramidal OME-TIFF or OME-zarr that can be viewed in software such asVitessce,vizarr,QuPath,OMEROor any platform that supports these formats.All transforms for complex registration paths are internally composited and only 1 interpolation step is performed, avoiding accumulation of interpolation error from many registrationsShape data (polygons, point sets, etc.) in GeoJSON format (future portable format for QuPath detection/annotation data) can be imported and transformations applied producing a modified GeoJSONSome support for reading native WSI formats: currently reads .czi and .scn but could be expanded to other formats supported by python packagetifffileHistory0.3.9 (2023-01-10)Deprecates unused aicsimageio dependency.0.3.8 (2023-01-10)Fix bug that occurs when file paths contain a period.0.3.7 (2022-04-28)Add support for translation transformation. Fix writing of merge modalities in cmd line configuration.0.3.6 (2022-04-28)Fixes bug in wsireg2d console script.0.3.5 (2022-04-28)Add support for python 3.10 with updated itk-elastix.0.3.4 (2022-04-27)Major refactor of RegImage class, various small improvements throughout to support napari-wsireg.0.3.2.2 (2022-02-04)This minor update adds the ability to draw binary or label masks using RegShapes.0.3.2.1 (2021-12-28)This releases fixes some small bugs around shape transforms.fix geojson import/exportfix bug with geojson reading0.3.0 (2021-09-22)add “ome.tiff-bytile” writer to write transformed images tile-by-tileunify data reading from tiffs to usedasknumerous improvements, bug fixes, and additional tests
Package: ws-joint-sbom-reports
WS Joint SBOM Tool in SPDX formatCLI Tool to generate joint SBOM report inSPDX formatfrom two SBOM reports.The tool can generate mutual report from two SBOM reports just inJSONformat.Both source files should be inJSONformat also.PrerequisitesPython 3.9+Installation and Execution by pulling package from PyPi:Execute pip installpip install ws-joint-sbom-reportsRun report:ws_joint_sbom_reports -f1 <FIRST_FILE> -f2 <SECOND_FILE> -o <OUTPUT_FILE> -hf <HEAD_FILE>Required and Optional arguments:-h,--helpshowthishelpmessageandexit-f1FIRST_FILE,--first_fileFIRST_FILE-f2SECOND_FILE,--second_fileSECOND_FILE-hfHEAD_FILE,--head_fileTakingheadofdatafromFirstfileifTrue(default)orfromsecondfileifFalse-oOUTPUT_FILE,--output_fileOUTPUT_FILEExamples:# Create output report with head data from first filews_joint_sbom_reports-f1<FIRST_FILE>-f2<SECOND_FILE>-o<OUTPUT_FILE># Create output report with head data from second filews_joint_sbom_reports-f1<FIRST_FILE>-f2<SECOND_FILE>-o<OUTPUT_FILE>-hfFalse
Package: wsjtx-srv
Author:Ralf Schlatterbeck <rsc@runtux.com>This implements a simple UDP server that binds to theWSJT-XUDP message
protocol port. It also provides everything for parsing and/or generatingWSJT-Xtelegrams.By default callingwsjtx-srvwill provide a simple server that
colors all callsigns not in the ADIF file for the current band. It uses
the ADIF logfile fromWSJT-Xwith a default path to that file. You can
specify the correct path for your installation either via
command-line (callwsjtx-srvwith the--helpoption) or in the
environment variableWBF_PATH. It has also an implementation that
looks up DXCC-entities in my log database, but only those that have been
confirmed via LOTW.The implementation ofwsjtx-srvshould give a rough idea of how to use
this in your own projects.There is a companion-programwbfstanding forworked beforethat
takes a number of callsigns on the command-line and tells you the worked
before status.ChangesVersion 0.5: Add pyproject.tomlInstallation with new setuptools again possibleVersion 0.4: Move to setuptoolsSeems previous releases had versioning problems with pypiVersion 0.3: Small fixesCompatibility with older protocol versions, thanks to Sampo Savolainen
for the patchFix band lookup if no QSO on bandVersion 0.2: Fix setup.py install_requiresVersion 0.1: Initial implementationImplement serialization and deserialization ofWSJT-Xtelegrams and a
simple serverFirst Release
Package: wskbb
Kemarin, 25 Juni 2022, aku mendengar kabar, dua sahabatku terserang stroke.
Mereka adalahPapindan kangAgung Botol.Mereka berdua adalah orang-orang yang tak henti menginspirasi, dan amatlah kebetulan bahwa keduanya memiliki bidang keahlian yang mirip, yaitu mengolah gambar. Output olahan gambar Kang Agung Botol adalah berbentuk vektor yang kemudian mewujud dalam kaos ataupun stiker. Sementara, karya pinot, sudah mendunia dalam bentul pixel art, retro.Saya percaya bahwadoaterbaik adalah yang disertailaku, maka biarlah koding tak seberapa ini menjadilakuku untuk mendoakan kesembuhan mereka berdua.Lekas sembuh dan teruslah berkarya, dulur-dulurku.Cara Menggunakan$ wskbb path_image –model=modelpath_image:: letak image yang ingin diproses.model:: model hasil yang dipilih. Pilihannya ada dua:papindanbotol.
Package: wsl2gpg
wsl2gpgwsl2gpg is a small utility making it possible to use gpg in WSL
(Windows Subsystem for Linux) with the agent
fromGpg4win.GnuPG's libassuan emulates sockets on Windows by listening on localhost
and writing the TCP port number and a key to the "socket" file.
This utility will listen on UNIX sockets in ~/.gnupg and proxy
connections to the localhost TCP port. The key is automatically sent first.With this, gpg in WSL can talk to the Gpg4win agent in Windows.UsageYou can either install wsl2gpg with pip:pipinstallwsl2gpgOr alternatively just copy__init__.pysomewhere
and make it executable withchmod +xThen, append a line to your.bashrc(or rc file of your favorite shell)
to run wsl2gpg when you log in:wsl2gpg-q-i&You should then be able to use gpg in WSL as usual. For example, to show
information on a Yubikey / smartcard:$gpg--card-status
Reader...........:YubicoYubikey4OTPU2FCCID0[...]Potential IssuesShould the Windows user detection not work, you can set the username manually:wsl2gpg-uyourwindowsuername
Package: wslconv
wslconvA utility for converting file paths between WSL (Windows Subsystem for Linux) and Windows formats.wslconvhelps developers working with WSL, bridge the path differences between Windows and Linux, making the
experience smoother and error-free.FeaturesDetect and convert paths automatically based on their format.Support for native Linux paths, native Windows paths, Linux paths on Windows, and Windows paths on Linux.Simple, intuitive API for developers.InstallationTo installwslconv, use pip:pip install wslconvQuickstartHere's a quick example:fromwslconvimportWSLPathConverter# Create an instance with the path and distro nameconverter=WSLPathConverter("C:\\Users\\user\\Documents","Ubuntu")# Convert to Linux formatlinux_path=converter.to_linux()print(linux_path)# Expected: /mnt/c/Users/user/Documents# Convert to Windows formatwindows_path=converter.to_windows()print(windows_path)# Expected: C:\Users\user\DocumentsAPI ReferenceWSLPathConverterMain class for the path conversion.Methods__init__(self, path, distro): Initialize with a path and the name of the WSL distro.filesystem_type(self): Return the filesystem type of the path (LinuxorWindows).os_type(self): Return the OS type based on the path format (LinuxorWindows).to_linux(self): Convert the path to its Linux representation.to_windows(self): Convert the path to its Windows representation.ContributingFeel free to open issues or PRs if you find any bugs or have suggestions for improvements!
Package: wslink
Wslink allows easy, bi-directional communication between a python server and a
javascript client over awebsocket. The client can make RPC calls to the
server, and the server can publish messages to topics that the client can
subscribe to. The server can include binary attachments in these messages,
which are communicated as a binary websocket message, avoiding the overhead of
encoding and decoding.RPC and publish/subscribeThe initial users of wslink driving its development areVTKandParaView.
ParaViewWeb and vtkWeb require:RPC - a remote procedure call that can be fired by the client and return
sometime later with a response from the server, possibly an error.Publish/subscribe - client can subscribe to a topic provided by the server,
possibly with a filter on the parts of interest. When the topic has updated
results, the server publishes them to the client, without further action on
the client’s part.Get the whole storyThis package is just the server side of wslink. See thegithub repofor
the full story - and to contribute or report issues!Configure from environment variablesThose only apply for the Python server and launcher.WSLINK_LAUNCHER_GET - If set to 1 this will enable the GET endpoint for session informationWSLINK_LAUNCHER_DELETE - If set to 1 this will enable the DELETE endpoint for killing a running sessionWSLINK_MAX_MSG_SIZE - Number of bytes for a message size (default: 4194304)WSLINK_HEART_BEAT - Number of seconds between heartbeats (default: 30)LicenseFree to use in open-source and commercial projects, under the BSD-3-Clause license.
Package: wslm
WSL Management ToolRepositoryhttps://gitee.com/itxq/wslm.gitInstallationpipinstallwslmHelp# eg:wslm-h
wslmport-h
wslmportadd-hBase# set encoding , PowerShell.exe PATHwslm-eutf-8-sPowerShell.exe# eg:wslm-eutf-8-sPowerShell.exeportadd-p33063307-w
wslm-egbk-sPowerShell.exeportadd-p33063307-wPorts info# view ports infowslmportinfo# showPortsInfo:
+---------------+------------+----------------+-------------+|ListenAddress|ListenPort|ConnectAddress|ConnectPort|+---------------+------------+----------------+-------------+|0.0.0.0|3306|172.23.60.88|3306||0.0.0.0|6379|172.23.60.88|6379|+---------------+------------+----------------+-------------+

NetFireWallRulesInfo:
+-------------------------------------+-----------+--------+---------+|DisplayName|Direction|Action|Enabled|+-------------------------------------+-----------+--------+---------+|WSL2FirewallUnlockOutbound3306|Outbound|Allow|True||WSL2FirewallUnlockInbound3306|Inbound|Allow|True||WSL2FirewallUnlockOutbound6379|Outbound|Allow|True||WSL2FirewallUnlockInbound6379|Inbound|Allow|True|+-------------------------------------+-----------+--------+---------+Add Ports# add portswslmportadd-p33063307# add ports with firewallwslmportadd-p33063307-w# add ports with firewall Inboundwslmportadd-p33063307-wInbound# add ports with firewall Outboundwslmportadd-p33063307-wOutboundDelete Ports# del portswslmportdel-p33063307# del ports with firewallwslmportdel-p33063307-w# del ports with firewall Inboundwslmportdel-p33063307-wInbound# del ports with firewall Outboundwslmportdel-p33063307-wOutboundReset Ports# reset portswslmportreset# reset ports with firewallwslmportreset-wWSL2 info# view wsl infowslmwslinfo# showWSL2Info:
+-------------+---------------+---------------+--------------------+|name|state|version|is_default|+-------------+---------------+---------------+--------------------+|Ubuntu|Running|2|True||WLE|Stopped|2|False|+-------------+---------------+---------------+--------------------+
Package: wslPath
wslPathwslPathis a Python module to convert between Windows and POSIX paths in WSLInstallFromPyPI:pipinstallwslPathFromConda:condainstall-cconda-forgewslPathUsagesimportwslPath# Windows to Posix## Relative pathpathwin="hoge\\fuga"wslPath.to_posix(pathwin)# -> "hoge/fuga"## Absolute pathpathwin="C:\\hoge\\fuga"wslPath.to_posix(pathwin)# -> "/mnt/c/hoge/fuga"# Posix to Windows## Relative pathpathposix="hoge/fuga"wslPath.to_windows(pathposix)# -> "hoge\\fuga"## Absolute pathpathposix="/mnt/c/hoge/fuga"wslPath.to_windows(pathposix)# -> "C:\\hoge\\fuga"# Identify path type (POSIX or Windows)path="hoge/fuga"wslPath.is_posix_path(path)# -> Truepath="hoge\\fuga"wslPath.is_posix_path(path)# -> Falsepath="hoge/fuga"wslPath.is_windows_path(path)# -> Falsepath="hoge\\fuga"wslPath.is_windows_path(path)# -> True
Package: wsl-path-converter
WSL path converterConvert between Linux and Windows path inWSL(Windows Subsystem for Linux).InstallationEither install the latest stable version hosted onPyPI:pip install wsl-path-converterOr clone the source repository and install the bleeding-edge version:git clone https://github.com/lamyj/wsl-path-converter.git
cd wsl-path-converter
pip install .If the latter case is run by a regular user, i.e. non-root, thewpcexecutable will be installed in~/.local/bin.UsageThis converter works with Windows path mounted in WSL, either through/etc/fstabor through themountcommand.The executable is calledwpc. To convert a Windows path to its Linux counterpart, run it with the-uoption:wpc -u C:\autoexec.batThis is also valid usingUNCpaths (e.g. remote shares):wpc -u \\samba.example.com\shareFor the converse operation, i.e. convert a Linux path to its Windows counterpart, use the-woption:wpc -w /mnt/c/autoexec.batIf a path unambiguously belongs to either Windows or Linux, the conversion option can be skipped; all previous examples can be run without the option:wpc C:\autoexec.bat
wpc \\samba.example.com\share
wpc /mnt/c/autoexec.bat
Package: wsl-path-exe
WSL-path-exe is a “script” that helps you use native software (.exe) more easily insideWSL, putting everyone in the PATH without ever having to put .exe at the end. The exe’s will behave like a WSL command, so theautocompleteof some application will work too (e.g Python). Onlybashandzshare supported.DependenciesWSL/UbuntuPython (apt install python)pip (apt installpython-pip)Install and UsageThe entire installation process is done within WSL, not in Powershell or CMD.$ pip installwsl-path-exe$wsl-path-exe-lYou may want to always leave the executables available in PATH add folder WSL:$ echo 'exportPATH=$PATH:$HOME/.wsl'>>~/.bashrcor$ echo 'exportPATH=$PATH:$HOME/.wsl'>>~/.zshrc