{ "info": { "author": "Andreas P. Cuny , Gotthold Fl\u00e4schner ", "author_email": "andreas.cuny@bsse.ethz.ch", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Natural Language :: English", "Operating System :: MacOS :: MacOS X", "Operating System :: Microsoft :: Windows :: Windows 7", "Operating System :: POSIX :: Linux", "Programming Language :: Python :: 3", "Topic :: Scientific/Engineering" ], "description": "Welcome to pyIMD!\n=================================\n\n.. image:: https://img.shields.io/badge/Made%20with-Python-brightgreen.svg\n :target: https://www.python.org/\n :alt: made-with-python\n\n.. image:: https://img.shields.io/pypi/pyversions/pyimd.svg\n :target: https://www.python.org/\n :alt: made-with-python3.6\n\n.. image:: https://img.shields.io/badge/platform-linux--x64%20%7C%20osx--x64%20%7C%20win--x64-lightgrey.svg\n :alt: supported-platform \n\n.. image:: https://img.shields.io/badge/license-GPLv3-brightgreen.svg\n :target: https://git.bsse.ethz.ch/cunya/pyimd/master/LICENSE\n :alt: License\n\n.. image:: https://readthedocs.org/projects/pyimd/badge/?version=latest\n :target: https://pyimd.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n.. image:: https://badge.fury.io/py/pyIMD.svg\n :target: https://pypi.org/project/pyIMD/\n\n.. image:: https://anaconda.org/cunya/pyimd/badges/installer/conda.svg\n :target: https://anaconda.org/cunya/pyimd\n\n.. image:: https://img.shields.io/travis/com/cunyap/pyIMD.svg?logo=travis\n :target: https://travis-ci.com/cunyap/pyIMD\n\n.. image:: https://ci.appveyor.com/api/projects/status/d4cjh9f6gx15n2y1?svg=true\n :target: https://ci.appveyor.com/project/cunyap/pyimd\n\n\n.. figure:: /pyIMD/examples/figures/pyIMD_ShowCaseFigure_web.png\n :width: 400 px\n\n Evolution of mass over time and the corresponding microscopy images are shown for a time span of 20min.\n The mass data was acquired every 10ms (data shown in black), overlaid in red is the rolling mean with a window of\n 1000. Images taken every 3 min over the observed times span, we see on average a steady increase of the cell mass.\n\nWith the introduction of a picoscopic cell balance that is compatible with optical microscopy, a new tool for the\ninvestigation of the cell state-dependent cell mass regulation is available for use in biophysics, cell biology,\nphysiology and medicine. However, the analysis of the data can be challenging due to a) the amount of high resolution\ndata or b) the structure of low-stress measurement (low resolution) data. Here, we introduce the software **pyIMD**, which\nallows to easily extract the mass as a function of time for non-moving cells out of the raw data. **pyIMD** Stands for\nPython inertial mass determination.\n\n\nThis documentation of **pyIMD** describes the API as well as gives provides a sample data set as well as sample scripts to\nrun **pyIMD** from Jupyter or the Python console but it also contains a tutorial about how pyIMD is used with the user\ninterface.\nThe aim of this module is the calculation of the total/inertial mass for measurements taken in the continuous sweep or in the phase-lock loop (PLL) mode.\n\nLinks\n=====\n\n* `Documentation `_\n* `PyPI `_\n\nInstallation\n------------\nIf you download the portable for your operating system there is no need for any installation and you can use **pyIMD**\ndirectly trough the user interface.\n\n* `Download the latest in one portable for WINDOWS, UNIX, OSX x64 systems `_\n\nOtherwise, to install this module from source, type on your terminal::\n\n >>> git clone https://git.bsse.ethz.ch/cunya/pyIMD\n >>> cd pyIMD\n >>> pip install .\n\nExample data\n------------\nExample data files can be found in this repo. We provide example data of the various devices used (Cytomass and Nanonis) in various formats.\n\n* Go to Example_data_.\n\n .. _Example_data: https://gitlab.com/csb.ethz/pyIMD/tree/master/pyIMD/examples/data/\n\n* Go to Example_scripts_.\n\n .. _Example_scripts: https://gitlab.com/csb.ethz/pyIMD/tree/master/pyIMD/examples/\n\nUsage\n-----\n\nTo use this module in a Python script, write::\n\n >>> from pyIMD.imd import InertialMassDetermination\n\nSet path to files either absolute or relative to where you run the script from, i.e. using the provided show case data::\n\n >>> file_path1 = \"/pyIMD/examples/data/show_case/0190110_ShowCase_PLL_B.txt\"\n >>> file_path2 = \"/pyIMD/examples/data/show_case/20190110_ShowCase_PLL_A.txt\"\n >>> file_path3 = \"/pyIMD/examples/data/show_case/20190110_ShowCase_PLL_LongTerm.txt\"\n >>> imd.create_pyimd_project(file_path1, file_path2, file_path3, '\\t', 23, 'PLL', figure_width=16.5, figure_height=20,\n initial_parameter_guess=[60.0, 2.0, 0.0, 0.0], cell_position=9.5, figure_format='pdf')\n >>> imd.run_intertial_mass_determination()\n\nList default settings for calculation::\n\n >>> imd.print_pyimd_project()\n\nChange settings for calculation and figure output the following way before calling run_intertial_mass_determination()::\n\n >>> imd.settings.spring_constant = 4\n\nMore info and examples can be found in the online `Documentation `_\n\nNote\n----\n\nUse tab completion to access the object's attributes (e.g. to get the calculated mass)::\n\n >>> mass = imd.calculated_cell_mass\n\nKnown Issues\n------------\n\nIn a IPython notebook the progress bar works not properly but has no effect on the calculations.\nIn a IPython notebook the calculation speed is much slower.\n\nContribute\n----------\n\nPlease do contribute! Issues and pull requests are welcome.\nThank you for your help improving software one changelog at a time!\n\n", "description_content_type": "", "docs_url": null, "download_url": "https://gitlab.com/csb.ethz/pyIMD/tree/master", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://gitlab.com/csb.ethz/pyIMD/tree/master", "keywords": "Inertial mass determination", "license": "GPL3.0", "maintainer": "", "maintainer_email": "", "name": "pyIMD", "package_url": "https://pypi.org/project/pyIMD/", "platform": "", "project_url": "https://pypi.org/project/pyIMD/", "project_urls": { "Download": "https://gitlab.com/csb.ethz/pyIMD/tree/master", "Homepage": "https://gitlab.com/csb.ethz/pyIMD/tree/master" }, "release_url": "https://pypi.org/project/pyIMD/0.0.8/", "requires_dist": [ "pandas (>=0.20.0)", "numpy (>=1.14.5)", "scipy (<1.3.0)", "nptdms (>=0.12.0)", "tqdm (>=4.23.4)", "plotnine", "PyQT5", "lxml", "xmltodict", "matplotlib", "pyyaml", "pyqtgraph", "xmlunittest" ], "requires_python": "", "summary": "Inertial mass determination", "version": "0.0.8" }, "last_serial": 5431434, "releases": { "0.0.7": [ { "comment_text": "", "digests": { "md5": "e2f099e436bd404db7308fb2dd57ee17", "sha256": "3109fb050328683e8f24da68138a59bbf811edd417697f36a2eb1d33ceeca7f6" }, "downloads": -1, "filename": "pyIMD-0.0.7-py3-none-any.whl", "has_sig": false, "md5_digest": "e2f099e436bd404db7308fb2dd57ee17", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 72631, "upload_time": "2019-03-29T17:32:53", "url": "https://files.pythonhosted.org/packages/97/e0/73338b85bc5cd1f868c6510676d144ae1132e54393903cf43ca61ae03c8c/pyIMD-0.0.7-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "4bc1032234203c0b14eabc32bcaea072", "sha256": "b0dfc830fedc2443b6d0c75aa72ccfc88ee064c7c998ebe9cdda05398ff82df1" }, "downloads": -1, "filename": "pyIMD-0.0.7.zip", "has_sig": false, "md5_digest": "4bc1032234203c0b14eabc32bcaea072", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 63862, "upload_time": "2019-03-29T17:32:56", "url": "https://files.pythonhosted.org/packages/e4/54/31ce4ece570102154c739d2c59db181866d3d7464b85b946d9cd64d112a2/pyIMD-0.0.7.zip" } ], "0.0.8": [ { "comment_text": "", "digests": { "md5": "ea2b07b0b08d12f459551a4dea358a5d", "sha256": "980df567d74d4151fd11476fe3eeadca2cd753857fd8c8def9eef6886caa7465" }, "downloads": -1, "filename": "pyIMD-0.0.8-py3-none-any.whl", "has_sig": false, "md5_digest": "ea2b07b0b08d12f459551a4dea358a5d", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 90915, "upload_time": "2019-06-21T15:30:21", "url": "https://files.pythonhosted.org/packages/aa/5b/2ddb4e47f795851ec4ad2b91aa8a349e6def3cca0487a1908928bcb4c1ed/pyIMD-0.0.8-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "2be6e6d720816ba8892a6c8d98b8fb86", "sha256": "a91b3a1f655b8f8cd0422bc4b99d2a72ed66a7708eae8c21bd6e23b8f7c8814c" }, "downloads": -1, "filename": "pyIMD-0.0.8.tar.gz", "has_sig": false, "md5_digest": "2be6e6d720816ba8892a6c8d98b8fb86", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 51472, "upload_time": "2019-06-21T15:30:24", "url": "https://files.pythonhosted.org/packages/39/72/726b18ce4293510dbd231e7c0071434dd972b7cfb4631f88e4478408dce0/pyIMD-0.0.8.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "ea2b07b0b08d12f459551a4dea358a5d", "sha256": "980df567d74d4151fd11476fe3eeadca2cd753857fd8c8def9eef6886caa7465" }, "downloads": -1, "filename": "pyIMD-0.0.8-py3-none-any.whl", "has_sig": false, "md5_digest": "ea2b07b0b08d12f459551a4dea358a5d", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 90915, "upload_time": "2019-06-21T15:30:21", "url": "https://files.pythonhosted.org/packages/aa/5b/2ddb4e47f795851ec4ad2b91aa8a349e6def3cca0487a1908928bcb4c1ed/pyIMD-0.0.8-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "2be6e6d720816ba8892a6c8d98b8fb86", "sha256": "a91b3a1f655b8f8cd0422bc4b99d2a72ed66a7708eae8c21bd6e23b8f7c8814c" }, "downloads": -1, "filename": "pyIMD-0.0.8.tar.gz", "has_sig": false, "md5_digest": "2be6e6d720816ba8892a6c8d98b8fb86", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 51472, "upload_time": "2019-06-21T15:30:24", "url": "https://files.pythonhosted.org/packages/39/72/726b18ce4293510dbd231e7c0071434dd972b7cfb4631f88e4478408dce0/pyIMD-0.0.8.tar.gz" } ] }