{ "info": { "author": "Casper van der Wel", "author_email": "caspervdw@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", "Operating System :: MacOS", "Operating System :: Microsoft :: Windows", "Operating System :: POSIX", "Operating System :: Unix", "Programming Language :: C", "Programming Language :: Python", "Programming Language :: Python :: 2", "Programming Language :: Python :: 3", "Topic :: Scientific/Engineering" ], "description": "pims\\_nd2 : A reader for Nikon .ND2\r\n===================================\r\n\r\n|build status|\r\n\r\n``pims_nd2`` contains a reader for nd2 files produced by NIS Elements.\r\nThe reader is based on the included `SDK `__ from\r\nNikon, which makes it compatible with older versions of nd2 files. The\r\nreader is written in the `pims `__\r\nframework, enabling easy access to multidimensional files, lazy slicing,\r\nand nice display in IPython.\r\n\r\nInstallation\r\n------------\r\n\r\n``pims_nd2`` is implemented on Windows, Linux and OSX systems. To obtain\r\nthe latest stable version, install via PyPi:\r\n\r\n::\r\n\r\n pip install pims_nd2\r\n\r\nThe ND2 SDK binaries are included in the package and will be copied into\r\nthe ``pims_nd2`` package folder.\r\n\r\nDependencies\r\n------------\r\n\r\nThis reader requires `pims `__\r\nversion 0.3.0.\r\n\r\nExamples\r\n--------\r\n\r\nThe following code opens a movie file and displays a frame. Note that\r\nframes are only actually read when necessary:\r\n\r\n::\r\n\r\n from pims import ND2_Reader\r\n frames = ND2_Reader('some_movie.nd2')\r\n frames[82] # display frame 82\r\n frames.close()\r\n\r\nThe following code opens the multidimensional demo file included in the\r\npackage and iterates through the first 3 frames. Note that we use a\r\ncontext manager here. We tell the reader which axis to iterate over and\r\nwhich axes to include in one frame. Also we select which channel to\r\nread.\r\n\r\n::\r\n\r\n from pims import ND2_Reader\r\n with ND2_Reader('cluster.nd2') as frames:\r\n frames.iter_axes = 't' # 't' is the default already\r\n frames.bundle_axes = 'zyx' # when 'z' is available, this will be default\r\n frames.default_coords['c'] = 1 # 0 is the default setting\r\n for frame in frames[:3]:\r\n # do something with 3D frames in channel 1\r\n\r\nThe best way to use the reader is using a context manager. If you do not\r\nuse a context manager, make sure to call ``frames.close()`` at the end\r\nof your script.\r\n\r\nMetadata access can be done on two levels: reader level and frame level.\r\n\r\n::\r\n\r\n frames.metadata['mpp'] # calibration in microns per pixel\r\n frames[0].metadata['t_ms'] # time of frame in milliseconds\r\n\r\nSupporting Grant\r\n----------------\r\n\r\nThis reader was developed by Casper van der Wel, as part of his PhD\r\nthesis work in Daniela Kraft's group at the Huygens-Kamerlingh-Onnes\r\nlaboratory, Institute of Physics, Leiden University, The Netherlands.\r\nThis work was supported by the Netherlands Organisation for Scientific\r\nResearch (NWO/OCW).\r\n\r\n.. |build status| image:: https://travis-ci.org/soft-matter/pims_nd2.png?branch=master\r\n :target: https://travis-ci.org/soft-matter/pims_nd2", "description_content_type": null, "docs_url": null, "download_url": "https://github.com/soft-matter/pims_nd2/tarball/1.0", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/soft-matter/pims_nd2", "keywords": null, "license": "UNKNOWN", "maintainer": null, "maintainer_email": null, "name": "pims_nd2", "package_url": "https://pypi.org/project/pims_nd2/", "platform": "MacOS X,Windows,Linux CentOs 6.5/7,Linux Debian 7/8", "project_url": "https://pypi.org/project/pims_nd2/", "project_urls": { "Download": "https://github.com/soft-matter/pims_nd2/tarball/1.0", "Homepage": "https://github.com/soft-matter/pims_nd2" }, "release_url": "https://pypi.org/project/pims_nd2/1.0/", "requires_dist": null, "requires_python": null, "summary": "An image reader for nd2 (NIS Elements) multidimensional images", "version": "1.0" }, "last_serial": 1893615, "releases": { "0.1": [ { "comment_text": "", "digests": { "md5": "b1f4030fa1416fee6ad5f9768ee81e01", "sha256": "6f4378c41f138efa6fddb89da1e356bda671d5fef691f70c95f17ee4981d0118" }, "downloads": -1, "filename": "pims_nd2-0.1.zip", "has_sig": false, "md5_digest": "b1f4030fa1416fee6ad5f9768ee81e01", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 19778576, "upload_time": "2015-10-13T18:08:41", "url": "https://files.pythonhosted.org/packages/89/14/10df3a83900459d320a81f793e2fc0c8d5ff3a4339a71013564d7166ed45/pims_nd2-0.1.zip" } ], "0.2": [ { "comment_text": "", "digests": { "md5": "fec2bcb82e3317883b8ce5504baf0e8d", "sha256": "627de394103241a0792f7e571a435ad9838d2424a596fc1d4e481fc745e8f046" }, "downloads": -1, "filename": "pims_nd2-0.2.zip", "has_sig": false, "md5_digest": "fec2bcb82e3317883b8ce5504baf0e8d", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 19779094, "upload_time": "2015-10-25T18:47:27", "url": "https://files.pythonhosted.org/packages/22/d6/6fba5970cd38e559d793b3c3879d4b1f71b6919205f8f257d11062afdb82/pims_nd2-0.2.zip" } ], "0.3": [ { "comment_text": "", "digests": { "md5": "0902e89f8041e294848c2a27f69ad0a1", "sha256": "ac9a9d8ec494f9d999474a34edab3083a03262d49e987ddbfa1b9660543ac2d1" }, "downloads": -1, "filename": "pims_nd2-0.3.zip", "has_sig": false, "md5_digest": "0902e89f8041e294848c2a27f69ad0a1", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 19779233, "upload_time": "2015-10-26T19:13:54", "url": "https://files.pythonhosted.org/packages/75/39/6521dc945436e362b483960c4a59f49966f7f3a7b16a7bb5152d50a722d0/pims_nd2-0.3.zip" } ], "0.4": [ { "comment_text": "", "digests": { "md5": "8097ba00e6a4e4693d4af575f6cd7ee3", "sha256": "e612b59be528fdaa2cb7c53031fbb58fe78c30258c51620ea83c0f86b8d36929" }, "downloads": -1, "filename": "pims_nd2-0.4.zip", "has_sig": false, "md5_digest": "8097ba00e6a4e4693d4af575f6cd7ee3", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 19779995, "upload_time": "2015-11-23T19:08:19", "url": "https://files.pythonhosted.org/packages/3f/f6/dbebd444af506b0202f078f6e4f5d9973cde09ade4ad2995cddad276fc02/pims_nd2-0.4.zip" } ], "1.0": [ { "comment_text": "", "digests": { "md5": "d43f58d7ac6c94729b862cbac52f5310", "sha256": "bc426802087b5a34c7ec020ca62c8bc6e01f635433eec40bdc50c33533f17b85" }, "downloads": -1, "filename": "pims_nd2-1.0.zip", "has_sig": false, "md5_digest": "d43f58d7ac6c94729b862cbac52f5310", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 19780402, "upload_time": "2015-11-25T20:20:02", "url": "https://files.pythonhosted.org/packages/4a/34/f81b114393dd61fe514ed7dfce05d3ff3eacb9ddcddafe5c1c4360e34fd1/pims_nd2-1.0.zip" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "d43f58d7ac6c94729b862cbac52f5310", "sha256": "bc426802087b5a34c7ec020ca62c8bc6e01f635433eec40bdc50c33533f17b85" }, "downloads": -1, "filename": "pims_nd2-1.0.zip", "has_sig": false, "md5_digest": "d43f58d7ac6c94729b862cbac52f5310", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 19780402, "upload_time": "2015-11-25T20:20:02", "url": "https://files.pythonhosted.org/packages/4a/34/f81b114393dd61fe514ed7dfce05d3ff3eacb9ddcddafe5c1c4360e34fd1/pims_nd2-1.0.zip" } ] }