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    "info": {
        "author": "Lumicks B.V.",
        "author_email": "devteam@lumicks.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Science/Research",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3 :: Only",
            "Programming Language :: Python :: Implementation :: CPython",
            "Topic :: Scientific/Engineering :: Physics"
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        "description": "# Lumicks pylake \n\n[![Build Status](https://travis-ci.org/lumicks/pylake.svg?branch=master)](https://travis-ci.org/lumicks/pylake)\n[![Documentation Status](https://readthedocs.org/projects/lumicks-pylake/badge/?version=latest)](https://lumicks-pylake.readthedocs.io/en/latest/?badge=latest)\n\nThis Python package includes data analysis tools for Bluelake HDF5 data.\n\n## Install\n\nFor general use, all you need to do is enter the following on the command line:\n\n```bash\npip install lumicks.pylake\n```\n\nTo upgrade to the latest version:\n\n```bash\npip install -U lumicks.pylake\n```\n\n## Reading HDF5 files\n\n```python\nfrom lumicks import pylake\n\nh5file = pylake.File(\"example.h5\")\n```\n\n### FD curves\n\n```python\nimport matplotlib.pyplot as plt\n\n# Plot all FD curves in a file\nfor name, fd in h5file.fdcurves.items():\n    fd.plot_scatter()\n    plt.savefig(name)\n\n# Pick a single FD curve\nfd = h5file.fdcurves[\"name\"]\n# By default, the FD channel pair is `downsampled_force2` and `distance1`\nfd.with_channels(force='1x', distance='2').plot_scatter()\n\n# Access the raw data: defaults\nforce = fd.f\ndistance = fd.d\n# Access the raw data: specific\nforce = fd.downsampled_force1y\ndistance = fd.distance2\n\n# Plot manually: FD curve\nplt.scatter(distance.data, force.data)\n# Plot manually: force timetrace\nplt.plot(force.timestamps, force.data)\n\n# By default `f` is `downsampled_force2` and `d` is `distance1`\naltenative_fd = fd.with_channels(force='1x', distance='2')\n\n# Baseline subtraction\nfd_baseline = h5file.fdcurves[\"Baseline\"]\nfd_measured = h5file.fdcurves[\"Measurement\"]\nfd = fd_measured - fd_baseline\nfd.plot_scatter()\n```\n\n### Force vs. time\n\n```python\n# Simple force plotting\nh5file.force1x.plot()\nplt.savefig(\"force1x\")\n\n# Accessing the raw data\nf1x_data = h5file.force1x.data\nf1x_timestamps = h5file.force1x.timestamps\nplt.plot(f1x_timestamps, f1x_data)\n```\n\n### Slicing data channels\n\n```python\n# Take the entire channel\neverything = h5file.force1x\neverything.plot()\n\n# Get the data between 1 and 1.5 seconds\npart = h5file.force1x['1s':'1.5s']\npart.plot()\n# Or manually\nf1x_data = part.data\nf1x_timestamps = part.timestamps\nplt.plot(f1x_timestamps, f1x_data)\n\n# More slicing examples\na = h5file.force1x[:'-5s']  # everything except the last 5 seconds\nb = h5file.force1x['-1m':]  # take the last minute\nc = h5file.force1x['-1m':'-500ms']  # last minute except the last 0.5 seconds\nd = h5file.force1x['1.2s':'-4s']  # between 1.2 seconds and 4 seconds from the end\ne = h5file.force1x['5.7m':'1h 40m']  # 5.7 minutes to an hour and 40 minutes\n```\n\n### Scans and kymographs\n\nThe following code uses kymographs as an example. \nScans work the same way -- just substitute `h5file.kymos` with `h5file.scans`.\n\n```python\n# Plot all kymographs in a file\nfor name, kymo in h5file.kymos.items():\n    kymo.plot_rgb()\n    plt.savefig(name)\n\n# Pick a single kymograph\nkymo = h5file.kymos[\"name\"]\n# Plot a single color channel\nkymo.plot_red()\n\n# Access the raw image data\nrgb = kymo.rgb_image  # matrix\nblue = kymo.blue_image\n# Plot manually\nplt.imshow(rgb)\n\n# Low-level raw data\nphotons = kymo.red_photons\nplt.plot(photons.timestamps, photons.data)\n\n# Saving photon counts to TIFF\nkymo.save_tiff(\"kymograph.tiff\")\n```\n\n```python\nscan = h5file.scans[\"name\"]\n\n# A scan can have multiple frames\nprint(scan.num_frames)\nprint(scan.blue_image.shape)  # (self.num_frames, h, w) -> single color channel\nprint(scan.rgb_image.shape)  # (self.num_frames, h, w, 3) -> three color channels\n```\n\n\n",
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