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    "info": {
        "author": "Sy Redding",
        "author_email": "",
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        "description": "=======\nsmtools\n=======\n\nSingle Molecule analysis Tools\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nThis package contains tools analysis package of the `Redding Lab`_, at the University of Cailfornia, San Francisco.\n\n.. _Redding Lab: https://www.reddinglab.com\n\nDependencies\n------------\n  * numpy\n  * scipy\n  * scikit-image\n  * matplotlib\n\n.. _numpy: http://www.numpy.org/\n.. _scipy: https://www.scipy.org/\n.. _scikit-image: https://scikit-image.org/\n.. _matplotlib: https://matplotlib.org/\n\nInstallation\n------------\n\nThe easiest way to install the package is via ``pip``::\n\n    $ pip install smtools\n\n\nDocumentation\n-------------\nDocumentation: https://smtools.readthedocs.io/en/latest/\n\nUsage\n-----\n\nThe `smtools.algnment` module is designed to align images split into separate\nchannels. It relies on using fluorescent particles that appear on both channels.\nWhen executed, the following code will yield the image output below.\n\n.. code-block:: python\n\n    import smtools.testdata as test\n    import smtools.alignment as al\n    import matplotlib.pyplot as plt\n    dx, dy, params = al.inspect_global_fit(test.image_stack(), showplot=False)\n    im = test.image_stack()[0]\n    im_old = al.overlay(im)\n    im_adj_image = al.align_by_offset(im,dx,dy)\n    im_new = al.overlay(im_adj_image)\n    fig = plt.figure(figsize=(12,12))\n    ax1 = fig.add_subplot(211)\n    ax2 = fig.add_subplot(212,sharex=ax1)\n    ax1.set_title('Original Image', fontsize = \"18\")\n    ax2.set_title('Aligned Image', fontsize = \"18\")\n    ax1.imshow(im_old)\n    ax2.imshow(im_new)\n    plt.show()\n\n.. figure:: https://github.com/ReddingLab/smtools/blob/master/images/alignment.png\n   :alt:\n\nThe `smtools.curtains` module is designed to locate individual DNA molecules within\na DNA curtain.\n\n.. code-block:: python\n\n    import smtools.curtains as cs\n    import smtools.alignment as al\n    from scipy.ndimage.interpolation import rotate\n    import matplotlib.pyplot as plt\n    import smtools.testdata as test\n    im = test.test_curtain()\n    ch1,ch2 = al.im_split(im)\n    angle = cs.find_rotang(ch2)\n    rotated_ch2 = rotate(ch2,angle)\n    bounds, mask = cs.find_curtain(rotated_ch2)\n    strands = cs.find_DNA(rotated_ch2,bounds)\n    DNAs = cs.fit_DNA(rotated_ch2, strands)\n    fig = plt.figure(figsize=(5,10))\n    plt.axis('off')\n    plt.imshow(rotated_ch2)\n    for x0,x1,y in DNAs:\n        plt.plot([x0,x1],[y,y],\"r.\", markersize = 5)\n    plt.show()\n\n.. figure:: https://github.com/ReddingLab/smtools/blob/master/images/curtain_finder.png\n   :alt: \n\n\nVersion History\n---------------\n  * 0.1.0  Initial release with `alignment`, `point_fitting` modules\n  * 0.2.0  Included `curtains` and `misc` modules\n\n\nReferences\n----------\n  * PyPI Page: https://pypi.org/project/smtools/\n  * Readthedocs: https://smtools.readthedocs.io/en/latest/\n\n",
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        "name": "smtools",
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