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        "author": "Dominic White",
        "author_email": "dewhite4@gmail.com",
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        "description": "# shapes\n\nshapes is a Python package for traditional and geometric morphometrics.\n\nIt can be used in a Python interpretator, or in a GUI online at [PhyloNimbus.com](http://www.phylonimbus.com/morphometrics/), where you can also digitize landmarks.\n\nUses include:\n\n* Procrustes superimposition.\n* Missing landmark estimation.\n\n## Installation\n\nshapes can be installed from the Python Package Index:\n\n`pip install shapes`\n\n## Usage\n\nRead files from Landmark editor:\n\n```\nimport shapes\nlms = shapes.read('/path/to/file')\n```\n\nThis returns a Shape object for that specimen.\n\nShape objects can be combined into ShapeSets:\n\n```\nshapeset = shapes.ShapeSet(name=\"Theropod skulls\")\nshapeset.append_shape(lms)\n```\n\nOnce you've added all relevant Shapes to a ShapeSet, the landmarks can be\naligned using \n[Procrustes Analysis](https://en.wikipedia.org/wiki/Procrustes_analysis):\n\n```\naligned_shapeset = shapes.procrustes_align(shapeset)\n```\n\nNote that this Procrustes alignment will work even if some landmarks are missing\n (in which case alignment will be based solely on the non-missing landmarks). \nThis could lead to systematic biases in your dataset depending on the \ndistribution of missing data. *Caveat emptor...*\n\nOnce the data set has been aligned as in the previous step, missing data can \nbe interpolated using one of two methods.\n\nUsing symmetry (for landmarks that are part of symmetrical pairs):\n\n```\npaired_landmarks = [(1,4),(2,5),(3,6)]\nsymmetrically_reconstructed = shapes.missing.estimate_from_symmetry(\n                                aligned_shapeset,\n                                paired_landmarks)\n```\n\nOr using the mean of the aligned homologous landmark in specimens where it is \npresent:\n\n```\nmean_reconstructed = shapes.missing.estimate_from_mean(aligned_shapeset)\n```\n\nLandmarks from all Shapes in a ShapeSet can be exported to csv:\n\n```\naligned_shapeset.export('output_file.csv')\n```\n\n## License\n\nshapes is available under the MIT license.\n\n## More information and citation\n\nWhite, D.E. (2016) Chapter 3 *of* The Evolution and Phylogenetic Analysis of \nthe Dinosaur Axial Skeleton. PhD Dissertation, George Washington University.",
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        "summary": "Tools for analyzing geometric morphometic shape",
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