06-26-17_test3.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import nbodykit.lab as nlab\n",
    "import numpy as np\n",
    "import h5py\n",
    "import matplotlib.pyplot as plt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Help on class BinaryCatalog in module abc:\n",
      "\n",
      "class BinaryCatalog(nbodykit.source.catalog.file.FileCatalogBase)\n",
      " |  A catalog source created using :class:`io.BinaryFile` to read data from disk\n",
      " |  \n",
      " |  Method resolution order:\n",
      " |      BinaryCatalog\n",
      " |      nbodykit.source.catalog.file.FileCatalogBase\n",
      " |      nbodykit.base.catalog.CatalogSource\n",
      " |      builtins.object\n",
      " |  \n",
      " |  Methods defined here:\n",
      " |  \n",
      " |  __init__(self, *args, **kwargs)\n",
      " |      Parameters\n",
      " |      ----------\n",
      " |      path : str\n",
      " |          the name of the binary file to load\n",
      " |      dtype : numpy.dtype or list of tuples\n",
      " |          the dtypes of the columns to load; this should be either a ``numpy.dtype``\n",
      " |          or be able to be converted to one via a :func:`numpy.dtype` call\n",
      " |      offsets : dict, optional\n",
      " |          a dictionay specifying the byte offsets of each column in the binary\n",
      " |          file; if not supplied, the offsets are inferred from the dtype size\n",
      " |          of each column, assuming a fixed header size, and contiguous storage\n",
      " |      header_size : int, optional\n",
      " |          the size of the header in bytes\n",
      " |      size : int, optional\n",
      " |          the number of objects in the binary file; if not provided, the value\n",
      " |          is inferred from the dtype and the total size of the file in bytes\n",
      " |      \n",
      " |      Additional Keyword Parameters\n",
      " |      -----------------------------\n",
      " |      comm : MPI Communicator, optional\n",
      " |          the MPI communicator instance; default (``None``) sets to the\n",
      " |          current communicator\n",
      " |      use_cache : bool, optional\n",
      " |          whether to cache data read from disk; default is ``False``\n",
      " |      attrs : dict; optional\n",
      " |          dictionary of meta-data to store in :attr:`attrs`\n",
      " |  \n",
      " |  ----------------------------------------------------------------------\n",
      " |  Data and other attributes defined here:\n",
      " |  \n",
      " |  __abstractmethods__ = frozenset()\n",
      " |  \n",
      " |  ----------------------------------------------------------------------\n",
      " |  Methods inherited from nbodykit.source.catalog.file.FileCatalogBase:\n",
      " |  \n",
      " |  get_hardcolumn(self, col)\n",
      " |      Return a column from the underlying file source\n",
      " |      \n",
      " |      Columns are returned as dask arrays\n",
      " |  \n",
      " |  ----------------------------------------------------------------------\n",
      " |  Data descriptors inherited from nbodykit.source.catalog.file.FileCatalogBase:\n",
      " |  \n",
      " |  hardcolumns\n",
      " |      The union of the columns in the file and any transformed columns\n",
      " |  \n",
      " |  size\n",
      " |      The local size\n",
      " |  \n",
      " |  ----------------------------------------------------------------------\n",
      " |  Methods inherited from nbodykit.base.catalog.CatalogSource:\n",
      " |  \n",
      " |  Selection(self)\n",
      " |      Override the ``Selection`` column to select a subset slice of a\n",
      " |      CatalogSource.\n",
      " |      \n",
      " |      By default, this column is set to ``True`` for all particles.\n",
      " |  \n",
      " |  Weight(self)\n",
      " |      When interpolating a CatalogSource on to a mesh, the value of this\n",
      " |      array is used as the Weight that each particle contributes to a given\n",
      " |      mesh cell.\n",
      " |      \n",
      " |      By default, this array is set to unity for all particles\n",
      " |  \n",
      " |  __contains__(self, col)\n",
      " |  \n",
      " |  __getitem__(self, sel)\n",
      " |      The following types of indexing supported are supported\n",
      " |      for CatalogSource:\n",
      " |      \n",
      " |          1.  strings specifying a column in the CatalogSource; returns\n",
      " |              a dask array holding the column data\n",
      " |          2.  boolean arrays specifying a slice of the CatalogSource;\n",
      " |              returns a CatalogSubset holding only the revelant slice\n",
      " |          3.  slice object specifying which particles to select\n",
      " |  \n",
      " |  __iter__(self)\n",
      " |  \n",
      " |  __len__(self)\n",
      " |      The length of CatalogSource is equal to :attr:`size`; this is the\n",
      " |      local size of the source on a given rank\n",
      " |  \n",
      " |  __setitem__(self, col, value)\n",
      " |      Add columns to the CatalogSource, overriding any existing columns\n",
      " |      with the name ``col``\n",
      " |  \n",
      " |  compute(self, *args, **kwargs)\n",
      " |      Our version of :func:`dask.compute` that computes\n",
      " |      multiple delayed dask collections at once\n",
      " |      \n",
      " |      This should be called on the return value of :func:`read`\n",
      " |      to converts any dask arrays to numpy arrays\n",
      " |      \n",
      " |      Parameters\n",
      " |      -----------\n",
      " |      args : object\n",
      " |          Any number of objects. If the object is a dask\n",
      " |          collection, it's computed and the result is returned.\n",
      " |          Otherwise it's passed through unchanged.\n",
      " |      \n",
      " |      Notes\n",
      " |      -----\n",
      " |      The dask default optimizer induces too many (unnecesarry)\n",
      " |      IO calls -- we turn this off feature off by default.\n",
      " |      \n",
      " |      Eventually we want our own optimizer probably.\n",
      " |  \n",
      " |  read(self, columns)\n",
      " |      Return the requested columns as dask arrays\n",
      " |      \n",
      " |      Parameters\n",
      " |      ----------\n",
      " |      columns : list of str\n",
      " |          the names of the requested columns\n",
      " |      \n",
      " |      Returns\n",
      " |      -------\n",
      " |      list of dask.array.Array :\n",
      " |          the list of column data, in the form of dask arrays\n",
      " |  \n",
      " |  save(self, output, columns, datasets=None, header='Header')\n",
      " |      Save the CatalogSource to a :class:`bigfile.BigFile`\n",
      " |      \n",
      " |      Only the selected columns are saved and :attr:`attrs` are saved in\n",
      " |      ``header``. The attrs of columns are stored in the datasets.\n",
      " |      \n",
      " |      Parameters\n",
      " |      ----------\n",
      " |      output : str\n",
      " |          the name of the file to write to\n",
      " |      columns : list of str\n",
      " |          the names of the columns to save in the file\n",
      " |      datasets : list of str, optional\n",
      " |          names for the data set where each column is stored; defaults to\n",
      " |          the name of the column\n",
      " |      header : str, optional\n",
      " |          the name of the data set holding the header information, where\n",
      " |          :attr:`attrs` is stored\n",
      " |  \n",
      " |  to_mesh(self, Nmesh=None, BoxSize=None, dtype='f4', interlaced=False, compensated=False, window='cic', weight='Weight', selection='Selection')\n",
      " |      Convert the CatalogSource to a MeshSource\n",
      " |      \n",
      " |      Parameters\n",
      " |      ----------\n",
      " |      Nmesh : int, optional\n",
      " |          the number of cells per side on the mesh; must be provided if\n",
      " |          not stored in :attr:`attrs`\n",
      " |      BoxSize : scalar, 3-vector, optional\n",
      " |          the size of the box; must be provided if\n",
      " |          not stored in :attr:`attrs`\n",
      " |      dtype : string, optional\n",
      " |          the data type of the mesh array\n",
      " |      interlaced : bool, optional\n",
      " |          use the interlacing technique of Sefusatti et al. 2015 to reduce\n",
      " |          the effects of aliasing on Fourier space quantities computed\n",
      " |          from the mesh\n",
      " |      compensated : bool, optional\n",
      " |          whether to correct for the window introduced by the grid\n",
      " |          interpolation scheme\n",
      " |      window : str, optional\n",
      " |          the string specifying which window interpolation scheme to use;\n",
      " |          see `pmesh.window.methods`\n",
      " |      weight : str, optional\n",
      " |          the name of the column specifying the weight for each particle\n",
      " |      selection : str, optional\n",
      " |          the name of the column that specifies which (if any) slice\n",
      " |          of the CatalogSource to take\n",
      " |      \n",
      " |      Returns\n",
      " |      -------\n",
      " |      mesh : CatalogMeshSource\n",
      " |          a mesh object that provides an interface for gridding particle\n",
      " |          data onto a specified mesh\n",
      " |  \n",
      " |  update_csize(self)\n",
      " |      Set the collective size, :attr:`csize`\n",
      " |      \n",
      " |      This function should be called in :func:`__init__` of a subclass,\n",
      " |      after :attr:`size` has been set to a valid value (not ``NotImplemented``)\n",
      " |  \n",
      " |  ----------------------------------------------------------------------\n",
      " |  Static methods inherited from nbodykit.base.catalog.CatalogSource:\n",
      " |  \n",
      " |  make_column(array)\n",
      " |      Utility function to convert a numpy array to a column object\n",
      " |      (dask.array.Array)\n",
      " |  \n",
      " |  ----------------------------------------------------------------------\n",
      " |  Data descriptors inherited from nbodykit.base.catalog.CatalogSource:\n",
      " |  \n",
      " |  __dict__\n",
      " |      dictionary for instance variables (if defined)\n",
      " |  \n",
      " |  __weakref__\n",
      " |      list of weak references to the object (if defined)\n",
      " |  \n",
      " |  attrs\n",
      " |      Dictionary storing relevant meta-data\n",
      " |  \n",
      " |  columns\n",
      " |      All columns in this Source, which include:\n",
      " |      \n",
      " |          1.  the columns hard-coded into the class's defintion\n",
      " |          2.  override columns provided by the user\n",
      " |  \n",
      " |  csize\n",
      " |      The total, collective size of the Source, i.e., summed across all\n",
      " |      ranks.\n",
      " |      \n",
      " |      It is the sum of :attr:`size` across all available ranks.\n",
      " |  \n",
      " |  use_cache\n",
      " |      If set to ``True``, use the builtin cache features of ``dask``\n",
      " |      to cache data in memory\n",
      " |  \n",
      " |  ----------------------------------------------------------------------\n",
      " |  Data and other attributes inherited from nbodykit.base.catalog.CatalogSource:\n",
      " |  \n",
      " |  logger = <Logger CatalogSource (WARNING)>\n",
      "\n"
     ]
    }
   ],
   "source": [
    "help(nlab.BinaryCatalog)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "halo_type = np.dtype([(\"gid\",np.int64),(\"N\",np.int64),(\"x\",np.float32,3),(\"v\",np.float32,3),(\"sigma_v\",np.float32,3),\n",
    "                      (\"r25\",np.float32),(\"r50\",np.float32),(\"r75\",np.float32),(\"r90\",np.float32),\n",
    "                      (\"vcirc_max\",np.float32),(\"rvcirc_max\",np.float32),\n",
    "                      (\"pf_start\",np.int64),(\"pf_np\",np.int64)])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "ename": "ValueError",
     "evalue": "byte size mismatch -- fractional rows found",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-9-55a6f0d506a3>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mcat\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnlab\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mBinaryCatalog\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'/Users/ding/Downloads/halos_1.field'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdtype\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mhalo_type\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m~/miniconda3/lib/python3.6/site-packages/nbodykit/source/catalog/file.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m    106\u001b[0m         \u001b[0muse_cache\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpop\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'use_cache'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    107\u001b[0m         \u001b[0mattrs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpop\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'attrs'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m{\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 108\u001b[0;31m         \u001b[0mFileCatalogBase\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfiletype\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mfiletype\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0margs\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    109\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mattrs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupdate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mattrs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    110\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/miniconda3/lib/python3.6/site-packages/nbodykit/__init__.py\u001b[0m in \u001b[0;36mwrapped\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m     21\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'comm'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     22\u001b[0m                 \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'comm'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mCurrentMPIComm\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 23\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     24\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mwrapped\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     25\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/miniconda3/lib/python3.6/site-packages/nbodykit/source/catalog/file.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, filetype, args, kwargs, comm, use_cache)\u001b[0m\n\u001b[1;32m     31\u001b[0m         \u001b[0;31m# bcast the FileStack\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     32\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcomm\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrank\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 33\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_source\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mFileStack\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfiletype\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     34\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     35\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_source\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/miniconda3/lib/python3.6/site-packages/nbodykit/io/stack.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, filetype, path, *args, **kwargs)\u001b[0m\n\u001b[1;32m     48\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     49\u001b[0m             \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"'path' should be a string or a list of strings\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 50\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfiles\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mfiletype\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mfn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mfilenames\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     51\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msizes\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnumpy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0marray\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mf\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfiles\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdtype\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'i8'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     52\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/miniconda3/lib/python3.6/site-packages/nbodykit/io/stack.py\u001b[0m in \u001b[0;36m<listcomp>\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m     48\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     49\u001b[0m             \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"'path' should be a string or a list of strings\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 50\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfiles\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mfiletype\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mfn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mfilenames\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     51\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msizes\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnumpy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0marray\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mf\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfiles\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdtype\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'i8'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     52\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/miniconda3/lib/python3.6/site-packages/nbodykit/io/binary.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, path, dtype, offsets, header_size, size)\u001b[0m\n\u001b[1;32m     81\u001b[0m             \u001b[0msize\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mlambda\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mgetsize\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mheader_size\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdtype\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mitemsize\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     82\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mcallable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msize\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 83\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msize\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msize\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     84\u001b[0m         \u001b[0;32melif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msize\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mint\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     85\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msize\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msize\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/miniconda3/lib/python3.6/site-packages/nbodykit/io/binary.py\u001b[0m in \u001b[0;36m<lambda>\u001b[0;34m(fn)\u001b[0m\n\u001b[1;32m     79\u001b[0m         \u001b[0;31m# determine the size (either an int or a function)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     80\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0msize\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 81\u001b[0;31m             \u001b[0msize\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mlambda\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mgetsize\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mheader_size\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdtype\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mitemsize\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     82\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mcallable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msize\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     83\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msize\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msize\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/miniconda3/lib/python3.6/site-packages/nbodykit/io/binary.py\u001b[0m in \u001b[0;36mgetsize\u001b[0;34m(filename, header_size, rowsize)\u001b[0m\n\u001b[1;32m     38\u001b[0m     \u001b[0msize\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mremainder\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mdivmod\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbytesize\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0mheader_size\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrowsize\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     39\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0mremainder\u001b[0m \u001b[0;34m!=\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 40\u001b[0;31m         \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"byte size mismatch -- fractional rows found\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     41\u001b[0m     \u001b[0;32mreturn\u001b[0m \u001b[0msize\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     42\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mValueError\u001b[0m: byte size mismatch -- fractional rows found"
     ]
    }
   ],
   "source": [
    "cat = nlab.BinaryCatalog('/Users/ding/Downloads/halos_1.field', dtype=halo_type)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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