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@blink1073
blink1073 / read_csv.py
Last active August 29, 2015 14:11
Read CSV to Numpy Record using Pandas Read_CSV
import pandas as pd
import numpy as np
def read_csv(fname, **kwargs):
df = pd.read_csv(fname, **kwargs)
arrs = [df.icol(i).data for i in range(df.shape[1])]
dtype = [(h, df.dtypes[h]) for h in df.columns]
arr = np.rec.fromarrays(arrs, dtype=dtype)
arr.columns = df.columns.tolist()
@blink1073
blink1073 / mpld3_rect_plugin.py
Last active August 29, 2015 14:11
MplD3 plugin to draw a rectangle that can be manipulated
"""
Rectangle Plugin
=================
This is a demo adapted from a `matplotlib gallery example
<http://matplotlib.org/examples/shapes_and_collections/path_patch_demo.html>`_
This example adds a custom D3 plugin allowing the user to drag a
rectangle and adjust the rectangle shape.
Use the toolbar buttons at the bottom-right of the plot to enable zooming
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@blink1073
blink1073 / mongo_hungry.py
Last active August 29, 2015 14:12
Read/write arbitrary data to Mongo
from pymongo.son_manipulator import SONManipulator
from bson import Binary
import numpy as np
import pickle
NUMPY_SUBTYPE = 128
class Transform(SONManipulator):
@blink1073
blink1073 / bson_adaptor.py
Last active August 29, 2015 14:12
BSON Adaptor
from bson import BSON, Binary
import numpy as np
import pickle
import struct
NUMPY_SUBTYPE = 128
def bson_dump(obj):
@blink1073
blink1073 / histogram_selector.py
Last active January 3, 2016 20:45
Matplotlib Image Histogram Selector
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
import numpy as np
from matplotlib.widgets import SpanSelector
class HistSelector(object):
def __init__(self, hist_ax, im, callback=None):
@blink1073
blink1073 / latex_test.ipynb
Last active August 29, 2015 14:17
latex_test.ipynb
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@blink1073
blink1073 / metatlas.spec
Last active August 29, 2015 14:17
MetAtlas Spec
/*
A KBase Atlas to liquid chromatography–mass spectrometry (LCMS) data
*/
module MetaboliteAtlas2 {
/* Metabolite Compound object
*
* name - common name of the compound
@blink1073
blink1073 / xonsh_metakernel.py
Last active March 17, 2022 17:10
Xonsh Jupyter Metakernel
from __future__ import absolute_import
from metakernel import MetaKernel
from xonsh.shell import Shell
import builtins
from xonsh import imphooks
import re
__version__ = '0.0'
@blink1073
blink1073 / xonsh_startup_errors
Created March 31, 2015 22:43
Xonsh Startup Output Errors
stevensilvester: ~
$ xonsh
/usr/local/etc/bash_completion.d/abook: line 3: have: command not found
/usr/local/etc/bash_completion.d/ant: line 45: syntax error in conditional expression: unexpected token `('
/usr/local/etc/bash_completion.d/ant: line 45: syntax error near `-@(?'
/usr/local/etc/bash_completion.d/ant: line 45: ` if [[ "${COMP_WORDS[i]}" == -@(?(build)file|f) ]]; then'
/usr/local/etc/bash_completion.d/apache2ctl: line 3: have: command not found
/usr/local/etc/bash_completion.d/apt: line 12: syntax error in conditional expression: unexpected token `('
/usr/local/etc/bash_completion.d/apt: line 12: syntax error near `@(i'
/usr/local/etc/bash_completion.d/apt: line 12: ` if [[ ${COMP_WORDS[i]} == @(install|remove|autoremove|purge|source|build-dep) ]]; then'