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In [8]: rf = RandomForestClassifier(100, max_depth=20, n_jobs=2, shared=True, compute_importances=True)

In [9]: rf = rf.fit(dat5[0], dat5[1][:, 0])
Exception AttributeError: AttributeError("'NoneType' object has no attribute 'tell'",) in <bound method memmap.__del__ of memmap([  2.00000000e+00,   1.50000006e-02,   2.25000018e-04,
         0.00000000e+00,   5.06250080e-08,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         9.54999954e-01,   1.22499975e-03,   1.11022302e-16,
         1.50062439e-06,   3.00000003e-02,   4.00000019e-04,
        -1.35525272e-20,   1.60000015e-07,   1.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,

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In [7]: rf = RandomForestClassifier(100, max_depth=20, n_jobs=8, shared=True, compute_importances=True)

In [8]: rf = rf.fit(dat5[0], dat5[1][:, 0])
---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
/groups/chklovskii/home/nuneziglesiasj/data/cropped_5um3_larva_fib_10x10x10nm/cl2/<ipython-input-8-16d0d527a259> in <module>()
----> 1 rf = rf.fit(dat5[0], dat5[1][:, 0])

/groups/chklovskii/home/nuneziglesiasj/projects/scikit-learn-sharedmem/sklearn/ensemble/forest.pyc in fit(self, X, y)
    273         # Pack inputs into shared-memory arrays

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 ~/projects/skimage (3d-slic)$ python setup.py install
non-existing path in 'skimage/_shared': 'tests'
cython -o /Volumes/Projects/skimage/skimage/segmentation/_slic.c /Volumes/Projects/skimage/skimage/segmentation/_slic.pyx

Error compiling Cython file:
------------------------------------------------------------
...
                 float ratio, int max_iter, int n_segments):
    """Helper function for SLIC segmentation."""

jni

nuneziglesiasj@jni-lscc-mbp Thu May 30 01:38
 ~ $ ipython --pylab
Activating auto-logging. Current session state plus future input saved.
Filename       : /Users/nuneziglesiasj/ipython-logs/automatic-log--2013.5.30--1.38.py
Mode           : backup
Output logging : False
Raw input log  : False
Timestamping   : False
State          : active

jni

In [28]: x = np.zeros((3, 3), float)

In [29]: x[0, 0] = -3.2

In [30]: x[2, 1] = -2.7

In [31]: s = sparse.csr_matrix(x)

In [32]: s.data
Out[32]: array([-3.2, -2.7])

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#!/usr/bin/env python
# -*- coding: utf-8 -*-

# copied with modifications from http://stackoverflow.com/a/15734251/224254 by @scls

import math

def to_si(d):
    incPrefixes = ['k', 'M', 'G', 'T', 'P', 'E', 'Z', 'Y']
    decPrefixes = ['m', 'µ', 'n', 'p', 'f', 'a', 'z', 'y']

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# run this from $GALADIR/tests
# This script was used to generate the matched random forest and training data for regression testing.
# However, the training data do not get reproduced between this run and a test run, presumably because
# of some problem setting the random state.

import numpy as np
from gala import imio, classify, features, agglo, evaluate as ev
gt_train, pr_train, p4_train, ws_train = map(imio.read_h5_stack, ['example-data/train-gt.lzf.h5', 'example-data/train-p1.lzf.h5', 'example-data/train-p4.lzf.h5', 'example-data/train-ws.lzf.h5'])
gt_test, pr_test, p4_test, ws_test = map(imio.read_h5_stack, ['example-data/test-gt.lzf.h5', 'example-data/test-p1.lzf.h5', 'example-data/test-p4.lzf.h5', 'example-data/test-ws.lzf.h5'])
fm = features.moments.Manager()

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nuneziglesiasj@jni-lscc-mbp Mon Apr 07 10:08 
 ~/projects/scikit-image/skimage/viewer/tests (master)$ python test_viewer.py 
Recommended matplotlib backend is `Agg` for full skimage.viewer functionality.
Qt internal error: qt_menu.nib could not be loaded. The .nib file should be placed in QtGui.framework/Versions/Current/Resources/  or in the resources directory of your application bundle.
Abort trap: 6

jni

%matplotlib inline
from skimage import img_as_float
import numpy as np
from matplotlib import pyplot as plt

def imshow_all(*images, **kwargs):
    """ Plot a series of images side-by-side.

    Convert all images to float so that images have a common intensity range.

jni

Process:               ImageJ-macosx [1330]
Path:                  /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx
Identifier:            org.fiji
Version:               1.0
Code Type:             X86-64 (Native)
Parent Process:        ??? [1]
Responsible:           ImageJ-macosx [1330]
User ID:               501

Date/Time:             2014-10-29 14:12:22.191 +1100