thouis

# OSX for Hackers (Mavericks/Yosemite)
#
# Source: https://gist.github.com/brandonb927/3195465

#!/bin/sh

# Some things taken from here
# https://github.com/mathiasbynens/dotfiles/blob/master/.osx

# Ask for the administrator password upfront

thouis

Some things we'd like to see discussed at the hackathon:

1. Modularity

• Can the alignment pipeline be separated into independent steps with a well-defined format for the intermediate results? This would help in parallelization on the cluster, as well as easy experimentation with new approaches. It also would help separate control parameters into groups based on which step they control.

2. 1D and 2D constraints

• Currently, filtering correspondences removes all of those except corner-like matches. Is it possible to classify correspondences into smooth/linear/corner? 1D correspondences can be used to constrain the solution to a subspace, and might result in improved results and solution times in some cases.

3. Cracks

• Some of our data has (long, linear) cracks from the microtoming process. We can detect them automatically. It would be useful to be able to eliminate cracked regions from correspondence finding, and to be able to do some mesh surgery on the structural mesh during the solving pr

thouis

thouis

##########################################################################
# Maximum Response filterbank from
# http://www.robots.ox.ac.uk/~vgg/research/texclass/filters.html
# based on several edge and bar filters.
# Adapted to Python by Andreas Mueller amueller@ais.uni-bonn.de
# Share and enjoy
#

import numpy as np
import matplotlib.pyplot as plt

thouis

import cpscript
from scipy import ndimage

labels = cpscript.Cells.segmented
background_labels = np.array(labels == 0, dtype=int)

dt_labels = ndimage.distance_transform_edt(background_labels)

imVSVG_pixels = cpscript.imVSVG.pixel_data
imVSVG_dt_pixels = imVSVG_pixels * dt_labels

thouis

#!/bin/sh

# TODO: check for virtualenv
# TODO: verify python is universal 32+64 bit

virtualenv -p /Library/Frameworks/Python.framework/Versions/2.7/bin/python --no-site-packages ${1}/cpdev
. ${1}/cpdev/bin/activate

pip install -U pip # to get git+https

thouis

    def recalculate_group(self, workspace, indexes):
        '''Recalculate all measurements once post_group has run
        
        workspace - the workspace being operated on
        indexes - the indexes of the group's image sets' measurements
        '''
        m = workspace.measurements
        object_name = self.object_name.value
        assert isinstance(m, cpmeas.Measurements)
        parent_object_numbers = m.get_all_measurements(

thouis

;;; from http://richardriley.net/projects/emacs/dotprogramming#sec-1.5
(when (load "flymake" t)
  (defun flymake-pycheckers-init ()
    (let* ((temp-file (flymake-init-create-temp-buffer-copy
                       'flymake-create-temp-inplace))
           (local-file (file-relative-name
                        temp-file
                        (file-name-directory buffer-file-name))))
      (list "/Users/tjones/elisp/pycheckers.sh"  (list local-file)))))

thouis

import xlrd
import sys
import numpy as np

book = xlrd.open_workbook(sys.argv[1])
sheet = book.sheet_by_name('Normalization 1')
headers = [c.value for c in sheet.row(0)]

# find columns
colidx = dict([(name, headers.index(name)) for name in ['Gene', 'rep1', 'rep2', 'rep3']])

thouis

"""Measurements.py - storage for image and object measurements

CellProfiler is distributed under the GNU General Public License.
See the accompanying file LICENSE for details.

Copyright (c) 2003-2009 Massachusetts Institute of Technology
Copyright (c) 2009-2011 Broad Institute
All rights reserved.

Please see the AUTHORS file for credits.