Thouis (Ray) Jones thouis

## Hackathon.md

      
              1 file
            
          
              0 forks
            
          
              0 comments
            
          
              0 stars
            
          
                thouis
                / Hackathon.md
            
            
              Last active
              August 29, 2015 13:57
            
              
                Issues to bring up at Hackathon
              
          
    Some things we'd like to see discussed at the hackathon:

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.


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.


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


## osx-for-hackers.sh
# 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

## Speeding up Python.ipynb

      
              1 file
            
          
              0 forks
            
          
              0 comments
            
          
              0 stars
            
          
                thouis
                / Speeding up Python.ipynb
            
            
              Last active
              August 29, 2015 14:10
            
          
      Sorry, something went wrong. Reload?
      Sorry, we cannot display this file.
      Sorry, this file is invalid so it cannot be displayed.
      
          Viewer requires iframe.
      
    
## current_machine.html
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
    "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta name="generator"  content="lshw-B.02.16" />
<style type="text/css">
  .first {font-weight: bold; margin-left: none; padding-right: 1em;vertical-align: top; }
  .second {padding-left: 1em; width: 100%; vertical-align: center; }
  .id {font-family: monospace;}

## gist:ed15adbfe620c8be064b
import plyfile
import pylab
import sys
import mcpi.minecraft as minecraft
import mcpi.block as block
import numpy as np

scale = 150


## Watershed - VI comparison.ipynb

      
              1 file
            
          
              0 forks
            
          
              0 comments
            
          
              0 stars
            
          
                thouis
                / Watershed - VI comparison.ipynb
            
            
              Created
              April 4, 2015 02:42
            
              
                watershed ipy
              
          
      Sorry, something went wrong. Reload?
      Sorry, we cannot display this file.
      Sorry, this file is invalid so it cannot be displayed.
      
          Viewer requires iframe.
      
    
## test.py
from math import tan, floor

def f5(element):
    assert len(element) % 2 == 0
    for idx in range(0 ,len(element), 2):
        sub = element[idx:idx+2].lower()
        v1 = ord(sub[0]) - ord('a') + 1
        v2 = ord(sub[1]) - ord('a') + 1
        if 8 - floor(tan(v1 * v2)) < 0:
            print v1 * v2, "bad"

## Ladder Games.ipynb

      
              1 file
            
          
              0 forks
            
          
              0 comments
            
          
              0 stars
            
          
                thouis
                / Ladder Games.ipynb
            
            
              Last active
              August 29, 2015 14:22
            
          
      Sorry, something went wrong. Reload?
      Sorry, we cannot display this file.
      Sorry, this file is invalid so it cannot be displayed.
      
          Viewer requires iframe.
      
    
## attempt at gridding
      for count, gene in countgenes:
            name = wx.StaticText(self, -1, gene)
            name.BackgroundColour = '#ffffff'
            self.grid_sizer.Add(name, 0, wx.EXPAND)
            c = wx.StaticText(self, -1, "%d"%(count))
            self.grid_sizer.Add(c, 0, wx.EXPAND)
            b1 = wx.RadioButton(self, -1, style=wx.RB_GROUP)
            b1.BackgroundColour = '#ffffff'
            b1.Alignment = wx.ALIGN_CENTER_HORIZONTAL
            self.grid_sizer.Add(b1, flag=wx.ALIGN_CENTER|wx.EXPAND)

## measurements.py
"""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.
	# 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
	<?xml version="1.0" encoding="utf-8"?>
	<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
	"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
	<html xmlns="http://www.w3.org/1999/xhtml">
	<head>
	<meta name="generator" content="lshw-B.02.16" />
	<style type="text/css">
	.first {font-weight: bold; margin-left: none; padding-right: 1em;vertical-align: top; }
	.second {padding-left: 1em; width: 100%; vertical-align: center; }
	.id {font-family: monospace;}
	import plyfile
	import pylab
	import sys
	import mcpi.minecraft as minecraft
	import mcpi.block as block
	import numpy as np

	scale = 150
	from math import tan, floor

	def f5(element):
	assert len(element) % 2 == 0
	for idx in range(0 ,len(element), 2):
	sub = element[idx:idx+2].lower()
	v1 = ord(sub[0]) - ord('a') + 1
	v2 = ord(sub[1]) - ord('a') + 1
	if 8 - floor(tan(v1 * v2)) < 0:
	print v1 * v2, "bad"
	for count, gene in countgenes:
	name = wx.StaticText(self, -1, gene)
	name.BackgroundColour = '#ffffff'
	self.grid_sizer.Add(name, 0, wx.EXPAND)
	c = wx.StaticText(self, -1, "%d"%(count))
	self.grid_sizer.Add(c, 0, wx.EXPAND)
	b1 = wx.RadioButton(self, -1, style=wx.RB_GROUP)
	b1.BackgroundColour = '#ffffff'
	b1.Alignment = wx.ALIGN_CENTER_HORIZONTAL
	self.grid_sizer.Add(b1, flag=wx.ALIGN_CENTER\|wx.EXPAND)
	"""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.