Leslie Evelyn Solorzano zloysmiertniy

## alpha.py
location="/home/leslie/Documents/alphaamd/"

imgs=["cells2little.png"]

def drawboxesat(pdx, iw, ih, q):
    step=1/q
    for x in range(iw):
        for y in range(ih):
            intensity=pdx[(x,y)][0]
            if intensity==0:

## mergiwild.ipynb

      
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                zloysmiertniy
                / mergiwild.ipynb
            
            
              Last active May 31, 2019
            
          
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## iwild.html
<html>

<head>
    <script src="https://d3js.org/d3.v4.min.js"></script>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/p5.js/0.8.0/p5.js"></script>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
    <script src="/home/leslie/Downloads/iWildCam_2019_iNat_Idaho.json"></script>
    <script src="/home/leslie/Downloads/iWildCam_2019_CCT_Bboxes.json"></script>
    <!-- Latest compiled and minified CSS -->
    <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/3.4.1/css/bootstrap.min.css"

## OSD-D3.js
var exampleapp={
    starCount:0,
    OSDviewer: null,
    init: function(){
        var OSDviewer = OpenSeadragon(this.OSDOptions);
        this.OSDviewer=OSDviewer;
        this.OSDsvgov=this.OSDviewer.svgOverlay();

        var click_handler= function(event) {
            if(event.quick){

## isosurfacespots.m
close all
clear all

fname ='C:\Users\Administrator\Documents\Leslie\Uppsala\registered161101\crops\b1-2-0001-1757-1887-White Top Hat.tif';

info = imfinfo(fname);
num_images = numel(info);
w =info.Width;
h= info.Height;

## screens.m
clear all;

base=5;

if(base==1)
b3=imread('MAX_base_1_ch3.tif');
b4=imread('MAX_base_1_ch4.tif');
b5=imread('MAX_base_1_ch5.tif');
b6=imread('MAX_base_1_ch6.tif');
finalname='b1-color.tif';

## voxelsimagetiff.py
from PIL import Image
import numpy

im=Image.open('C:/Users/Administrator/Documents/Leslie/Uppsala/registered161101/crops/b1-2-0001-1757-1887-White Top Hat.tif')

def makeMaterial(name, diffuse, specular, alpha):
    mat = bpy.data.materials.new(name)
    mat.diffuse_color = diffuse
    mat.diffuse_shader = 'LAMBERT'
    mat.diffuse_intensity = 1.0

## Python VTK MPR
def testBug(self):
        # Uncomment the next line if you want to run this via
        # `gdb python`.
        #raw_input('Hit Ctrl-C')

        # Load some data.
        v16 = vtk.vtkVolume16Reader()
        v16.SetDataDimensions(64, 64)
        v16.SetDataByteOrderToLittleEndian()
        v16.SetFilePrefix(os.path.join(Testing.VTK_DATA_ROOT,

## itk.cxx
/*
*  Create a float image the size of a short image
*  This is an example of how to create an image of
*  a different type but same size as a given image
*/
FloatImageType::Pointer ppRecruitImage = FloatImageType::New();

//define origin and size the same as the input

//get the biggest region (which usually is the whole image)

## commands.sh
#Copy directory structure

cd /path/to/directories &&
find . -type d -exec mkdir -p -- /path/to/backup/{} \;

#copy files of certain extension
#http://superuser.com/questions/299938/how-can-i-recursively-copy-files-by-file-extension-preserving-directory-structu

cd /source/path
find -type f -name \*.txt -exec install -D {} /dest/path/{} \;
	location="/home/leslie/Documents/alphaamd/"

	imgs=["cells2little.png"]

	def drawboxesat(pdx, iw, ih, q):
	step=1/q
	for x in range(iw):
	for y in range(ih):
	intensity=pdx[(x,y)][0]
	if intensity==0:
	<html>

	<head>
	<script src="https://d3js.org/d3.v4.min.js"></script>
	<script src="https://cdnjs.cloudflare.com/ajax/libs/p5.js/0.8.0/p5.js"></script>
	<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
	<script src="/home/leslie/Downloads/iWildCam_2019_iNat_Idaho.json"></script>
	<script src="/home/leslie/Downloads/iWildCam_2019_CCT_Bboxes.json"></script>
	<!-- Latest compiled and minified CSS -->
	<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/3.4.1/css/bootstrap.min.css"
	var exampleapp={
	starCount:0,
	OSDviewer: null,
	init: function(){
	var OSDviewer = OpenSeadragon(this.OSDOptions);
	this.OSDviewer=OSDviewer;
	this.OSDsvgov=this.OSDviewer.svgOverlay();

	var click_handler= function(event) {
	if(event.quick){
	close all
	clear all

	fname ='C:\Users\Administrator\Documents\Leslie\Uppsala\registered161101\crops\b1-2-0001-1757-1887-White Top Hat.tif';

	info = imfinfo(fname);
	num_images = numel(info);
	w =info.Width;
	h= info.Height;
	clear all;

	base=5;

	if(base==1)
	b3=imread('MAX_base_1_ch3.tif');
	b4=imread('MAX_base_1_ch4.tif');
	b5=imread('MAX_base_1_ch5.tif');
	b6=imread('MAX_base_1_ch6.tif');
	finalname='b1-color.tif';
	from PIL import Image
	import numpy

	im=Image.open('C:/Users/Administrator/Documents/Leslie/Uppsala/registered161101/crops/b1-2-0001-1757-1887-White Top Hat.tif')

	def makeMaterial(name, diffuse, specular, alpha):
	mat = bpy.data.materials.new(name)
	mat.diffuse_color = diffuse
	mat.diffuse_shader = 'LAMBERT'
	mat.diffuse_intensity = 1.0
	def testBug(self):
	# Uncomment the next line if you want to run this via
	# `gdb python`.
	#raw_input('Hit Ctrl-C')

	# Load some data.
	v16 = vtk.vtkVolume16Reader()
	v16.SetDataDimensions(64, 64)
	v16.SetDataByteOrderToLittleEndian()
	v16.SetFilePrefix(os.path.join(Testing.VTK_DATA_ROOT,
	/*
	* Create a float image the size of a short image
	* This is an example of how to create an image of
	* a different type but same size as a given image
	*/
	FloatImageType::Pointer ppRecruitImage = FloatImageType::New();

	//define origin and size the same as the input

	//get the biggest region (which usually is the whole image)
	#Copy directory structure

	cd /path/to/directories &&
	find . -type d -exec mkdir -p -- /path/to/backup/{} \;

	#copy files of certain extension
	#http://superuser.com/questions/299938/how-can-i-recursively-copy-files-by-file-extension-preserving-directory-structu

	cd /source/path
	find -type f -name \*.txt -exec install -D {} /dest/path/{} \;