miura

/* http://prismjs.com/download.html?themes=prism&languages=markup+css+clike+javascript+markdown&plugins=line-numbers+file-highlight */
var _self="undefined"!=typeof window?window:"undefined"!=typeof WorkerGlobalScope&&self instanceof WorkerGlobalScope?self:{},Prism=function(){var e=/\blang(?:uage)?-(\w+)\b/i,t=0,n=_self.Prism={manual:_self.Prism&&_self.Prism.manual,util:{encode:function(e){return e instanceof a?new a(e.type,n.util.encode(e.content),e.alias):"Array"===n.util.type(e)?e.map(n.util.encode):e.replace(/&/g,"&amp;").replace(/</g,"&lt;").replace(/\u00a0/g," ")},type:function(e){return Object.prototype.toString.call(e).match(/\[object (\w+)\]/)[1]},objId:function(e){return e.__id||Object.defineProperty(e,"__id",{value:++t}),e.__id},clone:function(e){var t=n.util.type(e);switch(t){case"Object":var a={};for(var r in e)e.hasOwnProperty(r)&&(a[r]=n.util.clone(e[r]));return a;case"Array":return e.map(function(e){return n.util.clone(e)})}return e}},languages:{extend:function(e,t){var a=n.util.clone(n.langua

miura

function doGet(request) {
  if (request.parameters.url != undefined && request.parameters.url != "") {
    var imageBlob = UrlFetchApp.fetch(request.parameters.url).getBlob();
    var resource = {
      title: imageBlob.getName(),
      mimeType: imageBlob.getContentType()
    };
    var options = {
      ocr: true
    };

miura

var npos = 0; // this variable is better be global. 
var directapply = 0; // "boolean" user input direct application of driftcorrect
var crop = 0;  // "boolean" user input crop to ROI 
var splitch = 0;  // "boolean" user input splitting of channels
var targetstack = 1 // ImageID of the stack that is to be processed 
var dir;
var cropxmax = 0;
var cropymax = 0;
var minout = 0;
var maxout = 0;

miura

macro "Ratiometric FRET" {

  path    = getDirectory("Choose a Directory");
  list    = getFileList(path);
  length  = list.length;

  File.makeDirectory(path + "Imaging/");

  //FRET map creation

miura

Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
error importing site
Traceback (most recent call last):
  File "/Users/miura/.m2/repository/org/scijava/jython-shaded/2.5.3/jython-shaded-2.5.3.jar/site$py.class", line 62, in <module>
  File "/Users/miura/.m2/repository/org/scijava/jython-shaded/2.5.3/jython-shaded-2.5.3.jar/os$py.class", line 50, in <module>
java.lang.ArrayIndexOutOfBoundsException: 8
	at org.python.objectweb.asm.ClassReader.a(Unknown Source)
	at org.python.objectweb.asm.ClassReader.accept(Unknown Source)
	at org.python.objectweb.asm.ClassReader.accept(Unknown Source)

miura

run("Blobs (25K)");
run("Radial Profile Angle", 
	"x_center=127.50 y_center=127.50 radius=127.50 starting_angle=0 integration_angle=180");
run("Clear Results"); 
for(j = 0; j < Ext.getBinSize; j++){
	setResult("Radius", j, Ext.getXValue(j)); 
	setResult("Intensity", j, Ext.getYValue(0, j)); 
}
updateResults(); 
saveAs("results", "");

miura

$cd ~/Applications/IBM/ILOG/CPLEX_Studio1251/concert/lib/x86-64_osx/static_pic
$g++ -fpic -shared -Wl,-all_load libconcert.a -Wl,-noall_load -o libconcert.dylib
ld: warning: option -noall_load is obsolete and being ignored

$cd ~/Applications/IBM/ILOG/CPLEX_Studio1251/cplex/lib/x86-64_osx/static_pic
$g++ -fpic -shared -Wl,-all_load libcplex.a -Wl,-noall_load -o libcplex.dylib
ld: warning: option -noall_load is obsolete and being ignored

$g++ -fpic -shared -Wl,-all_load libilocplex.a -Wl,-noall_load -L.:../../../../concert/lib/x86-64_osx/static_pic -lcplex -lconcert -o libilocplex.dylib
ld: warning: option -noall_load is obsolete and being ignored

miura

ld: warning: option -noall_load is obsolete and being ignored
Undefined symbols for architecture x86_64:
  "_CPXEaddabs", referenced from:
      IloCplexI::addAbs(IloExtractableI const*, int*, int*, char const*) in libilocplex.a(ilocplex.o)
  "_CPXEaddindconstr", referenced from:
      IloCplexI::addIndicator(IloExtractableI const*, int*, double, int, IloCarray<int*> const&, IloCarray<double> const&) in libilocplex.a(ilocplex.o)
  "_CPXEaddmaxexpr", referenced from:
      IloCplexI::addMax(IloExtractableI const*, int*, IloCarray<int*> const&, double, char const*) in libilocplex.a(ilocplex.o)
  "_CPXEaddminexpr", referenced from:
      IloCplexI::addMin(IloExtractableI const*, int*, IloCarray<int*> const&, double, char const*) in libilocplex.a(ilocplex.o)

miura

from de.embl.cmci.radial import RadialProfile

def radMeasure(rp, rt, slicenum):
	imp.setSlice(slicenum)
	rp.doit(imp, "")
	data = rp.getAccumulator()
	for d in data:
		print d
	index = data[0]
	intensity = data[1]

miura

t1 = System.currentTimeMillis()
imp = IJ.getImage()
imps = ChannelSplitter.split(imp)
ch1A = imps[0].getProcessor().convertToFloat().getPixels()
ch2A = imps[1].getProcessor().convertToFloat().getPixels()
t2 = System.currentTimeMillis()
min1 = min(ch1A)
max1 = max(ch1A)
min2 = min(ch2A)
max2 = max(ch2A)