Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
// Creates stack projections for subgroups
// and saves them to disk.
macro "Grouped Projections Batch" {
// Parameters
extension = ".BTF";
method="Max Intensity"; //one of Max Intensity", "Min Intensity","Median","Average Intensity","Standard Deviation"
subStackSize = 300;
overlap = 10;
// Get user input if requiered
inargs = getArgument();
if (inargs=="") {
//Display dialog and ask for paths
inputDir = getDirectory("Input directory");
outputDir = getDirectory("Output directory");
} else {
//Parse input and output paths from argumet string
paths = split(files," ");
inputDir = paths[1]:
outputDir = paths[2];
}
processFolder(inputDir);
// Process all files and recurse into subdirs
function processFolder(input) {
list = getFileList(input);
for (i = 0; i < list.length; i++) {
if(File.isDirectory(input + list[i]))
processFolder("" + input + list[i]);
if(endsWith(list[i], extension))
processFile(input, outputDir, list[i]);
}
}
// Single file projections
function processFile(inputFile,basePath) {
// open input input file
open(inputFile);
run("Bio-Formats Importer", "open="+inputFile+" color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT use_virtual_stack");
inputID = getImageID();
// Input checking
if (nSlices() == 1) {exit("This macro only operates on stacks.")};
if (overlap >= subStackSize) {error("Overlap must be smaller than size of substack");}
//Check if sub stack will fit in memory
maxMem = parseInt(IJ.maxMemory());
stackMem = getWidth()*getHeight()*bitDepth()/8*subStackSize;
if (stackMem > maxMem) {
exit("Substack is too large for available memory");
}
//FIXME calculate iMax correctly for non zero overlaps
iMax = floor(nSlices()/subStackSize)+1;
methodPrefix = replace(method,' ','-');
resultName = methodPrefix;
inputInfo = getImageInfo;
inputName = getInfo("image.filename");
dotIndex = lastIndexOf(inputName, ".");
if (dotIndex >= 0) {
inputName = substring(inputName, 0, dotIndex);
}
progressTitle = "[Progress]";
run("Text Window...", "name="+ progressTitle +" width=30 height=3 monospaced");
print(progressTitle,"\\Update:0/"+iMax+" substacks (0%)\n"+getBar(0, 100));
print("Calculating the grouped "+method+" projection...");
setBatchMode(true);
tStart = getTime();
for (i=0; i<iMax; i++) {
print(progressTitle,"\\Update:"+i+"/"+iMax+" substacks ("+round(i/iMax*100)+"%)\n"+getBar(i, 100));
start=i*subStackSize+1;
stop=start+subStackSize+overlap;
if (stop > nSlices()) {
stop=nSlices();
i = iMax+1;
}
sliceName = methodPrefix+"_"+IJ.pad(start,5)+"-"+IJ.pad(stop,5);
calculateProjection(start,stop,"SubStack",method);
rename(sliceName);
if (i>1) {
addSlice(resultName,resultName,getTitle());
selectImage(resultName);
setSlice(nSlices);
setMetadata("Label", sliceName);
}
else if (i==1) {
addSlice(resultName,slice1,sliceName);
selectImage(resultName);
setSlice(1);
setMetadata("Label", slice1);
setSlice(2);
setMetadata("Label", sliceName);
setMetadata("Info", inputInfo);
}
else if (i==0) {
slice1=getTitle();
}
selectImage("SubStack");
close();
selectImage(inputID);
}
selectImage(resultName);
setSlice(1);
run("Enhance Contrast...", "saturated=0.4 process_all");
if (saveToDisk) {
saveAs("Tiff",basePath+inputName+"_"+resultName+"-grouped");
}
close();
close(inputID);
setBatchMode(false);
tStop = getTime();
walltime = (tStop-tStart)/1000/60;
print("Done! (took "+d2s(walltime,1)+" min to process "+i+" substacks.");
print(progressTitle, "\\Close");
//Subfunctions
function calculateProjection(iStart,iStop,resultTitle,method) {
run("Duplicate...", "title="+resultTitle+" duplicate range="+iStart+"-"+iStop);
if (nSlices>1) {
run("Z Project...", "start=1 stop="+(iStop-iStart+1)+" projection=["+method+"]");
}
}
//add projection in2 to existing result stack in2
function addSlice(resultTitle,in1,in2) {
run("Concatenate...", " title=["+resultTitle+"] image1="+in1+" image2="+in2);
showStatus("Grouped Stack Proj. ("+i+"/"+iMax+"):");
showProgress(i/iMax);
}
//get string representation of progress bar with p1 out of p2 done
function getBar(p1, p2) {
n = 20;
bar1 = "--------------------";
bar2 = "********************";
index = round(n*(p1/p2));
if (index<1) index = 1;
if (index>n-1) index = n-1;
return substring(bar2, 0, index) + substring(bar1, index+1, n);
}
}
}