-
Notifications
You must be signed in to change notification settings - Fork 0
/
YellowLine.ijm
233 lines (188 loc) · 7.47 KB
/
YellowLine.ijm
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
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
TILL = 25;
// Characteristics: This does the whole workflow, and avoids creating an entire mess-of-a-folder.
// It takes less memory, and the final finished product is nice and concise. Must save then, though.
// Selection functions:
// 1- selectImage(id)
// 2- selectWindow("name")
// Tasks:
/*
* 1) Dialog prompt
* 2) Basic operation using COMBINE
* 3) For loop
* 4)
*/
// TODO:
// 1) pixel-scale reset (maybe can preserve thing by using toUnscaled(length)
// 2) make a 2-bit line...
/* Tidywork:
// Close all windows, establish standard settings
// also, could ensure the new title is relevant to the first
// will NOT auto-save, bc it produces a tangible and it is important the interacting scientist knows
// where it is saved, as it will most likely be used on an ad-hoc basis.
- could ensure the video is of proper "A" format...
- set titles if desired
*/
//Clearing Fiji of all open images and windows
showMessageWithCancel("WARNING", "First, all files open in FIJI will be closed. \n \nSave desired image-files.");
// If no cancel...
while (nImages>0) {selectImage(nImages); close();}
if (isOpen("Results")) {selectWindow("Results"); run("Close");}
if(isOpen("ROI Manager")){selectWindow("ROI Manager");run("Close");}
if(isOpen("Log")){selectWindow("Log");run("Close");}
if(isOpen("Debug")){selectWindow("Debug");run("Close");}
///// 1) Dialog prompt(s)
// Which video (z-stack-by-time)?
filepath=File.openDialog("Select a Movie");
open(filepath);
fp_name=getTitle();
mainID=getImageID();
// Change the scale to pixels so integers can promote a clean re-slice into the kymos
run("Properties...",
"channels=1 slices=561 frames=1 unit=µm pixel_width=1 pixel_height=1 voxel_depth=1.0000000 frame=[1 sec]");
// Which kymo?
Dialog.create("Choose the visualization-type")
// Features:
// which X? --- menu items must match the argument-flags of Z-Project
Dialog.addChoice("X Kymograph type:", newArray("None", "Average Intensity", "Max Intensity", "Min Intensity", "Sum Slices", "Standard Deviation", "Median"), "None");
//Dialog.addChoice("X Kymograph type:", newArray("None", "Average", "Max", "Min", "Sum", "SD", "Median"), "None");
Dialog.addCheckbox("Type-label?", true);
// which Y?
Dialog.addChoice("Y Kymograph type:", newArray("None", "Average Intensity", "Max Intensity", "Min Intensity", "Sum Slices", "Standard Deviation", "Median"), "None");
Dialog.addCheckbox("Type-label?", true);
Dialog.setLocation(400,250);
// add help box...
html = "<html>"
+"<h2>What are these options?</h2>"
+"<font size=-1>
+"<b>X-Kymo:</b> <font color=red>Preserves the X-dimension</font>, while switching the orientation of the Time-dimension & Y-dimension,<br>"
+ "then collapsing the Y-dimension's associated pixel intensities with the chosen operation.<br>"
+ "e.g. 'Max' yielding the highest 8-bit value <i>out-of-all</i> the Y-values<br>"
+ "<font color=red>tl;dr</font> - The 'classic' Kymograph– looks like a broken wish-bone."
+"<br><br/>"
+"<b>Type-Label?:</b> Burns in (or 'flattens' in ijm-jargon) a label of which operation was performed on the Kymograph.<br>"
+"Changes the pixel-data; avoid if further calculations are desired.<br>"
+"<br>"
+"<b>Y-Kymo:</b> <font color=red>Preserves the Y-dimension</font>, while switching the orientation of the Time-dimension & Y-dimension,<br>"
+ "then collapsing the Y-dimension's associated pixel intensities with the chosen operation.<br>"
+ "e.g. 'Max' yielding the highest 8-bit value <i>out-of-all</i> the Y-values<br>"
+ "<font color=red>tl;dr</font> - The 'classic' Kymograph– looks like a broken wish-bone."
+"<br><br/>"
+"<b>Choosing both:</b> A scrollable image will be formatted as would be expected."
+"<br><br/>"
+"</font>";
Dialog.addHelp(html);
// Trigger the interaction
Dialog.show();
// Harvest the information
// The X-Kymograph...
x_type = Dialog.getChoice();
x_type_arg = "projection=[" + x_type + "]";
x_label_flag = Dialog.getCheckbox();
//print("The x_type is..." + x_type);
//print(x_label_flag);
// The Y-Kymograph...
y_type = Dialog.getChoice();
y_type_arg = "projection=[" + y_type + "]";
y_label_flag = Dialog.getCheckbox();
//print("The y_type is..." + y_type);
//print(y_label_flag);
// So far... original video is OPEN... the kymographs are NOT made
// Make X Kymograph (will run macros to accomplish this)
if(x_type!= "None") {
//make the main video active
selectImage(mainID);
run("Reslice [/]...", "output=1.000 start=Bottom flip");
// now i have a new stack
// open: original + kymo-stack
run("Z Project...", x_type_arg);
// get the image ID
XID=getImageID();
rename("X: " + x_type);
Stack.getDimensions(Xw, Xh, Xc, Xs, Xf);
// open: original + kymo-slice + kymograph
close("Reslice*");
}
// Make Y Kymograph
if(y_type!= "None") {
//make the main video active
selectImage(mainID);
run("Reslice [/]...", "output=1.000 start=Left rotate");
// now i have a new stack
// open: original + kymo-stack
run("Z Project...", y_type_arg);
// get the image ID
YID=getImageID();
rename("Y: " + y_type);
Stack.getDimensions(Yw, Yh, Yc, Ys, Yf);
// open: original + kymo-slice + kymograph
close("Reslice*");
}
// open at end of this section: 1) ORIGINAL + 2) KYMOGRAPH, to be yellow-lined'
// will close main video for now to increase the available memory to make the CONCATENATED image
close(fp_name);
//// TTL (Time-Tracer-Line) loop
// CONCATENATE
print(getValue("color.foreground"));
print(getValue("color.background"));
setLineWidth(1);
setForegroundColor(255, 255, 255);
setColor(255);
print(getValue("color.foreground"));
print(getValue("color.background"));
///////// X-Kymo//////////
if(x_type!= "None") {
selectImage(XID);
makeRectangle(0,0,Xw,1);
changeValues(0,255,200);
// set the first flattened image equal to the soon-to-be accumulating concatenation
AccX_ID = getImageID();
rename("Concats-X!");
for (i=1; i <= TILL; i++) {
//make the X Kymograph active, that will have lines, iteratively, painted onto it
selectImage(XID);
run("Duplicate...", "title=[The d00p]");
makeRectangle(0,Xh-i,Xw, 1);
changeValues(0,255,200);
// after Flatten, the newly-created & selected image will be ACTIVE
// This must be combined with the Accumulating line-series concatenation, and then deleted itself
run("Concatenate...", " title=Concats-X! image1=[Concats-X!] image2=[" + getTitle + "]");
}
}
// Y Kymo
if(y_type!= "None") {
selectImage(YID);
makeRectangle(0,0,1,Yh);
changeValues(0,255,200);
// set the first flattened image equal to the soon-to-be accumulating concatenation
AccY_ID = getImageID();
rename("Concats-Y!");
for (i=1;i <= TILL; i++) {
// make the Y Kymograph active, each time painting a line onto it
selectImage(YID);
run("Duplicate...", "title=[The d00p]");
makeRectangle(i,0,1,Yh);
changeValues(0,255,200);
run("Concatenate...", " title=Concats-Y! image1=[Concats-Y!] image2=[" + getTitle + "]");
}
}
// COMBINE
open(filepath); // the video is now active
videoName = getTitle();
//
print(videoName + "'s dimensions are...");
print("Time..." + getTime());
print("Height: " + getHeight());
print("Width: " + getWidth());
//
if(y_type!= "None") {
run("RGB Color");
run("Combine...", "stack1=" + videoName + " stack2=Concats-Y!");
videoName = getTitle();
}
if (x_type!= "None") {
run("RGB Color");
run("Combine...", "stack1=Concats-X! stack2=[" + videoName + "] combine");
videoName = getTitle();
}
//////////////////////////////////////////////////////////////////////////////////////////////////////
// Scratch-Pad