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Output.java
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/*
* DeconvolutionLab2
*
* Conditions of use: You are free to use this software for research or
* educational purposes. In addition, we expect you to include adequate
* citations and acknowledgments whenever you present or publish results that
* are based on it.
*
* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
*/
/*
* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
*
* This file is part of DeconvolutionLab2 (DL2).
*
* DL2 is free software: you can redistribute it and/or modify it under the
* terms of the GNU General Public License as published by the Free Software
* Foundation, either version 3 of the License, or (at your option) any later
* version.
*
* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with
* DL2. If not, see <http://www.gnu.org/licenses/>.
*/
package deconvolutionlab;
import java.io.File;
import lab.tools.NumFormat;
import signal.Constraint;
import signal.RealSignal;
import deconvolution.algorithm.Controller;
import deconvolutionlab.monitor.Monitors;
public class Output {
public enum View {
STACK, SERIES, ORTHO, MIP, PLANAR, FIGURE
};
public enum Dynamic {
INTACT, RESCALED, NORMALIZED, CLIPPED
};
private int px = 0;
private int py = 0;
private int pz = 0;
private boolean center = true;
private String name = "";
private boolean save = true;
private boolean show = true;
private View view = View.STACK;
private PlatformImager.Type type = PlatformImager.Type.FLOAT;
private Dynamic dynamic = Dynamic.INTACT;
private int frequency = 0;
private String path = "";
public Output(View view, int frequency, String param) {
String[] tokens = param.trim().split(" ");
this.view = view;
this.frequency = frequency;
this.name = "";
this.center = true;
this.save = true;
this.show = true;
for (int i = 0; i < tokens.length; i++) {
boolean found = false;
String p = tokens[i].trim().toLowerCase();
if (p.startsWith("@")) {
found = true;
}
if (p.startsWith("noshow")) {
show = false;
found = true;
}
if (p.startsWith("nosave")) {
save = false;
found = true;
}
for (Dynamic d : Dynamic.values()) {
if (p.toLowerCase().equals(d.name().toLowerCase())) {
dynamic = d;
found = true;
}
}
for (View v : View.values()) {
if (p.toLowerCase().equals(v.name().toLowerCase())) {
view = v;
found = true;
}
}
for (PlatformImager.Type t : PlatformImager.Type.values()) {
if (p.toLowerCase().equals(t.name().toLowerCase())) {
type = t;
found = true;
}
}
if (p.startsWith("(") && p.endsWith(")")) {
double pos[] = NumFormat.parseNumbers(p);
if (pos.length > 0) px = (int) Math.round(pos[0]);
if (pos.length > 1) py = (int) Math.round(pos[1]);
if (pos.length > 2) pz = (int) Math.round(pos[2]);
found = true;
center = false;
}
if (!found) name += tokens[i] + " ";
name = name.trim();
}
}
public Output(View view, boolean show, boolean save, int frequency, String name, Dynamic dynamic, PlatformImager.Type type, boolean center) {
this.name = name;
this.show = show;
this.save = save;
this.view = view;
this.type = type;
this.dynamic = dynamic;
this.center = center;
this.frequency = frequency;
}
public Output(View view, boolean show, boolean save, int frequency, String name, Dynamic dynamic, PlatformImager.Type type, int px, int py, int pz) {
this.name = name;
this.show = show;
this.save = save;
this.view = view;
this.type = type;
this.dynamic = dynamic;
this.center = false;
this.px = px;
this.py = py;
this.pz = pz;
this.frequency = frequency;
}
public boolean is(int iterations) {
if (frequency == 0) return false;
return iterations % frequency == 0;
}
public View getView() {
return view;
}
public String getName() {
return name;
}
public void setPath1(String path) {
this.path = path;
}
public int extractFrequency(String param) {
String line = param.trim();
if (!line.startsWith("@")) line = "@0 " + line;
String parts[] = line.split(" ");
if (parts.length >= 1) {
return (int) Math.round(NumFormat.parseNumber(parts[0], 0));
}
return 0;
}
public void setKeypoint(int px, int py, int pz) {
this.px = px;
this.py = py;
this.pz = pz;
this.center = false;
}
public String[] getAsString() {
String t = (type == PlatformImager.Type.FLOAT ? "" : type.name().toLowerCase());
String d = (dynamic == Dynamic.INTACT ? "" : dynamic.name().toLowerCase());
String k = "";
if (!center)
k = " (" + px + "," + py + "," + pz + ")";
else
k = "";
String sa = save ? "\u2713" : "";
String sh = show ? "\u2713" : "";
String fr = frequency > 0 ? " @" + frequency : "";
return new String[] { view.name().toLowerCase() + fr, name, d, t, k, sh, sa, "" };
}
public void execute(Monitors monitors, RealSignal signal, Controller controller, boolean live) {
if (signal == null) return;
String title = name;
if (controller != null && live) {
if (controller.getIterations() > 0) {
title += "@" + controller.getIterations();
}
}
RealSignal x = null;
Constraint constraint = new Constraint(monitors);
switch (dynamic) {
case RESCALED:
x = signal.duplicate();
constraint.rescaled(x, 0, 255);
break;
case CLIPPED:
x = signal.duplicate();
float[] stats = controller.getStatsInput();
if (stats != null) constraint.clipped(x, stats[1], stats[2]);
break;
case NORMALIZED:
x = signal.duplicate();
float[] stats1 = controller.getStatsInput();
if (stats1 != null) constraint.normalized(x, stats1[0], stats1[3]);
break;
default:
x = signal;
}
String filename = path + File.separator + title + ".tif";
String key = name + "-" + type.name() + "-" + view.name() + "-" + dynamic.name() + "-" + (px + py + pz);
switch (view) {
case STACK:
if (show && !live) Lab.show(monitors, x, title, type, (center ? x.nz / 2 : pz));
if (save && !live) Lab.save(monitors, x, filename, type);
break;
case SERIES:
for (int k = 0; k < x.nz; k++) {
RealSignal slice = x.getSlice(k);
if (show && !live) Lab.show(monitors, slice, title, type);
if (save && !live) Lab.save(monitors, slice, filename, type);
}
break;
case ORTHO:
orthoview(monitors, x, title, filename, live, key);
break;
case FIGURE:
figure(monitors, x, title, filename, live, key);
break;
case MIP:
mip(monitors, x, title, filename, live, key);
break;
case PLANAR:
planar(monitors, x, title, filename, live, key);
break;
default:
break;
}
}
private void mip(Monitors monitors, RealSignal signal, String title, String filename, boolean live, String key) {
RealSignal plane = signal.createMIP();
if (show && live) Lab.appendShowLive(monitors, key, plane, title, type);
if (show && !live) Lab.show(monitors, plane, title, type);
if (save) Lab.save(monitors, plane, filename, type);
}
private void orthoview(Monitors monitors, RealSignal signal, String title, String filename, boolean live, String key) {
int cx = px;
int cy = py;
int cz = pz;
if (center) {
cx = signal.nx / 2;
cy = signal.ny / 2;
cz = signal.nz / 2;
}
RealSignal plane = signal.createOrthoview(cx, cy, cz);
if (show && live) Lab.appendShowLive(monitors, key, plane, title, type);
if (show && !live) Lab.show(monitors, plane, title, type);
if (save) Lab.save(monitors, plane, filename, type);
}
private void figure(Monitors monitors, RealSignal signal, String title, String filename, boolean live, String key) {
int cx = px;
int cy = py;
int cz = pz;
if (center) {
cx = signal.nx / 2;
cy = signal.ny / 2;
cz = signal.nz / 2;
}
RealSignal plane = signal.createFigure(cx, cy, cz);
if (show && live) Lab.appendShowLive(monitors, key, plane, title, type);
if (show && !live) Lab.show(monitors, plane, title, type);
if (save) Lab.save(monitors, plane, filename, type);
}
private void planar(Monitors monitors, RealSignal signal, String title, String filename, boolean live, String key) {
RealSignal plane = signal.createMontage();
if (show && live) Lab.appendShowLive(monitors, key, plane, title, type);
if (show && !live) Lab.show(monitors, plane, title, type);
if (save) Lab.save(monitors, plane, filename, type);
}
@Override
public String toString() {
String t = type.name().toLowerCase();
String v = view.name().toLowerCase();
String d = dynamic.name().toLowerCase();
String f = frequency > 0 ? " every " + frequency + " iterations" : "";
String k = (center ? "" : " keypoint = (" + px + "," + py + "," + pz + ")");
return v + " " + name + " format = (" + d + ", " + t + ") " + k + f;
}
}

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