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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.output;
import java.io.File;
import bilib.tools.NumFormat;
import deconvolution.algorithm.Controller;
import deconvolutionlab.Imager;
import deconvolutionlab.Imager.ContainerImage;
import deconvolutionlab.Lab;
import deconvolutionlab.monitor.Monitors;
import signal.Constraint;
import signal.RealSignal;
public class Output {
public enum View {
STACK, SERIES, ORTHO, MIP, PLANAR, FIGURE
};
public enum Dynamic {
INTACT, RESCALED, NORMALIZED, CLIPPED
};
public enum Action {
SHOW, SAVE, SHOWSAVE;
}
private ContainerImage container = null;
private int ox = 0;
private int oy = 0;
private int oz = 0;
private boolean center = true;
private String name = "";
private boolean save = true;
private boolean show = true;
private View view = View.STACK;
private Imager.Type type = Imager.Type.FLOAT;
private Dynamic dynamic = Dynamic.INTACT;
private String customPath = "$";
private int frequency = 0;
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;
this.container = Lab.createContainer(Monitors.createDefaultMonitor(), "");
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 (Imager.Type t : Imager.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)
ox = (int) Math.round(pos[0]);
if (pos.length > 1)
oy = (int) Math.round(pos[1]);
if (pos.length > 2)
oz = (int) Math.round(pos[2]);
found = true;
center = false;
}
if (!found)
name += tokens[i] + " ";
name = name.trim();
}
}
public Output(View view, Action action, String name) {
this.name = name;
this.show = action == Action.SHOW || action == Action.SHOWSAVE;
this.save = action == Action.SAVE || action == Action.SHOWSAVE;
this.view = view;
this.type = Imager.Type.FLOAT;
this.dynamic = Dynamic.INTACT;
this.center = true;
this.frequency = 0;
}
public Output rescale() {
this.dynamic = Dynamic.RESCALED;
return this;
}
public Output clip() {
this.dynamic = Dynamic.CLIPPED;
return this;
}
public Output normalize() {
this.dynamic = Dynamic.NORMALIZED;
return this;
}
public Output toFloat() {
this.type = Imager.Type.FLOAT;
return this;
}
public Output toShort() {
this.type = Imager.Type.SHORT;
return this;
}
public Output toByte() {
this.type = Imager.Type.BYTE;
return this;
}
public Output frequency(int frequency) {
this.frequency = frequency;
return this;
}
public Output origin(int ox, int oy, int oz) {
this.ox = ox;
this.oy = oy;
this.oz = oz;
this.center = false;
return this;
}
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 setPath(String customPath) {
this.customPath = customPath;
}
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 String[] getAsString() {
String t = (type == Imager.Type.FLOAT ? "" : type.name().toLowerCase());
String d = (dynamic == Dynamic.INTACT ? "" : dynamic.name().toLowerCase());
String o = "";
if (!center)
o = " (" + ox + "," + oy + "," + oz + ")";
String sa = save ? "\u2713" : "";
String sh = show ? "\u2713" : "";
String fr = frequency > 0 ? " @" + frequency : "";
return new String[] { view.name().toLowerCase() + fr, name, d, t, o, sh, sa, "\u232B" };
}
public void executeStarting(Monitors monitors, RealSignal signal, Controller controller) {
if (signal == null)
return;
execute(monitors, signal, controller, true, false, false, 0);
}
public void executeFinal(Monitors monitors, RealSignal signal, Controller controller) {
if (signal == null)
return;
execute(monitors, signal, controller, false, false, true, 0);
}
public void executeIterative(Monitors monitors, RealSignal signal, Controller controller, int iter) {
if (signal == null)
return;
execute(monitors, signal, controller, false, true, false, iter);
}
private void execute(Monitors monitors, RealSignal signal, Controller controller, boolean start, boolean live, boolean finish, int iter) {
String title = name;
if (live)
if (!is(iter))
return;
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.getStats().getStatsInput();
if (stats != null)
constraint.clipped(x, stats[1], stats[2]);
break;
case NORMALIZED:
x = signal.duplicate();
float[] stats1 = controller.getStats().getStatsInput();
if (stats1 != null)
constraint.normalized(x, stats1[0], stats1[3]);
break;
default:
x = signal;
}
String path = (customPath.equals("$") ? controller.getPath() : customPath) + File.separator;
String filename = path + title + ".tif";
switch (view) {
case STACK:
if (show && !live)
Lab.show(monitors, x, title, type, (center ? x.nz / 2 : oz));
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);
String z = "-z" + String.format("%06d", k) ;
if (show && !live)
Lab.show(monitors, slice, title + z, type);
if (save && !live) {
String zfilename = path + title + z + ".tif";
Lab.save(monitors, slice, zfilename, type);
}
}
break;
case ORTHO:
if (!start)
orthoview(monitors, x, title, filename, live);
break;
case FIGURE:
if (!start)
figure(monitors, x, title, filename, live);
break;
case MIP:
if (!start)
mip(monitors, x, title, filename, live);
break;
case PLANAR:
if (!start)
planar(monitors, x, title, filename, live);
break;
default:
break;
}
}
private void mip(Monitors monitors, RealSignal signal, String title, String filename, boolean live) {
RealSignal plane = signal.createMIP();
if (show && live) {
Lab.append(monitors, container, 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) {
int cx = ox;
int cy = oy;
int cz = oz;
if (center) {
cx = signal.nx / 2;
cy = signal.ny / 2;
cz = signal.nz / 2;
}
RealSignal plane = signal.createOrthoview(cx, cy, cz);
if (show && live) {
if (container == null)
container = Lab.createContainer(monitors, title);
Lab.append(monitors, container, 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) {
int cx = ox;
int cy = oy;
int cz = oz;
if (center) {
cx = signal.nx / 2;
cy = signal.ny / 2;
cz = signal.nz / 2;
}
RealSignal plane = signal.createFigure(cx, cy, cz);
if (show && live) {
if (container == null)
container = Lab.createContainer(monitors, title);
Lab.append(monitors, container, 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) {
RealSignal plane = signal.createPlanar();
if (show && live) {
if (container == null)
container = Lab.createContainer(monitors, title);
Lab.append(monitors, container, 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 = (" + ox + "," + oy + "," + oz + ")");
return v + " " + name + " format = (" + d + ", " + t + ") " + k + f;
}
}

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