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Plugins: Configure slice label name using pattern #2891

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merged 20 commits into from Aug 28, 2017
Merged

Plugins: Configure slice label name using pattern #2891

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1b2056c
Configuration option for slice label
dgault Jul 9, 2017
e01cdd9
Add missing series index
dgault Jul 9, 2017
557e4d6
Use reader to return dimension order
dgault Jul 12, 2017
9872e23
Update getFilename to use optional brackets and indexing
dgault Aug 3, 2017
e618ace
Add option for base index on slice label
dgault Aug 3, 2017
ffd7629
Replace constructSliceLabel with FormatTools
dgault Aug 3, 2017
e73b089
Update config window description
dgault Aug 4, 2017
e259e0a
Prevent exception in getFilename
dgault Aug 7, 2017
f503e5d
Revert "Prevent exception in getFilename"
dgault Aug 10, 2017
a2c53bd
Revert "Update config window description"
dgault Aug 10, 2017
42568a0
Revert "Update getFilename to use optional brackets and indexing"
dgault Aug 10, 2017
1ed9f39
Plugins: Revert to use constructSliceLabel rather than FormatTools
dgault Aug 10, 2017
ab78102
Plugins: Update default slice label
dgault Aug 10, 2017
70d5126
Plugins: Fix slice label channel params
dgault Aug 10, 2017
54d9c6f
Resolve conflict in LociPrefs
dgault Aug 11, 2017
5c90daa
Merge CellSens changes
dgault Aug 11, 2017
4447b86
Merge from openmicroscopy/develop
dgault Aug 11, 2017
b6d77a9
Plugins - configure label with channel name
dgault Aug 21, 2017
915fea6
Plugins - reorder config window
dgault Aug 21, 2017
5802178
Plugins configuration - use retrieve for channel count
dgault Aug 22, 2017
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86 changes: 66 additions & 20 deletions components/bio-formats-plugins/src/loci/plugins/config/ConfigWindow.java
View file
Open in desktop
Expand Up @@ -70,6 +70,7 @@
import loci.common.Constants;
import loci.common.DateTools;
import loci.formats.FormatTools;
import loci.plugins.util.LociPrefs;
import loci.plugins.util.WindowTools;

/**
Expand All @@ -91,13 +92,16 @@ public class ConfigWindow extends JFrame
private DefaultListModel formatsListModel;
private JList formatsList;
private JPanel formatInfo;
private JTextField extensions;
private JTextField extensions, sliceLabel;
private JCheckBox enabledBox, windowlessBox, upgradeBox;

private DefaultListModel libsListModel;
private JList libsList;
private JTextField type, status, version, path, url, license;
private JTextArea notes;
private JButton installButton;
private JButton setSliceLabelButton;
private JButton resetSliceLabelButton;

private PrintWriter log;

Expand All @@ -115,10 +119,56 @@ public ConfigWindow() {
tabs.setBorder(new EmptyBorder(PAD, PAD, PAD, PAD));
setContentPane(tabs);

JPanel bfOptionsPanel = new JPanel(new SpringLayout());
tabs.addTab("General", bfOptionsPanel);

JPanel upgradePanel = new JPanel(new SpringLayout());
JLabel upgradeLabel =
new JLabel("Automatically check for new versions of the Bio-Formats plugins");
upgradePanel.add(upgradeLabel);

final boolean checkForUpgrades = Prefs.get(UPGRADE_CHECK_KEY, true);
upgradeBox = new JCheckBox("", checkForUpgrades);
upgradeBox.addItemListener(this);
upgradePanel.add(upgradeBox);

SpringUtilities.makeCompactGrid(upgradePanel,1, 2, PAD, PAD, PAD, PAD);

JPanel sliceNamePanel = new JPanel(new SpringLayout());
JLabel sliceNameLabel = new JLabel("Slice Label Pattern");
sliceNamePanel.add(sliceNameLabel);

final String sliceLabelPattern = LociPrefs.getSliceLabelPattern();
sliceLabel = new JTextField(sliceLabelPattern);
int prefHeight = sliceLabel.getPreferredSize().height;
sliceLabel.setMaximumSize(new Dimension(Integer.MAX_VALUE, prefHeight));
sliceNamePanel.add(sliceLabel);

setSliceLabelButton = new JButton("Set");
resetSliceLabelButton = new JButton("Reset");
setSliceLabelButton.addActionListener(this);
resetSliceLabelButton.addActionListener(this);
sliceNamePanel.add(setSliceLabelButton);
sliceNamePanel.add(resetSliceLabelButton);
SpringUtilities.makeCompactGrid(sliceNamePanel,1, 4, PAD, PAD, PAD, PAD);

bfOptionsPanel.add(upgradePanel);
bfOptionsPanel.add(sliceNamePanel);
JLabel sliceDescription = new JLabel("<html>Customize the slice label by specifying a pattern string:"
+ "<br>%s - series index"
+ "<br>%n - series name"
+ "<br>%c - channel index"
+ "<br>%w - channel name"
+ "<br>%z - Z index"
+ "<br>%t - T index"
+ "<br>%A - acquisition timestamp</html>");
bfOptionsPanel.add(sliceDescription);
SpringUtilities.makeCompactGrid(bfOptionsPanel,3, 1, PAD, PAD, PAD, PAD);

JPanel installPanel = new JPanel();
//tabs.addTab("Install", installPanel);

JButton installButton = new JButton(
installButton = new JButton(
"<html><center><br><font size=\"+1\">Check my system,<br>" +
"install missing libraries,<br>" +
"and upgrade old files</font><br>" +
Expand Down Expand Up @@ -192,22 +242,6 @@ public ConfigWindow() {

// TODO: "How to install" for each library?

JPanel upgradePanel = new JPanel();
tabs.addTab("Upgrade", upgradePanel);

upgradePanel.setLayout(new SpringLayout());

JLabel upgradeLabel =
new JLabel("Automatically check for new versions of the Bio-Formats plugins");
upgradePanel.add(upgradeLabel);

final boolean checkForUpgrades = Prefs.get(UPGRADE_CHECK_KEY, true);
upgradeBox = new JCheckBox("", checkForUpgrades);
upgradeBox.addItemListener(this);
upgradePanel.add(upgradeBox);

SpringUtilities.makeCompactGrid(upgradePanel, 1, 2, PAD, PAD, PAD, PAD);

JPanel logPanel = new JPanel();
tabs.addTab("Log", logPanel);

Expand All @@ -232,8 +266,20 @@ public ConfigWindow() {

@Override
public void actionPerformed(ActionEvent e) {
new LociInstaller().run(null);
dispose();
Object src = e.getSource();
if (src == installButton) {
new LociInstaller().run(null);
dispose();
}
else if (src == setSliceLabelButton) {
Prefs.set(LociPrefs.PREF_SLICE_LABEL_PATTERN, sliceLabel.getText());
return;
}
else if (src == resetSliceLabelButton) {
Prefs.set(LociPrefs.PREF_SLICE_LABEL_PATTERN, null);
sliceLabel.setText(LociPrefs.getSliceLabelPattern());
return;
}
}

// -- ItemListener API methods --
Expand Down
175 changes: 125 additions & 50 deletions components/bio-formats-plugins/src/loci/plugins/in/ImagePlusReader.java
View file
Open in desktop
Expand Up @@ -40,6 +40,7 @@
import java.util.List;
import java.util.Vector;

import loci.common.DateTools;
import loci.common.Location;
import loci.common.Region;
import loci.common.StatusEvent;
Expand All @@ -50,12 +51,20 @@
import loci.formats.FormatTools;
import loci.formats.IFormatReader;
import loci.formats.Modulo;
import loci.formats.meta.DummyMetadata;
import loci.formats.meta.IMetadata;
import loci.formats.meta.MetadataRetrieve;
import loci.formats.meta.MetadataStore;
import loci.plugins.Slicer;
import loci.plugins.util.BFVirtualStack;
import loci.plugins.util.ImageProcessorReader;
import loci.plugins.util.LociPrefs;
import loci.plugins.util.LuraWave;
import loci.plugins.util.VirtualImagePlus;
import ome.units.UNITS;
import ome.units.quantity.Time;
import ome.xml.model.enums.DimensionOrder;
import ome.xml.model.primitives.Timestamp;

/**
* A high-level reader for {@link ij.ImagePlus} objects.
Expand Down Expand Up @@ -330,8 +339,7 @@ private ImageStack createVirtualStack(ImportProcess process, int s,
final BFVirtualStack virtualStack = new BFVirtualStack(options.getId(),
reader, false, false, false);
for (int i=0; i<imageCount; i++) {
final String label = constructSliceLabel(i,
reader, meta, s, zCount, cCount, tCount);
String label = constructSliceLabel(i, reader, meta, s, zCount, cCount, tCount);
virtualStack.addSlice(label);
}

Expand Down Expand Up @@ -381,8 +389,7 @@ private ImageStack readPlanes(ImportProcess process, int s, List<LUT> luts,
throw new FormatException("Cannot read plane #" + i);
}
// generate a label for ith plane
final String label = constructSliceLabel(i,
reader, meta, s, zCount, cCount, tCount);
String label = constructSliceLabel(i, reader, meta, s, zCount, cCount, tCount);

for (ImageProcessor ip : p) {
procs.add(ip);
Expand Down Expand Up @@ -572,60 +579,128 @@ private String constructSliceLabel(int ndx, IFormatReader r,
IMetadata meta, int series, int zCount, int cCount, int tCount)
{
r.setSeries(series);
String sliceLabelPattern = LociPrefs.getSliceLabelPattern();

String order = r.getDimensionOrder();
int sizeC = r.getEffectiveSizeC();
int sizeT = r.getSizeT();
int sizeZ = r.getSizeZ();
int seriesCount = r.getImageCount();
int indexBase = LociPrefs.getSliceLabelBaseIndex();
int[] coordinates = FormatTools.getZCTCoords(order, sizeZ, sizeC, sizeT, sizeZ*sizeC*sizeT, ndx);

MetadataStore store = r.getMetadataStore();
MetadataRetrieve retrieve = store instanceof MetadataRetrieve ? (MetadataRetrieve) store : new DummyMetadata();
String filename = sliceLabelPattern.replaceAll(FormatTools.SERIES_NUM, String.format("%d", series));

String imageName = retrieve.getImageName(series);
if (imageName == null) imageName = "Series" + series;
filename = sliceLabelPattern;

filename = filename.replaceAll(FormatTools.SERIES_NUM, String.format("%d", series));
filename = filename.replaceAll(FormatTools.SERIES_NAME, imageName);
if (sizeC > 1) {
int[] subC;
String[] subCTypes;
Modulo moduloC = r.getModuloC();
if (moduloC.length() > 1) {
subC = new int[] {r.getSizeC() / moduloC.length(), moduloC.length()};
subCTypes = new String[] {moduloC.parentType, moduloC.type};
} else {
subC = new int[] {r.getSizeC()};
subCTypes = new String[] {FormatTools.CHANNEL};
}
int[] subCPos = FormatTools.rasterToPosition(subC, coordinates[1]);
StringBuffer channelString = new StringBuffer();
for (int i=0; i<subC.length; i++) {
boolean ch = subCTypes[i] == null || FormatTools.CHANNEL.equals(subCTypes[i]);
channelString.append(ch ? "c" : subCTypes[i]);
channelString.append(":");
channelString.append(subCPos[i] + 1);
channelString.append("/");
channelString.append(subC[i]);
if (i < subC.length - 1) channelString.append(", ");
}
filename = filename.replaceAll(FormatTools.CHANNEL_NUM, channelString.toString() + " ");

final int[] zct = r.getZCTCoords(ndx);
final StringBuffer sb = new StringBuffer();

int[] subC;
String[] subCTypes;
Modulo moduloC = r.getModuloC();
if (moduloC.length() > 1) {
subC = new int[] {r.getSizeC() / moduloC.length(), moduloC.length()};
subCTypes = new String[] {moduloC.parentType, moduloC.type};
} else {
subC = new int[] {r.getSizeC()};
subCTypes = new String[] {FormatTools.CHANNEL};
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Does it make sense to keep a way to include the modulo information in the slice labels?

int channelCount = retrieve.getChannelCount(series);
if (coordinates[1] < channelCount) {
String channelName = retrieve.getChannelName(series, coordinates[1]);
if (channelName == null) channelName = String.valueOf(coordinates[1]);
filename = filename.replaceAll(FormatTools.CHANNEL_NAME, channelName);
}
else {
filename = filename.replaceAll(FormatTools.CHANNEL_NAME, String.valueOf(coordinates[1]));
}
}
else {
filename = filename.replaceAll(FormatTools.CHANNEL_NUM, "");
filename = filename.replaceAll(FormatTools.CHANNEL_NAME, "");
}
if (sizeZ > 1) {
filename = filename.replaceAll(FormatTools.Z_NUM, "z:" + String.format("%d", coordinates[0] + 1) + "/" + String.format("%d", sizeZ) + " ");
}
else {
filename = filename.replaceAll(FormatTools.Z_NUM, "");
}
if (sizeT > 1) {
filename = filename.replaceAll(FormatTools.T_NUM, "t:" + String.format("%d", coordinates[2] + 1) + "/" + String.format("%d", sizeT) + " ");
}
else {
filename = filename.replaceAll(FormatTools.T_NUM, "");
}

boolean first = true;
if (cCount > 1) {
if (first) first = false;
else sb.append("; ");
int[] subCPos = FormatTools.rasterToPosition(subC, zct[1]);
for (int i=0; i<subC.length; i++) {
boolean ch =
subCTypes[i] == null || FormatTools.CHANNEL.equals(subCTypes[i]);
sb.append(ch ? "c" : subCTypes[i]);
sb.append(":");
sb.append(subCPos[i] + 1);
sb.append("/");
sb.append(subC[i]);
if (i < subC.length - 1) sb.append(", ");
Timestamp timestamp = retrieve.getImageAcquisitionDate(series);
long stamp = 0;
String date = null;
if (timestamp != null) {
date = timestamp.getValue();
if (retrieve.getPlaneCount(series) > ndx) {
Time deltaT = retrieve.getPlaneDeltaT(series, ndx);
if (deltaT != null) {
stamp = (long) (deltaT.value(UNITS.SECOND).doubleValue() * 1000);
}
}
stamp += DateTools.getTime(date, DateTools.ISO8601_FORMAT);
}
if (zCount > 1) {
if (first) first = false;
else sb.append("; ");
sb.append("z:");
sb.append(zct[0] + 1);
sb.append("/");
sb.append(r.getSizeZ());
else {
stamp = System.currentTimeMillis();
}
if (tCount > 1) {
if (first) first = false;
else sb.append("; ");
sb.append("t:");
sb.append(zct[2] + 1);
sb.append("/");
sb.append(r.getSizeT());
date = DateTools.convertDate(stamp, (int) DateTools.UNIX_EPOCH);

filename = filename.replaceAll(FormatTools.TIMESTAMP, date);
return filename;
}

private static String[] substringsBetween(String str, String open, String close) {
if (str == null || open == null || close == null || open.length() == 0 || close.length() == 0) {
return null;
}
int strLen = str.length();
if (strLen == 0) {
return new String [0];
}
// put image name at the end, in case it is long
String imageName = meta.getImageName(series);
if (imageName != null && !imageName.trim().equals("")) {
sb.append(" - ");
sb.append(imageName);
int closeLen = close.length();
int openLen = open.length();
List<String> list = new ArrayList<String>();
int pos = 0;
while (pos < (strLen - closeLen)) {
int start = str.indexOf(open, pos);
if (start < 0) {
break;
}
start += openLen;
int end = str.indexOf(close, start);
if (end < 0) {
break;
}
list.add(str.substring(start, end));
pos = end + closeLen;
}
return sb.toString();
if (list.isEmpty()) {
return null;
}
return (String[]) list.toArray(new String [list.size()]);
}

private static void saveLUTs(ImagePlus imp, List<LUT> luts) {
Expand Down
11 changes: 11 additions & 0 deletions components/bio-formats-plugins/src/loci/plugins/util/LociPrefs.java
View file
Open in desktop
Expand Up @@ -30,6 +30,7 @@
import ij.Prefs;

import loci.formats.ClassList;
import loci.formats.FormatTools;
import loci.formats.IFormatReader;
import loci.formats.ImageReader;
import loci.formats.in.CellSensReader;
Expand Down Expand Up @@ -68,6 +69,8 @@ public final class LociPrefs {
"bioformats.nativend2.chunkmap";
public static final String PREF_LEICA_LIF_PHYSICAL_SIZE =
"bioformats.leicalif.physicalsize.compatibility";
public static final String PREF_SLICE_LABEL_PATTERN = "bioformats.sliceLabelPattern";
public static final String PREF_SLICE_LABEL_BASE_INDEX = "bioformats.sliceLabelBaseIndex";
public static final String PREF_CELLSENS_FAIL =
"bioformats.cellsens.fail_on_missing_ets";

Expand Down Expand Up @@ -195,6 +198,14 @@ public static boolean isLeicaLIFPhysicalSizeBackwardsCompatible() {
LIFReader.OLD_PHYSICAL_SIZE_DEFAULT);
}

public static String getSliceLabelPattern() {
return Prefs.get(PREF_SLICE_LABEL_PATTERN, "%c%z%t- %n");
}

public static int getSliceLabelBaseIndex() {
return Prefs.getInt(PREF_SLICE_LABEL_BASE_INDEX, 1);
}

public static boolean isCellsensFailOnMissing() {
return Prefs.get(PREF_CELLSENS_FAIL, CellSensReader.FAIL_ON_MISSING_DEFAULT);
}
Expand Down