diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/data/CameraData.java b/src/main/java/org/micromanager/lightsheetmanager/api/data/CameraData.java index e3dcff72..741c0164 100644 --- a/src/main/java/org/micromanager/lightsheetmanager/api/data/CameraData.java +++ b/src/main/java/org/micromanager/lightsheetmanager/api/data/CameraData.java @@ -3,28 +3,28 @@ // Used to track imaging camera order for simultaneous imaging cameras. public class CameraData { - private String name_; - private boolean isActive_; + private String name; + private boolean isActive; public CameraData(final String name, final boolean isActive) { - name_ = name; - isActive_ = isActive; + this.name = name; + this.isActive = isActive; } public String name() { - return name_; + return name; } public void name(final String name) { - name_ = name; + this.name = name; } public boolean isActive() { - return isActive_; + return isActive; } public void isActive(final boolean isActive) { - isActive_ = isActive; + this.isActive = isActive; } public static boolean isCameraActive(final CameraData[] cameras, final String cameraName) { @@ -38,7 +38,7 @@ public static boolean isCameraActive(final CameraData[] cameras, final String ca @Override public String toString() { - return String.format("%s[name=%s]", getClass().getSimpleName(), name_); + return String.format("%s[name=%s]", getClass().getSimpleName(), name); } } diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/internal/BaseAcquisitionSettings.java b/src/main/java/org/micromanager/lightsheetmanager/api/internal/BaseAcquisitionSettings.java index 0828785d..8b50a25b 100644 --- a/src/main/java/org/micromanager/lightsheetmanager/api/internal/BaseAcquisitionSettings.java +++ b/src/main/java/org/micromanager/lightsheetmanager/api/internal/BaseAcquisitionSettings.java @@ -23,43 +23,43 @@ public abstract class BaseAcquisitionSettings implements AcquisitionSettings { public abstract static class Builder> implements AcquisitionSettings.Builder { - private String saveDirectory_ = System.getProperty("user.home"); - private String saveNamePrefix_ = "Experiment"; - private boolean saveDuringAcq_ = false; - private boolean demoMode_ = false; - private SaveMode saveMode_ = SaveMode.ND_TIFF; - private CameraMode cameraMode_ = CameraMode.EDGE; - private CameraData[] imagingCameraOrder_ = {}; - private boolean useMultiplePositions_ = false; - private int postMoveDelay_ = 0; - private boolean useTimePoints_ = false; - private int numTimePoints_ = 1; - private double timePointIntervalSec_ = 0.0; - private AcquisitionMode acquisitionMode_ = AcquisitionMode.NO_SCAN; - - private DefaultAutofocusSettings.Builder afBuilder_ = DefaultAutofocusSettings.builder(); - private ChannelSettings.Builder channelBuilder_ = DefaultChannelSettings.builder(); + private String saveDirectory = System.getProperty("user.home"); + private String saveNamePrefix = "Experiment"; + private boolean saveDuringAcq = false; + private boolean demoMode = false; + private SaveMode saveMode = SaveMode.ND_TIFF; + private CameraMode cameraMode = CameraMode.EDGE; + private CameraData[] imagingCameraOrder = {}; + private boolean useMultiplePositions = false; + private int postMoveDelay = 0; + private boolean useTimePoints = false; + private int numTimePoints = 1; + private double timePointIntervalSec = 0.0; + private AcquisitionMode acquisitionMode = AcquisitionMode.NO_SCAN; + + private DefaultAutofocusSettings.Builder afBuilder = DefaultAutofocusSettings.builder(); + private ChannelSettings.Builder channelBuilder = DefaultChannelSettings.builder(); private VolumeSettings.Builder volumeBuilder_ = DefaultVolumeSettings.builder(); public Builder() { } public Builder(final AcquisitionSettings settings) { - saveDirectory_ = settings.saveDirectory(); - saveNamePrefix_ = settings.saveNamePrefix(); - saveDuringAcq_ = settings.isSavingImagesDuringAcquisition(); - demoMode_ = settings.demoMode(); - saveMode_ = settings.saveMode(); - cameraMode_ = settings.cameraMode(); - imagingCameraOrder_ = settings.imagingCameraOrder(); - useMultiplePositions_ = settings.isUsingMultiplePositions(); - postMoveDelay_ = settings.postMoveDelay(); - useTimePoints_ = settings.isUsingTimePoints(); - numTimePoints_ = settings.numTimePoints(); - timePointIntervalSec_ = settings.timePointIntervalSec(); - acquisitionMode_ = settings.acquisitionMode(); - afBuilder_ = settings.autofocus().copyBuilder(); - channelBuilder_ = settings.channels().copyBuilder(); + saveDirectory = settings.saveDirectory(); + saveNamePrefix = settings.saveNamePrefix(); + saveDuringAcq = settings.isSavingImagesDuringAcquisition(); + demoMode = settings.demoMode(); + saveMode = settings.saveMode(); + cameraMode = settings.cameraMode(); + imagingCameraOrder = settings.imagingCameraOrder(); + useMultiplePositions = settings.isUsingMultiplePositions(); + postMoveDelay = settings.postMoveDelay(); + useTimePoints = settings.isUsingTimePoints(); + numTimePoints = settings.numTimePoints(); + timePointIntervalSec = settings.timePointIntervalSec(); + acquisitionMode = settings.acquisitionMode(); + afBuilder = settings.autofocus().copyBuilder(); + channelBuilder = settings.channels().copyBuilder(); volumeBuilder_ = settings.volume().copyBuilder(); } @@ -70,7 +70,7 @@ public Builder(final AcquisitionSettings settings) { */ @Override public T saveDirectory(final String directory) { - saveDirectory_ = directory; + saveDirectory = directory; return self(); } @@ -81,7 +81,7 @@ public T saveDirectory(final String directory) { */ @Override public T saveNamePrefix(final String name) { - saveNamePrefix_ = name; + saveNamePrefix = name; return self(); } @@ -92,7 +92,7 @@ public T saveNamePrefix(final String name) { */ @Override public T saveImagesDuringAcquisition(final boolean state) { - saveDuringAcq_ = state; + saveDuringAcq = state; return self(); } @@ -103,7 +103,7 @@ public T saveImagesDuringAcquisition(final boolean state) { */ @Override public T demoMode(final boolean state) { - demoMode_ = state; + demoMode = state; return self(); } @@ -114,7 +114,7 @@ public T demoMode(final boolean state) { */ @Override public T saveMode(final SaveMode saveMode) { - saveMode_ = saveMode; + this.saveMode = saveMode; return self(); } @@ -126,7 +126,7 @@ public T saveMode(final SaveMode saveMode) { */ @Override public T cameraMode(final CameraMode mode) { - cameraMode_ = mode; + cameraMode = mode; return self(); } @@ -138,7 +138,7 @@ public T cameraMode(final CameraMode mode) { */ @Override public T imagingCameraOrder(final CameraData[] order) { - imagingCameraOrder_ = order; + imagingCameraOrder = order; return self(); } @@ -150,7 +150,7 @@ public T imagingCameraOrder(final CameraData[] order) { */ @Override public T useMultiplePositions(final boolean state) { - useMultiplePositions_ = state; + useMultiplePositions = state; return self(); } @@ -162,7 +162,7 @@ public T useMultiplePositions(final boolean state) { */ @Override public T postMoveDelay(final int postMoveDelay) { - postMoveDelay_ = postMoveDelay; + this.postMoveDelay = postMoveDelay; return self(); } @@ -174,7 +174,7 @@ public T postMoveDelay(final int postMoveDelay) { */ @Override public T useTimePoints(final boolean state) { - useTimePoints_ = state; + useTimePoints = state; return self(); } @@ -186,7 +186,7 @@ public T useTimePoints(final boolean state) { */ @Override public T numTimePoints(final int numTimePoints) { - numTimePoints_ = numTimePoints; + this.numTimePoints = numTimePoints; return self(); } @@ -198,7 +198,7 @@ public T numTimePoints(final int numTimePoints) { */ @Override public T timePointIntervalSec(final double timePointIntervalSec) { - timePointIntervalSec_ = timePointIntervalSec; + this.timePointIntervalSec = timePointIntervalSec; return self(); } @@ -213,7 +213,7 @@ public T timePointIntervalSec(final double timePointIntervalSec) { */ @Override public T acquisitionMode(final AcquisitionMode mode) { - acquisitionMode_ = mode; + acquisitionMode = mode; final boolean scanEnabled = (mode == AcquisitionMode.STAGE_SCAN || mode == AcquisitionMode.STAGE_SCAN_INTERLEAVED || mode == AcquisitionMode.STAGE_SCAN_UNIDIRECTIONAL); @@ -232,11 +232,11 @@ public T acquisitionMode(final AcquisitionMode mode) { @Override public DefaultAutofocusSettings.Builder autofocusBuilder() { - return afBuilder_; + return afBuilder; } public ChannelSettings.Builder channelBuilder() { - return channelBuilder_; + return channelBuilder; } public VolumeSettings.Builder volumeBuilder() { @@ -266,23 +266,23 @@ public VolumeSettings.Builder volumeBuilder() { // ); // } - private final String saveNamePrefix_; - private final String saveDirectory_; - private final boolean saveDuringAcq_; - private final boolean demoMode_; - private final SaveMode saveMode_; - private final CameraMode cameraMode_; - private final CameraData[] imagingCameraOrder_; - private final boolean useMultiplePositions_; - private final int postMoveDelay_; - private final boolean useTimePoints_; - private final int numTimePoints_; - private final double timePointIntervalSec_; - private final AcquisitionMode acquisitionMode_; - - private final DefaultAutofocusSettings autofocus_; - private final ChannelSettings channels_; - private final VolumeSettings volume_; + private final String saveNamePrefix; + private final String saveDirectory; + private final boolean saveDuringAcq; + private final boolean demoMode; + private final SaveMode saveMode; + private final CameraMode cameraMode; + private final CameraData[] imagingCameraOrder; + private final boolean useMultiplePositions; + private final int postMoveDelay; + private final boolean useTimePoints; + private final int numTimePoints; + private final double timePointIntervalSec; + private final AcquisitionMode acquisitionMode; + + private final DefaultAutofocusSettings autofocus; + private final ChannelSettings channels; + private final VolumeSettings volume; // public DefaultAcquisitionSettings() { // saveNamePrefix_ = ""; @@ -291,22 +291,22 @@ public VolumeSettings.Builder volumeBuilder() { // } protected BaseAcquisitionSettings(Builder builder) { - saveDirectory_ = builder.saveDirectory_; - saveNamePrefix_ = builder.saveNamePrefix_; - saveDuringAcq_ = builder.saveDuringAcq_; - demoMode_ = builder.demoMode_; - saveMode_ = builder.saveMode_; - cameraMode_ = builder.cameraMode_; - imagingCameraOrder_ = builder.imagingCameraOrder_.clone(); - useMultiplePositions_ = builder.useMultiplePositions_; - postMoveDelay_ = builder.postMoveDelay_; - useTimePoints_ = builder.useTimePoints_; - numTimePoints_ = builder.numTimePoints_; - timePointIntervalSec_ = builder.timePointIntervalSec_; - acquisitionMode_ = builder.acquisitionMode_; - autofocus_ = builder.afBuilder_.build(); - channels_ = builder.channelBuilder_.build(); - volume_ = builder.volumeBuilder_.build(); + saveDirectory = builder.saveDirectory; + saveNamePrefix = builder.saveNamePrefix; + saveDuringAcq = builder.saveDuringAcq; + demoMode = builder.demoMode; + saveMode = builder.saveMode; + cameraMode = builder.cameraMode; + imagingCameraOrder = builder.imagingCameraOrder.clone(); + useMultiplePositions = builder.useMultiplePositions; + postMoveDelay = builder.postMoveDelay; + useTimePoints = builder.useTimePoints; + numTimePoints = builder.numTimePoints; + timePointIntervalSec = builder.timePointIntervalSec; + acquisitionMode = builder.acquisitionMode; + autofocus = builder.afBuilder.build(); + channels = builder.channelBuilder.build(); + volume = builder.volumeBuilder_.build(); } /** @@ -316,7 +316,7 @@ protected BaseAcquisitionSettings(Builder builder) { */ @Override public String saveNamePrefix() { - return saveNamePrefix_; + return saveNamePrefix; } /** @@ -326,7 +326,7 @@ public String saveNamePrefix() { */ @Override public String saveDirectory() { - return saveDirectory_; + return saveDirectory; } /** @@ -336,7 +336,7 @@ public String saveDirectory() { */ @Override public boolean isSavingImagesDuringAcquisition() { - return saveDuringAcq_; + return saveDuringAcq; } /** @@ -346,7 +346,7 @@ public boolean isSavingImagesDuringAcquisition() { */ @Override public boolean demoMode() { - return demoMode_; + return demoMode; } /** @@ -356,7 +356,7 @@ public boolean demoMode() { */ @Override public SaveMode saveMode() { - return saveMode_; + return saveMode; } /** @@ -366,7 +366,7 @@ public SaveMode saveMode() { */ @Override public CameraMode cameraMode() { - return cameraMode_; + return cameraMode; } /** @@ -376,7 +376,7 @@ public CameraMode cameraMode() { */ @Override public CameraData[] imagingCameraOrder() { - return imagingCameraOrder_; + return imagingCameraOrder; } /** @@ -386,7 +386,7 @@ public CameraData[] imagingCameraOrder() { */ @Override public boolean isUsingMultiplePositions() { - return useMultiplePositions_; + return useMultiplePositions; } /** @@ -396,7 +396,7 @@ public boolean isUsingMultiplePositions() { */ @Override public int postMoveDelay() { - return postMoveDelay_; + return postMoveDelay; } /** @@ -406,7 +406,7 @@ public int postMoveDelay() { */ @Override public boolean isUsingTimePoints() { - return useTimePoints_; + return useTimePoints; } /** @@ -416,7 +416,7 @@ public boolean isUsingTimePoints() { */ @Override public int numTimePoints() { - return numTimePoints_; + return numTimePoints; } /** @@ -426,7 +426,7 @@ public int numTimePoints() { */ @Override public double timePointIntervalSec() { - return timePointIntervalSec_; + return timePointIntervalSec; } /** @@ -436,7 +436,7 @@ public double timePointIntervalSec() { */ @Override public AcquisitionMode acquisitionMode() { - return acquisitionMode_; + return acquisitionMode; } /** @@ -446,7 +446,7 @@ public AcquisitionMode acquisitionMode() { */ @Override public DefaultAutofocusSettings autofocus() { - return autofocus_; + return autofocus; } /** @@ -456,7 +456,7 @@ public DefaultAutofocusSettings autofocus() { */ @Override public ChannelSettings channels() { - return channels_; + return channels; } /** @@ -466,14 +466,14 @@ public ChannelSettings channels() { */ @Override public VolumeSettings volume() { - return volume_; + return volume; } @Override public String toString() { return String.format( "%s[saveDirectory=%s, saveNamePrefix=%s, saveDuringAcq=%s, demoMode=%s, saveMode=%s]", - getClass().getSimpleName(), saveDirectory_, saveNamePrefix_, saveDuringAcq_, demoMode_, saveMode_ + getClass().getSimpleName(), saveDirectory, saveNamePrefix, saveDuringAcq, demoMode, saveMode ); } diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultAutofocusSettings.java b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultAutofocusSettings.java index e7b9bd20..30e35db8 100644 --- a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultAutofocusSettings.java +++ b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultAutofocusSettings.java @@ -8,24 +8,24 @@ public class DefaultAutofocusSettings implements AutofocusSettings { - private final boolean enabled_; - private final int numImages_; - private final double stepSizeUm_; - private final boolean showImages_; - private final boolean showGraph_; - private final AutofocusMode mode_; - private final AutofocusType scoringMethod_; - private final String channel_; + private final boolean enabled; + private final int numImages; + private final double stepSizeUm; + private final boolean showImages; + private final boolean showGraph; + private final AutofocusMode mode; + private final AutofocusType scoringMethod; + private final String channel; private DefaultAutofocusSettings(Builder builder) { - enabled_ = builder.enabled_; - numImages_ = builder.numImages_; - stepSizeUm_ = builder.stepSizeUm_; - showImages_ = builder.showImages_; - showGraph_ = builder.showGraph_; - mode_ = builder.mode_; - scoringMethod_ = builder.scoringMethod_; - channel_ = builder.channel_; + enabled = builder.enabled; + numImages = builder.numImages; + stepSizeUm = builder.stepSizeUm; + showImages = builder.showImages; + showGraph = builder.showGraph; + mode = builder.mode; + scoringMethod = builder.scoringMethod; + channel = builder.channel; } public static Builder builder() { @@ -44,7 +44,7 @@ public Builder copyBuilder() { @Override public boolean enabled() { - return enabled_; + return enabled; } /** @@ -54,7 +54,7 @@ public boolean enabled() { */ @Override public int numImages() { - return numImages_; + return numImages; } /** @@ -64,7 +64,7 @@ public int numImages() { */ @Override public double stepSizeUm() { - return stepSizeUm_; + return stepSizeUm; } /** @@ -74,7 +74,7 @@ public double stepSizeUm() { */ @Override public AutofocusMode mode() { - return mode_; + return mode; } /** @@ -83,7 +83,7 @@ public AutofocusMode mode() { * @return {@code true} if displaying images */ public boolean showImages() { - return showImages_; + return showImages; } /** @@ -92,7 +92,7 @@ public boolean showImages() { * @return {@code true} if displaying the graph */ public boolean showGraph() { - return showGraph_; + return showGraph; } /** @@ -102,7 +102,7 @@ public boolean showGraph() { */ @Override public AutofocusType scoringMethod() { - return scoringMethod_; + return scoringMethod; } /** @@ -112,7 +112,7 @@ public AutofocusType scoringMethod() { */ @Override public String channel() { - return channel_; + return channel; } @Override @@ -124,20 +124,20 @@ public boolean equals(Object obj) { return false; } DefaultAutofocusSettings other = (DefaultAutofocusSettings) obj; - return enabled_ == other.enabled_ && - numImages_ == other.numImages_ && - Double.compare(stepSizeUm_, other.stepSizeUm_) == 0 && - showImages_ == other.showImages_ && - showGraph_ == other.showGraph_ && - mode_ == other.mode_ && - scoringMethod_ == other.scoringMethod_ && - channel_.equals(other.channel_); + return enabled == other.enabled && + numImages == other.numImages && + Double.compare(stepSizeUm, other.stepSizeUm) == 0 && + showImages == other.showImages && + showGraph == other.showGraph && + mode == other.mode && + scoringMethod == other.scoringMethod && + channel.equals(other.channel); } @Override public int hashCode() { - return Objects.hash(enabled_, numImages_, stepSizeUm_, - showImages_, showGraph_, mode_, scoringMethod_, channel_); + return Objects.hash(enabled, numImages, stepSizeUm, + showImages, showGraph, mode, scoringMethod, channel); } @Override @@ -145,37 +145,37 @@ public String toString() { return String.format("%s[enabled=%s, numImages=%s, stepSizeUm=%s, " + "showImages=%s, showGraph=%s, mode=%s, scoringMethod=%s, channel=%s]", getClass().getSimpleName(), - enabled_, numImages_, stepSizeUm_, showImages_, showGraph_, mode_, scoringMethod_, channel_); + enabled, numImages, stepSizeUm, showImages, showGraph, mode, scoringMethod, channel); } public static class Builder implements AutofocusSettings.Builder { - private boolean enabled_ = false; - private int numImages_ = 10; - private double stepSizeUm_ = 1.0; - private boolean showImages_ = false; - private boolean showGraph_ = false; - private AutofocusMode mode_ = AutofocusMode.FIXED_PIEZO_SWEEP_SLICE; - private AutofocusType scoringMethod_ = AutofocusType.VOLATH5; - private String channel_ = ""; + private boolean enabled = false; + private int numImages = 10; + private double stepSizeUm = 1.0; + private boolean showImages = false; + private boolean showGraph = false; + private AutofocusMode mode = AutofocusMode.FIXED_PIEZO_SWEEP_SLICE; + private AutofocusType scoringMethod = AutofocusType.VOLATH5; + private String channel = ""; private Builder() { } private Builder(final AutofocusSettings settings) { - enabled_ = settings.enabled(); - numImages_ = settings.numImages(); - stepSizeUm_ = settings.stepSizeUm(); - showImages_ = settings.showImages(); - showGraph_ = settings.showGraph(); - mode_ = settings.mode(); - scoringMethod_ = settings.scoringMethod(); - channel_ = settings.channel(); + enabled = settings.enabled(); + numImages = settings.numImages(); + stepSizeUm = settings.stepSizeUm(); + showImages = settings.showImages(); + showGraph = settings.showGraph(); + mode = settings.mode(); + scoringMethod = settings.scoringMethod(); + channel = settings.channel(); } @Override public Builder enabled(final boolean state) { - enabled_ = state; + enabled = state; return this; } @@ -186,7 +186,7 @@ public Builder enabled(final boolean state) { */ @Override public Builder numImages(final int numImages) { - numImages_ = numImages; + this.numImages = numImages; return this; } @@ -197,7 +197,7 @@ public Builder numImages(final int numImages) { */ @Override public Builder stepSizeUm(final double stepSize) { - stepSizeUm_ = stepSize; + stepSizeUm = stepSize; return this; } @@ -208,7 +208,7 @@ public Builder stepSizeUm(final double stepSize) { */ @Override public Builder showImages(boolean state) { - showImages_ = state; + showImages = state; return this; } @@ -219,7 +219,7 @@ public Builder showImages(boolean state) { */ @Override public Builder showGraph(boolean state) { - showGraph_ = state; + showGraph = state; return this; } @@ -230,7 +230,7 @@ public Builder showGraph(boolean state) { */ @Override public Builder mode(final AutofocusMode mode) { - mode_ = mode; + this.mode = mode; return this; } @@ -241,7 +241,7 @@ public Builder mode(final AutofocusMode mode) { */ @Override public Builder scoringMethod(final AutofocusType type) { - scoringMethod_ = type; + scoringMethod = type; return this; } @@ -252,7 +252,7 @@ public Builder scoringMethod(final AutofocusType type) { */ @Override public Builder channel(final String channel) { - channel_ = channel; + this.channel = channel; return this; } diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultChannelSettings.java b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultChannelSettings.java index 4495f474..03cdf450 100644 --- a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultChannelSettings.java +++ b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultChannelSettings.java @@ -12,19 +12,19 @@ public class DefaultChannelSettings implements ChannelSettings { - private final boolean enabled_; - private final ChannelMode mode_; - private final String group_; - private final HashMap groups_; + private final boolean enabled; + private final ChannelMode mode; + private final String group; + private final HashMap groups; // default value for when the channel group key is not found private static final ChannelSpec[] EMPTY_CHANNELS = new ChannelSpec[0]; private DefaultChannelSettings(Builder builder) { - enabled_ = builder.enabled_; - mode_ = builder.mode_; - group_ = builder.group_; - groups_ = builder.groups_; + enabled = builder.enabled; + mode = builder.mode; + group = builder.group; + groups = builder.groups; } // Note: used by GSON library for deserialization @@ -53,7 +53,7 @@ public Builder copyBuilder() { */ @Override public boolean enabled() { - return enabled_; + return enabled; } /** @@ -63,7 +63,7 @@ public boolean enabled() { */ @Override public int count() { - if (enabled_) { + if (enabled) { return used().length; } else { return 1; @@ -77,7 +77,7 @@ public int count() { */ @Override public int numGroups() { - return groups_.size(); + return groups.size(); } /** @@ -87,7 +87,7 @@ public int numGroups() { */ @Override public String group() { - return group_; + return group; } /** @@ -97,7 +97,7 @@ public String group() { */ @Override public ChannelMode mode() { - return mode_; + return mode; } /** @@ -107,7 +107,7 @@ public ChannelMode mode() { */ @Override public String[] groupNames() { - return groups_.keySet().toArray(String[]::new); + return groups.keySet().toArray(String[]::new); } /** @@ -117,7 +117,7 @@ public String[] groupNames() { */ @Override public ChannelSpec[] used() { - return Arrays.stream(groups_.getOrDefault(group_, EMPTY_CHANNELS)) + return Arrays.stream(groups.getOrDefault(group, EMPTY_CHANNELS)) .filter(ChannelSpec::useChannel) .toArray(ChannelSpec[]::new); } @@ -129,12 +129,12 @@ public ChannelSpec[] used() { */ @Override public ChannelSpec[] data() { - return groups_.getOrDefault(group_, EMPTY_CHANNELS); + return groups.getOrDefault(group, EMPTY_CHANNELS); } @Override public Map groups() { - return Collections.unmodifiableMap(groups_); + return Collections.unmodifiableMap(groups); } // TODO: add groups_ to toString, equals, and hashCode methods @@ -142,7 +142,7 @@ public Map groups() { @Override public String toString() { return String.format("%s[enabled=%s, group=%s, mode=%s]", - getClass().getSimpleName(), enabled_, group_, mode_); + getClass().getSimpleName(), enabled, group, mode); } @Override @@ -154,62 +154,62 @@ public boolean equals(Object obj) { return false; } DefaultChannelSettings other = (DefaultChannelSettings) obj; - return enabled_ == other.enabled_ - && group_.equals(other.group_) - && mode_ == other.mode_; + return enabled == other.enabled + && group.equals(other.group) + && mode == other.mode; } @Override public int hashCode() { - return Objects.hash(enabled_, group_, mode_); + return Objects.hash(enabled, group, mode); } public static class Builder implements ChannelSettings.Builder { - private boolean enabled_ = false; - private ChannelMode mode_ = ChannelMode.VOLUME; - private String group_ = ""; - private HashMap groups_ = new HashMap<>(); + private boolean enabled = false; + private ChannelMode mode = ChannelMode.VOLUME; + private String group = ""; + private HashMap groups = new HashMap<>(); private Builder() { } public Builder(final ChannelSettings settings) { - enabled_ = settings.enabled(); - mode_ = settings.mode(); - group_ = settings.group(); - groups_ = new HashMap<>(); + enabled = settings.enabled(); + mode = settings.mode(); + group = settings.group(); + groups = new HashMap<>(); // deep copy settings.groups().forEach((name, channels) -> { ChannelSpec[] array = new ChannelSpec[channels.length]; for (int i = 0; i < channels.length; i++) { array[i] = new ChannelSpec(channels[i]); } - groups_.put(name, array); + groups.put(name, array); }); } @Override public Builder enabled(final boolean state) { - enabled_ = state; + enabled = state; return this; } @Override public Builder group(final String group) { - group_ = group; + this.group = group; return this; } @Override public Builder mode(final ChannelMode mode) { - mode_ = mode; + this.mode = mode; return this; } @Override public Builder data(final ChannelSpec[] channels) { - groups_.put(group_, channels); + groups.put(group, channels); return this; } diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSheetCalibration.java b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSheetCalibration.java index fd5dbd1e..ee2134c3 100644 --- a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSheetCalibration.java +++ b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSheetCalibration.java @@ -6,22 +6,22 @@ public class DefaultSheetCalibration implements SheetCalibration { - private final double imagingCenter_; - private final double sheetWidth_; - private final double sheetOffset_; - private final boolean autoSheetWidthEnabled_; - private final double autoSheetWidthPerPixel_; - private final double scanSpeed_; - private final double scanOffset_; + private final double imagingCenter; + private final double sheetWidth; + private final double sheetOffset; + private final boolean autoSheetWidthEnabled; + private final double autoSheetWidthPerPixel; + private final double scanSpeed; + private final double scanOffset; private DefaultSheetCalibration(Builder builder) { - imagingCenter_ = builder.imagingCenter_; - sheetWidth_ = builder.sheetWidth_; - sheetOffset_ = builder.sheetOffset_; - autoSheetWidthEnabled_ = builder.autoSheetWidthEnabled_; - autoSheetWidthPerPixel_ = builder.autoSheetWidthPerPixel_; - scanSpeed_ = builder.scanSpeed_; - scanOffset_ = builder.scanOffset_; + imagingCenter = builder.imagingCenter; + sheetWidth = builder.sheetWidth; + sheetOffset = builder.sheetOffset; + autoSheetWidthEnabled = builder.autoSheetWidthEnabled; + autoSheetWidthPerPixel = builder.autoSheetWidthPerPixel; + scanSpeed = builder.scanSpeed; + scanOffset = builder.scanOffset; } // Note: used by GSON library for deserialization @@ -45,41 +45,41 @@ public Builder copyBuilder() { @Override public double imagingCenter() { - return imagingCenter_; + return imagingCenter; } // standard camera modes @Override public double sheetWidth() { - return sheetWidth_; + return sheetWidth; } @Override public double sheetOffset() { - return sheetOffset_; + return sheetOffset; } @Override public boolean autoSheetWidthEnabled() { - return autoSheetWidthEnabled_; + return autoSheetWidthEnabled; } @Override public double autoSheetWidthPerPixel() { - return autoSheetWidthPerPixel_; + return autoSheetWidthPerPixel; } // virtual slit camera mode @Override public double scanSpeed() { - return scanSpeed_; + return scanSpeed; } @Override public double scanOffset() { - return scanOffset_; + return scanOffset; } @Override @@ -91,19 +91,19 @@ public boolean equals(Object obj) { return false; } DefaultSheetCalibration other = (DefaultSheetCalibration) obj; - return Double.compare(imagingCenter_, other.imagingCenter_) == 0 && - Double.compare(sheetWidth_, other.sheetWidth_) == 0 && - Double.compare(sheetOffset_, other.sheetOffset_) == 0 && - autoSheetWidthEnabled_ == other.autoSheetWidthEnabled_ && - Double.compare(autoSheetWidthPerPixel_, other.autoSheetWidthPerPixel_) == 0 && - Double.compare(scanSpeed_, other.scanSpeed_) == 0 && - Double.compare(scanOffset_, other.scanOffset_) == 0; + return Double.compare(imagingCenter, other.imagingCenter) == 0 && + Double.compare(sheetWidth, other.sheetWidth) == 0 && + Double.compare(sheetOffset, other.sheetOffset) == 0 && + autoSheetWidthEnabled == other.autoSheetWidthEnabled && + Double.compare(autoSheetWidthPerPixel, other.autoSheetWidthPerPixel) == 0 && + Double.compare(scanSpeed, other.scanSpeed) == 0 && + Double.compare(scanOffset, other.scanOffset) == 0; } @Override public int hashCode() { - return Objects.hash(imagingCenter_, sheetWidth_, sheetOffset_, - autoSheetWidthEnabled_, autoSheetWidthPerPixel_, scanSpeed_, scanOffset_); + return Objects.hash(imagingCenter, sheetWidth, sheetOffset, + autoSheetWidthEnabled, autoSheetWidthPerPixel, scanSpeed, scanOffset); } @Override @@ -111,62 +111,62 @@ public String toString() { return String.format("%s[imagingCenter=%s, sheetWidth=%s, sheetOffset=%s, " + "autoSheetWidthEnabled=%s, autoSheetWidthPerPixel=%s, scanSpeed=%s, scanOffset=%s]", getClass().getSimpleName(), - imagingCenter_, sheetWidth_, sheetOffset_, - autoSheetWidthEnabled_, autoSheetWidthPerPixel_, scanSpeed_, scanOffset_); + imagingCenter, sheetWidth, sheetOffset, + autoSheetWidthEnabled, autoSheetWidthPerPixel, scanSpeed, scanOffset); } public static class Builder implements SheetCalibration.Builder { - private double imagingCenter_ = 0.0; - private double sheetWidth_ = 0.0; - private double sheetOffset_ = 0.0; - private boolean autoSheetWidthEnabled_ = false; - private double autoSheetWidthPerPixel_ = 0.0; - private double scanSpeed_ = 0.0; - private double scanOffset_ = 0.0; + private double imagingCenter = 0.0; + private double sheetWidth = 0.0; + private double sheetOffset = 0.0; + private boolean autoSheetWidthEnabled = false; + private double autoSheetWidthPerPixel = 0.0; + private double scanSpeed = 0.0; + private double scanOffset = 0.0; private Builder() { } private Builder(final SheetCalibration settings) { - imagingCenter_ = settings.imagingCenter(); - sheetWidth_ = settings.sheetWidth(); - sheetOffset_ = settings.sheetOffset(); - autoSheetWidthEnabled_ = settings.autoSheetWidthEnabled(); - autoSheetWidthPerPixel_ = settings.autoSheetWidthPerPixel(); - scanSpeed_ = settings.scanSpeed(); - scanOffset_ = settings.scanOffset(); + imagingCenter = settings.imagingCenter(); + sheetWidth = settings.sheetWidth(); + sheetOffset = settings.sheetOffset(); + autoSheetWidthEnabled = settings.autoSheetWidthEnabled(); + autoSheetWidthPerPixel = settings.autoSheetWidthPerPixel(); + scanSpeed = settings.scanSpeed(); + scanOffset = settings.scanOffset(); } // normal camera modes @Override public Builder imagingCenter(double center) { - imagingCenter_ = center; + imagingCenter = center; return this; } @Override public Builder sheetWidth(double width) { - sheetWidth_ = width; + sheetWidth = width; return this; } @Override public Builder sheetOffset(double offset) { - sheetOffset_ = offset; + sheetOffset = offset; return this; } @Override public Builder autoSheetWidthEnabled(boolean state) { - autoSheetWidthEnabled_ = state; + autoSheetWidthEnabled = state; return this; } @Override public Builder autoSheetWidthPerPixel(double widthPerPixel) { - autoSheetWidthPerPixel_ = widthPerPixel; + autoSheetWidthPerPixel = widthPerPixel; return this; } @@ -174,13 +174,13 @@ public Builder autoSheetWidthPerPixel(double widthPerPixel) { @Override public Builder scanSpeed(double speed) { - scanSpeed_ = speed; + scanSpeed = speed; return this; } @Override public Builder scanOffset(double offset) { - scanOffset_ = offset; + scanOffset = offset; return this; } diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSliceCalibration.java b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSliceCalibration.java index 0c99ef39..989e3d08 100644 --- a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSliceCalibration.java +++ b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSliceCalibration.java @@ -6,12 +6,12 @@ public class DefaultSliceCalibration implements SliceCalibration { - private final double slope_; - private final double offset_; + private final double slope; + private final double offset; private DefaultSliceCalibration(Builder builder) { - slope_ = builder.slope_; - offset_ = builder.offset_; + slope = builder.slope; + offset = builder.offset; } // Note: used by GSON library for deserialization @@ -35,12 +35,12 @@ public Builder copyBuilder() { @Override public double slope() { - return slope_; + return slope; } @Override public double offset() { - return offset_; + return offset; } @Override @@ -52,42 +52,43 @@ public boolean equals(Object obj) { return false; } DefaultSliceCalibration other = (DefaultSliceCalibration) obj; - return Double.compare(slope_, other.slope_) == 0 && - Double.compare(offset_, other.offset_) == 0; + return Double.compare(slope, other.slope) == 0 && + Double.compare(offset, other.offset) == 0; } @Override public int hashCode() { - return Objects.hash(slope_, offset_); + return Objects.hash(slope, offset); } @Override public String toString() { return String.format("%s[slope=%s, offset=%s]", - getClass().getSimpleName(), slope_, offset_); + getClass().getSimpleName(), slope, offset); } public static class Builder implements SliceCalibration.Builder { - private double slope_ = 0.0; - private double offset_ = 0.0; + + private double slope = 0.0; + private double offset = 0.0; private Builder() { } private Builder(final SliceCalibration settings) { - slope_ = settings.slope(); - offset_ = settings.offset(); + slope = settings.slope(); + offset = settings.offset(); } @Override public Builder slope(final double slope) { - slope_ = slope; + this.slope = slope; return this; } @Override public Builder offset(final double offset) { - offset_ = offset; + this.offset = offset; return this; } diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSliceSettings.java b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSliceSettings.java index 706f2b2f..930e9df9 100644 --- a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSliceSettings.java +++ b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSliceSettings.java @@ -6,14 +6,14 @@ public class DefaultSliceSettings implements SliceSettings { - private final double period_; - private final double sampleExposure_; - private final boolean periodMinimized_; + private final double period; + private final double sampleExposure; + private final boolean periodMinimized; private DefaultSliceSettings(Builder builder) { - period_ = builder.period_; - sampleExposure_ = builder.sampleExposure_; - periodMinimized_ = builder.periodMinimized_; + period = builder.period; + sampleExposure = builder.sampleExposure; + periodMinimized = builder.periodMinimized; } // Note: used by GSON library for deserialization @@ -37,17 +37,17 @@ public Builder copyBuilder() { @Override public double period() { - return period_; + return period; } @Override public double sampleExposure() { - return sampleExposure_; + return sampleExposure; } @Override public boolean periodMinimized() { - return periodMinimized_; + return periodMinimized; } @Override @@ -59,14 +59,14 @@ public boolean equals(Object obj) { return false; } DefaultSliceSettings other = (DefaultSliceSettings) obj; - return Double.compare(period_, other.period_) == 0 && - Double.compare(sampleExposure_, other.sampleExposure_) == 0 && - periodMinimized_ == other.periodMinimized_; + return Double.compare(period, other.period) == 0 && + Double.compare(sampleExposure, other.sampleExposure) == 0 && + periodMinimized == other.periodMinimized; } @Override public int hashCode() { - return Objects.hash(period_, sampleExposure_, periodMinimized_); + return Objects.hash(period, sampleExposure, periodMinimized); } @Override @@ -74,40 +74,40 @@ public String toString() { return String.format( "%s[period=%s, sampleExposure=%s, periodMinimized=%s]", getClass().getSimpleName(), - period_, sampleExposure_, periodMinimized_ + period, sampleExposure, periodMinimized ); } public static class Builder implements SliceSettings.Builder { - private double period_ = 10.0; - private double sampleExposure_ = 1.0; - private boolean periodMinimized_ = false; + private double period = 10.0; + private double sampleExposure = 1.0; + private boolean periodMinimized = false; private Builder() { } private Builder(final SliceSettings settings) { - period_ = settings.period(); - sampleExposure_ = settings.sampleExposure(); - periodMinimized_ = settings.periodMinimized(); + period = settings.period(); + sampleExposure = settings.sampleExposure(); + periodMinimized = settings.periodMinimized(); } @Override public Builder period(double periodMs) { - period_ = periodMs; + period = periodMs; return this; } @Override public Builder sampleExposure(double exposureMs) { - sampleExposure_ = exposureMs; + sampleExposure = exposureMs; return this; } @Override public Builder periodMinimized(boolean state) { - periodMinimized_ = state; + periodMinimized = state; return this; } diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSliceSettingsLS.java b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSliceSettingsLS.java index ddff878a..71c5193e 100644 --- a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSliceSettingsLS.java +++ b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSliceSettingsLS.java @@ -6,16 +6,16 @@ public class DefaultSliceSettingsLS implements SliceSettingsLightSheet { - private final double scanResetTime_; - private final double scanSettleTime_; - private final double shutterWidth_; - private final double shutterSpeedFactor_; + private final double scanResetTime; + private final double scanSettleTime; + private final double shutterWidth; + private final double shutterSpeedFactor; private DefaultSliceSettingsLS(Builder builder) { - scanResetTime_ = builder.scanResetTime_; - scanSettleTime_ = builder.scanSettleTime_; - shutterWidth_ = builder.shutterWidth_; - shutterSpeedFactor_ = builder.shutterSpeedFactor_; + scanResetTime = builder.scanResetTime; + scanSettleTime = builder.scanSettleTime; + shutterWidth = builder.shutterWidth; + shutterSpeedFactor = builder.shutterSpeedFactor; } public static Builder builder() { @@ -34,22 +34,22 @@ public Builder copyBuilder() { @Override public double scanResetTime() { - return scanResetTime_; + return scanResetTime; } @Override public double scanSettleTime() { - return scanSettleTime_; + return scanSettleTime; } @Override public double shutterWidth() { - return shutterWidth_; + return shutterWidth; } @Override public double shutterSpeedFactor() { - return shutterSpeedFactor_; + return shutterSpeedFactor; } @Override @@ -61,15 +61,15 @@ public boolean equals(Object obj) { return false; } DefaultSliceSettingsLS other = (DefaultSliceSettingsLS) obj; - return Double.compare(scanResetTime_, other.scanResetTime_) == 0 && - Double.compare(scanSettleTime_, other.scanSettleTime_) == 0 && - Double.compare(shutterWidth_, other.shutterWidth_) == 0 && - Double.compare(shutterSpeedFactor_, other.shutterSpeedFactor_) == 0; + return Double.compare(scanResetTime, other.scanResetTime) == 0 && + Double.compare(scanSettleTime, other.scanSettleTime) == 0 && + Double.compare(shutterWidth, other.shutterWidth) == 0 && + Double.compare(shutterSpeedFactor, other.shutterSpeedFactor) == 0; } @Override public int hashCode() { - return Objects.hash(scanResetTime_, scanSettleTime_, shutterWidth_, shutterSpeedFactor_); + return Objects.hash(scanResetTime, scanSettleTime, shutterWidth, shutterSpeedFactor); } @Override @@ -77,48 +77,48 @@ public String toString() { return String.format( "%s[scanResetTime=%s, scanSettleTime=%s, shutterWidth=%s, shutterSpeedFactor=%s]", getClass().getSimpleName(), - scanResetTime_, scanSettleTime_, shutterWidth_, shutterSpeedFactor_ + scanResetTime, scanSettleTime, shutterWidth, shutterSpeedFactor ); } public static class Builder implements SliceSettingsLightSheet.Builder { - private double scanResetTime_ = 3.0; - private double scanSettleTime_ = 1.0; - private double shutterWidth_ = 5.0; - private double shutterSpeedFactor_ = 1.0; + private double scanResetTime = 3.0; + private double scanSettleTime = 1.0; + private double shutterWidth = 5.0; + private double shutterSpeedFactor = 1.0; private Builder() { } private Builder(final SliceSettingsLightSheet settings) { - scanResetTime_ = settings.scanResetTime(); - scanSettleTime_ = settings.scanSettleTime(); - shutterWidth_ = settings.shutterWidth(); - shutterSpeedFactor_ = settings.shutterSpeedFactor(); + scanResetTime = settings.scanResetTime(); + scanSettleTime = settings.scanSettleTime(); + shutterWidth = settings.shutterWidth(); + shutterSpeedFactor = settings.shutterSpeedFactor(); } @Override public Builder shutterWidth(final double um) { - shutterWidth_ = um; + shutterWidth = um; return this; } @Override public Builder shutterSpeedFactor(final double factor) { - shutterSpeedFactor_ = factor; + shutterSpeedFactor = factor; return this; } @Override public Builder scanSettleTime(final double ms) { - scanSettleTime_ = ms; + scanSettleTime = ms; return this; } @Override public Builder scanResetTime(final double ms) { - scanResetTime_ = ms; + scanResetTime = ms; return this; } diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultStageScanSettings.java b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultStageScanSettings.java index a2b55ac7..13002162 100644 --- a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultStageScanSettings.java +++ b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultStageScanSettings.java @@ -6,24 +6,24 @@ public class DefaultStageScanSettings implements StageScanSettings { - private final boolean enabled_; - private final double accelerationFactor_; - private final int overshootDistance_; - private final double retraceSpeed_; - private final double firstViewAngle_; - private final boolean returnToStart_; - private final boolean fromCurrentPosition_; - private final boolean fromNegativeDirection_; + private final boolean enabled; + private final double accelerationFactor; + private final int overshootDistance; + private final double retraceSpeed; + private final double firstViewAngle; + private final boolean returnToStart; + private final boolean fromCurrentPosition; + private final boolean fromNegativeDirection; private DefaultStageScanSettings(Builder builder) { - enabled_ = builder.enabled_; - accelerationFactor_ = builder.accelerationFactor_; - overshootDistance_ = builder.overshootDistance_; - retraceSpeed_ = builder.retraceSpeed_; - firstViewAngle_ = builder.firstViewAngle_; - returnToStart_ = builder.returnToStart_; - fromCurrentPosition_ = builder.fromCurrentPosition_; - fromNegativeDirection_ = builder.fromNegativeDirection_; + enabled = builder.enabled; + accelerationFactor = builder.accelerationFactor; + overshootDistance = builder.overshootDistance; + retraceSpeed = builder.retraceSpeed; + firstViewAngle = builder.firstViewAngle; + returnToStart = builder.returnToStart; + fromCurrentPosition = builder.fromCurrentPosition; + fromNegativeDirection = builder.fromNegativeDirection; } // Note: used by GSON library for deserialization @@ -47,42 +47,42 @@ public StageScanSettings.Builder copyBuilder() { @Override public boolean enabled() { - return enabled_; + return enabled; } @Override public double accelerationFactor() { - return accelerationFactor_; + return accelerationFactor; } @Override public int overshootDistance() { - return overshootDistance_; + return overshootDistance; } @Override public double retraceSpeed() { - return retraceSpeed_; + return retraceSpeed; } @Override public double firstViewAngle() { - return firstViewAngle_; + return firstViewAngle; } @Override public boolean returnToStart() { - return returnToStart_; + return returnToStart; } @Override public boolean fromCurrentPosition() { - return fromCurrentPosition_; + return fromCurrentPosition; } @Override public boolean fromNegativeDirection() { - return fromNegativeDirection_; + return fromNegativeDirection; } @Override @@ -94,27 +94,27 @@ public boolean equals(Object obj) { return false; } DefaultStageScanSettings other = (DefaultStageScanSettings) obj; - return enabled_ == other.enabled_ && - Double.compare(other.accelerationFactor_, accelerationFactor_) == 0 && - overshootDistance_ == other.overshootDistance_ && - Double.compare(other.retraceSpeed_, retraceSpeed_) == 0 && - Double.compare(other.firstViewAngle_, firstViewAngle_) == 0 && - returnToStart_ == other.returnToStart_ && - fromCurrentPosition_ == other.fromCurrentPosition_ && - fromNegativeDirection_ == other.fromNegativeDirection_; + return enabled == other.enabled && + Double.compare(other.accelerationFactor, accelerationFactor) == 0 && + overshootDistance == other.overshootDistance && + Double.compare(other.retraceSpeed, retraceSpeed) == 0 && + Double.compare(other.firstViewAngle, firstViewAngle) == 0 && + returnToStart == other.returnToStart && + fromCurrentPosition == other.fromCurrentPosition && + fromNegativeDirection == other.fromNegativeDirection; } @Override public int hashCode() { return Objects.hash( - enabled_, - accelerationFactor_, - overshootDistance_, - retraceSpeed_, - firstViewAngle_, - returnToStart_, - fromCurrentPosition_, - fromNegativeDirection_ + enabled, + accelerationFactor, + overshootDistance, + retraceSpeed, + firstViewAngle, + returnToStart, + fromCurrentPosition, + fromNegativeDirection ); } @@ -124,81 +124,81 @@ public String toString() { "%s[enabled=%s, accelerationFactor=%s, overshootDistance=%s, retraceSpeed=%s, firstViewAngle=%s, " + "returnToStart=%s, fromCurrentPosition=%s, fromNegativeDirection=%s]", getClass().getSimpleName(), - enabled_, accelerationFactor_, overshootDistance_, retraceSpeed_, firstViewAngle_, - returnToStart_, fromCurrentPosition_, fromNegativeDirection_ + enabled, accelerationFactor, overshootDistance, retraceSpeed, firstViewAngle, + returnToStart, fromCurrentPosition, fromNegativeDirection ); } public static class Builder implements StageScanSettings.Builder { - private boolean enabled_ = false; - private double accelerationFactor_ = 1.0; - private int overshootDistance_ = 0; - private double retraceSpeed_ = 67.0; - private double firstViewAngle_ = 45.0; - private boolean returnToStart_ = false; - private boolean fromCurrentPosition_ = false; - private boolean fromNegativeDirection_ = false; + private boolean enabled = false; + private double accelerationFactor = 1.0; + private int overshootDistance = 0; + private double retraceSpeed = 67.0; + private double firstViewAngle = 45.0; + private boolean returnToStart = false; + private boolean fromCurrentPosition = false; + private boolean fromNegativeDirection = false; private Builder() { } private Builder(StageScanSettings settings) { - enabled_ = settings.enabled(); - accelerationFactor_ = settings.accelerationFactor(); - overshootDistance_ = settings.overshootDistance(); - retraceSpeed_ = settings.retraceSpeed(); - firstViewAngle_ = settings.firstViewAngle(); - returnToStart_ = settings.returnToStart(); - fromCurrentPosition_ = settings.fromCurrentPosition(); - fromNegativeDirection_ = settings.fromNegativeDirection(); + enabled = settings.enabled(); + accelerationFactor = settings.accelerationFactor(); + overshootDistance = settings.overshootDistance(); + retraceSpeed = settings.retraceSpeed(); + firstViewAngle = settings.firstViewAngle(); + returnToStart = settings.returnToStart(); + fromCurrentPosition = settings.fromCurrentPosition(); + fromNegativeDirection = settings.fromNegativeDirection(); } @Override public Builder enabled(final boolean state) { - enabled_ = state; + enabled = state; return this; } @Override public Builder accelerationFactor(final double factor) { - accelerationFactor_ = factor; + accelerationFactor = factor; return this; } @Override public Builder overshootDistance(final int distance) { - overshootDistance_ = distance; + overshootDistance = distance; return this; } @Override public Builder retraceSpeed(final double speed) { - retraceSpeed_ = speed; + retraceSpeed = speed; return this; } @Override public Builder firstViewAngle(final double angle) { - firstViewAngle_ = angle; + firstViewAngle = angle; return this; } @Override public Builder returnToStart(final boolean state) { - returnToStart_ = state; + returnToStart = state; return this; } @Override public Builder fromCurrentPosition(final boolean state) { - fromCurrentPosition_ = state; + fromCurrentPosition = state; return this; } @Override public Builder fromNegativeDirection(final boolean state) { - fromNegativeDirection_ = state; + fromNegativeDirection = state; return this; } diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultTimingSettings.java b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultTimingSettings.java index b8d6cfb6..f3c9c74a 100644 --- a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultTimingSettings.java +++ b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultTimingSettings.java @@ -6,28 +6,28 @@ public class DefaultTimingSettings implements TimingSettings { - private final int scansPerSlice_; - private final double delayBeforeScanMs_; - private final double scanDurationMs_; - private final double delayBeforeLaserMs_; - private final double laserTriggerDurationMs_; - private final double delayBeforeCameraMs_; - private final double cameraTriggerDurationMs_; - private final double cameraExposureMs_; - private final double sliceDurationMs_; - private final boolean alternateScanDirection_; + private final int scansPerSlice; + private final double delayBeforeScanMs; + private final double scanDurationMs; + private final double delayBeforeLaserMs; + private final double laserTriggerDurationMs; + private final double delayBeforeCameraMs; + private final double cameraTriggerDurationMs; + private final double cameraExposureMs; + private final double sliceDurationMs; + private final boolean alternateScanDirection; private DefaultTimingSettings(Builder builder) { - scansPerSlice_ = builder.scansPerSlice_; - delayBeforeScanMs_ = builder.delayBeforeScanMs_; - scanDurationMs_ = builder.scanDurationMs_; - delayBeforeLaserMs_ = builder.delayBeforeLaserMs_; - laserTriggerDurationMs_ = builder.laserTriggerDurationMs_; - delayBeforeCameraMs_ = builder.delayBeforeCameraMs_; - cameraTriggerDurationMs_ = builder.cameraTriggerDurationMs_; - cameraExposureMs_ = builder.cameraExposureMs_; - sliceDurationMs_ = builder.sliceDurationMs(); - alternateScanDirection_ = builder.alternateScanDirection_; + scansPerSlice = builder.scansPerSlice; + delayBeforeScanMs = builder.delayBeforeScanMs; + scanDurationMs = builder.scanDurationMs; + delayBeforeLaserMs = builder.delayBeforeLaserMs; + laserTriggerDurationMs = builder.laserTriggerDurationMs; + delayBeforeCameraMs = builder.delayBeforeCameraMs; + cameraTriggerDurationMs = builder.cameraTriggerDurationMs; + cameraExposureMs = builder.cameraExposureMs; + sliceDurationMs = builder.sliceDurationMs(); + alternateScanDirection = builder.alternateScanDirection; } // Note: used by GSON library for deserialization @@ -61,7 +61,7 @@ public DefaultTimingSettings.Builder copyBuilder() { */ @Override public double delayBeforeScanMs() { - return delayBeforeScanMs_; + return delayBeforeScanMs; } /** @@ -71,7 +71,7 @@ public double delayBeforeScanMs() { */ @Override public int scansPerSlice() { - return scansPerSlice_; + return scansPerSlice; } /** @@ -81,7 +81,7 @@ public int scansPerSlice() { */ @Override public double scanDurationMs() { - return scanDurationMs_; + return scanDurationMs; } /** @@ -91,7 +91,7 @@ public double scanDurationMs() { */ @Override public double delayBeforeLaserMs() { - return delayBeforeLaserMs_; + return delayBeforeLaserMs; } /** @@ -101,7 +101,7 @@ public double delayBeforeLaserMs() { */ @Override public double laserTriggerDurationMs() { - return laserTriggerDurationMs_; + return laserTriggerDurationMs; } /** @@ -111,7 +111,7 @@ public double laserTriggerDurationMs() { */ @Override public double delayBeforeCameraMs() { - return delayBeforeCameraMs_; + return delayBeforeCameraMs; } /** @@ -121,7 +121,7 @@ public double delayBeforeCameraMs() { */ @Override public double cameraTriggerDurationMs() { - return cameraTriggerDurationMs_; + return cameraTriggerDurationMs; } /** @@ -131,7 +131,7 @@ public double cameraTriggerDurationMs() { */ @Override public double cameraExposureMs() { - return cameraExposureMs_; + return cameraExposureMs; } /** @@ -141,7 +141,7 @@ public double cameraExposureMs() { */ @Override public double sliceDurationMs() { - return sliceDurationMs_; + return sliceDurationMs; } /** @@ -151,7 +151,7 @@ public double sliceDurationMs() { */ @Override public boolean useAlternateScanDirection() { - return alternateScanDirection_; + return alternateScanDirection; } @Override @@ -163,23 +163,23 @@ public boolean equals(Object obj) { return false; } DefaultTimingSettings other = (DefaultTimingSettings) obj; - return scansPerSlice_ == other.scansPerSlice_ && - Double.compare(delayBeforeScanMs_, other.delayBeforeScanMs_) == 0 && - Double.compare(scanDurationMs_, other.scanDurationMs_) == 0 && - Double.compare(delayBeforeLaserMs_, other.delayBeforeLaserMs_) == 0 && - Double.compare(laserTriggerDurationMs_, other.laserTriggerDurationMs_) == 0 && - Double.compare(delayBeforeCameraMs_, other.delayBeforeCameraMs_) == 0 && - Double.compare(cameraTriggerDurationMs_, other.cameraTriggerDurationMs_) == 0 && - Double.compare(cameraExposureMs_, other.cameraExposureMs_) == 0 && - Double.compare(sliceDurationMs_, other.sliceDurationMs_) == 0 && - alternateScanDirection_ == other.alternateScanDirection_; + return scansPerSlice == other.scansPerSlice && + Double.compare(delayBeforeScanMs, other.delayBeforeScanMs) == 0 && + Double.compare(scanDurationMs, other.scanDurationMs) == 0 && + Double.compare(delayBeforeLaserMs, other.delayBeforeLaserMs) == 0 && + Double.compare(laserTriggerDurationMs, other.laserTriggerDurationMs) == 0 && + Double.compare(delayBeforeCameraMs, other.delayBeforeCameraMs) == 0 && + Double.compare(cameraTriggerDurationMs, other.cameraTriggerDurationMs) == 0 && + Double.compare(cameraExposureMs, other.cameraExposureMs) == 0 && + Double.compare(sliceDurationMs, other.sliceDurationMs) == 0 && + alternateScanDirection == other.alternateScanDirection; } @Override public int hashCode() { - return Objects.hash(scansPerSlice_, delayBeforeScanMs_, scanDurationMs_, delayBeforeLaserMs_, - laserTriggerDurationMs_, delayBeforeCameraMs_, cameraTriggerDurationMs_, cameraExposureMs_, - sliceDurationMs_, alternateScanDirection_); + return Objects.hash(scansPerSlice, delayBeforeScanMs, scanDurationMs, delayBeforeLaserMs, + laserTriggerDurationMs, delayBeforeCameraMs, cameraTriggerDurationMs, cameraExposureMs, + sliceDurationMs, alternateScanDirection); } @Override @@ -190,37 +190,37 @@ public String toString() { + " delayBeforeCameraMs=%s, cameraTriggerDurationMs=%s," + " cameraExposureMs=%s, sliceDurationMs=%s, alternateScanDirection=%s]", getClass().getSimpleName(), - scansPerSlice_, delayBeforeScanMs_, scanDurationMs_, delayBeforeLaserMs_, - laserTriggerDurationMs_, delayBeforeCameraMs_, cameraTriggerDurationMs_, - cameraExposureMs_, sliceDurationMs_, alternateScanDirection_ + scansPerSlice, delayBeforeScanMs, scanDurationMs, delayBeforeLaserMs, + laserTriggerDurationMs, delayBeforeCameraMs, cameraTriggerDurationMs, + cameraExposureMs, sliceDurationMs, alternateScanDirection ); } public static class Builder implements TimingSettings.Builder { - private int scansPerSlice_ = 1; - private double delayBeforeScanMs_ = 0.0; - private double scanDurationMs_ = 10.0; - private double delayBeforeLaserMs_ = 1.0; - private double laserTriggerDurationMs_ = 1.0; - private double delayBeforeCameraMs_ = 0.0; - private double cameraTriggerDurationMs_ = 1.0; - private double cameraExposureMs_ = 1.0; - private boolean alternateScanDirection_ = false; + private int scansPerSlice = 1; + private double delayBeforeScanMs = 0.0; + private double scanDurationMs = 10.0; + private double delayBeforeLaserMs = 1.0; + private double laserTriggerDurationMs = 1.0; + private double delayBeforeCameraMs = 0.0; + private double cameraTriggerDurationMs = 1.0; + private double cameraExposureMs = 1.0; + private boolean alternateScanDirection = false; private Builder() { } private Builder(final TimingSettings settings) { - scansPerSlice_ = settings.scansPerSlice(); - delayBeforeScanMs_ = settings.delayBeforeScanMs(); - scanDurationMs_ = settings.scanDurationMs(); - delayBeforeLaserMs_ = settings.delayBeforeLaserMs(); - laserTriggerDurationMs_ = settings.laserTriggerDurationMs(); - delayBeforeCameraMs_ = settings.delayBeforeCameraMs(); - cameraTriggerDurationMs_ = settings.cameraTriggerDurationMs(); - cameraExposureMs_ = settings.cameraExposureMs(); - alternateScanDirection_ = settings.useAlternateScanDirection(); + scansPerSlice = settings.scansPerSlice(); + delayBeforeScanMs = settings.delayBeforeScanMs(); + scanDurationMs = settings.scanDurationMs(); + delayBeforeLaserMs = settings.delayBeforeLaserMs(); + laserTriggerDurationMs = settings.laserTriggerDurationMs(); + delayBeforeCameraMs = settings.delayBeforeCameraMs(); + cameraTriggerDurationMs = settings.cameraTriggerDurationMs(); + cameraExposureMs = settings.cameraExposureMs(); + alternateScanDirection = settings.useAlternateScanDirection(); } /** @@ -230,7 +230,7 @@ private Builder(final TimingSettings settings) { */ @Override public Builder delayBeforeScanMs(final double delayMs) { - delayBeforeScanMs_ = delayMs; + delayBeforeScanMs = delayMs; return this; } @@ -241,7 +241,7 @@ public Builder delayBeforeScanMs(final double delayMs) { */ @Override public Builder scansPerSlice(final int numScans) { - scansPerSlice_ = numScans; + scansPerSlice = numScans; return this; } @@ -252,7 +252,7 @@ public Builder scansPerSlice(final int numScans) { */ @Override public Builder scanDurationMs(final double durationMs) { - scanDurationMs_ = durationMs; + scanDurationMs = durationMs; return this; } @@ -263,7 +263,7 @@ public Builder scanDurationMs(final double durationMs) { */ @Override public Builder delayBeforeLaserMs(final double delayMs) { - delayBeforeLaserMs_ = delayMs; + delayBeforeLaserMs = delayMs; return this; } @@ -274,7 +274,7 @@ public Builder delayBeforeLaserMs(final double delayMs) { */ @Override public Builder laserTriggerDurationMs(final double durationMs) { - laserTriggerDurationMs_ = durationMs; + laserTriggerDurationMs = durationMs; return this; } @@ -285,7 +285,7 @@ public Builder laserTriggerDurationMs(final double durationMs) { */ @Override public Builder delayBeforeCameraMs(final double delayMs) { - delayBeforeCameraMs_ = delayMs; + delayBeforeCameraMs = delayMs; return this; } @@ -296,7 +296,7 @@ public Builder delayBeforeCameraMs(final double delayMs) { */ @Override public Builder cameraTriggerDurationMs(final double durationMs) { - cameraTriggerDurationMs_ = durationMs; + cameraTriggerDurationMs = durationMs; return this; } @@ -307,7 +307,7 @@ public Builder cameraTriggerDurationMs(final double durationMs) { */ @Override public Builder cameraExposureMs(final double exposureMs) { - cameraExposureMs_ = exposureMs; + cameraExposureMs = exposureMs; return this; } @@ -318,7 +318,7 @@ public Builder cameraExposureMs(final double exposureMs) { */ @Override public Builder useAlternateScanDirection(final boolean state) { - alternateScanDirection_ = state; + alternateScanDirection = state; return this; } @@ -328,10 +328,10 @@ public Builder useAlternateScanDirection(final boolean state) { @Override public double sliceDurationMs() { return Math.max(Math.max( - delayBeforeScanMs_ + (scanDurationMs_ * scansPerSlice_), // scan time - delayBeforeLaserMs_ + laserTriggerDurationMs_ // laser time + delayBeforeScanMs + (scanDurationMs * scansPerSlice), // scan time + delayBeforeLaserMs + laserTriggerDurationMs // laser time ), - delayBeforeCameraMs_ + cameraTriggerDurationMs_ // camera time + delayBeforeCameraMs + cameraTriggerDurationMs // camera time ); } @@ -342,9 +342,9 @@ public String toString() { "cameraTriggerDurationMs=%s, cameraExposureMs=%s, " + "sliceDurationMs=%s, alternateScanDirection=%s]", getClass().getSimpleName(), - scansPerSlice_, delayBeforeScanMs_, scanDurationMs_, delayBeforeLaserMs_, laserTriggerDurationMs_, - delayBeforeCameraMs_, cameraTriggerDurationMs_, cameraExposureMs_, - sliceDurationMs(), alternateScanDirection_ + scansPerSlice, delayBeforeScanMs, scanDurationMs, delayBeforeLaserMs, laserTriggerDurationMs, + delayBeforeCameraMs, cameraTriggerDurationMs, cameraExposureMs, + sliceDurationMs(), alternateScanDirection ); } diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultVolumeSettings.java b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultVolumeSettings.java index ace4cd0c..882552f8 100644 --- a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultVolumeSettings.java +++ b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultVolumeSettings.java @@ -6,24 +6,24 @@ public class DefaultVolumeSettings implements VolumeSettings { - private final int firstView_; - private final int numViews_; - private final int slicesPerView_; - private final double delayBeforeView_; - private final double sliceStepSize_; - private final double startPosition_; - private final double centerPosition_; - private final double endPosition_; + private final int firstView; + private final int numViews; + private final int slicesPerView; + private final double delayBeforeView; + private final double sliceStepSize; + private final double startPosition; + private final double centerPosition; + private final double endPosition; private DefaultVolumeSettings(Builder builder) { - firstView_ = builder.firstView_; - numViews_ = builder.numViews_; - slicesPerView_ = builder.slicesPerView_; - delayBeforeView_ = builder.delayBeforeView_; - sliceStepSize_ = builder.sliceStepSize_; - startPosition_ = builder.startPosition_; - centerPosition_ = builder.centerPosition_; - endPosition_ = builder.endPosition_; + firstView = builder.firstView; + numViews = builder.numViews; + slicesPerView = builder.slicesPerView; + delayBeforeView = builder.delayBeforeView; + sliceStepSize = builder.sliceStepSize; + startPosition = builder.startPosition; + centerPosition = builder.centerPosition; + endPosition = builder.endPosition; } // Note: used by GSON library for deserialization @@ -47,42 +47,42 @@ public Builder copyBuilder() { @Override public int firstView() { - return firstView_; + return firstView; } @Override public int numViews() { - return numViews_; + return numViews; } @Override public int slicesPerView() { - return slicesPerView_; + return slicesPerView; } @Override public double delayBeforeView() { - return delayBeforeView_; + return delayBeforeView; } @Override public double sliceStepSize() { - return sliceStepSize_; + return sliceStepSize; } @Override public double startPosition() { - return startPosition_; + return startPosition; } @Override public double centerPosition() { - return centerPosition_; + return centerPosition; } @Override public double endPosition() { - return endPosition_; + return endPosition; } @Override @@ -94,20 +94,20 @@ public boolean equals(Object obj) { return false; } DefaultVolumeSettings other = (DefaultVolumeSettings) obj; - return firstView_ == other.firstView_ && - numViews_ == other.numViews_ && - slicesPerView_ == other.slicesPerView_ && - Double.compare(delayBeforeView_, other.delayBeforeView_) == 0 && - Double.compare(sliceStepSize_, other.sliceStepSize_) == 0 && - Double.compare(startPosition_, other.startPosition_) == 0 && - Double.compare(centerPosition_, other.centerPosition_) == 0 && - Double.compare(endPosition_, other.endPosition_) == 0; + return firstView == other.firstView && + numViews == other.numViews && + slicesPerView == other.slicesPerView && + Double.compare(delayBeforeView, other.delayBeforeView) == 0 && + Double.compare(sliceStepSize, other.sliceStepSize) == 0 && + Double.compare(startPosition, other.startPosition) == 0 && + Double.compare(centerPosition, other.centerPosition) == 0 && + Double.compare(endPosition, other.endPosition) == 0; } @Override public int hashCode() { - return Objects.hash(firstView_, numViews_, slicesPerView_, delayBeforeView_, sliceStepSize_, - startPosition_, centerPosition_, endPosition_); + return Objects.hash(firstView, numViews, slicesPerView, delayBeforeView, sliceStepSize, + startPosition, centerPosition, endPosition); } @Override @@ -116,95 +116,95 @@ public String toString() { "%s[firstView=%s, numViews=%s, numSlices=%s, viewDelayMs=%s, stepSizeUm=%s, " + "startPosition=%s, centerPosition=%s, endPosition=%s]", getClass().getSimpleName(), - firstView_, numViews_, slicesPerView_, delayBeforeView_, sliceStepSize_, - startPosition_, centerPosition_, endPosition_ + firstView, numViews, slicesPerView, delayBeforeView, sliceStepSize, + startPosition, centerPosition, endPosition ); } public static class Builder implements VolumeSettings.Builder { - private int firstView_ = 1; - private int numViews_ = 1; - private int slicesPerView_ = 10; - private double delayBeforeView_ = 50; - private double sliceStepSize_ = 0.5; - private double startPosition_ = 0.0; - private double centerPosition_ = 0.0; - private double endPosition_ = 0.0; + private int firstView = 1; + private int numViews = 1; + private int slicesPerView = 10; + private double delayBeforeView = 50; + private double sliceStepSize = 0.5; + private double startPosition = 0.0; + private double centerPosition = 0.0; + private double endPosition = 0.0; private Builder() { } private Builder(final VolumeSettings settings) { - firstView_ = settings.firstView(); - numViews_ = settings.numViews(); - slicesPerView_ = settings.slicesPerView(); - delayBeforeView_ = settings.delayBeforeView(); - sliceStepSize_ = settings.sliceStepSize(); - startPosition_ = settings.startPosition(); - centerPosition_ = settings.centerPosition(); - endPosition_ = settings.endPosition(); + firstView = settings.firstView(); + numViews = settings.numViews(); + slicesPerView = settings.slicesPerView(); + delayBeforeView = settings.delayBeforeView(); + sliceStepSize = settings.sliceStepSize(); + startPosition = settings.startPosition(); + centerPosition = settings.centerPosition(); + endPosition = settings.endPosition(); } @Override public Builder numViews(final int numViews) { - numViews_ = numViews; + this.numViews = numViews; return this; } @Override public Builder firstView(final int firstView) { - firstView_ = firstView; + this.firstView = firstView; return this; } @Override public Builder delayBeforeView(final double viewDelayMs) { - delayBeforeView_ = viewDelayMs; + delayBeforeView = viewDelayMs; return this; } @Override public Builder slicesPerView(final int numSlices) { - slicesPerView_ = numSlices; + slicesPerView = numSlices; return this; } @Override public Builder sliceStepSize(final double stepSizeUm) { - sliceStepSize_ = stepSizeUm; + sliceStepSize = stepSizeUm; return this; } // TODO: what happens when stepSize is not evenly divided by range? maybe just remove? @Override public Builder volumeBounds(final double startPosition, final double endPosition, final double stepSizeUm) { - startPosition_ = startPosition; - endPosition_ = endPosition; - sliceStepSize_ = stepSizeUm; - centerPosition_ = (startPosition + endPosition) / 2.0; - slicesPerView_ = (int)Math.floor((Math.abs(startPosition) + Math.abs(endPosition)) / stepSizeUm); + this.startPosition = startPosition; + this.endPosition = endPosition; + sliceStepSize = stepSizeUm; + centerPosition = (startPosition + endPosition) / 2.0; + slicesPerView = (int)Math.floor((Math.abs(startPosition) + Math.abs(endPosition)) / stepSizeUm); return this; } @Override public Builder volumeBounds(final double startPosition, final double endPosition, final int numSlices) { - startPosition_ = startPosition; - endPosition_ = endPosition; - slicesPerView_ = numSlices; - centerPosition_ = (startPosition + endPosition) / 2.0; - sliceStepSize_ = (Math.abs(startPosition) + Math.abs(endPosition)) / numSlices; + this.startPosition = startPosition; + this.endPosition = endPosition; + slicesPerView = numSlices; + centerPosition = (startPosition + endPosition) / 2.0; + sliceStepSize = (Math.abs(startPosition) + Math.abs(endPosition)) / numSlices; return this; } @Override public Builder volumeBounds(final double centerPosition, final int numSlices, final double stepSizeUm) { final double halfDistance = (stepSizeUm * numSlices) / 2.0; - centerPosition_ = centerPosition; - sliceStepSize_ = stepSizeUm; - slicesPerView_ = numSlices; - startPosition_ = centerPosition - halfDistance; - endPosition_ = centerPosition + halfDistance; + this.centerPosition = centerPosition; + sliceStepSize = stepSizeUm; + slicesPerView = numSlices; + startPosition = centerPosition - halfDistance; + endPosition = centerPosition + halfDistance; return this; } diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DispimAcquisitionSettings.java b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DispimAcquisitionSettings.java index 8bd3f4ba..68cf036e 100644 --- a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DispimAcquisitionSettings.java +++ b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DispimAcquisitionSettings.java @@ -13,33 +13,33 @@ public class DispimAcquisitionSettings extends BaseAcquisitionSettings implements AcquisitionSettingsDispim { - private final TimingSettings timing_; - private final SliceSettings slice_; - private final SliceSettingsLightSheet sliceLS_; - private final StageScanSettings stageScan_; - private final SheetCalibration[] sheetCalibrations_; - private final SliceCalibration[] sliceCalibrations_; + private final TimingSettings timing; + private final SliceSettings slice; + private final SliceSettingsLightSheet sliceLS; + private final StageScanSettings stageScan; + private final SheetCalibration[] sheetCalibrations; + private final SliceCalibration[] sliceCalibrations; - private final boolean useHardwareTimePoints_; - private final boolean useAdvancedTiming_; + private final boolean useHardwareTimePoints; + private final boolean useAdvancedTiming; - private final double liveScanPeriod_; + private final double liveScanPeriod; private DispimAcquisitionSettings(Builder builder) { super(builder); - timing_ = builder.timingBuilder().build(); - slice_ = builder.sliceBuilder().build(); - sliceLS_ = builder.sliceLSBuilder().build(); - stageScan_ = builder.stageScanBuilder().build(); - sheetCalibrations_ = new DefaultSheetCalibration[2]; - sliceCalibrations_ = new DefaultSliceCalibration[2]; // TODO: populate with numViews instead of magic number + timing = builder.timingBuilder().build(); + slice = builder.sliceBuilder().build(); + sliceLS = builder.sliceLSBuilder().build(); + stageScan = builder.stageScanBuilder().build(); + sheetCalibrations = new DefaultSheetCalibration[2]; + sliceCalibrations = new DefaultSliceCalibration[2]; // TODO: populate with numViews instead of magic number for (int i = 0; i < 2; i++) { - sheetCalibrations_[i] = builder.shcb_[i].build(); - sliceCalibrations_[i] = builder.slcb_[i].build(); + sheetCalibrations[i] = builder.shcb[i].build(); + sliceCalibrations[i] = builder.slcb[i].build(); } - useHardwareTimePoints_ = builder.useHardwareTimePoints_; - useAdvancedTiming_ = builder.useAdvancedTiming_; - liveScanPeriod_= builder.liveScanPeriod_; + useHardwareTimePoints = builder.useHardwareTimePoints; + useAdvancedTiming = builder.useAdvancedTiming; + liveScanPeriod = builder.liveScanPeriod; } public static Builder builder() { @@ -58,47 +58,47 @@ public Builder copyBuilder() { @Override public TimingSettings timing() { - return timing_; + return timing; } @Override public SliceSettings slice() { - return slice_; + return slice; } @Override public SliceSettingsLightSheet sliceLS() { - return sliceLS_; + return sliceLS; } @Override public StageScanSettings stageScan() { - return stageScan_; + return stageScan; } @Override public SheetCalibration sheetCalibration(final int view) { - return sheetCalibrations_[view-1]; + return sheetCalibrations[view-1]; } @Override public SliceCalibration sliceCalibration(final int view) { - return sliceCalibrations_[view-1]; + return sliceCalibrations[view-1]; } @Override public boolean isUsingHardwareTimePoints() { - return useHardwareTimePoints_; + return useHardwareTimePoints; } @Override public boolean isUsingAdvancedTiming() { - return useAdvancedTiming_; + return useAdvancedTiming; } @Override public double liveScanPeriod() { - return liveScanPeriod_; + return liveScanPeriod; } // TODO: finish this @@ -112,11 +112,11 @@ public boolean equals(Object obj) { } DispimAcquisitionSettings other = (DispimAcquisitionSettings) obj; return Objects.equals(channels(), other.channels()) && - Objects.equals(timing_, other.timing_) && + Objects.equals(timing, other.timing) && Objects.equals(volume(), other.volume()) && - Objects.equals(slice_, other.slice_) && - Objects.equals(sliceLS_, other.sliceLS_) && - Objects.equals(stageScan_, other.stageScan_) && + Objects.equals(slice, other.slice) && + Objects.equals(sliceLS, other.sliceLS) && + Objects.equals(stageScan, other.stageScan) && // Objects.equals(sheetCalibration_, other.sheetCalibration_) && // Objects.equals(sliceCalibration_, other.sliceCalibration_) && acquisitionMode() == other.acquisitionMode() && @@ -124,8 +124,8 @@ public boolean equals(Object obj) { Arrays.equals(imagingCameraOrder(), other.imagingCameraOrder()) && isUsingTimePoints() == other.isUsingTimePoints() && isUsingMultiplePositions() == other.isUsingMultiplePositions() && - useHardwareTimePoints_ == other.useHardwareTimePoints_ && - useAdvancedTiming_ == other.useAdvancedTiming_ && + useHardwareTimePoints == other.useHardwareTimePoints && + useAdvancedTiming == other.useAdvancedTiming && numTimePoints() == other.numTimePoints() && Double.compare(other.timePointIntervalSec(), timePointIntervalSec()) == 0 && postMoveDelay() == other.postMoveDelay(); @@ -136,11 +136,11 @@ public boolean equals(Object obj) { public int hashCode() { return Objects.hash( channels(), - timing_, + timing, volume(), - slice_, - sliceLS_, - stageScan_, + slice, + sliceLS, + stageScan, // sheetCalibration_, // sliceCalibration_, acquisitionMode(), @@ -148,8 +148,8 @@ public int hashCode() { Arrays.hashCode(imagingCameraOrder()), isUsingTimePoints(), isUsingMultiplePositions(), - useHardwareTimePoints_, - useAdvancedTiming_, + useHardwareTimePoints, + useAdvancedTiming, numTimePoints(), timePointIntervalSec(), postMoveDelay() @@ -160,93 +160,93 @@ public int hashCode() { @Override public String toString() { return String.format("%s[channels=%s, timing=%s, volume=%s, slice=%s, sliceLS=%s, stageScan=%s]", - getClass().getSimpleName(), channels(), timing_, volume(), slice_, sliceLS_, stageScan_); + getClass().getSimpleName(), channels(), timing, volume(), slice, sliceLS, stageScan); } public static class Builder extends BaseAcquisitionSettings.Builder implements AcquisitionSettingsDispim.Builder { - private TimingSettings.Builder timingBuilder_ = DefaultTimingSettings.builder(); - private SliceSettings.Builder sliceBuilder_ = DefaultSliceSettings.builder(); - private SliceSettingsLightSheet.Builder ssbLS_ = DefaultSliceSettingsLS.builder(); // maybe this should be LightSheetSliceSettings? replace ssb_? - private StageScanSettings.Builder stageScanBuilder_ = DefaultStageScanSettings.builder(); - private SheetCalibration.Builder[] shcb_ = new DefaultSheetCalibration.Builder[2]; - private SliceCalibration.Builder[] slcb_ = new DefaultSliceCalibration.Builder[2]; + private TimingSettings.Builder timingBuilder = DefaultTimingSettings.builder(); + private SliceSettings.Builder sliceBuilder = DefaultSliceSettings.builder(); + private SliceSettingsLightSheet.Builder ssbLS = DefaultSliceSettingsLS.builder(); // maybe this should be LightSheetSliceSettings? replace ssb_? + private StageScanSettings.Builder stageScanBuilder = DefaultStageScanSettings.builder(); + private SheetCalibration.Builder[] shcb = new DefaultSheetCalibration.Builder[2]; + private SliceCalibration.Builder[] slcb = new DefaultSliceCalibration.Builder[2]; - private boolean useHardwareTimePoints_ = false; - private boolean useAdvancedTiming_ = false; + private boolean useHardwareTimePoints = false; + private boolean useAdvancedTiming = false; - private double liveScanPeriod_ = 20.0; // TODO: this could go in user settings since it has to do with the live view + private double liveScanPeriod = 20.0; // TODO: this could go in user settings since it has to do with the live view private Builder() { for (int i = 0; i < 2; i++) { - shcb_[i] = DefaultSheetCalibration.builder(); - slcb_[i] = DefaultSliceCalibration.builder(); + shcb[i] = DefaultSheetCalibration.builder(); + slcb[i] = DefaultSliceCalibration.builder(); } } public Builder(final DispimAcquisitionSettings settings) { super(settings); - timingBuilder_ = settings.timing().copyBuilder(); - sliceBuilder_ = settings.slice().copyBuilder(); - ssbLS_ = settings.sliceLS_.copyBuilder(); - stageScanBuilder_ = settings.stageScan().copyBuilder(); + timingBuilder = settings.timing().copyBuilder(); + sliceBuilder = settings.slice().copyBuilder(); + ssbLS = settings.sliceLS.copyBuilder(); + stageScanBuilder = settings.stageScan().copyBuilder(); for (int i = 0; i < 2; i++) { - slcb_[i] = settings.sliceCalibrations_[i].copyBuilder(); - shcb_[i] = settings.sheetCalibrations_[i].copyBuilder(); + slcb[i] = settings.sliceCalibrations[i].copyBuilder(); + shcb[i] = settings.sheetCalibrations[i].copyBuilder(); } - useHardwareTimePoints_ = settings.isUsingHardwareTimePoints(); - useAdvancedTiming_ = settings.isUsingAdvancedTiming(); - liveScanPeriod_ = settings.liveScanPeriod(); + useHardwareTimePoints = settings.isUsingHardwareTimePoints(); + useAdvancedTiming = settings.isUsingAdvancedTiming(); + liveScanPeriod = settings.liveScanPeriod(); } @Override public Builder useHardwareTimePoints(final boolean state) { - useHardwareTimePoints_ = state; + useHardwareTimePoints = state; return this; } @Override public Builder useAdvancedTiming(final boolean state) { - useAdvancedTiming_ = state; + useAdvancedTiming = state; return this; } @Override public Builder liveScanPeriod(double liveScanPeriod) { - liveScanPeriod_ = liveScanPeriod; + this.liveScanPeriod = liveScanPeriod; return this; } // getters for sub-builders public TimingSettings.Builder timingBuilder() { - return timingBuilder_; + return timingBuilder; } public SliceSettings.Builder sliceBuilder() { - return sliceBuilder_; + return sliceBuilder; } public SliceSettingsLightSheet.Builder sliceLSBuilder() { - return ssbLS_; + return ssbLS; } @Override public StageScanSettings.Builder stageScanBuilder() { - return stageScanBuilder_; + return stageScanBuilder; } public SheetCalibration.Builder sheetCalibrationBuilder(final int view) { - return shcb_[view-1]; + return shcb[view-1]; } public SliceCalibration.Builder sliceCalibrationBuilder(final int view) { - return slcb_[view-1]; + return slcb[view-1]; } public void timingBuilder(DefaultTimingSettings.Builder builder) { - timingBuilder_ = builder; + timingBuilder = builder; } @Override @@ -262,7 +262,7 @@ public Builder self() { // TODO: finish toString with rest of properties @Override public String toString() { - return String.format("[timingBuilder_=%s]", timingBuilder_); + return String.format("[timingBuilder_=%s]", timingBuilder); } } diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/internal/ScapeAcquisitionSettings.java b/src/main/java/org/micromanager/lightsheetmanager/api/internal/ScapeAcquisitionSettings.java index e93611e8..d7a352e6 100644 --- a/src/main/java/org/micromanager/lightsheetmanager/api/internal/ScapeAcquisitionSettings.java +++ b/src/main/java/org/micromanager/lightsheetmanager/api/internal/ScapeAcquisitionSettings.java @@ -12,24 +12,24 @@ public class ScapeAcquisitionSettings extends BaseAcquisitionSettings implements AcquisitionSettingsScape { - private final TimingSettings timing_; - private final SliceSettings slice_; - private final StageScanSettings stageScan_; - private final SheetCalibration sheetCalibration_; - private final SliceCalibration sliceCalibration_; + private final TimingSettings timing; + private final SliceSettings slice; + private final StageScanSettings stageScan; + private final SheetCalibration sheetCalibration; + private final SliceCalibration sliceCalibration; - private final boolean useHardwareTimePoints_; - private final boolean useAdvancedTiming_; + private final boolean useHardwareTimePoints; + private final boolean useAdvancedTiming; private ScapeAcquisitionSettings(Builder builder) { super(builder); - timing_ = builder.timingBuilder().build(); - slice_ = builder.sliceBuilder().build(); - stageScan_ = builder.stageScanBuilder().build(); - sheetCalibration_ = builder.sheetCalibrationBuilder().build(); - sliceCalibration_ = builder.sliceCalibrationBuilder().build(); - useHardwareTimePoints_ = builder.useHardwareTimePoints_; - useAdvancedTiming_ = builder.useAdvancedTiming_; + timing = builder.timingBuilder().build(); + slice = builder.sliceBuilder().build(); + stageScan = builder.stageScanBuilder().build(); + sheetCalibration = builder.sheetCalibrationBuilder().build(); + sliceCalibration = builder.sliceCalibrationBuilder().build(); + useHardwareTimePoints = builder.useHardwareTimePoints; + useAdvancedTiming = builder.useAdvancedTiming; } public static Builder builder() { @@ -48,37 +48,37 @@ public Builder copyBuilder() { @Override public TimingSettings timing() { - return timing_; + return timing; } @Override public SliceSettings slice() { - return slice_; + return slice; } @Override public StageScanSettings stageScan() { - return stageScan_; + return stageScan; } @Override public SheetCalibration sheetCalibration() { - return sheetCalibration_; + return sheetCalibration; } @Override public SliceCalibration sliceCalibration() { - return sliceCalibration_; + return sliceCalibration; } @Override public boolean isUsingHardwareTimePoints() { - return useHardwareTimePoints_; + return useHardwareTimePoints; } @Override public boolean isUsingAdvancedTiming() { - return useAdvancedTiming_; + return useAdvancedTiming; } @Override @@ -91,19 +91,19 @@ public boolean equals(Object obj) { } ScapeAcquisitionSettings other = (ScapeAcquisitionSettings) obj; return Objects.equals(channels(), other.channels()) && - Objects.equals(timing_, other.timing_) && + Objects.equals(timing, other.timing) && Objects.equals(volume(), other.volume()) && - Objects.equals(slice_, other.slice_) && - Objects.equals(stageScan_, other.stageScan_) && - Objects.equals(sheetCalibration_, other.sheetCalibration_) && - Objects.equals(sliceCalibration_, other.sliceCalibration_) && + Objects.equals(slice, other.slice) && + Objects.equals(stageScan, other.stageScan) && + Objects.equals(sheetCalibration, other.sheetCalibration) && + Objects.equals(sliceCalibration, other.sliceCalibration) && acquisitionMode() == other.acquisitionMode() && cameraMode() == other.cameraMode() && Arrays.equals(imagingCameraOrder(), other.imagingCameraOrder()) && isUsingTimePoints() == other.isUsingTimePoints() && isUsingMultiplePositions() == other.isUsingMultiplePositions() && - useHardwareTimePoints_ == other.useHardwareTimePoints_ && - useAdvancedTiming_ == other.useAdvancedTiming_ && + useHardwareTimePoints == other.useHardwareTimePoints && + useAdvancedTiming == other.useAdvancedTiming && numTimePoints() == other.numTimePoints() && Double.compare(other.timePointIntervalSec(), timePointIntervalSec()) == 0 && postMoveDelay() == other.postMoveDelay(); @@ -113,19 +113,19 @@ public boolean equals(Object obj) { public int hashCode() { return Objects.hash( channels(), - timing_, + timing, volume(), - slice_, - stageScan_, - sheetCalibration_, - sliceCalibration_, + slice, + stageScan, + sheetCalibration, + sliceCalibration, acquisitionMode(), cameraMode(), Arrays.hashCode(imagingCameraOrder()), isUsingTimePoints(), isUsingMultiplePositions(), - useHardwareTimePoints_, - useAdvancedTiming_, + useHardwareTimePoints, + useAdvancedTiming, numTimePoints(), timePointIntervalSec(), postMoveDelay() @@ -136,72 +136,72 @@ public int hashCode() { @Override public String toString() { return String.format("%s[channels=%s, timing=%s, volume=%s, slice=%s]", - getClass().getSimpleName(), channels(), timing_, volume(), slice_); + getClass().getSimpleName(), channels(), timing, volume(), slice); } public static class Builder extends BaseAcquisitionSettings.Builder implements AcquisitionSettingsScape.Builder { - private TimingSettings.Builder timingBuilder_ = DefaultTimingSettings.builder(); - private SliceSettings.Builder sliceBuilder_ = DefaultSliceSettings.builder(); - private StageScanSettings.Builder stageScanBuilder_ = DefaultStageScanSettings.builder(); - private SheetCalibration.Builder sheetCalibBuilder_ = DefaultSheetCalibration.builder(); - private SliceCalibration.Builder sliceCalibBuilder_ = DefaultSliceCalibration.builder(); + private TimingSettings.Builder timingBuilder = DefaultTimingSettings.builder(); + private SliceSettings.Builder sliceBuilder = DefaultSliceSettings.builder(); + private StageScanSettings.Builder stageScanBuilder = DefaultStageScanSettings.builder(); + private SheetCalibration.Builder sheetCalibBuilder = DefaultSheetCalibration.builder(); + private SliceCalibration.Builder sliceCalibBuilder = DefaultSliceCalibration.builder(); - private boolean useHardwareTimePoints_ = false; - private boolean useAdvancedTiming_ = false; + private boolean useHardwareTimePoints = false; + private boolean useAdvancedTiming = false; private Builder() { } public Builder(final ScapeAcquisitionSettings settings) { super(settings); - timingBuilder_ = settings.timing().copyBuilder(); - sliceBuilder_ = settings.slice().copyBuilder(); - stageScanBuilder_ = settings.stageScan().copyBuilder(); - sheetCalibBuilder_ = settings.sheetCalibration().copyBuilder(); - sliceCalibBuilder_ = settings.sliceCalibration().copyBuilder(); - useHardwareTimePoints_ = settings.isUsingHardwareTimePoints(); - useAdvancedTiming_ = settings.isUsingAdvancedTiming(); + timingBuilder = settings.timing().copyBuilder(); + sliceBuilder = settings.slice().copyBuilder(); + stageScanBuilder = settings.stageScan().copyBuilder(); + sheetCalibBuilder = settings.sheetCalibration().copyBuilder(); + sliceCalibBuilder = settings.sliceCalibration().copyBuilder(); + useHardwareTimePoints = settings.isUsingHardwareTimePoints(); + useAdvancedTiming = settings.isUsingAdvancedTiming(); } @Override public Builder useHardwareTimePoints(final boolean state) { - useHardwareTimePoints_ = state; + useHardwareTimePoints = state; return this; } @Override public Builder useAdvancedTiming(final boolean state) { - useAdvancedTiming_ = state; + useAdvancedTiming = state; return this; } // getters for sub-builders public TimingSettings.Builder timingBuilder() { - return timingBuilder_; + return timingBuilder; } public SliceSettings.Builder sliceBuilder() { - return sliceBuilder_; + return sliceBuilder; } @Override public StageScanSettings.Builder stageScanBuilder() { - return stageScanBuilder_; + return stageScanBuilder; } public SheetCalibration.Builder sheetCalibrationBuilder() { - return sheetCalibBuilder_; + return sheetCalibBuilder; } public SliceCalibration.Builder sliceCalibrationBuilder() { - return sliceCalibBuilder_; + return sliceCalibBuilder; } public void timingBuilder(DefaultTimingSettings.Builder builder) { - timingBuilder_ = builder; + timingBuilder = builder; } @Override @@ -218,7 +218,7 @@ public ScapeAcquisitionSettings build() { @Override public String toString() { return String.format("%s[timingBuilder=%s]", - getClass().getSimpleName(), timingBuilder_); + getClass().getSimpleName(), timingBuilder); } } diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/PluginSettings.java b/src/main/java/org/micromanager/lightsheetmanager/model/PluginSettings.java index 749cd278..8044ead0 100644 --- a/src/main/java/org/micromanager/lightsheetmanager/model/PluginSettings.java +++ b/src/main/java/org/micromanager/lightsheetmanager/model/PluginSettings.java @@ -8,37 +8,37 @@ */ public class PluginSettings { - private boolean isPollingPositions_ = true; + private boolean isPollingPositions = true; // volatile: written from the EDT (Settings tab) and read from the acquisition thread - private volatile boolean acquireFailQuietly_ = false; + private volatile boolean acquireFailQuietly = false; - private final JoystickData joystick_ = new JoystickData(); + private final JoystickData joystick = new JoystickData(); - private final XYZGrid xyzGrid_ = new XYZGrid(); + private final XYZGrid xyzGrid = new XYZGrid(); public JoystickData joystickPanel() { - return joystick_; + return joystick; } public XYZGrid xyzGrid() { - return xyzGrid_; + return xyzGrid; } public void setPollingPositions(final boolean state) { - isPollingPositions_ = state; + isPollingPositions = state; } public boolean isPollingPositions() { - return isPollingPositions_; + return isPollingPositions; } public void setAcquireFailQuietly(final boolean state) { - acquireFailQuietly_ = state; + acquireFailQuietly = state; } public boolean isAcquireFailQuietly() { - return acquireFailQuietly_; + return acquireFailQuietly; } public String toJson() { @@ -56,38 +56,38 @@ public static PluginSettings fromJson(final String json) { public static class JoystickData { - private String joystick_; - private String leftWheel_; - private String rightWheel_; + private String joystick; + private String leftWheel; + private String rightWheel; JoystickData() { - joystick_ = "None"; - leftWheel_ = "None"; - rightWheel_ = "None"; + joystick = "None"; + leftWheel = "None"; + rightWheel = "None"; } public String joystick() { - return joystick_; + return joystick; } public String leftWheel() { - return leftWheel_; + return leftWheel; } public String rightWheel() { - return rightWheel_; + return rightWheel; } public void joystick(final String joystick) { - joystick_ = joystick; + this.joystick = joystick; } public void leftWheel(final String leftWheel) { - leftWheel_ = leftWheel; + this.leftWheel = leftWheel; } public void rightWheel(final String rightWheel) { - rightWheel_ = rightWheel; + this.rightWheel = rightWheel; } } } diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/XYZGrid.java b/src/main/java/org/micromanager/lightsheetmanager/model/XYZGrid.java index a2656c6d..7095d863 100644 --- a/src/main/java/org/micromanager/lightsheetmanager/model/XYZGrid.java +++ b/src/main/java/org/micromanager/lightsheetmanager/model/XYZGrid.java @@ -16,31 +16,31 @@ */ public class XYZGrid { - private boolean useX_; - private boolean useY_; - private boolean useZ_; + private boolean useX; + private boolean useY; + private boolean useZ; - private double startX_; - private double startY_; - private double startZ_; + private double startX; + private double startY; + private double startZ; - private double stopX_; - private double stopY_; - private double stopZ_; + private double stopX; + private double stopY; + private double stopZ; - private double deltaX_; - private double deltaY_; - private double deltaZ_; + private double deltaX; + private double deltaY; + private double deltaZ; - private int overlapPercentYZ_; - private boolean clearPositions_; + private int overlapPercentYZ; + private boolean clearPositions; public XYZGrid() { } private int updateGridXCount() { - double delta = deltaX_; - final double range = startX_ - stopX_; + double delta = deltaX; + final double range = startX - stopX; if (Math.signum(range) != Math.signum(delta) && !NumberUtils.doublesEqual(Math.abs(range), 0.0)) { delta *= -1; @@ -52,8 +52,8 @@ private int updateGridXCount() { } private int updateGridYCount() { - double delta = deltaY_; - final double range = startY_ - stopY_; + double delta = deltaY; + final double range = startY - stopY; if (Math.signum(range) != Math.signum(delta) && !NumberUtils.doublesEqual(Math.abs(range), 0.0)) { delta *= -1; @@ -65,8 +65,8 @@ private int updateGridYCount() { } private int updateGridZCount() { - double delta = deltaZ_; - final double range = startX_ - stopX_; + double delta = deltaZ; + final double range = startX - stopX; if (Math.signum(range) != Math.signum(delta) && !NumberUtils.doublesEqual(Math.abs(range), 0.0)) { delta *= -1; @@ -85,26 +85,26 @@ public void computeGrid(final LightSheetManager model) { XYStage xyStage = model.devices().device("SampleXY"); Stage zStage = model.devices().device("SampleZ"); - final int numX = useX_ ? updateGridXCount() : 1; - final int numY = useY_ ? updateGridYCount() : 1; - final int numZ = useZ_ ? updateGridZCount() : 1; + final int numX = useX ? updateGridXCount() : 1; + final int numY = useY ? updateGridYCount() : 1; + final int numZ = useZ ? updateGridZCount() : 1; // computer the center of each range - double centerX = (startX_ + stopX_) / 2; - double centerY = (startY_ + stopY_) / 2; - double centerZ = (startZ_ + stopZ_) / 2; + double centerX = (startX + stopX) / 2; + double centerY = (startY + stopY) / 2; + double centerZ = (startZ + stopZ) / 2; - double startY = centerY - deltaY_ * (numY-1) / 2; - double startZ = centerZ - deltaZ_ * (numZ-1) / 2; + double startY = centerY - deltaY * (numY-1) / 2; + double startZ = centerZ - deltaZ * (numZ-1) / 2; - if (useX_) { + if (useX) { // TODO: update GUI with values, aliases for asb and vsb? final double speedFactor = GeometryUtils.getStageGeometricSpeedFactor( model.acquisitions().settings().stageScan().firstViewAngle(),true); - model.acquisitions().settingsBuilder().volumeBuilder().sliceStepSize(Math.abs(deltaX_)/speedFactor); + model.acquisitions().settingsBuilder().volumeBuilder().sliceStepSize(Math.abs(deltaX)/speedFactor); model.acquisitions().settingsBuilder().volumeBuilder().slicesPerView(numX); // move to X center if we aren't generating a position list with it - if (!useY_ && !useZ_) { + if (!useY && !useZ) { xyStage.setXYPosition(centerX, xyStage.getXYPosition().y); // TODO: make convenience method? xyStage.waitForDevice(); } @@ -114,14 +114,14 @@ public void computeGrid(final LightSheetManager model) { } // if we aren't using one axis, use the current position instead of GUI position - if (useY_ && !useZ_) { + if (useY && !useZ) { startZ = zStage.getPosition(); } - if (useZ_ && !useY_) { + if (useZ && !useY) { startY = xyStage.getXYPosition().y; // Note: only the Y coordinate } - if (!useY_ && !useZ_ && !clearPositions_) { + if (!useY && !useZ && !clearPositions) { return; // early exit => YZ unused } @@ -135,20 +135,20 @@ public void computeGrid(final LightSheetManager model) { // } // } PositionList positionList = new PositionList(); - if (useY_ || useZ_) { + if (useY || useZ) { for (int iz = 0; iz < numZ; ++iz) { for (int iy = 0; iy < numY; ++iy) { MultiStagePosition msp = new MultiStagePosition(); - if (useY_) { + if (useY) { msp.add(StagePosition.create2D( xyStage.getDeviceName(), centerX, - startY + iy * deltaY_)); + startY + iy * deltaY)); } - if (useZ_) { + if (useZ) { msp.add(StagePosition.create1D( zStage.getDeviceName(), - startZ + iz * deltaZ_)); + startZ + iz * deltaZ)); } msp.setLabel("Pos_" + iz + "_" + iy); positionList.addPosition(msp); @@ -159,115 +159,115 @@ public void computeGrid(final LightSheetManager model) { } public boolean getUseX() { - return useX_; + return useX; } public void setUseX(final boolean state) { - useX_ = state; + useX = state; } public boolean getUseY() { - return useY_; + return useY; } public void setUseY(final boolean state) { - useY_ = state; + useY = state; } public boolean getUseZ() { - return useZ_; + return useZ; } public void setUseZ(final boolean state) { - useZ_ = state; + useZ = state; } public boolean getClearYZ() { - return clearPositions_; + return clearPositions; } public void setClearYZ(final boolean state) { - clearPositions_ = state; + clearPositions = state; } public void setOverlapYZ(final int value) { - overlapPercentYZ_ = value; + overlapPercentYZ = value; } public int getOverlapYZ() { - return overlapPercentYZ_; + return overlapPercentYZ; } public double getStartX() { - return startX_; + return startX; } public void setStartX(final double value) { - startX_ = value; + startX = value; } public double getStopX() { - return stopX_; + return stopX; } public void setStopX(final double value) { - stopX_ = value; + stopX = value; } public double getDeltaX() { - return deltaX_; + return deltaX; } public void setDeltaX(final double value) { - deltaX_ = value; + deltaX = value; } public double getStartY() { - return startY_; + return startY; } public void setStartY(final double value) { - startY_ = value; + startY = value; } public double getStopY() { - return stopY_; + return stopY; } public void setStopY(final double value) { - stopY_ = value; + stopY = value; } public double getDeltaY() { - return deltaY_; + return deltaY; } public void setDeltaY(final double value) { - deltaY_ = value; + deltaY = value; } public double getStartZ() { - return startZ_; + return startZ; } public void setStartZ(final double value) { - startZ_ = value; + startZ = value; } public double getStopZ() { - return stopZ_; + return stopZ; } public void setStopZ(final double value) { - stopZ_ = value; + stopZ = value; } public double getDeltaZ() { - return deltaZ_; + return deltaZ; } public void setDeltaZ(final double value) { - deltaZ_ = value; + deltaZ = value; } }