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Merge pull request #131 from henrypinkard/main
removed storage callbacks in favor of acquisiton notifications. Add a…
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169 changes: 169 additions & 0 deletions
169
java/src/main/java/org/micromanager/ndtiffstorage/NDRAMStorage.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,169 @@ | ||
| package org.micromanager.ndtiffstorage; | ||
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| import java.util.HashMap; | ||
| import java.util.Set; | ||
| import java.util.concurrent.Callable; | ||
| import java.util.concurrent.CompletableFuture; | ||
| import java.util.concurrent.Future; | ||
| import java.util.concurrent.FutureTask; | ||
| import java.util.function.Consumer; | ||
| import mmcorej.TaggedImage; | ||
| import mmcorej.org.json.JSONObject; | ||
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| /** | ||
| * A class that implements the NDTiff API, but holds images in memory | ||
| */ | ||
| public class NDRAMStorage implements NDTiffAPI { | ||
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| private boolean finished_ = false; | ||
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| private HashMap<HashMap<String, Object>, Object> images_ = new HashMap<HashMap<String, Object>, Object>(); | ||
| private HashMap<HashMap<String, Object>, JSONObject> metadata_ = new HashMap<HashMap<String, Object>, JSONObject>(); | ||
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| private boolean rgb_; | ||
| private int bitDepth_; | ||
| private int imageHeight_ = -1; | ||
| private int imageWidth_ = -1; | ||
| private JSONObject displaySettings_; | ||
| private JSONObject summaryMetadata_; | ||
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| public NDRAMStorage(JSONObject summaryMetadata) { | ||
| summaryMetadata_ = summaryMetadata; | ||
| } | ||
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| @Override | ||
| public Future<IndexEntryData> putImage(Object pixels, JSONObject metadata, HashMap<String, Object> axes, | ||
| boolean rgb, int bitDepth, int imageHeight, int imageWidth) { | ||
| images_.put(axes, pixels); | ||
| metadata_.put(axes, metadata); | ||
| rgb_ = rgb; | ||
| bitDepth_ = bitDepth; | ||
| imageHeight_ = imageHeight; | ||
| imageWidth_ = imageWidth; | ||
| Future<IndexEntryData> future = CompletableFuture.completedFuture(null); | ||
| return future; | ||
| } | ||
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| @Override | ||
| public boolean isFinished() { | ||
| return finished_; | ||
| } | ||
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| @Override | ||
| public void checkForWritingException() throws Exception {} | ||
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| @Override | ||
| public void setDisplaySettings(JSONObject displaySettings) { | ||
| displaySettings_ = displaySettings; | ||
| } | ||
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| @Override | ||
| public JSONObject getDisplaySettings() { | ||
| return displaySettings_; | ||
| } | ||
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| @Override | ||
| public JSONObject getSummaryMetadata() { | ||
| return summaryMetadata_; | ||
| } | ||
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| @Override | ||
| public void finishedWriting() { | ||
| finished_ = true; | ||
| } | ||
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| @Override | ||
| public void addImageWrittenListener(ImageWrittenListener iwc) { | ||
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| } | ||
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| @Override | ||
| public String getDiskLocation() { | ||
| return null; | ||
| } | ||
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| @Override | ||
| public void close() { | ||
| images_.clear(); | ||
| metadata_.clear(); | ||
| } | ||
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| @Override | ||
| public void closeAndWait() throws InterruptedException { | ||
| images_.clear(); | ||
| metadata_.clear(); | ||
| } | ||
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| @Override | ||
| public int[] getImageBounds() { | ||
| if (imageHeight_ == -1 || imageWidth_ == -1) { | ||
| return null; // not initialized | ||
| } | ||
| return new int[]{0, 0, imageWidth_, imageHeight_}; | ||
| } | ||
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| @Override | ||
| public TaggedImage getImage(HashMap<String, Object> axes) { | ||
| return new TaggedImage(images_.get(axes), metadata_.get(axes)); | ||
| } | ||
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| @Override | ||
| public TaggedImage getSubImage(HashMap<String, Object> axes, int xOffset, int yOffset, int width, | ||
| int height) { | ||
| TaggedImage ti = getImage(axes); | ||
| if (ti.pix == null) { | ||
| return null; | ||
| } | ||
| if (ti.pix instanceof byte[]) { | ||
| byte[] original = (byte[]) ti.pix; | ||
| byte[] cropped = new byte[width * height]; | ||
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| for (int y = 0; y < height; y++) { | ||
| System.arraycopy(original, ((y + yOffset) * this.imageWidth_) + xOffset, cropped, y * width, width); | ||
| } | ||
| return new TaggedImage(cropped, ti.tags); | ||
| } | ||
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| if (ti.pix instanceof short[]) { | ||
| short[] original = (short[]) ti.pix; | ||
| short[] cropped = new short[width * height]; | ||
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| for (int y = 0; y < height; y++) { | ||
| System.arraycopy(original, ((y + yOffset) * this.imageWidth_) + xOffset, cropped, y * width, width); | ||
| } | ||
| return new TaggedImage(cropped, ti.tags); | ||
| } | ||
| throw new UnsupportedOperationException("Unsupported pixel type"); | ||
| } | ||
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| @Override | ||
| public EssentialImageMetadata getEssentialImageMetadata(HashMap<String, Object> axes) { | ||
| return new EssentialImageMetadata(imageWidth_, imageHeight_, bitDepth_, rgb_); | ||
| } | ||
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| @Override | ||
| public boolean hasImage(HashMap<String, Object> axes) { | ||
| return images_.containsKey(axes); | ||
| } | ||
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| @Override | ||
| public Set<HashMap<String, Object>> getAxesSet() { | ||
| return images_.keySet(); | ||
| } | ||
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| @Override | ||
| public String getUniqueAcqName() { | ||
| return null; | ||
| } | ||
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| @Override | ||
| public int getWritingQueueTaskSize() { | ||
| return 0; | ||
| } | ||
|
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| @Override | ||
| public int getWritingQueueTaskMaxSize() { | ||
| return 0; | ||
| } | ||
| } |
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