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MicroManager: use PositionName key/value for storing the ImageName (rebased onto metadata54) #3092

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MicroManager: use PositionName key/value for storing the ImageName (rebased onto metadata54) #3092

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MicroManager: use PositionName key/value for storing the ImageName
sbesson Mar 1, 2018
6d851b0
Escape cases where "PositionName": null is stored in the metadata
sbesson Mar 1, 2018
7f3f0f7
Make new name field transient
sbesson Mar 1, 2018
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14 changes: 11 additions & 3 deletions components/formats-bsd/src/loci/formats/in/MicromanagerReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -317,9 +317,13 @@ private void populateMetadata() throws FormatException, IOException {
}
}

if (positions.size() > 1) {
Location parent = new Location(p.metadataFile).getParentFile();
store.setImageName(parent.getName(), i);
if (p.name != null) {
store.setImageName(p.name, i);
} else {
if (positions.size() > 1) {
Location parent = new Location(p.metadataFile).getParentFile();
store.setImageName(parent.getName(), i);
}
}

if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
Expand Down Expand Up @@ -850,6 +854,9 @@ else if (key.equals(p.cameraRef + "-CCDMode")) {
else if (key.startsWith("DAC-") && key.endsWith("-Volts")) {
p.voltage.add(new Double(value));
}
else if (key.equals("PositionName") && !value.equals("null")) {
p.name = value;
}
else if (key.equals("FileName")) {
p.fileNameMap.put(new Index(slice), value);
Location realFile = new Location(parent, value);
Expand Down Expand Up @@ -1097,6 +1104,7 @@ class Position {

public String metadataFile;
public String xmlFile;
public transient String name;

public String[] channels;

Expand Down