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CV7000: handle case where wells are recorded, but all files were removed #4006

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merged 2 commits into from
Jun 14, 2023
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CV7000: handle case where wells are recorded, but all files were removed #4006

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CV7000: handle case where wells are recorded, but all files were removed
melissalinkert May 15, 2023
8e1dac2
Cache well acquisition status
melissalinkert May 16, 2023
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16 changes: 16 additions & 0 deletions components/formats-gpl/src/loci/formats/in/CV7000Reader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -92,6 +92,8 @@ public class CV7000Reader extends FormatReader {
private String startTime, endTime;
private ArrayList<String> extraFiles;

private transient Map<String, Boolean> acquiredWells = new HashMap<String, Boolean>();

// -- Constructor --

/** Constructs a new Yokogawa CV7000 reader. */
Expand Down Expand Up @@ -206,6 +208,7 @@ public void close(boolean fileOnly) throws IOException {
endTime = null;
reversePlaneLookup = null;
extraFiles = null;
acquiredWells.clear();
}
}

Expand Down Expand Up @@ -309,6 +312,10 @@ public int compare(Channel c1, Channel c2) {

for (Plane p : planeData) {
if (p != null) {
if (!isWellAcquired(p.field.row, p.field.column)) {
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Overall, the logic is to populate a more faithful uniqueWells (excluding the missing wells) and then initialize and populate a reversePlaneLookup map only for the existing wells which makes total sense.

My primary concern with the proposed fix is its computational cost and the potential performance impact on large plates. isWellAcquired returns the existence of a particular well from a loop on PlaneData itself. Having this call nested within a PlaneData loop means an increase of complexity which will scale with the number of wells/fields in a plate.

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Agreed. I wasn't really thinking about performance for the initial fix, was really trying to verify that it worked. 8e1dac2 is one option that should make isWellAcquired inexpensive for repeated checks on the same well.

continue;
}

p.channelIndex = getChannelIndex(p);

int wellIndex = p.field.row * plate.getPlateColumns() + p.field.column;
Expand Down Expand Up @@ -383,6 +390,9 @@ public int compare(Channel c1, Channel c2) {
for (int i=0; i<planeData.size(); i++) {
Plane p = planeData.get(i);
Field f = p.field;
if (!isWellAcquired(f.row, f.column)) {
continue;
}
int wellNumber = f.row * plate.getPlateColumns() + f.column;
int wellIndex = Arrays.binarySearch(wells, wellNumber);
p.series = FormatTools.positionToRaster(seriesLengths,
Expand Down Expand Up @@ -639,13 +649,19 @@ private String readSanitizedXML(String filename) throws IOException {
}

private boolean isWellAcquired(int row, int col) {
String key = row + "-" + col;
if (acquiredWells.containsKey(key)) {
return acquiredWells.get(key);
}
if (planeData != null) {
for (Plane p : planeData) {
if (p != null && p.file != null && p.field.row == row && p.field.column == col) {
acquiredWells.put(key, true);
return true;
}
}
}
acquiredWells.put(key, false);
return false;
}

Expand Down