Skip to content

Commit

Permalink
another metadata improvement
Browse files Browse the repository at this point in the history
  • Loading branch information
@NicoKiaru
NicoKiaru committed Aug 24, 2023
1 parent 5d557bc commit 6b41286
Showing 1 changed file with 69 additions and 9 deletions.
78 changes: 69 additions & 9 deletions src/main/java/ch/epfl/biop/formats/in/ZeissQuickStartCZIReader.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3181,7 +3181,7 @@ private void setSpaceAndTimeInformation( // of series and of planes
int nChannels = reader.getSizeC();
List<MinimalDimensionEntry> blocks;

Length planePosX, planePosY, planePosZ; // plane position of the current coreindex - do not vary over z and t, but that could happen
Length planePosX, planePosY, planePosZ = null; // plane position of the current coreindex - do not vary over z and t, but that could happen

blocks = mapCoreCZTToBlocks.get(iCoreIndex).get(new CZTKey(0,0,0));

Expand All @@ -3192,14 +3192,54 @@ private void setSpaceAndTimeInformation( // of series and of planes
planePosY = planePosYResolutionLevel0;
planePosZ = planePosZResolutionLevel0;
} else {
// The most complicated logic
// ------ Here's the available data:

// XYZ - Plane position according to the block position (should not be null - compulsory in czi file)
Corner blocksCorner = new Corner().fromBlocks(blocks, iCoreIndex, unitLength);
// XYZ - Plane position according to the subblock xml metadata (could be null)
Corner subBlockMetaCorner = new Corner().fromSubBlockMeta(blocks, iCoreIndex, unitLength, parser);
// XY - (offsetXInMicrons, offsetYInMicrons) : the top left corner, according to the xml czi header (could be NaN)
// Z - scenePosZ : the z location of the current scene, according to the xml czi header (could be Null)
/*System.out.println("- Id = "+reader.currentId);
System.out.println("- CoreIndex = "+reader.coreIndex+" Res Lev 0 = "+resolutionLevel0);
System.out.println("Min XYZ location according to block start position:");
System.out.println("\tX="+blocksCorner.x);
System.out.println("\tY="+blocksCorner.y);
System.out.println("\tZ="+blocksCorner.z);
System.out.println("Min XYZ location according to subblock metadata position:");
System.out.println("\tX="+subBlockMetaCorner.x);
System.out.println("\tY="+subBlockMetaCorner.y);
System.out.println("\tZ="+subBlockMetaCorner.z);
System.out.println("XY Global offset according to main xml document:");
System.out.println("\tX="+offsetXInMicrons);
System.out.println("\tY="+offsetYInMicrons);
System.out.println("Z position of current scene according to main xml document:");
System.out.println("\tZ="+scenePosZ);*/

// XY : keep blocks only
planePosX = blocksCorner.x;
planePosY = blocksCorner.y;

if ((blocksCorner.z!=null)&&(subBlockMetaCorner.z!=null)&&(blocksCorner.z.unit().equals(subBlockMetaCorner.z.unit()))) {
Unit<Length> u = blocksCorner.z.unit();
planePosZ = new Length(blocksCorner.z.value(u).doubleValue()+subBlockMetaCorner.z.value(u).doubleValue(), u);
} else if ((blocksCorner.z!=null)&&(scenePosZ!=null)&&(scenePosZ.unit().equals(blocksCorner.z.unit()))) {
Unit<Length> u = blocksCorner.z.unit();
planePosZ = new Length(blocksCorner.z.value(u).doubleValue()+scenePosZ.value(u).doubleValue(), u);
} else if (blocksCorner.z!=null) {
planePosZ = blocksCorner.z;
} else if (subBlockMetaCorner.z!=null) {
planePosZ = subBlockMetaCorner.z;
} else if (scenePosZ!=null) {
planePosZ = scenePosZ;
}

// Look for the min X and Y position from blocks
planePosX=(blocksCorner.x==null)?subBlockMetaCorner.x:blocksCorner.x;
planePosY=(blocksCorner.y==null)?subBlockMetaCorner.y:blocksCorner.y;
//planePosX=(blocksCorner.x==null)?subBlockMetaCorner.x:blocksCorner.x;
//planePosY=(blocksCorner.y==null)?subBlockMetaCorner.y:blocksCorner.y;
// To match the previous reader, using the meta instead
planePosZ=(subBlockMetaCorner.z==null)?blocksCorner.z:subBlockMetaCorner.z;
/*planePosZ=(subBlockMetaCorner.z==null)?blocksCorner.z:subBlockMetaCorner.z;
// There's an offset potentially
// Scene offset = scenePosX.value(u) scenePosY.value(u) scenePosZ.value(u)
Expand All @@ -3226,7 +3266,7 @@ private void setSpaceAndTimeInformation( // of series and of planes
Unit<Length> u = planePosZ.unit();
planePosZ = new Length(scenePosZ.value(u).doubleValue() + planePosZ.value(u).doubleValue(), u);
}
}
}*/
}

if (resolutionLevel0) {
Expand Down Expand Up @@ -3316,8 +3356,28 @@ private void setSpaceAndTimeInformation( // of series and of planes
double[] currentTimeStamps = timeStampsResolutionLevel0.get(iChannel);
int planeCounter = 0;
if ((reader.flattenedResolutions)||(resolutionLevel0)) { // Avoid setting the metadata not for lower resolution levels, because this override proper metadata if flattenresolution = false
for (int iZori = 0; iZori < reader.getSizeZ(); iZori++) {
for (int iTori = 0; iTori < reader.getSizeT(); iTori++) {
for (int iTori = 0; iTori < reader.getSizeT(); iTori++) {
int iT = iTori % (reader.getSizeT() / reader.nPhases);
double timeStartCurrentFrame = 0;
if (interpolateZTPlanePosition) {
// We can afford to read the first block of the first timepoint
LibCZI.SubBlockMeta sbmzt = getSubBlockMeta(
iChannel,
0,
iT,
iCoreIndex, mapCoreCZTToBlocks, parser);
if (Double.isNaN(sbmzt.timestamp)) {
if (cziSegments.timeStamps.length>iT) {
timeStartCurrentFrame = cziSegments.timeStamps[iT];
}
} else {
timeStartCurrentFrame = sbmzt.timestamp - realT0;
}
}

for (int iZori = 0; iZori < reader.getSizeZ(); iZori++) {


int planeIndex = reader.getIndex(iZori, iChannel, iTori);
// rotations -> modulo Z
// illuminations -> modulo C
Expand All @@ -3330,13 +3390,13 @@ private void setSpaceAndTimeInformation( // of series and of planes
reader.store.setPlaneExposureTime(exposure, reader.series, planeIndex); // 0 exposure do not make sense
}
int iZ = iZori % (reader.getSizeZ() / reader.nRotations);
int iT = iTori % (reader.getSizeT() / reader.nPhases);

Time dT = null;
Length pZ = null;

if (interpolateZTPlanePosition) {
if ((incrementTimeOverZ >= 0) || (incrementTimeOverT >= 0)) {
dT = new Time(offsetT0 + incrementTimeOverT * iT + incrementTimeOverZ * iZ,
dT = new Time(timeStartCurrentFrame + incrementTimeOverZ * iZ,
UNITS.SECOND);
}
pZ = new Length(offsetZ0 + iZ * stepZ, unitLength);
Expand Down

0 comments on commit 6b41286

Please sign in to comment.