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Add a few options for working with CZI files that have multiple scenes #3681

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merged 4 commits into from
Jul 23, 2021
Merged

Add a few options for working with CZI files that have multiple scenes #3681

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b195e8f
Calculate XY sizes based upon actual tiles available
melissalinkert Mar 11, 2021
5b3343a
Add zeissczi.trim_dimensions option
melissalinkert Mar 18, 2021
fd1c1ac
Add zeissczi.relative_positions option
melissalinkert Mar 21, 2021
5346a43
Refine relative position calculation
melissalinkert Mar 22, 2021
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72 changes: 68 additions & 4 deletions components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -90,6 +90,10 @@ public class ZeissCZIReader extends FormatReader {
public static final String INCLUDE_ATTACHMENTS_KEY =
"zeissczi.attachments";
public static final boolean INCLUDE_ATTACHMENTS_DEFAULT = true;
public static final String TRIM_DIMENSIONS_KEY = "zeissczi.trim_dimensions";
public static final boolean TRIM_DIMENSIONS_DEFAULT = false;
public static final String RELATIVE_POSITIONS_KEY = "zeissczi.relative_positions";
public static final boolean RELATIVE_POSITIONS_DEFAULT = false;

private static final int ALIGNMENT = 32;
private static final int HEADER_SIZE = 32;
Expand Down Expand Up @@ -585,6 +589,8 @@ protected ArrayList<String> getAvailableOptions() {
ArrayList<String> optionsList = super.getAvailableOptions();
optionsList.add(ALLOW_AUTOSTITCHING_KEY);
optionsList.add(INCLUDE_ATTACHMENTS_KEY);
optionsList.add(TRIM_DIMENSIONS_KEY);
optionsList.add(RELATIVE_POSITIONS_KEY);
return optionsList;
}

Expand Down Expand Up @@ -1044,6 +1050,9 @@ else if (seriesCount > mosaics && mosaics > 1 && prestitched != null && prestitc
keepMissingPyramid = true;
}
}
if (trimDimensions()) {
calculateDimensions(s, true);
}
s += core.get(s).resolutionCount;
}
}
Expand Down Expand Up @@ -1367,7 +1376,15 @@ else if (p.resolutionIndex == 0) {
for (Integer q : index) {
SubBlock currentPlane = planes.get(q);
if (currentPlane == null) continue;
if (currentPlane.stageX != null) {
if (storeRelativePositions()) {
if (minStageX == null || currentPlane.col < minStageX) {
minStageX = (double) currentPlane.col;
}
if (maxStageX == null || currentPlane.col > maxStageX) {
maxStageX = (double) currentPlane.col;
}
}
else if (currentPlane.stageX != null) {
if (minStageX == null ||
currentPlane.stageX.value().doubleValue() < minStageX)
{
Expand All @@ -1379,7 +1396,15 @@ else if (p.resolutionIndex == 0) {
maxStageX = currentPlane.stageX.value().doubleValue();
}
}
if (currentPlane.stageY != null) {
if (storeRelativePositions()) {
if (minStageY == null || currentPlane.row < minStageY) {
minStageY = (double) currentPlane.row;
}
if (maxStageY == null || currentPlane.row > maxStageY) {
maxStageY = (double) currentPlane.row;
}
}
else if (currentPlane.stageY != null) {
if (minStageY == null ||
currentPlane.stageY.value().doubleValue() < minStageY)
{
Expand All @@ -1397,7 +1422,10 @@ else if (p.resolutionIndex == 0) {
// assign the same position to each resolution in a pyramid

Length x = null;
if (minStageX != null && maxStageX != null) {
if (storeRelativePositions()) {
x = new Length(minStageX, UNITS.PIXEL);
}
else if (minStageX != null && maxStageX != null) {
double diff = (maxStageX - minStageX) / 2;
x = new Length(minStageX + diff, UNITS.MICROMETER);
if (positionsX != null) {
Expand All @@ -1423,7 +1451,10 @@ else if (p.stageX != null) {
}

Length y = null;
if (minStageY != null && maxStageY != null) {
if (storeRelativePositions()) {
y = new Length(minStageY, UNITS.PIXEL);
}
else if (minStageY != null && maxStageY != null) {
double diff = (maxStageY - minStageY) / 2;
y = new Length(minStageY + diff, UNITS.MICROMETER);
if (positionsY != null) {
Expand Down Expand Up @@ -1619,6 +1650,24 @@ public boolean canReadAttachments() {
return INCLUDE_ATTACHMENTS_DEFAULT;
}

public boolean trimDimensions() {
MetadataOptions options = getMetadataOptions();
if (options instanceof DynamicMetadataOptions) {
return ((DynamicMetadataOptions) options).getBoolean(
TRIM_DIMENSIONS_KEY, TRIM_DIMENSIONS_DEFAULT);
}
return TRIM_DIMENSIONS_DEFAULT;
}

public boolean storeRelativePositions() {
MetadataOptions options = getMetadataOptions();
if (options instanceof DynamicMetadataOptions) {
return ((DynamicMetadataOptions) options).getBoolean(
RELATIVE_POSITIONS_KEY, RELATIVE_POSITIONS_DEFAULT);
}
return RELATIVE_POSITIONS_DEFAULT;
}

// -- Helper methods --

private void readSegments(String id) throws IOException {
Expand Down Expand Up @@ -1707,6 +1756,11 @@ private void calculateDimensions(int coreIndex, boolean xyOnly) {
int minPositions = Integer.MAX_VALUE;
int maxPositions = Integer.MIN_VALUE;

int minX = Integer.MAX_VALUE;
int maxX = Integer.MIN_VALUE;
int minY = Integer.MAX_VALUE;
int maxY = Integer.MIN_VALUE;

for (SubBlock plane : planes) {
if (xyOnly && plane.coreIndex != coreIndex) {
continue;
Expand All @@ -1724,6 +1778,8 @@ private void calculateDimensions(int coreIndex, boolean xyOnly) {
case 'X':
plane.x = dimension.size;
plane.col = dimension.start;
minX = (int) Math.min(plane.col, minX);
maxX = (int) Math.max(plane.col + plane.x, maxX);
if ((prestitched == null || prestitched) &&
getSizeX() > 0 && dimension.size != getSizeX() && allowAutostitching())
{
Expand All @@ -1737,6 +1793,8 @@ private void calculateDimensions(int coreIndex, boolean xyOnly) {
case 'Y':
plane.y = dimension.size;
plane.row = dimension.start;
minY = (int) Math.min(plane.row, minY);
maxY = (int) Math.max(plane.row + plane.y, maxY);
if ((prestitched == null || prestitched) &&
getSizeY() > 0 && dimension.size != getSizeY() && allowAutostitching())
{
Expand Down Expand Up @@ -1817,6 +1875,12 @@ else if (dimension.size > getSizeZ()) {
if (maxPositions > Integer.MIN_VALUE && minPositions < Integer.MAX_VALUE) {
positions = maxPositions - minPositions + 1;
}

if (xyOnly && trimDimensions()) {
ms0.sizeX = maxX - minX;
ms0.sizeY = maxY - minY;
}

setCoreIndex(previousCoreIndex);
}

Expand Down