Fix downsampling issue

[lguerard]

Just changing this line fixes the issue with the TileConfiguration reported here : https://forum.image.sc/t/fusion-of-label-images-using-downsampling/73150

Closes #38.

[lguerard]

@imagejan Thanks for cleaning up a bit the PR ;)

However, I'm not sure if that closes the issue aryehw was mentioning, but it at least closes mine. (I probably should have made a different issue for this, sorry..)

[imagejan]

Good point, @lguerard, sorry, I maybe was a bit fast to add the "Closes #38" to your PR description.

#38 actually talks about "Filename defined position", which is grid type 4 according to here:

Stitching/src/main/java/plugin/GridType.java

Line 48 in 340ab11

"Filename defined position", // 4

So how about relaxing to gridType >= 4 even?

[lguerard]

I would be fine but I don't have any files to test the other types which is why I asked if there was a reason to keep it only for 5 and 7.

[imagejan]

@lguerard wrote in #38 (comment)

Was there a reason to only do the downsampling if GridType was 5 or 7 ?

The Downsampler logic was introduced with f37c98f.

There's actually two code paths, for grid type {5,7} and for all others:

• !( gridType == 5 || gridType == 7) (note the ds arguments in the function calls):
  

  Stitching/src/main/java/plugin/Stitching_Grid.java

  Lines 406 to 418 in 340ab11

  	Downsampler ds = null;
  	if ( downSample && !( gridType == 5 || gridType == 7) ) ds = new Downsampler();
  	if ( gridType < 5 )
  	elements = getGridLayout( grid, gridSizeX, gridSizeY, overlapX, overlapY, directory, filenames, startI, startX, startY, params.virtual, ds );
  	//John Lapage modified this: copying setup for Unknown Positions
  	else if ( gridType == 5 || gridType == 7)
  	elements = getAllFilesInDirectory( directory, confirmFiles );
  	else if ( gridType == 6 && gridOrder == 1 ) // positions from file metadata
  	elements = getLayoutFromMultiSeriesFile( seriesFile, increaseOverlap,
  	ignoreCalibration, invertX, invertY, ignoreZStage, ds );
  	else if ( gridType == 6 ) // positions from tile configuration file
  	elements = getLayoutFromFile( directory, outputFile, ds );

• ( gridType == 5 || gridType == 7)
  

  Stitching/src/main/java/plugin/Stitching_Grid.java

  Lines 460 to 466 in 340ab11

  	if (downSample && ( gridType == 5 || gridType == 7)) {
  	if (ds == null) {
  	ds = new Downsampler();
  	ds.getInput(imp.getWidth(), imp.getHeight());
  	}
  	ds.run(imp);
  	}

So while the fix might work for your case, @lguerard, I believe there was some other breakage since f37c98f. It would be good to have unit test cases for this 😄

[lguerard]

Indeed, sorry about this. I'll investigate a bit more and update this PR when I have found something !

[lguerard]

Actually, I think I was right.

If I understand correctly what the ImageCollection corresponds to, this part

Stitching/src/main/java/plugin/Stitching_Grid.java

Lines 417 to 418 in 340ab11

	else if ( gridType == 6 ) // positions from tile configuration file
	elements = getLayoutFromFile( directory, outputFile, ds );

only changes the grid elements which corresponds to the position of the tiles no ? The real downsampling of the ImagePlus is happening here and only if the GridType is 5 or 7.

Stitching/src/main/java/plugin/Stitching_Grid.java

Lines 460 to 466 in 340ab11

	if (downSample && ( gridType == 5 || gridType == 7)) {
	if (ds == null) {
	ds = new Downsampler();
	ds.getInput(imp.getWidth(), imp.getHeight());
	}
	ds.run(imp);
	}