Bug: Pyramid tiff reader treats nonflat series as timepoints

[rleigh]

Note the sizeT below when using -noflat.

I can't see any obvious defect in PyramidTiffReader?--it looks like it's setting resolutionCount correctly, and sizeT==1.

% showinf -noflat ~/images/test_images_good/pyramid/101_pyramid
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/Users/rleigh/bioformats/artifacts/slf4j-log4j12-1.5.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [file:/Users/rleigh/bioformats/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
Checking file format [Tagged Image File Format]
Initializing reader
Reading IFDs
Populating metadata
Checking comment style
Populating OME metadata
Expected positive value for PhysicalSizeX; got Infinity
Expected positive value for PhysicalSizeY; got Infinity
Initialization took 0.104s

Reading core metadata
Filename = /Users/rleigh/images/test_images_good/pyramid/101_pyramid
Series count = 1
Series #0 :
	Image count = 9
	RGB = false (1) 
	Interleaved = false
	Indexed = false (false color)
	Width = 1834
	Height = 1993
	SizeZ = 1
	SizeT = 9
	SizeC = 1
	Thumbnail size = 117 x 128
	Endianness = intel (little)
	Dimension order = XYCZT (uncertain)
	Pixel type = uint8
	Valid bits per pixel = 8
	Metadata complete = true
	Thumbnail series = false
	-----
	Plane #0 <=> Z 0, C 0, T 0
	Plane #2 <=> Z 0, C 0, T 2
	Plane #3 <=> Z 0, C 0, T 3
	Plane #4 <=> Z 0, C 0, T 4
	Plane #5 <=> Z 0, C 0, T 5
	Plane #6 <=> Z 0, C 0, T 6
	Plane #8 <=> Z 0, C 0, T 8


Reading pixel data (0-8)
	Read 1/9 planes (11%)
	Read 3/9 planes (33%)
	Read 9/9 planes (100%)
[done]
2.459s elapsed (273.22223ms per plane)

Launching image viewer

Reading global metadata
BitsPerSample: 8
Compression: JPEG-2000
ImageLength: 1993
ImageWidth: 1834
MetaDataPhotometricInterpretation: Monochrome
MetaMorph: no
NumberOfChannels: 1
PhotometricInterpretation: BlackIsZero
PlanarConfiguration: Chunky
ResolutionUnit: Centimeter
SampleFormat: unsigned integer
SamplesPerPixel: 1
Software: OME Bio-Formats
TileByteCounts: 24812
TileLength: 240
TileOffsets: 1586
TileWidth: 240
XResolution: 0
YResolution: 0

Reading metadata

[mlinkert]

Fixed with: ​https://github.com/melissalinkert/bioformats/commit/e972ab6779b7dffa5934d6688d95bf76de44d51f

The files in the 'pyramid' directories are not read by the PyramidTiffReader?, but by MinimalTiffReader/BaseTiffReader/TiffReader?.