Leica TCS: make sure XML file is on used files list #4252
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Note Series002.xml will appear at the end of the list, which at first glance looks like it should cause test failures due to the changes in #4172. However, the use of initFile(...) on the first TIFF file found in line 263 means that the initialized file in the end is not Series002.xml.
From the reader logic, the XML file is treated an optional file with additional metadata so appending it to the end of the used files list rather makes sense.
With the current release of Bio-Formats using the sample dataset listed in the description, the XML file is not included in the the used files list after initialization when selecting either a TIFF file of the XML file. With this change, the XML is added to the used files:
sbesson@Sebastiens-MacBook-Pro-3 bioformats % ./tools/showinf -nopix ~/bf-data-repo/automated-tests/curated/leica-tcs/brian/Series002.xml
Checking file format [Leica TCS TIFF]
Initializing reader
TCSReader initializing /Users/sbesson/bf-data-repo/automated-tests/curated/leica-tcs/brian/Series002.xml
Reading IFDs
Populating metadata
Checking comment style
Populating OME metadata
unknown creation date format: 0:00:00 00:00:00
Initialization took 0.064s
Reading core metadata
filename = /Users/sbesson/bf-data-repo/automated-tests/curated/leica-tcs/brian/Series002_z00_ch00.tif
Used files:
/Users/sbesson/bf-data-repo/automated-tests/curated/leica-tcs/brian/Series002_z00_ch00.tif
/Users/sbesson/bf-data-repo/automated-tests/curated/leica-tcs/brian/Series002_z00_ch01.tif
/Users/sbesson/bf-data-repo/automated-tests/curated/leica-tcs/brian/Series002.xml
Series count = 1
Series #0 :
Image count = 2
RGB = false (1)
Interleaved = false
Indexed = true (false color, 8-bit LUT: 3 x 256)
Width = 512
Height = 512
SizeZ = 1
SizeT = 1
SizeC = 2
Tile size = 512 x 512
Thumbnail size = 128 x 128
Endianness = intel (little)
Dimension order = XYCTZ (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = false
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Plane #1 <=> Z 0, C 1, T 0
Reading global metadata
Number of image files: 2
Reading metadata
When selecting the TIFF file as an input, the XML file is not returned by getUsedFiles, should this be the case?
sbesson@Sebastiens-MacBook-Pro-3 bioformats % ./tools/showinf -nopix ~/bf-data-repo/automated-tests/curated/leica-tcs/brian/Series002_z00_ch00.tif
Checking file format [Leica TCS TIFF]
Initializing reader
TCSReader initializing /Users/sbesson/bf-data-repo/automated-tests/curated/leica-tcs/brian/Series002_z00_ch00.tif
Reading IFDs
Populating metadata
Checking comment style
Populating OME metadata
unknown creation date format: 0:00:00 00:00:00
Initialization took 0.065s
Reading core metadata
filename = /Users/sbesson/bf-data-repo/automated-tests/curated/leica-tcs/brian/Series002_z00_ch00.tif
Used files:
/Users/sbesson/bf-data-repo/automated-tests/curated/leica-tcs/brian/Series002_z00_ch00.tif
/Users/sbesson/bf-data-repo/automated-tests/curated/leica-tcs/brian/Series002_z00_ch01.tif
Series count = 1
Series #0 :
Image count = 2
RGB = false (1)
Interleaved = false
Indexed = true (false color, 8-bit LUT: 3 x 256)
Width = 512
Height = 512
SizeZ = 1
SizeT = 1
SizeC = 2
Tile size = 512 x 512
Thumbnail size = 128 x 128
Endianness = intel (little)
Dimension order = XYCTZ (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = false
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Plane #1 <=> Z 0, C 1, T 0
Reading global metadata
Number of image files: 2
Reading metadata
One inline question about a possible redundant call.
| @@ -247,6 +247,7 @@ protected void initFile(String id) throws FormatException, IOException { | |||
| Arrays.sort(list); | |||
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| boolean isXML = checkSuffix(id, XML_SUFFIX); | |||
| if (isXML) xmlFile = l.getAbsolutePath(); | |||
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Is this effectively redundant with the call after initFile(new Location(parent, file).getAbsolutePath()) below?
In particular, the pinhole size may be present in the XML, but just hasn't been parsed yet.
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This ended up being quite a bit more involved than I originally anticipated. Last 3 commits here should mean that the XML file ends up on the used files list no matter what. However, the XML file being missing from the list meant that it wasn't being parsed at all - so several fixes were needed to address a Given the larger scope, I would be more comfortable with this going into 8.1.0 than 8.0.1, so have updated the milestone accordingly. |
Fixes #4229 (cc @mabruce).
As indicated in the original issue,
showinf curated/leica-tcs/brian/Series002.xmlwithout this change will not includeSeries002.xmlon the used file list. With this change, it should be included on the used file list.Note
Series002.xmlwill appear at the end of the list, which at first glance looks like it should cause test failures due to the changes in #4172. However, the use ofinitFile(...)on the first TIFF file found in line 263 means that the initialized file in the end is notSeries002.xml.Adding to 8.0.1 since this should be safe for a patch release, but this could easily be moved to a later milestone.