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imagej_metadata failed with ValueError

See original GitHub issue

When opening a TiffFile the method imagej_metadata raises this exception:

imagej_metadata failed with ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

Line: 15365 @ tifffile.py:

if not bytecounts:

Maybe replace with something like:

if not bytecounts.size > 0:

Issue Analytics

State:
Created 2 years ago
Comments:9 (5 by maintainers)

Top GitHub Comments

1reaction

cgohlkecommented, Feb 3, 2022

Fixed in v2022.2.2.

0reactions

FirefoxMetzgercommented, Feb 4, 2022

I just tried this on my end with a problematic file, and I can confirm that this fixes the problem.

Before (tifffile 2022.11.2):

>>> import tifffile
>>> foo = tifffile.TiffFile("Substack (1-1023).tif") 
<tifffile.TiffPage 0 @8> imagej_metadata failed with ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
>>> foo.imagej_metadata
{'ImageJ': '1.53e', 'images': 1023, 'slices': 1023, 'unit': 'micron', 'finterval': 0.06870408356189728, 'loop': False}

After (tifffile 2022.02.2):

>>> import tifffile
>>> foo = tifffile.TiffFile("Substack (1-1023).tif")
>>> foo.imagej_metadata
{'ImageJ': '1.53e', 'images': 1023, 'slices': 1023, 'unit': 'micron', 'finterval': 0.06870408356189728, 'loop': False, 'Info': ' BitsPerPixel = 8\n DimensionOrder = XYCZT\n IsInterleaved = false\n IsRGB = false\n LittleEndian = true\n PixelType = uint8\n Series 4 Name = Series006\n SizeC = 1\n SizeT = 1765\n SizeX = 512\n SizeY = 350\n SizeZ = 1\nImage name = Series006\nImage|ATLConfocalSettingDefinition|ActiveCS_SubModeForRLD = 1000\n [... lets avoid flooding the thread ... ]\nImage|ChannelDescription|DataType = 0\nImage|ChannelDescription|IsLUTInverted = 0\nImage|ChannelDescription|LUTName = Green\nImage|ChannelDescription|Max = 2.550000e+002\nImage|ChannelDescription|Min = 0.000000e+000\nImage|ChannelDescription|Resolution = 8\nImage|ChannelScalingInfo|Automatic = 0\nImage|ChannelScalingInfo|BlackValue = 0\nImage|ChannelScalingInfo|GammaValue = 1\nImage|ChannelScalingInfo|WhiteValue = 1\nImage|DimensionDescription|BitInc = 0\nImage|DimensionDescription|BytesInc = 179200\nImage|DimensionDescription|DimID = 4\nImage|DimensionDescription|Length = 1.211940e+002\nImage|DimensionDescription|NumberOfElements = 1765\nImage|DimensionDescription|Origin = 0.000000e+000\nImage|DimensionDescription|Unit = s\nImage|TimeStampList|NumberOfTimeStamps = 1765\nLocation = D:\\Zebrafish\\190205_nanoKTP_kif5a\\190205_nanoKTP_kif5a.lif\n', 'Labels': ['t:2/1765 - Series006', 't:3/1765 - Series006', 't:4/1765 - Series006',[... lets avoid flooding the thread ... ] 't:1023/1765 - Series006', 't:1024/1765 - Series006']}
>>>

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