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<class 'TypeError'> Inappropriate argument type. __init__() should return None, not 'int' #304

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csittz opened this issue Jun 3, 2024 · 10 comments
Open

<class 'TypeError'> Inappropriate argument type. __init__() should return None, not 'int' #304

csittz opened this issue Jun 3, 2024 · 10 comments
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@nanli-emory

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@csittz
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csittz commented Jun 3, 2024

Hi i downloaded ovarian cancer tissue svs files from public imaging portal and try to run histoqc
python3 -m histoqc -c first *.svs

but i encounter this error

2024-06-03 14:46:39,094 - ERROR - XX.svs: Has unknown or uncalculated base magnification, cannot specify magnification scale! Did you try getMag?
2024-06-03 14:46:39,095 - ERROR - XX.svs - Error analyzing file (skipping):      <class 'TypeError'> Inappropriate argument type. __init__() should return None, not 'int'

any idea what is wrong and how to work around it?
@jacksonjacobs1
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Hi @csittz,

Thank you for reaching out! This error message is quite common and usually means an image file (usually .tif or .tiff but potentially also .svs) you are using does not contain key metadata.

Can you run tifftools dump <your-image-filepath> and paste it into this thread? tifftools can be installed with pip.

@csittz
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csittz commented Jun 4, 2024

Thanks for your help. here's the tifftools dump output for one of the svs file.

Header: 0x4949 <little-endian> <ClassicTIFF>
Directory 0: offset 1632748420 (0x6151c384)
  NewSubfileType 254 (0xFE) LONG: 0
  ImageWidth 256 (0x100) SHORT: 55776
  ImageLength 257 (0x101) SHORT: 44390
  BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
  Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
  Photometric 262 (0x106) SHORT: 2 (RGB 2 (0x2))
  ImageDescription 270 (0x10E) ASCII:
  SamplesPerPixel 277 (0x115) SHORT: 3
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  TileWidth 322 (0x142) SHORT: 240
  TileLength 323 (0x143) SHORT: 240
  TileOffsets 324 (0x144) LONG: <43105> 16 618720 1217723 1787803 2379501 3017643 3696718 5267520 8480459 12321670 16792658 21986177 27694392 33785911 39917332 46281676 52436451 58681098 65522289 72494063 ...
  TileByteCounts 325 (0x145) LONG: <43105> 7830 7276 6220 6661 7299 6608 6975 7042 6581 6918 6437 6603 8897 7467 7356 7613 7406 7323 6725 6176 ...
  JPEGTables 347 (0x15B) UNDEFINED: <574> b'\xff\xd8\xff\xdb\x00C\x00\x06\x04\x05\x06\x05\x04\x06\x06\x05\x06\x07\x07\x06' ... (estimated quality: 80)
  YCbCrSubsampling 530 (0x212) SHORT: <2> 2 2
  ImageDepth 32997 (0x80E5) LONG: 1
  ICCProfile 34675 (0x8773) UNDEFINED: <1687824> b'\x00\x19\xc1\x10SICC\x04\x00\x00\x00scnrRGB ' ...
Directory 1: offset 1635150692 (0x61766b64)
  NewSubfileType 254 (0xFE) LONG: 0
  ImageWidth 256 (0x100) SHORT: 964
  ImageLength 257 (0x101) SHORT: 768
  BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
  Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
  Photometric 262 (0x106) SHORT: 2 (RGB 2 (0x2))
  ImageDescription 270 (0x10E) ASCII:
  StripOffsets 273 (0x111) LONG: <48> 1634782444 1634789563 1634797090 1634805388 1634813969 1634822840 1634831845 1634840851 1634849645 1634857910 1634865848 1634874485 1634883434 1634892259 1634901226 1634910366 1634919462 1634928287 1634937525 1634946178 ...
  SamplesPerPixel 277 (0x115) SHORT: 3
  RowsPerStrip 278 (0x116) SHORT: 16
  StripByteCounts 279 (0x117) LONG: <48> 7119 7527 8298 8581 8871 9005 9006 8794 8265 7938 8637 8949 8825 8967 9140 9096 8825 9238 8653 8289 ...
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  JPEGTables 347 (0x15B) UNDEFINED: <289> b'\xff\xd8\xff\xdb\x00C\x00\n\x07\x07\x08\x07\x06\n\x08\x08\x08\x0b\n\n' ... (estimated quality: 70)
  YCbCrSubsampling 530 (0x212) SHORT: <2> 2 2
  ImageDepth 32997 (0x80E5) LONG: 1
Directory 2: offset 1824388758 (0x6cbdf696)
  NewSubfileType 254 (0xFE) LONG: 0
  ImageWidth 256 (0x100) SHORT: 13944
  ImageLength 257 (0x101) SHORT: 11097
  BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
  Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
  Photometric 262 (0x106) SHORT: 2 (RGB 2 (0x2))
  ImageDescription 270 (0x10E) ASCII: Aperio Image Library v12.0.15
56896x44490 [0,100 55776x44390] (240x240) -> 13944x11097 JPEG/RGB Q=90
  SamplesPerPixel 277 (0x115) SHORT: 3
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  TileWidth 322 (0x142) SHORT: 240
  TileLength 323 (0x143) SHORT: 240
  TileOffsets 324 (0x144) LONG: <2773> 1635152095 1635157168 1635162285 1635166986 1635172441 1635202298 1635245907 1635255519 1635260143 1635265475 1635279386 1635332942 1635396740 1635469496 1635513700 1635534331 1635583469 1635648927 1635713375 1635764314 ...
  TileByteCounts 325 (0x145) LONG: <2773> 5073 5117 4701 5455 29857 43609 9612 4624 5332 13911 53556 63798 72756 44204 20631 49138 65458 64448 50939 43980 ...
  JPEGTables 347 (0x15B) UNDEFINED: <574> b'\xff\xd8\xff\xdb\x00C\x00\x03\x02\x02\x03\x02\x02\x03\x03\x03\x03\x04\x03\x03' ... (estimated quality: 90)
  YCbCrSubsampling 530 (0x212) SHORT: <2> 2 2
  ImageDepth 32997 (0x80E5) LONG: 1
Directory 3: offset 1839677964 (0x6da7420c)
  NewSubfileType 254 (0xFE) LONG: 0
  ImageWidth 256 (0x100) SHORT: 3486
  ImageLength 257 (0x101) SHORT: 2774
  BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
  Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
  Photometric 262 (0x106) SHORT: 2 (RGB 2 (0x2))
  ImageDescription 270 (0x10E) ASCII: Aperio Image Library v12.0.15
56896x44490 [0,100 55776x44390] (240x240) -> 3486x2774 JPEG/RGB Q=95
  SamplesPerPixel 277 (0x115) SHORT: 3
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  TileWidth 322 (0x142) SHORT: 240
  TileLength 323 (0x143) SHORT: 240
  TileOffsets 324 (0x144) LONG: <180> 1824411824 1824438385 1824528753 1824620812 1824720922 1824821844 1824928333 1825030531 1825128877 1825219971 1825314952 1825400379 1825488168 1825561623 1825589824 1825626718 1825677975 1825787997 1825893985 1825998468 ...
  TileByteCounts 325 (0x145) LONG: <180> 26561 90368 92059 100110 100922 106489 102198 98346 91094 94981 85427 87789 73455 28201 36894 51257 110022 105988 104483 102681 ...
  JPEGTables 347 (0x15B) UNDEFINED: <574> b'\xff\xd8\xff\xdb\x00C\x00\x02\x01\x01\x01\x01\x01\x02\x01\x01\x01\x02\x02\x02' ... (estimated quality: 95)
  YCbCrSubsampling 530 (0x212) SHORT: <2> 2 2
  ImageDepth 32997 (0x80E5) LONG: 1
Directory 4: offset 1840303924 (0x6db0cf34)
  NewSubfileType 254 (0xFE) LONG: 9 (ReducedImage 1 (0x1), Macro 8 (0x8))
  ImageWidth 256 (0x100) SHORT: 1600
  ImageLength 257 (0x101) SHORT: 652
  BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
  Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
  Photometric 262 (0x106) SHORT: 2 (RGB 2 (0x2))
  ImageDescription 270 (0x10E) ASCII: Aperio Image Library v12.0.15
macro 1600x652
  StripOffsets 273 (0x111) LONG: <41> 1840113604 1840124406 1840131681 1840136564 1840141357 1840146552 1840151491 1840156221 1840160475 1840164812 1840169214 1840173800 1840178995 1840183631 1840188329 1840192928 1840197094 1840201267 1840205668 1840209991 ...
  SamplesPerPixel 277 (0x115) SHORT: 3
  RowsPerStrip 278 (0x116) SHORT: 16
  StripByteCounts 279 (0x117) LONG: <41> 10802 7275 4883 4793 5195 4939 4730 4254 4337 4402 4586 5195 4636 4698 4599 4166 4173 4401 4323 4267 ...
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  JPEGTables 347 (0x15B) UNDEFINED: <289> b'\xff\xd8\xff\xdb\x00C\x00\x10\x0b\x0c\x0e\x0c\n\x10\x0e\r\x0e\x12\x11\x10' ... (estimated quality: 50)
  YCbCrSubsampling 530 (0x212) SHORT: <2> 2 2
  ImageDepth 32997 (0x80E5) LONG: 1

@bsauty
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bsauty commented Jul 17, 2024

Hi :) I'm running into the same issue, do you know if there is a fix?

@jacksonjacobs1
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My apologies for the delay.

@csittz your dumped output indicates that your file is lacking metadata which HistoQC requires. Specifically, the ImageDescription header is empty.

I would recommend following the "Adding Metadata" section of this blog post to inject "fake" metadata into your image.
https://andrewjanowczyk.com/converting-an-existing-image-into-an-openslide-compatible-format/

Also note that your injected metadata should reflect e.g., the true base magnification and microns per pixel of the original image.

Please let me know if you have additional issues.

@bsauty
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bsauty commented Jul 23, 2024 •
edited
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Thank's for the answer! Actually it's not exactly the same problem since the ImageDescription field is not empty (instead rather huge)

Directory 0: offset 16 (0x10)
  NewSubfileType 254 (0xFE) LONG: 1 (ReducedImage 1 (0x1))
  ImageWidth 256 (0x100) LONG: 22016
  ImageLength 257 (0x101) LONG: 31232
  BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
  Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
  Photometric 262 (0x106) SHORT: 6 (YCbCr 6 (0x6))
  ImageDescription 270 (0x10E) ASCII: {"@xmlns": "http://www.openmicroscopy.org/Schemas/OME/2016-06", "@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance", "@xsi:schemaLocation": "http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd", "Instrument": {"@ID": "Instrument:0", "Detector": [{"@Gain": "0.0", "@ID": "Detector:0:0", "@Manufacturer": "iDS", "@Model": "VS-264C", "@SerialNumber": "21954560", "@Type": "CCD"}, {"@Gain": "0.0", "@ID": "Detector:0:1", "@Manufacturer": "iDS", "@Model": "VS-264C", "@SerialNumber": "21954560", "@Type": "CCD"}], "Objective": [{"@ID": "Objective:0:0", "@LensNA": "0.06", "@Model": "PLN", "@NominalMagnification": "2.0", "@WorkingDistance": "5800.0", "@WorkingDistanceUnit": "\u00b5m"}, {"@ID": "Objective:0:1", "@LensNA": "0.8", "@Model": "UPLXAPO", "@NominalMagnification": "20.0", "@WorkingDistance": "600.0", "@WorkingDistanceUnit": "\u00b5m"}]}, "Image": {"@ID": "Image:7", "@Name": "20x_BF_01", "AcquisitionDate": "2024-01-23T12:05:45", "InstrumentRef": {"@ID": "Instrument:0"}, "ObjectiveSettings": {"@ID": "Objective:0:1", "@RefractiveIndex": "1.0"}, "Pixels": {"@BigEndian": "true", "@DimensionOrder": "XYCZT", "@ID": "Pixels:7", "@Interleaved": "true", "@PhysicalSizeX": "0.27372249550400146", "@PhysicalSizeXUnit": "\u00b5m", "@PhysicalSizeY": "0.2737273248209411", "@PhysicalSizeYUnit": "\u00b5m", "@SignificantBits": "8", "@SizeC": "3", "@SizeT": "1", "@SizeX": "21850", "@SizeY": "31136", "@SizeZ": "1", "@Type": "uint8", "Channel": {"@ID": "Channel:7:0", "@Name": "BF", "@SamplesPerPixel": "3", "DetectorSettings": {"@Binning": "1x1", "@Gain": "1.8468625188257375", "@ID": "Detector:0:1"}, "LightPath": null}, "MetadataOnly": null, "Plane": {"@ExposureTime": "4.62E-4", "@ExposureTimeUnit": "s", "@PositionX": "52904.98751836284", "@PositionXUnit": "\u00b5m", "@PositionY": "7826.101007850231", "@PositionYUnit": "\u00b5m", "@TheC": "0", "@TheT": "0", "@TheZ": "0"}}}, "StructuredAnnotations": {"XMLAnnotation": [{"@ID": "Annotation:0", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "overview Calibration units", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:1", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "Layer selection", "Value": "[952697198]"}}}, {"@ID": "Annotation:2", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Microscope Objective Description", "Value": "20x"}}}, {"@ID": "Annotation:3", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "Original magnification", "Value": "[20x, Overview]"}}}, {"@ID": "Annotation:4", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "Canvas background color 2", "Value": "[0]"}}}, {"@ID": "Annotation:5", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "Canvas background color 1", "Value": "[0]"}}}, {"@ID": "Annotation:6", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "overview Objective Working Distance Units", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:7", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "overview Microscope Device Position #7", "Value": "0"}}}, {"@ID": "Annotation:8", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "overview Microscope Device Position #6", "Value": "75"}}}, {"@ID": "Annotation:9", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #31", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:10", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "overview Microscope Device Position #5", "Value": "0"}}}, {"@ID": "Annotation:11", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #30", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:12", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "overview Microscope Device Position #4", "Value": "0"}}}, {"@ID": "Annotation:13", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "overview Microscope Device Position #3", "Value": "0"}}}, {"@ID": "Annotation:14", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "overview Microscope Device Position #2", "Value": "0"}}}, {"@ID": "Annotation:15", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "overview Microscope Device Position #1", "Value": "1"}}}, {"@ID": "Annotation:16", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "overview Microscope Aperture Max Mode", "Value": "0"}}}, {"@ID": "Annotation:17", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "Slide Name", "Value": "[Lame303]"}}}, {"@ID": "Annotation:18", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Channel name", "Value": "BF"}}}, {"@ID": "Annotation:19", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "overview Microscope Camera Gain Unit", "Value": "10^0#^1"}}}, {"@ID": "Annotation:20", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #29", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:21", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #28", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:22", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #27", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:23", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Microscope Device Manufacturer #15", "Value": "Olympus"}}}, {"@ID": "Annotation:24", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #26", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:25", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Microscope Device Manufacturer #14", "Value": "Olympus"}}}, {"@ID": "Annotation:26", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #25", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:27", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Microscope Device Manufacturer #13", "Value": "Olympus"}}}, {"@ID": "Annotation:28", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #24", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:29", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Microscope Device Manufacturer #12", "Value": "Olympus"}}}, {"@ID": "Annotation:30", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #23", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:31", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Microscope Device Manufacturer #11", "Value": "Olympus"}}}, {"@ID": "Annotation:32", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #22", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:33", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Microscope Device Manufacturer #10", "Value": "Olympus"}}}, {"@ID": "Annotation:34", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #21", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:35", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #20", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:36", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Microscope Device Manufacturer #09", "Value": "Olympus"}}}, {"@ID": "Annotation:37", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Microscope Device Manufacturer #08", "Value": "Olympus"}}}, {"@ID": "Annotation:38", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #19", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:39", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Microscope Device Manufacturer #07", "Value": "Olympus"}}}, {"@ID": "Annotation:40", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #18", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:41", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Microscope Device Manufacturer #06", "Value": "Olympus"}}}, {"@ID": "Annotation:42", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #17", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:43", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Microscope Device Manufacturer #05", "Value": "Olympus"}}}, {"@ID": "Annotation:44", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #16", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:45", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Microscope Device Manufacturer #04", "Value": "Olympus"}}}, {"@ID": "Annotation:46", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #15", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:47", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Microscope Device Manufacturer #03", "Value": "Olympus"}}}, {"@ID": "Annotation:48", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "Display processor type", "Value": "[1, 1, -1, 1, -1, -1]"}}}, {"@ID": "Annotation:49", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Units #14", "Value": "10^-6m^1"}}}, {"@ID": "Annotation:50", "@Namespace": "openmicroscopy.org/OriginalMetadata", "Value": {"OriginalMetadata": {"Key": "20x_BF_01 Microscope Device Manufacturer #02", "Value": "Olympus"}}}, {"@ID": "Annotation:51", "@Namespace": 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  TileOffsets 324 (0x144) LONG8: <13860> 253536 272390 291126 309895 328813 347460 366121 384804 403463 422073 440843 459807 478682 497375 515970 534786 553567 572193 590860 609363 ...
  TileByteCounts 325 (0x145) LONG: <13860> 18854 18736 18769 18918 18647 18661 18683 18659 18610 18770 18964 18875 18693 18595 18816 18781 18626 18667 18503 18575 ...
  YCbCrSubsampling 530 (0x212) SHORT: <2> 2 2
  ReferenceBlackWhite 532 (0x214) RATIONAL: <6> 0 1 (0) 255 1 (255) 128 1 (128) 255 1 (255) 128 1 (128) 255 1 (255)
Directory 1: offset 299207168 (0x11d58a00)
  NewSubfileType 254 (0xFE) LONG: 1 (ReducedImage 1 (0x1))
  ImageWidth 256 (0x100) LONG: 11008
  ImageLength 257 (0x101) LONG: 15616
  BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
  Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
  Photometric 262 (0x106) SHORT: 6 (YCbCr 6 (0x6))
  ImageDescription 270 (0x10E) ASCII: [... Too long for github comments]
  SamplesPerPixel 277 (0x115) SHORT: 3
  XResolution 282 (0x11A) RATIONAL: 36533 64 (570.82812)
  YResolution 283 (0x11B) RATIONAL: 9133 16 (570.8125)
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  ResolutionUnit 296 (0x128) SHORT: 3 (Centimeter 3 (0x3))
  Software 305 (0x131) ASCII: tifffile.py
  TileWidth 322 (0x142) LONG: 224
  TileLength 323 (0x143) LONG: 224
  TileOffsets 324 (0x144) LONG8: <6> 443755936 443786105 443803237 443827435 443840411 443846764
  TileByteCounts 325 (0x145) LONG: <6> 30169 17132 24198 12976 6353 2555
  YCbCrSubsampling 530 (0x212) SHORT: <2> 2 2
  ReferenceBlackWhite 532 (0x214) RATIONAL: <6> 0 1 (0) 255 1 (255) 128 1 (128) 255 1 (255) 128 1 (128) 255 1 (255)

Do you where the error may come from?

@jacksonjacobs1
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Hi @bsauty. What file format is your image? ome-tiff?

@Himanshunitrr
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Himanshunitrr commented Jul 24, 2024 •
edited
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getting the same error, what can be a workaround for it?

output of tifftools dump file_path:

Header: 0x4949
Directory 0: offset 5674472 (0x5695e8)
NewSubfileType 254 (0xFE) LONG: 2 (Page 2 (0x2))
ImageWidth 256 (0x100) SHORT: 4096
ImageLength 257 (0x101) SHORT: 2112
BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
Photometric 262 (0x106) SHORT: 2 (RGB 2 (0x2))
FillOrder 266 (0x10A) SHORT: 1 (MSBToLSB 1 (0x1))
Orientation 274 (0x112) SHORT: 1 (TopLeft 1 (0x1))
SamplesPerPixel 277 (0x115) SHORT: 3
XResolution 282 (0x11A) RATIONAL: 72 1 (72)
YResolution 283 (0x11B) RATIONAL: 72 1 (72)
PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
ResolutionUnit 296 (0x128) SHORT: 2 (Inch 2 (0x2))
PageNumber 297 (0x129) SHORT: <2> 0 7
WhitePoint 318 (0x13E) RATIONAL: <2> 1343036287 4294967295 (0.3127) 1413044223 4294967295 (0.329)
PrimaryChromaticities 319 (0x13F) RATIONAL: <6> 2748779007 4294967295 (0.63999999) 1417339263 4294967295 (0.33000001) 1288490239 4294967295 (0.30000001) 2576980479 4294967295 (0.60000002) 644245119 4294967295 (0.15000001) 257698031 4294967295 (0.059999998)
TileWidth 322 (0x142) SHORT: 256
TileLength 323 (0x143) SHORT: 256
TileOffsets 324 (0x144) LONG: <144> 8 8589 21115 49564 97217 149847 179115 211976 262365 284763 297055 305574 315545 323976 358566 376250 386241 412680 452264 513805 ...
TileByteCounts 325 (0x145) LONG: <144> 8581 12526 28449 47653 52630 29268 32861 50389 22398 12292 8519 9971 8431 34590 17684 9991 26439 39584 61541 55093 ...
JPEGTables 347 (0x15B) UNDEFINED: <289> b'\xff\xd8\xff\xdb\x00C\x00\x08\x06\x06\x07\x06\x05\x08\x07\x07\x07\t\t\x08' ... (estimated quality: 75)
Directory 1: offset 7247020 (0x6e94ac)
NewSubfileType 254 (0xFE) LONG: 2 (Page 2 (0x2))
ImageWidth 256 (0x100) SHORT: 2048
ImageLength 257 (0x101) SHORT: 1056
BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
Photometric 262 (0x106) SHORT: 2 (RGB 2 (0x2))
FillOrder 266 (0x10A) SHORT: 1 (MSBToLSB 1 (0x1))
Orientation 274 (0x112) SHORT: 1 (TopLeft 1 (0x1))
SamplesPerPixel 277 (0x115) SHORT: 3
XResolution 282 (0x11A) RATIONAL: 36 1 (36)
YResolution 283 (0x11B) RATIONAL: 36 1 (36)
PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
ResolutionUnit 296 (0x128) SHORT: 2 (Inch 2 (0x2))
PageNumber 297 (0x129) SHORT: <2> 0 7
WhitePoint 318 (0x13E) RATIONAL: <2> 1343036287 4294967295 (0.3127) 1413044223 4294967295 (0.329)
PrimaryChromaticities 319 (0x13F) RATIONAL: <6> 2748779007 4294967295 (0.63999999) 1417339263 4294967295 (0.33000001) 1288490239 4294967295 (0.30000001) 2576980479 4294967295 (0.60000002) 644245119 4294967295 (0.15000001) 257698031 4294967295 (0.059999998)
TileWidth 322 (0x142) SHORT: 256
TileLength 323 (0x143) SHORT: 256
TileOffsets 324 (0x144) LONG: <40> 5676258 5697137 5742952 5791648 5836358 5861105 5876841 5897616 5907459 5964385 6033088 6103051 6158170 6212783 6274441 6302831 6334857 6387015 6462835 6520616 ...
TileByteCounts 325 (0x145) LONG: <40> 20879 45815 48696 44710 24747 15736 20775 9843 56926 68703 69963 55119 54613 61658 28390 32026 52158 75820 57781 36260 ...
JPEGTables 347 (0x15B) UNDEFINED: <289> b'\xff\xd8\xff\xdb\x00C\x00\x08\x06\x06\x07\x06\x05\x08\x07\x07\x07\t\t\x08' ... (estimated quality: 75)
Directory 2: offset 7697542 (0x757486)
NewSubfileType 254 (0xFE) LONG: 2 (Page 2 (0x2))
ImageWidth 256 (0x100) SHORT: 1024
ImageLength 257 (0x101) SHORT: 528
BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
Photometric 262 (0x106) SHORT: 2 (RGB 2 (0x2))
FillOrder 266 (0x10A) SHORT: 1 (MSBToLSB 1 (0x1))
Orientation 274 (0x112) SHORT: 1 (TopLeft 1 (0x1))
SamplesPerPixel 277 (0x115) SHORT: 3
XResolution 282 (0x11A) RATIONAL: 18 1 (18)
YResolution 283 (0x11B) RATIONAL: 18 1 (18)
PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
ResolutionUnit 296 (0x128) SHORT: 2 (Inch 2 (0x2))
PageNumber 297 (0x129) SHORT: <2> 0 7
WhitePoint 318 (0x13E) RATIONAL: <2> 1343036287 4294967295 (0.3127) 1413044223 4294967295 (0.329)
PrimaryChromaticities 319 (0x13F) RATIONAL: <6> 2748779007 4294967295 (0.63999999) 1417339263 4294967295 (0.33000001) 1288490239 4294967295 (0.30000001) 2576980479 4294967295 (0.60000002) 644245119 4294967295 (0.15000001) 257698031 4294967295 (0.059999998)
TileWidth 322 (0x142) SHORT: 256
TileLength 323 (0x143) SHORT: 256
TileOffsets 324 (0x144) LONG: <12> 7247974 7294760 7348260 7388129 7409788 7454640 7492213 7511560 7550494 7587099 7624360 7661021
TileByteCounts 325 (0x145) LONG: <12> 46786 53500 39869 21659 44852 37573 19347 38934 36605 37261 36661 36520
JPEGTables 347 (0x15B) UNDEFINED: <289> b'\xff\xd8\xff\xdb\x00C\x00\x08\x06\x06\x07\x06\x05\x08\x07\x07\x07\t\t\x08' ... (estimated quality: 75)
Directory 3: offset 7831140 (0x777e64)
NewSubfileType 254 (0xFE) LONG: 2 (Page 2 (0x2))
ImageWidth 256 (0x100) SHORT: 512
ImageLength 257 (0x101) SHORT: 264
BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
Photometric 262 (0x106) SHORT: 2 (RGB 2 (0x2))
FillOrder 266 (0x10A) SHORT: 1 (MSBToLSB 1 (0x1))
Orientation 274 (0x112) SHORT: 1 (TopLeft 1 (0x1))
SamplesPerPixel 277 (0x115) SHORT: 3
XResolution 282 (0x11A) RATIONAL: 9 1 (9)
YResolution 283 (0x11B) RATIONAL: 9 1 (9)
PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
ResolutionUnit 296 (0x128) SHORT: 2 (Inch 2 (0x2))
PageNumber 297 (0x129) SHORT: <2> 0 7
WhitePoint 318 (0x13E) RATIONAL: <2> 1343036287 4294967295 (0.3127) 1413044223 4294967295 (0.329)
PrimaryChromaticities 319 (0x13F) RATIONAL: <6> 2748779007 4294967295 (0.63999999) 1417339263 4294967295 (0.33000001) 1288490239 4294967295 (0.30000001) 2576980479 4294967295 (0.60000002) 644245119 4294967295 (0.15000001) 257698031 4294967295 (0.059999998)
TileWidth 322 (0x142) SHORT: 256
TileLength 323 (0x143) SHORT: 256
TileOffsets 324 (0x144) LONG: <4> 7698272 7742199 7771771 7801578
TileByteCounts 325 (0x145) LONG: <4> 43927 29572 29807 29561
JPEGTables 347 (0x15B) UNDEFINED: <289> b'\xff\xd8\xff\xdb\x00C\x00\x08\x06\x06\x07\x06\x05\x08\x07\x07\x07\t\t\x08' ... (estimated quality: 75)
Directory 4: offset 7852384 (0x77d160)
NewSubfileType 254 (0xFE) LONG: 2 (Page 2 (0x2))
ImageWidth 256 (0x100) SHORT: 256
ImageLength 257 (0x101) SHORT: 132
BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
Photometric 262 (0x106) SHORT: 2 (RGB 2 (0x2))
FillOrder 266 (0x10A) SHORT: 1 (MSBToLSB 1 (0x1))
Orientation 274 (0x112) SHORT: 1 (TopLeft 1 (0x1))
SamplesPerPixel 277 (0x115) SHORT: 3
XResolution 282 (0x11A) RATIONAL: 4294967295 954437176 (4.5)
YResolution 283 (0x11B) RATIONAL: 4294967295 954437176 (4.5)
PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
ResolutionUnit 296 (0x128) SHORT: 2 (Inch 2 (0x2))
PageNumber 297 (0x129) SHORT: <2> 0 7
WhitePoint 318 (0x13E) RATIONAL: <2> 1343036287 4294967295 (0.3127) 1413044223 4294967295 (0.329)
PrimaryChromaticities 319 (0x13F) RATIONAL: <6> 2748779007 4294967295 (0.63999999) 1417339263 4294967295 (0.33000001) 1288490239 4294967295 (0.30000001) 2576980479 4294967295 (0.60000002) 644245119 4294967295 (0.15000001) 257698031 4294967295 (0.059999998)
TileWidth 322 (0x142) SHORT: 256
TileLength 323 (0x143) SHORT: 256
TileOffsets 324 (0x144) LONG: 7831806
TileByteCounts 325 (0x145) LONG: 20577
JPEGTables 347 (0x15B) UNDEFINED: <289> b'\xff\xd8\xff\xdb\x00C\x00\x08\x06\x06\x07\x06\x05\x08\x07\x07\x07\t\t\x08' ... (estimated quality: 75)
Directory 5: offset 7860542 (0x77f13e)
NewSubfileType 254 (0xFE) LONG: 2 (Page 2 (0x2))
ImageWidth 256 (0x100) SHORT: 128
ImageLength 257 (0x101) SHORT: 66
BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
Photometric 262 (0x106) SHORT: 2 (RGB 2 (0x2))
FillOrder 266 (0x10A) SHORT: 1 (MSBToLSB 1 (0x1))
Orientation 274 (0x112) SHORT: 1 (TopLeft 1 (0x1))
SamplesPerPixel 277 (0x115) SHORT: 3
XResolution 282 (0x11A) RATIONAL: 4294967295 1908874353 (2.25)
YResolution 283 (0x11B) RATIONAL: 4294967295 1908874353 (2.25)
PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
ResolutionUnit 296 (0x128) SHORT: 2 (Inch 2 (0x2))
PageNumber 297 (0x129) SHORT: <2> 0 7
WhitePoint 318 (0x13E) RATIONAL: <2> 1343036287 4294967295 (0.3127) 1413044223 4294967295 (0.329)
PrimaryChromaticities 319 (0x13F) RATIONAL: <6> 2748779007 4294967295 (0.63999999) 1417339263 4294967295 (0.33000001) 1288490239 4294967295 (0.30000001) 2576980479 4294967295 (0.60000002) 644245119 4294967295 (0.15000001) 257698031 4294967295 (0.059999998)
TileWidth 322 (0x142) SHORT: 256
TileLength 323 (0x143) SHORT: 256
TileOffsets 324 (0x144) LONG: 7853018
TileByteCounts 325 (0x145) LONG: 7524
JPEGTables 347 (0x15B) UNDEFINED: <289> b'\xff\xd8\xff\xdb\x00C\x00\x08\x06\x06\x07\x06\x05\x08\x07\x07\x07\t\t\x08' ... (estimated quality: 75)
Directory 6: offset 7865204 (0x780374)
NewSubfileType 254 (0xFE) LONG: 2 (Page 2 (0x2))
ImageWidth 256 (0x100) SHORT: 64
ImageLength 257 (0x101) SHORT: 33
BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
Photometric 262 (0x106) SHORT: 2 (RGB 2 (0x2))
FillOrder 266 (0x10A) SHORT: 1 (MSBToLSB 1 (0x1))
Orientation 274 (0x112) SHORT: 1 (TopLeft 1 (0x1))
SamplesPerPixel 277 (0x115) SHORT: 3
XResolution 282 (0x11A) RATIONAL: 4294967295 3817748706 (1.125)
YResolution 283 (0x11B) RATIONAL: 4294967295 3817748706 (1.125)
PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
ResolutionUnit 296 (0x128) SHORT: 2 (Inch 2 (0x2))
PageNumber 297 (0x129) SHORT: <2> 0 7
WhitePoint 318 (0x13E) RATIONAL: <2> 1343036287 4294967295 (0.3127) 1413044223 4294967295 (0.329)
PrimaryChromaticities 319 (0x13F) RATIONAL: <6> 2748779007 4294967295 (0.63999999) 1417339263 4294967295 (0.33000001) 1288490239 4294967295 (0.30000001) 2576980479 4294967295 (0.60000002) 644245119 4294967295 (0.15000001) 257698031 4294967295 (0.059999998)
TileWidth 322 (0x142) SHORT: 256
TileLength 323 (0x143) SHORT: 256
TileOffsets 324 (0x144) LONG: 7861176

related errorlog:
<class 'TypeError'> Inappropriate argument type. __init__() should return None, not 'int'

024-07-24 18:28:12,242 - INFO - -----Working on: /data/TMH_69.tiff 57 of 63 2024-07-24 18:28:12,296 - INFO - TMH_26.tiff - getMag 2024-07-24 18:28:12,296 - ERROR - TMH_26.tiff: Has unknown or uncalculated base magnification, cannot specify magnification scale! Did you try getMag? 2024-07-24 18:28:12,296 - ERROR - /data/TMH_26.tiff - Error analyzing file (skipping): <class 'TypeError'> Inappropriate argument type. __init__() should return None, not 'int'

I tried adding base_mag=40x in config_v2.1.ini but it did not help

@jacksonjacobs1
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Hi @Himanshunitrr ,

It seems your problematic image has a .tiff file format but does not have an ImageDescription header.

I would recommend the solution suggested above: #304 (comment) to inject the missing metadata into your image.

@bsauty
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bsauty commented Jul 29, 2024

Hi @bsauty. What file format is your image? ome-tiff?

It's vsi format that was later converted to tiff using tifffile.

@jacksonjacobs1
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Okay, thanks. In that case it seems like ImageDescription does not contain the required metadata for HistoQC to run correctly.

I would again recommend "spoofing" the Aperio format by following the above tutorial. You may want to hold on to the xml namespace stuff which currently populates the ImageDescription.

@jacksonjacobs1 jacksonjacobs1 moved this from Todo to Done in @jacksonjacobs1's HistoTools Nov 19, 2024
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