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Error Handling #141

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manthey opened this issue Jul 25, 2023 · 2 comments
Open

Error Handling #141

manthey opened this issue Jul 25, 2023 · 2 comments

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@manthey
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manthey commented Jul 25, 2023

Running on a few files on windows, the server stops due to an exception:

  + Exception Group Traceback (most recent call last):
  |   File "imagedephi\__main__.py", line 4, in <module>
  |   File "click\core.py", line 1130, in __call__
  |   File "click\core.py", line 1055, in main
  |   File "imagedephi\utils\cli.py", line 48, in invoke
  |   File "click\core.py", line 1657, in invoke
  |   File "click\core.py", line 1404, in invoke
  |   File "click\core.py", line 760, in invoke
  |   File "imagedephi\utils\cli.py", line 17, in wrapper
  |   File "asyncio\runners.py", line 190, in run
  |   File "asyncio\runners.py", line 118, in run
  |   File "asyncio\base_events.py", line 653, in run_until_complete
  |   File "imagedephi\main.py", line 108, in gui
  |   File "asyncio\taskgroups.py", line 147, in __aexit__
  | ExceptionGroup: unhandled errors in a TaskGroup (1 sub-exception)
  +-+---------------- 1 ----------------
    | Traceback (most recent call last):
    |   File "starlette\routing.py", line 677, in lifespan
    |   File "contextlib.py", line 211, in __aexit__
    |   File "imagedephi\gui.py", line 35, in lifespan
    |   File "hypercorn\asyncio\task_group.py", line 23, in _handle
    |   File "hypercorn\app_wrappers.py", line 33, in __call__
    |   File "fastapi\applications.py", line 289, in __call__
    |   File "starlette\applications.py", line 122, in __call__
    |   File "starlette\middleware\errors.py", line 184, in __call__
    |   File "starlette\middleware\errors.py", line 162, in __call__
    |   File "starlette\middleware\exceptions.py", line 79, in __call__
    |   File "starlette\middleware\exceptions.py", line 68, in __call__
    |   File "fastapi\middleware\asyncexitstack.py", line 20, in __call__
    |   File "fastapi\middleware\asyncexitstack.py", line 17, in __call__
    |   File "starlette\routing.py", line 718, in __call__
    |   File "starlette\routing.py", line 276, in handle
    |   File "starlette\routing.py", line 66, in app
    |   File "fastapi\routing.py", line 273, in app
    |   File "fastapi\routing.py", line 192, in run_endpoint_function
    |   File "starlette\concurrency.py", line 41, in run_in_threadpool
    |   File "anyio\to_thread.py", line 33, in run_sync
    |   File "anyio\_backends\_asyncio.py", line 877, in run_sync_in_worker_thread
    |   File "anyio\_backends\_asyncio.py", line 807, in run
    |   File "imagedephi\gui.py", line 122, in redact
    |   File "imagedephi\redact\redact.py", line 77, in redact_images
    |   File "imagedephi\redact\redact.py", line 106, in show_redaction_plan
    |   File "imagedephi\redact\build_redaction_plan.py", line 32, in build_redaction_plan
    |   File "imagedephi\redact\svs.py", line 84, in __init__
    |   File "imagedephi\redact\tiff.py", line 133, in __init__
    |   File "imagedephi\redact\svs.py", line 115, in get_associated_image_key_for_ifd
    | KeyError: 270
    | 
    | During handling of the above exception, another exception occurred:
    | 
    | Traceback (most recent call last):
    |   File "hypercorn\asyncio\__init__.py", line 49, in serve
    |   File "hypercorn\asyncio\run.py", line 173, in worker_serve
    |   File "hypercorn\asyncio\lifespan.py", line 43, in handle_lifespan
    |   File "hypercorn\app_wrappers.py", line 33, in __call__
    |   File "fastapi\applications.py", line 289, in __call__
    |   File "starlette\applications.py", line 122, in __call__
    |   File "starlette\middleware\errors.py", line 149, in __call__
    |   File "starlette\middleware\exceptions.py", line 55, in __call__
    |   File "fastapi\middleware\asyncexitstack.py", line 20, in __call__
    |   File "fastapi\middleware\asyncexitstack.py", line 17, in __call__
    |   File "starlette\routing.py", line 707, in __call__
    |   File "starlette\routing.py", line 690, in lifespan
    |   File "hypercorn\asyncio\lifespan.py", line 104, in asgi_send
    | hypercorn.utils.LifespanFailureError: Lifespan failure in shutdown. 'Traceback (most recent call last):
  File "starlette\routing.py", line 677, in lifespan
  File "contextlib.py", line 211, in __aexit__
  File "imagedephi\gui.py", line 35, in lifespan
  File "hypercorn\asyncio\task_group.py", line 23, in _handle
  File "hypercorn\app_wrappers.py", line 33, in __call__
  File "fastapi\applications.py", line 289, in __call__
  File "starlette\applications.py", line 122, in __call__
  File "starlette\middleware\errors.py", line 184, in __call__
  File "starlette\middleware\errors.py", line 162, in __call__
  File "starlette\middleware\exceptions.py", line 79, in __call__
  File "starlette\middleware\exceptions.py", line 68, in __call__
  File "fastapi\middleware\asyncexitstack.py", line 20, in __call__
  File "fastapi\middleware\asyncexitstack.py", line 17, in __call__
  File "starlette\routing.py", line 718, in __call__
  File "starlette\routing.py", line 276, in handle
  File "starlette\routing.py", line 66, in app
  File "fastapi\routing.py", line 273, in app
  File "fastapi\routing.py", line 192, in run_endpoint_function
  File "starlette\concurrency.py", line 41, in run_in_threadpool
  File "anyio\to_thread.py", line 33, in run_sync
  File "anyio\_backends\_asyncio.py", line 877, in run_sync_in_worker_thread
  File "anyio\_backends\_asyncio.py", line 807, in run
  File "imagedephi\gui.py", line 122, in redact
  File "imagedephi\redact\redact.py", line 77, in redact_images
  File "imagedephi\redact\redact.py", line 106, in show_redaction_plan
  File "imagedephi\redact\build_redaction_plan.py", line 32, in build_redaction_plan
  File "imagedephi\redact\svs.py", line 84, in __init__
  File "imagedephi\redact\tiff.py", line 133, in __init__
  File "imagedephi\redact\svs.py", line 115, in get_associated_image_key_for_ifd
KeyError: 270
'
    +------------------------------------
[12480] Failed to execute script '__main__' due to unhandled exception!

We should catch (and log) exceptions rather than halting the program.
@manthey manthey mentioned this issue Jul 25, 2023
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@naglepuff
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Do you recall what file this happened to? I'm trying to figure out a root cause.

Is it valid for an svs file to have IFDs with no ImageDescription? I think that this line of code should only be hit if we determine that a given image is an svs file. Maybe our method of relying on file extension has caught up with us?

@manthey
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manthey commented Aug 8, 2023

Yes, it appears to be a valid svs file (at least according to a version of ImageScope). If I run tifftools dump on the file, I get the text below. I can provide a synthetic test file or the original (the synthetic file just runs the ttdump_to_tiff.py program on the dump below). It looks like the macro and label images within the svs don't have ImageDescriptions (but the pyramidal images do).

-- /mnt/transfer/nomacrodescription.svs --
Header: 0x4949 <little-endian> <BigTIFF>
Directory 0: offset 625945748 (0x254f2c94)
  NewSubfileType 254 (0xFE) LONG: 0
  ImageWidth 256 (0x100) SHORT: 57201
  ImageLength 257 (0x101) LONG: 93897
  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: Aperio Leica Biosystems Segue v1.0 
57201x93897 [0,0,57201x93897] (256x256) JPEG/YCC Q=91|AppMag = 40|Gamma = 2.2|Left = 0|MPP = 0.263158|ScanScope ID = alpha5|StripeWidth = 4096|Top = 0
  SamplesPerPixel 277 (0x115) SHORT: 3
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  TileWidth 322 (0x142) SHORT: 256
  TileLength 323 (0x143) SHORT: 256
  TileOffsets 324 (0x144) LONG8: <82208> 16 2208671 4352655 6444943 8483123 10470627 12442988 14401228 16353995 18295573 20235202 22189119 24178011 26193868 28259835 30387541 32587950 34896332 37149521 39366259 ...
  TileByteCounts 325 (0x145) LONG8: <82208> 6153 5892 5911 5636 5518 5409 5374 5392 5403 5323 5371 5469 5488 5416 5601 5772 6026 5811 5681 5562 ...
  ImageDepth 32997 (0x80E5) LONG: 1
  ICCProfile 34675 (0x8773) UNDEFINED: <13113264> b'\x00\xc8\x17\xb0SICC\x04\x00\x00\x00scnrRGB ' ...
Directory 1: offset 640401894 (0x262bc1e6)
  NewSubfileType 254 (0xFE) LONG: 0
  ImageWidth 256 (0x100) SHORT: 467
  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: 6 (YCbCr 6 (0x6))
  ImageDescription 270 (0x10E) ASCII: Aperio Leica Biosystems Segue v1.0 
467x768 [0,0,467x768] (467x768) JPEG/YCC Q=100|CompressedFile = \\uscavs-eng-is1.aperio.int\is1\Images\alpha5\dfd77469-ba7f-8d82-e768-42efc297d999.svs|Left = 0|MPP = 32.233179|ScanScope ID = alpha5|Top = 0
  StripOffsets 273 (0x111) LONG8: 640374844
  SamplesPerPixel 277 (0x115) SHORT: 3
  RowsPerStrip 278 (0x116) SHORT: 768
  StripByteCounts 279 (0x117) LONG8: 27049
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
Directory 2: offset 669891302 (0x27edbae6)
  NewSubfileType 254 (0xFE) LONG: 0
  ImageWidth 256 (0x100) SHORT: 14300
  ImageLength 257 (0x101) SHORT: 23474
  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: Aperio Leica Biosystems Segue v1.0 
14300x23474 [0,0,14300x23474] (256x256) JPEG/YCC Q=91|AppMag = 10|Gamma = 2.2|Left = 0|MPP = 1.052632|ScanScope ID = alpha5|StripeWidth = 4096|Top = 0
  SamplesPerPixel 277 (0x115) SHORT: 3
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  TileWidth 322 (0x142) SHORT: 256
  TileLength 323 (0x143) SHORT: 256
  TileOffsets 324 (0x144) LONG8: <5152> 640402392 640404973 640407102 640409130 640411238 640413365 640415388 640417368 640419455 640421704 640423829 640425920 640428133 640430307 640432472 640434529 640436640 640438765 640440862 640442951 ...
  TileByteCounts 325 (0x145) LONG8: <5152> 2581 2129 2028 2108 2127 2023 1980 2087 2249 2125 2091 2213 2174 2165 2057 2111 2125 2097 2089 2166 ...
  ICCProfile 34675 (0x8773) UNDEFINED: <13113264> b'\x00\xc8\x17\xb0SICC\x04\x00\x00\x00scnrRGB ' ...
Directory 3: offset 684883546 (0x28d27e5a)
  NewSubfileType 254 (0xFE) LONG: 0
  ImageWidth 256 (0x100) SHORT: 3575
  ImageLength 257 (0x101) SHORT: 5868
  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: Aperio Leica Biosystems Segue v1.0 
3575x5868 [0,0,3575x5868] (256x256) JPEG/YCC Q=91|AppMag = 2.5|Gamma = 2.2|Left = 0|MPP = 4.210526|ScanScope ID = alpha5|StripeWidth = 4096|Top = 0
  SamplesPerPixel 277 (0x115) SHORT: 3
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  TileWidth 322 (0x142) SHORT: 256
  TileLength 323 (0x143) SHORT: 256
  TileOffsets 324 (0x144) LONG8: <322> 683087482 683089738 683091634 683093492 683095365 683097201 683099205 683101577 683103661 683106972 683111427 683113871 683116130 683118448 683120601 683122735 683124645 683126642 683128644 683130622 ...
  TileByteCounts 325 (0x145) LONG8: <322> 2256 1896 1858 1873 1836 2004 2372 2084 3311 4455 2444 2259 2318 2153 2134 1910 1997 2002 1978 1852 ...
  ICCProfile 34675 (0x8773) UNDEFINED: <13113264> b'\x00\xc8\x17\xb0SICC\x04\x00\x00\x00scnrRGB ' ...
Directory 4: offset 704373032 (0x29fbe128)
  NewSubfileType 254 (0xFE) LONG: 1 (ReducedImage 1 (0x1))
  ImageWidth 256 (0x100) SHORT: 1961
  ImageLength 257 (0x101) SHORT: 1601
  BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
  Compression 259 (0x103) SHORT: 5 (LZW 5 (0x5))
  Photometric 262 (0x106) SHORT: 2 (RGB 2 (0x2))
  StripOffsets 273 (0x111) LONG8: 698002442
  SamplesPerPixel 277 (0x115) SHORT: 3
  RowsPerStrip 278 (0x116) SHORT: 1601
  StripByteCounts 279 (0x117) LONG8: 6370589
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  Predictor 317 (0x13D) SHORT: 2 (Horizontal 2 (0x2))
Directory 5: offset 705278412 (0x2a09b1cc)
  NewSubfileType 254 (0xFE) LONG: 9 (ReducedImage 1 (0x1), Macro 8 (0x8))
  ImageWidth 256 (0x100) SHORT: 1831
  ImageLength 257 (0x101) SHORT: 4201
  BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
  Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
  Photometric 262 (0x106) SHORT: 2 (RGB 2 (0x2))
  StripOffsets 273 (0x111) LONG8: 704373288
  SamplesPerPixel 277 (0x115) SHORT: 3
  RowsPerStrip 278 (0x116) SHORT: 4201
  StripByteCounts 279 (0x117) LONG8: 905124
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))

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@naglepuff @manthey