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NVIDIA / nvImageCodec

A nvImageCodec library of GPU- and CPU- accelerated codecs featuring a unified interface
https://docs.nvidia.com/cuda/nvimagecodec/index.html
Apache License 2.0
52 stars 4 forks source link

Incorrect decoding of 16-bit TIFF images #5

Open Crackvignoule opened 2 months ago

Crackvignoule commented 2 months ago

Version

0.2.0.7

Describe the bug.

Hi, I'm encountering an issue when decoding 16-bit TIFF images using the nvImageCodec library. The decoded image appears to be duplicated and the range of pixel values is different from the expected range.

Expected result: The decoded image should match the original image, both in terms of pixel values and visual appearance.

Actual result: The decoded image appears to be duplicated and the range of pixel values is different from the expected range.

Expected Output: image

Actual Output: image

Minimum reproducible example

import cupy as cp
import numpy as np
from nvidia import nvimgcodec
import matplotlib.pyplot as plt
from tifffile import imread, imwrite

def sh_info(img, header=""):
    print(header)
    print(f"\tShape: {img.shape}")
    print(f"\tMin value: {img.min()}")
    print(f"\tMax value: {img.max()}")
    print(f"\tData type: {img.dtype}")

# Creating a random 16-bit image
arr = np.random.random((4096, 4096))
arr *= 60000
arr[100:400, 100:400] = 61000
arr = arr.astype(np.uint16)
sh_info(arr, "Original Image")

# Writing the image to a tif file and reading it back
imwrite('test.tif', arr, dtype=np.uint16)
img0 = imread('test.tif')
sh_info(img0, "tifffile Decoded Image")

# Decode the image using nvimgcodec
params = nvimgcodec.DecodeParams(color_spec=nvimgcodec.ColorSpec.UNCHANGED, allow_any_depth=True)
dec = nvimgcodec.Decoder()
img_decoded = dec.read('test.tif', params)

# Convert the decoded image to a CuPy array
cp_img = cp.asarray(img_decoded).get()
sh_info(cp_img, "nvImageCodec Decoded Image")

# Create a figure with 3 subplots
plt.figure(figsize=(15, 5))

plt.subplot(1, 3, 1)
plt.title('Original Image')
plt.imshow(arr)

plt.subplot(1, 3, 2)
plt.title("tifffile Decoded Image")
plt.imshow(img0)

plt.subplot(1, 3, 3)
plt.title('nvImageCodec Decoded Image')
plt.imshow(cp_img)

plt.tight_layout()
plt.show()

Environment details

<details><summary>Click here to see environment details</summary><pre>

     **git***
     commit b1b3f28d3bd52804370bc246d145164cf412f8df (HEAD -> data-loading-enhancement, origin/data-loading-enhancement)
     Author: Crackvignoule <kiki.kalagan@gmail.com>
     Date:   Tue Apr 23 14:52:58 2024 +0200

     update tests
     **git submodules***

     ***OS Information***
     DISTRIB_ID=Ubuntu
     DISTRIB_RELEASE=20.04
     DISTRIB_CODENAME=focal
     DISTRIB_DESCRIPTION="Ubuntu 20.04.6 LTS"
     NAME="Ubuntu"
     VERSION="20.04.6 LTS (Focal Fossa)"
     ID=ubuntu
     ID_LIKE=debian
     PRETTY_NAME="Ubuntu 20.04.6 LTS"
     VERSION_ID="20.04"
     HOME_URL="https://www.ubuntu.com/"
     SUPPORT_URL="https://help.ubuntu.com/"
     BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
     PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
     VERSION_CODENAME=focal
     UBUNTU_CODENAME=focal
     Linux aar164 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:28 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

     ***GPU Information***
     Wed Apr 24 09:44:28 2024
     +-----------------------------------------------------------------------------+
     | NVIDIA-SMI 510.39.01    Driver Version: 510.39.01    CUDA Version: 11.6     |
     |-------------------------------+----------------------+----------------------+
     | GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
     | Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
     |                               |                      |               MIG M. |
     |===============================+======================+======================|
     |   0  NVIDIA A100 80G...  On   | 00000000:CA:00.0 Off |                    0 |
     | N/A   29C    P0    64W / 300W |   5982MiB / 81920MiB |      0%      Default |
     |                               |                      |             Disabled |
     +-------------------------------+----------------------+----------------------+

     +-----------------------------------------------------------------------------+
     | Processes:                                                                  |
     |  GPU   GI   CI        PID   Type   Process name                  GPU Memory |
     |        ID   ID                                                   Usage      |
     |=============================================================================|
     |    0   N/A  N/A     12726      C   .../envs/env_cuda/bin/python      539MiB |
     |    0   N/A  N/A     13127      C   ...a_v11/ollama_llama_server     5441MiB |
     +-----------------------------------------------------------------------------+

     ***CPU***
     Architecture:                       x86_64
     CPU op-mode(s):                     32-bit, 64-bit
     Byte Order:                         Little Endian
     Address sizes:                      46 bits physical, 57 bits virtual
     CPU(s):                             128
     On-line CPU(s) list:                0-127
     Thread(s) per core:                 2
     Core(s) per socket:                 32
     Socket(s):                          2
     NUMA node(s):                       2
     Vendor ID:                          GenuineIntel
     CPU family:                         6
     Model:                              106
     Model name:                         Intel(R) Xeon(R) Platinum 8362 CPU @ 2.80GHz
     Stepping:                           6
     CPU MHz:                            800.101
     BogoMIPS:                           5600.00
     Virtualization:                     VT-x
     L1d cache:                          3 MiB
     L1i cache:                          2 MiB
     L2 cache:                           80 MiB
     L3 cache:                           96 MiB
     NUMA node0 CPU(s):                  0,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78,80,82,84,86,88,90,92,94,96,98,100,102,104,106,108,110,112,114,116,118,120,122,124,126
     NUMA node1 CPU(s):                  1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,87,89,91,93,95,97,99,101,103,105,107,109,111,113,115,117,119,121,123,125,127
     Vulnerability Gather data sampling: Mitigation; Microcode
     Vulnerability Itlb multihit:        Not affected
     Vulnerability L1tf:                 Not affected
     Vulnerability Mds:                  Not affected
     Vulnerability Meltdown:             Not affected
     Vulnerability Mmio stale data:      Mitigation; Clear CPU buffers; SMT vulnerable
     Vulnerability Retbleed:             Not affected
     Vulnerability Spec store bypass:    Mitigation; Speculative Store Bypass disabled via prctl and seccomp
     Vulnerability Spectre v1:           Mitigation; usercopy/swapgs barriers and __user pointer sanitization
     Vulnerability Spectre v2:           Mitigation; Enhanced IBRS, IBPB conditional, RSB filling, PBRSB-eIBRS SW sequence
     Vulnerability Srbds:                Not affected
     Vulnerability Tsx async abort:      Not affected
     Flags:                              fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 invpcid_single ssbd mba ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm rdt_a avx512f avx512dq rdseed adx smap avx512ifma clflushopt clwb intel_pt avx512cd sha_ni avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local wbnoinvd dtherm ida arat pln pts avx512vbmi umip pku ospke avx512_vbmi2 gfni vaes vpclmulqdq avx512_vnni avx512_bitalg tme avx512_vpopcntdq rdpid md_clear pconfig flush_l1d arch_capabilities

     ***CMake***
     /bin/cmake
     cmake version 3.16.3

     CMake suite maintained and supported by Kitware (kitware.com/cmake).

     ***g++***
     /bin/g++
     g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
     Copyright (C) 2019 Free Software Foundation, Inc.
     This is free software; see the source for copying conditions.  There is NO
     warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

     ***nvcc***
     /usr/local/cuda-11/bin/nvcc
     nvcc: NVIDIA (R) Cuda compiler driver
     Copyright (c) 2005-2021 NVIDIA Corporation
     Built on Fri_Dec_17_18:16:03_PST_2021
     Cuda compilation tools, release 11.6, V11.6.55
     Build cuda_11.6.r11.6/compiler.30794723_0

     ***Python***
     /nobackup/kp276129/envs/env_cuda/bin/python
     Python 3.10.13

     ***Environment Variables***
     PATH                            : /nobackup/kp276129/envs/env_cuda/bin:/nobackup/kp276129/data/miniconda3/condabin:/home/kp276129/.local/bin:/usr/local/cuda-11/bin:/bin:/sbin:/usr/X11R6/bin:/usr/sbin:/usr/bin:/etc:/home/cmd:/usr/ccs/bin:/usr/openwin/bin:/usr/dt/bin:/opt/sfw/bin:/home/prog/SUNWspro/bin:/home/prog/s1studio/ee/bin:/home/systeme/SUNWspro/bin:/home/systeme/SUNWste/bin:/usr/ucb:/usr/local/bin:.
     LD_LIBRARY_PATH                 : /nobackup/Python/envs//lib:/usr/local/cuda/lib64:/usr/lib:/usr/openwin/lib:/home/prog/SUNWspro/lib:/home/prog/s1studio/ee/lib:/home/systeme/SUNWspro/lib:/home/systeme/SUNWspro/lib/v9:/opt/sfw/lib:/usr/ucblib:/home/prog/librairies/nag:/home/systeme/hpnp.6.15/lib:/usr/dt/lib:/opt/SUNWits/Graphics-sw/xil/lib/pipelines:/usr/local/lib:/usr/local/mysql/lib/mysql
     NUMBAPRO_NVVM                   :
     NUMBAPRO_LIBDEVICE              :
     CONDA_PREFIX                    : /nobackup/kp276129/envs/env_cuda
     PYTHON_PATH                     :

     ***conda packages***
     /nobackup/kp276129/data/miniconda3/condabin/conda
     # packages in environment at /nobackup/kp276129/envs/env_cuda:
     #
     # Name                    Version                   Build  Channel
     _libgcc_mutex             0.1                        main
     _openmp_mutex             5.1                       1_gnu
     appdirs                   1.4.4                    pypi_0    pypi
     asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
     astunparse                1.6.3                    pypi_0    pypi
     blessed                   1.20.0                   pypi_0    pypi
     build                     1.0.3                    pypi_0    pypi
     bzip2                     1.0.8                h7b6447c_0
     ca-certificates           2023.11.17           hbcca054_0    conda-forge
     cachecontrol              0.13.1                   pypi_0    pypi
     certifi                   2023.11.17               pypi_0    pypi
     cffi                      1.16.0                   pypi_0    pypi
     charset-normalizer        3.3.2                    pypi_0    pypi
     cleo                      2.1.0                    pypi_0    pypi
     click                     8.1.7                    pypi_0    pypi
     click-default-group       1.2.4                    pypi_0    pypi
     cloudpickle               3.0.0                    pypi_0    pypi
     cloup                     2.1.2                    pypi_0    pypi
     comm                      0.1.4              pyhd8ed1ab_0    conda-forge
     contourpy                 1.2.0                    pypi_0    pypi
     crashtest                 0.4.1                    pypi_0    pypi
     cryptography              41.0.7                   pypi_0    pypi
     cupy-cuda11x              12.3.0                   pypi_0    pypi
     cycler                    0.12.1                   pypi_0    pypi
     debugpy                   1.6.7           py310h6a678d5_0
     decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
     distlib                   0.3.8                    pypi_0    pypi
     dm-tree                   0.1.8                    pypi_0    pypi
     dulwich                   0.21.7                   pypi_0    pypi
     entrypoints               0.4                pyhd8ed1ab_0    conda-forge
     exceptiongroup            1.0.4           py310h06a4308_0
     executing                 2.0.1              pyhd8ed1ab_0    conda-forge
     fastjsonschema            2.19.0                   pypi_0    pypi
     fastrlock                 0.8.2                    pypi_0    pypi
     filelock                  3.13.1                   pypi_0    pypi
     fonttools                 4.45.1                   pypi_0    pypi
     fsspec                    2024.3.1                 pypi_0    pypi
     gast                      0.5.4                    pypi_0    pypi
     gitdb                     4.0.11                   pypi_0    pypi
     glcontext                 2.5.0                    pypi_0    pypi
     gpustat                   1.1.1                    pypi_0    pypi
     idna                      3.6                      pypi_0    pypi
     imageio                   2.33.0                   pypi_0    pypi
     importlib-metadata        7.0.0                    pypi_0    pypi
     iniconfig                 1.1.1              pyhd3eb1b0_0
     installer                 0.7.0                    pypi_0    pypi
     ipykernel                 6.26.0             pyhf8b6a83_0    conda-forge
     ipympl                    0.9.3                    pypi_0    pypi
     ipython                   8.18.1             pyh707e725_3    conda-forge
     ipython-genutils          0.2.0                    pypi_0    pypi
     ipywidgets                8.1.1                    pypi_0    pypi
     isosurfaces               0.1.0                    pypi_0    pypi
     jaraco-classes            3.3.0                    pypi_0    pypi
     jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
     jeepney                   0.8.0                    pypi_0    pypi
     jupyter_client            7.3.4              pyhd8ed1ab_0    conda-forge
     jupyter_core              5.5.0           py310hff52083_0    conda-forge
     jupyterlab-widgets        3.0.9                    pypi_0    pypi
     keyring                   24.3.0                   pypi_0    pypi
     kiwisolver                1.4.5                    pypi_0    pypi
     lazy-loader               0.3                      pypi_0    pypi
     ld_impl_linux-64          2.38                 h1181459_1
     libffi                    3.4.4                h6a678d5_0
     libgcc-ng                 11.2.0               h1234567_1
     libgomp                   11.2.0               h1234567_1
     libsodium                 1.0.18               h36c2ea0_1    conda-forge
     libstdcxx-ng              11.2.0               h1234567_1
     libuuid                   1.41.5               h5eee18b_0
     line-profiler             4.1.2                    pypi_0    pypi
     llvmlite                  0.42.0                   pypi_0    pypi
     locket                    1.0.0                    pypi_0    pypi
     mako                      1.2.4                    pypi_0    pypi
     manim                     0.18.0                   pypi_0    pypi
     manimpango                0.5.0                    pypi_0    pypi
     mapbox-earcut             1.0.1                    pypi_0    pypi
     markdown-it-py            3.0.0                    pypi_0    pypi
     markupsafe                2.1.3                    pypi_0    pypi
     matplotlib                3.8.2                    pypi_0    pypi
     matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
     mdurl                     0.1.2                    pypi_0    pypi
     memory-profiler           0.61.0                   pypi_0    pypi
     moderngl                  5.9.0                    pypi_0    pypi
     moderngl-window           2.4.4                    pypi_0    pypi
     more-itertools            10.1.0                   pypi_0    pypi
     msgpack                   1.0.7                    pypi_0    pypi
     multipledispatch          1.0.0                    pypi_0    pypi
     ncurses                   6.4                  h6a678d5_0
     nest-asyncio              1.5.8              pyhd8ed1ab_0    conda-forge
     networkx                  3.2.1                    pypi_0    pypi
     numpy                     1.26.0                   pypi_0    pypi
     nvidia-ml-py              12.535.133               pypi_0    pypi
     nvidia-nvimgcodec-cu11    0.2.0.7                  pypi_0    pypi
     openssl                   3.0.12               h7f8727e_0
     packaging                 23.1            py310h06a4308_0
     parso                     0.8.3              pyhd8ed1ab_0    conda-forge
     partd                     1.4.1                    pypi_0    pypi
     pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
     pickleshare               0.7.5                   py_1003    conda-forge
     pillow                    9.5.0                    pypi_0    pypi
     pip                       23.2.1          py310h06a4308_0
     pkginfo                   1.9.6                    pypi_0    pypi
     platformdirs              3.11.0                   pypi_0    pypi
     pluggy                    1.0.0           py310h06a4308_1
     poetry                    1.7.1                    pypi_0    pypi
     poetry-core               1.8.1                    pypi_0    pypi
     poetry-plugin-export      1.6.0                    pypi_0    pypi
     prompt-toolkit            3.0.41             pyha770c72_0    conda-forge
     psutil                    5.9.0           py310h5eee18b_0
     ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
     pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
     pycairo                   1.25.1                   pypi_0    pypi
     pycparser                 2.21                     pypi_0    pypi
     pycuda                    2022.2.2                 pypi_0    pypi
     pydub                     0.25.1                   pypi_0    pypi
     pyglet                    2.0.10                   pypi_0    pypi
     pygments                  2.17.2             pyhd8ed1ab_0    conda-forge
     pyparsing                 3.1.1                    pypi_0    pypi
     pyproject-hooks           1.0.0                    pypi_0    pypi
     pyrr                      0.10.3                   pypi_0    pypi
     pytest                    7.4.0           py310h06a4308_0
     python                    3.10.13              h955ad1f_0
     python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
     python_abi                3.10                    2_cp310    conda-forge
     pytools                   2023.1.1                 pypi_0    pypi
     pyyaml                    6.0.1                    pypi_0    pypi
     pyzmq                     25.1.0          py310h6a678d5_0
     rapidfuzz                 3.5.2                    pypi_0    pypi
     readline                  8.2                  h5eee18b_0
     requests                  2.31.0                   pypi_0    pypi
     requests-toolbelt         1.0.0                    pypi_0    pypi
     rich                      13.7.0                   pypi_0    pypi
     scikit-image              0.22.0                   pypi_0    pypi
     scipy                     1.11.4                   pypi_0    pypi
     screeninfo                0.8.1                    pypi_0    pypi
     secretstorage             3.3.3                    pypi_0    pypi
     setuptools                68.0.0          py310h06a4308_0
     shellingham               1.5.4                    pypi_0    pypi
     six                       1.16.0             pyh6c4a22f_0    conda-forge
     skia-pathops              0.7.4                    pypi_0    pypi
     smmap                     5.0.1                    pypi_0    pypi
     sqlite                    3.41.2               h5eee18b_0
     srt                       3.5.3                    pypi_0    pypi
     stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
     svgelements               1.9.6                    pypi_0    pypi
     tifffile                  2023.9.26                pypi_0    pypi
     tk                        8.6.12               h1ccaba5_0
     tomli                     2.0.1           py310h06a4308_0
     tomlkit                   0.12.3                   pypi_0    pypi
     toolz                     0.12.1                   pypi_0    pypi
     tornado                   6.1             py310h5764c6d_3    conda-forge
     tqdm                      4.66.1                   pypi_0    pypi
     traitlets                 5.14.0             pyhd8ed1ab_0    conda-forge
     trove-classifiers         2023.11.29               pypi_0    pypi
     typing_extensions         4.8.0              pyha770c72_0    conda-forge
     tzdata                    2023c                h04d1e81_0
     urllib3                   2.1.0                    pypi_0    pypi
     virtualenv                20.25.0                  pypi_0    pypi
     watchdog                  3.0.0                    pypi_0    pypi
     wcwidth                   0.2.12             pyhd8ed1ab_0    conda-forge
     wheel                     0.41.2          py310h06a4308_0
     widgetsnbextension        4.0.9                    pypi_0    pypi
     xz                        5.4.2                h5eee18b_0
     zeromq                    4.3.4                h2531618_0
     zipp                      3.17.0                   pypi_0    pypi
     zlib                      1.2.13               h5eee18b_0

</pre></details>

Relevant log output

No response

Other/Misc.

The allow_any_depth=True parameter in DecodeParams seems to be causing the issue. However, setting it to False is not a viable solution for me, as I need to preserve the original data type of the image. When allow_any_depth is set to False, the only remaining issue is the incorrect range of pixel values.

image

Check for duplicates

jantonguirao commented 2 months ago

~@Crackvignoule Thanks for reporting this. Could you please share the TIFF image so that I can reproduce on my end? Thank you~

Nevermind, I see in the snippet it is generated.

jantonguirao commented 2 months ago

@Crackvignoule Thank you for reporting this. We can confirm it is indeed a bug and it will be fixed in the next nvImageCodec release.

Crackvignoule commented 3 weeks ago

@Crackvignoule Thank you for reporting this. We can confirm it is indeed a bug and it will be fixed in the next nvImageCodec release.

Hi, it's me again, do you have any clue when the next release should arrive ? Thank you

jantonguirao commented 3 weeks ago

@Crackvignoule We are targeting July (next month) for this release. Thank you for your patience.