weecology
Compatibility issue when running base model on images
The code runs well when ussing Deepforest 1.1, when uprgading to 1.3.3 ussing a virtual enviroment it starts returning a compatibility problem, the torch and torchvision versions are compatible acording to the official webpage
**Environment
- OS: windows 10
- Python version and environment : 3.11.9 conda VE with DeepForest 1.3.3
Screenshots and Context
Cell In[1], [line 24](vscode-notebook-cell:?execution_count=1&line=24)
[21](vscode-notebook-cell:?execution_count=1&line=21) model.use_release()
[23](vscode-notebook-cell:?execution_count=1&line=23) sample_image_path = r"C:\Users\zer0a\OneDrive\Escritorio\Test/Prueba3.png"
---> [24](vscode-notebook-cell:?execution_count=1&line=24) img = model.predict_image(path=sample_image_path, return_plot=True)
[26](vscode-notebook-cell:?execution_count=1&line=26) #predict_image returns plot in BlueGreenRed (opencv style), but matplotlib likes RedGreenBlue, switch the channel order. Many functions in deepforest will automatically perform this flip for you and give a warning.
[27](vscode-notebook-cell:?execution_count=1&line=27) plt.imshow(img[:,:,::-1])
File c:\Users\zer0a\miniconda3\envs\DiegoTest\Lib\site-packages\deepforest\main.py:347, in deepforest.predict_image(self, image, path, return_plot, color, thickness)
[344](file:///C:/Users/zer0a/miniconda3/envs/DiegoTest/Lib/site-packages/deepforest/main.py:344) image = torch.tensor(image, device=self.device).permute(2, 0, 1)
[345](file:///C:/Users/zer0a/miniconda3/envs/DiegoTest/Lib/site-packages/deepforest/main.py:345) image = image / 255
--> [347](file:///C:/Users/zer0a/miniconda3/envs/DiegoTest/Lib/site-packages/deepforest/main.py:347) result = predict._predict_image_(model=self.model,
[348](file:///C:/Users/zer0a/miniconda3/envs/DiegoTest/Lib/site-packages/deepforest/main.py:348) image=image,
[349](file:///C:/Users/zer0a/miniconda3/envs/DiegoTest/Lib/site-packages/deepforest/main.py:349) path=path,
[350](file:///C:/Users/zer0a/miniconda3/envs/DiegoTest/Lib/site-packages/deepforest/main.py:350) nms_thresh=self.config["nms_thresh"],
[351](file:///C:/Users/zer0a/miniconda3/envs/DiegoTest/Lib/site-packages/deepforest/main.py:351) return_plot=return_plot,
[352](file:///C:/Users/zer0a/miniconda3/envs/DiegoTest/Lib/site-packages/deepforest/main.py:352) thickness=thickness,
[353](file:///C:/Users/zer0a/miniconda3/envs/DiegoTest/Lib/site-packages/deepforest/main.py:353) color=color)
[355](file:///C:/Users/zer0a/miniconda3/envs/DiegoTest/Lib/site-packages/deepforest/main.py:355) if return_plot:
[356](file:///C:/Users/zer0a/miniconda3/envs/DiegoTest/Lib/site-packages/deepforest/main.py:356) return result
File c:\Users\zer0a\miniconda3\envs\DiegoTest\Lib\site-packages\deepforest\predict.py:38, in _predict_image_(model, image, path, nms_thresh, return_plot, thickness, color)
[23](file:///C:/Users/zer0a/miniconda3/envs/DiegoTest/Lib/site-packages/deepforest/predict.py:23) """Predict a single image with a deepforest model
[24](file:///C:/Users/zer0a/miniconda3/envs/DiegoTest/Lib/site-packages/deepforest/predict.py:24)
...
[54](file:///C:/Users/zer0a/miniconda3/envs/DiegoTest/Lib/site-packages/torchvision/extension.py:54) "version with torchvision.__version__ and verify if they are compatible, and if not "
[55](file:///C:/Users/zer0a/miniconda3/envs/DiegoTest/Lib/site-packages/torchvision/extension.py:55) "please reinstall torchvision so that it matches your PyTorch install."
[56](file:///C:/Users/zer0a/miniconda3/envs/DiegoTest/Lib/site-packages/torchvision/extension.py:56) )
RuntimeError: Couldn't load custom C++ ops. This can happen if your PyTorch and torchvision versions are incompatible, or if you had errors while compiling torchvision from source. For further information on the compatible versions, check https://github.com/pytorch/vision#installation for the compatibility matrix. Please check your PyTorch version with torch.__version__ and your torchvision version with torchvision.__version__ and verify if they are compatible, and if not please reinstall torchvision so that it matches your PyTorch install.
User Story
“As a student Im working on a school project”
I already did, maybe its an issue with the versions of pytorch and torchvision, now the error runs in the IoU call from DeepForest main.py, it asks for version 0.8 or newer, wich i have
You'll need to show full and reproducible logs for me to help, to much to guess at.
Created a VE with python 3.11.9
conda install pytorch torchvision -c pytorch
conda install deepforest=1.3.3 -c conda-forge (this was done beacuse if not specified it would install DeepForest 1.1.3)
Run the "Getting started demo" from the readthedocs DeepForest page, after I run the code I get the compatibility error previously mentioned
snipet of the code:
import deepforest from deepforest import main from deepforest import get_data import matplotlib.pyplot as plt
model = main.deepforest() model.use_release()
sample_image_path = r"C:\Users\zer0a\OneDrive\Escritorio\DiegoTrees\TIF\Prueba3.png" img = model.predict_image(path=sample_image_path, return_plot=True) plt.imshow(img[:,:,::-1])
RuntimeError: Couldn't load custom C++ ops. This can happen if your PyTorch and torchvision versions are incompatible, or if you had errors while compiling torchvision from source. For further information on the compatible versions, check https://github.com/pytorch/vision#installation for the compatibility matrix. Please check your PyTorch version with torch.version and your torchvision version with torchvision.version and verify if they are compatible, and if not please reinstall torchvision so that it matches your PyTorch install. Output is truncated. View as a scrollable element or open in a text editor. Adjust cell output settings...
Start with pip install DeepForest and let's see. Conda installs are getting weaker and weaker, hard to mantain. (@henrykironde)
@henrykironde I start to wonder whether we should drop conda support. Its just not worth it? @ethanwhite.
Hi, I tried using a pip install, but it keeps outputing errors once I run the code, this time with lightning, after running the same code shown before I get OSError: [WinError 126] No se puede encontrar el módulo especificado. Error loading "C:\Users\zer0a\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\torch\lib\shm.dll" or one of its dependencies.
please run and paste entire output.
conda create python=3.10 --name DeepForest_env
conda activate DeepForest_env
pip install deepforest
Here it is!: PS C:\Users\zer0a> conda create python=3.10 --name DeepForest_env Retrieving notices: ...working... done Channels:
- soumith
- conda-forge
- defaults
Platform: win-64 Collecting package metadata (repodata.json): done Solving environment: done
Package Plan
environment location: A:\Anaconda\envs\DeepForest_env
added / updated specs: - python=3.10
The following packages will be downloaded:
package | build
---------------------------|-----------------
openssl-3.3.1 | h2466b09_1 8.0 MB conda-forge
python-3.10.14 |h4de0772_0_cpython 15.1 MB conda-forge
------------------------------------------------------------
Total: 23.1 MB
The following NEW packages will be INSTALLED:
bzip2 conda-forge/win-64::bzip2-1.0.8-hcfcfb64_5 ca-certificates conda-forge/win-64::ca-certificates-2024.6.2-h56e8100_0 libffi conda-forge/win-64::libffi-3.4.2-h8ffe710_5 libsqlite conda-forge/win-64::libsqlite-3.46.0-h2466b09_0 libzlib conda-forge/win-64::libzlib-1.3.1-h2466b09_1 openssl conda-forge/win-64::openssl-3.3.1-h2466b09_1 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/win-64::python-3.10.14-h4de0772_0_cpython setuptools conda-forge/noarch::setuptools-70.1.1-pyhd8ed1ab_0 tk conda-forge/win-64::tk-8.6.13-h5226925_1 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 ucrt conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_0 vc conda-forge/win-64::vc-14.3-h8a93ad2_20 vc14_runtime conda-forge/win-64::vc14_runtime-14.40.33810-ha82c5b3_20 vs2015_runtime conda-forge/win-64::vs2015_runtime-14.40.33810-h3bf8584_20 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/win-64::xz-5.2.6-h8d14728_0
Proceed ([y]/n)? y
Downloading and Extracting Packages:
Preparing transaction: done Verifying transaction: done Executing transaction: done
To activate this environment, use
To deactivate an active environment, use
$ conda deactivate
PS C:\Users\zer0a> conda activate DeepForest_env PS C:\Users\zer0a> pip install deepforest Collecting deepforest Downloading deepforest-1.3.3-py3-none-any.whl.metadata (1.9 kB) Collecting albumentations>=1.0.0 (from deepforest) Downloading albumentations-1.4.10-py3-none-any.whl.metadata (38 kB) Collecting geopandas (from deepforest) Downloading geopandas-1.0.0-py3-none-any.whl.metadata (2.2 kB) Requirement already satisfied: imagecodecs in a:\anaconda\lib\site-packages (from deepforest) (2023.1.23) Requirement already satisfied: matplotlib in a:\anaconda\lib\site-packages (from deepforest) (3.8.0) Requirement already satisfied: numpy in a:\anaconda\lib\site-packages (from deepforest) (1.26.4) Collecting opencv-python>=4.5.4 (from deepforest) Downloading opencv_python-4.10.0.84-cp37-abi3-win_amd64.whl.metadata (20 kB) Requirement already satisfied: pandas in a:\anaconda\lib\site-packages (from deepforest) (2.1.4) Requirement already satisfied: Pillow>6.2.0 in a:\anaconda\lib\site-packages (from deepforest) (10.2.0) Collecting progressbar2 (from deepforest) Downloading progressbar2-4.4.2-py3-none-any.whl.metadata (17 kB) Collecting pycocotools (from deepforest) Downloading pycocotools-2.0.8-cp311-cp311-win_amd64.whl.metadata (1.1 kB) Collecting pytorch-lightning>=1.5.8 (from deepforest) Downloading pytorch_lightning-2.3.1-py3-none-any.whl.metadata (21 kB) Collecting rasterio (from deepforest) Downloading rasterio-1.3.10-cp311-cp311-win_amd64.whl.metadata (15 kB) Collecting recommonmark (from deepforest) Downloading recommonmark-0.7.1-py2.py3-none-any.whl.metadata (463 bytes) Requirement already satisfied: rtree in a:\anaconda\lib\site-packages (from deepforest) (1.0.1) Requirement already satisfied: scipy>1.5 in a:\anaconda\lib\site-packages (from deepforest) (1.11.4) Requirement already satisfied: six in a:\anaconda\lib\site-packages (from deepforest) (1.16.0) Collecting slidingwindow (from deepforest) Downloading slidingwindow-0.0.14-py3-none-any.whl.metadata (309 bytes) Requirement already satisfied: sphinx in a:\anaconda\lib\site-packages (from deepforest) (5.0.2) Collecting torch (from deepforest) Downloading torch-2.3.1-cp311-cp311-win_amd64.whl.metadata (26 kB) Collecting torchvision>=0.13 (from deepforest) Downloading torchvision-0.18.1-cp311-cp311-win_amd64.whl.metadata (6.6 kB) Requirement already satisfied: tqdm in a:\anaconda\lib\site-packages (from deepforest) (4.65.0) Collecting xmltodict (from deepforest) Downloading xmltodict-0.13.0-py2.py3-none-any.whl.metadata (7.7 kB) Requirement already satisfied: scikit-image>=0.21.0 in a:\anaconda\lib\site-packages (from albumentations>=1.0.0->deepforest) (0.22.0) Requirement already satisfied: PyYAML in a:\anaconda\lib\site-packages (from albumentations>=1.0.0->deepforest) (6.0.1) Requirement already satisfied: typing-extensions>=4.9.0 in a:\anaconda\lib\site-packages (from albumentations>=1.0.0->deepforest) (4.9.0) Collecting scikit-learn>=1.3.2 (from albumentations>=1.0.0->deepforest) Downloading scikit_learn-1.5.0-cp311-cp311-win_amd64.whl.metadata (11 kB) Collecting pydantic>=2.7.0 (from albumentations>=1.0.0->deepforest) Using cached pydantic-2.7.4-py3-none-any.whl.metadata (109 kB) Collecting albucore>=0.0.11 (from albumentations>=1.0.0->deepforest) Downloading albucore-0.0.12-py3-none-any.whl.metadata (3.1 kB) Collecting opencv-python-headless>=4.9.0.80 (from albumentations>=1.0.0->deepforest) Downloading opencv_python_headless-4.10.0.84-cp37-abi3-win_amd64.whl.metadata (20 kB) Requirement already satisfied: fsspec>=2022.5.0 in a:\anaconda\lib\site-packages (from fsspec[http]>=2022.5.0->pytorch-lightning>=1.5.8->deepforest) (2023.10.0) Collecting torchmetrics>=0.7.0 (from pytorch-lightning>=1.5.8->deepforest) Using cached torchmetrics-1.4.0.post0-py3-none-any.whl.metadata (19 kB) Requirement already satisfied: packaging>=20.0 in a:\anaconda\lib\site-packages (from pytorch-lightning>=1.5.8->deepforest) (23.1) Collecting lightning-utilities>=0.10.0 (from pytorch-lightning>=1.5.8->deepforest) Downloading lightning_utilities-0.11.3.post0-py3-none-any.whl.metadata (4.7 kB) Requirement already satisfied: filelock in a:\anaconda\lib\site-packages (from torch->deepforest) (3.13.1) Requirement already satisfied: sympy in a:\anaconda\lib\site-packages (from torch->deepforest) (1.12) Requirement already satisfied: networkx in a:\anaconda\lib\site-packages (from torch->deepforest) (3.1) Requirement already satisfied: jinja2 in a:\anaconda\lib\site-packages (from torch->deepforest) (3.1.3) Collecting mkl<=2021.4.0,>=2021.1.1 (from torch->deepforest) Using cached mkl-2021.4.0-py2.py3-none-win_amd64.whl.metadata (1.4 kB) Requirement already satisfied: colorama in a:\anaconda\lib\site-packages (from tqdm->deepforest) (0.4.6) Collecting pyogrio>=0.7.2 (from geopandas->deepforest) Downloading pyogrio-0.9.0-cp311-cp311-win_amd64.whl.metadata (3.9 kB) Collecting pyproj>=3.3.0 (from 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click-plugins (from rasterio->deepforest) Downloading click_plugins-1.1.1-py2.py3-none-any.whl.metadata (6.4 kB) Requirement already satisfied: setuptools in a:\anaconda\lib\site-packages (from rasterio->deepforest) (68.2.2) Collecting commonmark>=0.8.1 (from recommonmark->deepforest) Downloading commonmark-0.9.1-py2.py3-none-any.whl.metadata (5.7 kB) Requirement already satisfied: docutils>=0.11 in a:\anaconda\lib\site-packages (from recommonmark->deepforest) (0.18.1) Requirement already satisfied: sphinxcontrib-applehelp in a:\anaconda\lib\site-packages (from sphinx->deepforest) (1.0.2) Requirement already satisfied: sphinxcontrib-devhelp in a:\anaconda\lib\site-packages (from sphinx->deepforest) (1.0.2) Requirement already satisfied: sphinxcontrib-jsmath in a:\anaconda\lib\site-packages (from sphinx->deepforest) (1.0.1) Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.0 in a:\anaconda\lib\site-packages (from sphinx->deepforest) (2.0.0) Requirement already satisfied: 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slidingwindow->deepforest) (5.9.0) Collecting tomli>=2.0.1 (from albucore>=0.0.11->albumentations>=1.0.0->deepforest) Downloading tomli-2.0.1-py3-none-any.whl.metadata (8.9 kB) Requirement already satisfied: aiohttp!=4.0.0a0,!=4.0.0a1 in a:\anaconda\lib\site-packages (from fsspec[http]>=2022.5.0->pytorch-lightning>=1.5.8->deepforest) (3.9.3) Requirement already satisfied: MarkupSafe>=2.0 in a:\anaconda\lib\site-packages (from jinja2->torch->deepforest) (2.1.3) Collecting intel-openmp==2021.* (from mkl<=2021.4.0,>=2021.1.1->torch->deepforest) Using cached intel_openmp-2021.4.0-py2.py3-none-win_amd64.whl.metadata (1.2 kB) Collecting tbb==2021.* (from mkl<=2021.4.0,>=2021.1.1->torch->deepforest) Downloading tbb-2021.13.0-py3-none-win_amd64.whl.metadata (1.1 kB) Collecting annotated-types>=0.4.0 (from pydantic>=2.7.0->albumentations>=1.0.0->deepforest) Using cached annotated_types-0.7.0-py3-none-any.whl.metadata (15 kB) Collecting pydantic-core==2.18.4 (from 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click-plugins, albucore, torchvision, torchmetrics, recommonmark, rasterio, pycocotools, geopandas, albumentations, pytorch-lightning, deepforest Attempting uninstall: threadpoolctl Found existing installation: threadpoolctl 2.2.0 Uninstalling threadpoolctl-2.2.0: Successfully uninstalled threadpoolctl-2.2.0
after running that installation and then running the test code on the VE it can`t recognize any of the libraries that where installed by deepforest installation.
ModuleNotFoundError Traceback (most recent call last) Cell In[5], line 1 ----> 1 import matplotlib.pyplot as plt 2 import pandas as pd 3 import numpy as np
ModuleNotFoundError: No module named 'matplotlib'
Thanks, but don't skip steps, its going to be something really subtle, so you need to show everything. Show me
which python
and the terminal state right before you invoke python. I am guessing its looking at a python version that supercedes what you just installed. The module traceback should also give you a path, which i'm guess is not in the DeepForest_env conda directory. The fact that you are getting 'no module named matplotlib' is good news is the sense that unless all of python ecosystem has suddenly crashed (-> world ending) this is very unlikely to be a bug and much more something specific to your system setup.
There is something wrong with your setup. Please revisit how to manage / setup conda or python environments.
The environment location use is: A:\Anaconda\envs\DeepForest_env
however you are installing the packages outside the environment to the base environment
Requirement already satisfied: sphinxcontrib-qthelp in a:\anaconda\lib\site-packages (from sphinx->deepforest) (1.0.3)
Requirement already satisfied: Pygments>=2.0 in a:\anaconda\lib\site-packages (from sphinx->deepforest) (2.15.1)
Closing this due to lack of response. @Diego-asutralgis - feel free to open a new discussion if you are still having issues with your conda install and hopefully someone will have time to help.
