Windows Anaconda: pip install lama_phenotype_detection fails to install pyradiomics

[dorkylever]

Hi guys,

I followed the steps outlined in the wiki for installing LAMA within windows. Anaconda = Python 3.6, R = version 4.0.0 and elastix was successfully installed (shown below)

(C:\Users\Kyle\Anaconda3) C:\Users\Kyle>elastix
Use "elastix --help" for information about elastix-usage.

Running pip install lama_phenotype_detections fails to install pyradiomics due to a version conflict between scikit and Pywavelets 1.0.0. This can be fixed by manually installing pyradiomics (I wasn't able to edit the wiki to make this change).

Install before manually installing pyradiomics

(C:\Users\Kyle\Anaconda3) C:\Users\Kyle>pip install lama_phenotype_detection
Collecting lama_phenotype_detection
Downloading lama_phenotype_detection-0.9.51-py3-none-any.whl (156 kB)
|████████████████████████████████| 156 kB 2.2 MB/s
Requirement already satisfied: pandas>=0.23.4 in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (1.0.3)
Requirement already satisfied: logzero in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (1.5.0)
Requirement already satisfied: pytest in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (3.0.7)
Requirement already satisfied: scikit-learn>=0.19.2 in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (0.23.1)
Requirement already satisfied: numpy>=1.15.0 in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (1.18.4)
Requirement already satisfied: PyYAML>=3.13 in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (5.3.1)
Requirement already satisfied: toml in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (0.10.1)
Requirement already satisfied: addict in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (2.2.1)
Requirement already satisfied: seaborn>=0.9.0 in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (0.10.1)
Requirement already satisfied: psutil in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (5.2.2)
Requirement already satisfied: scipy>=1.1.0 in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (1.4.1)
Requirement already satisfied: filelock in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (3.0.12)
Requirement already satisfied: scikit-image>=0.15.0 in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (0.17.2)
Requirement already satisfied: appdirs in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (1.4.4)
Requirement already satisfied: statsmodels>=0.9.0 in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (0.11.1)
Requirement already satisfied: SimpleITK>=1.1.0 in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (1.2.4)
Requirement already satisfied: pynrrd in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (0.4.2)
Requirement already satisfied: matplotlib>=2.2.0 in c:\users\kyle\anaconda3\lib\site-packages (from lama_phenotype_detection) (3.2.1)
Requirement already satisfied: python-dateutil>=2.6.1 in c:\users\kyle\anaconda3\lib\site-packages (from pandas>=0.23.4->lama_phenotype_detection) (2.8.1)
Requirement already satisfied: pytz>=2017.2 in c:\users\kyle\anaconda3\lib\site-packages (from pandas>=0.23.4->lama_phenotype_detection) (2017.2)
Requirement already satisfied: colorama; sys_platform == "win32" in c:\users\kyle\anaconda3\lib\site-packages (from logzero->lama_phenotype_detection) (0.3.9)
Requirement already satisfied: py>=1.4.29 in c:\users\kyle\anaconda3\lib\site-packages (from pytest->lama_phenotype_detection) (1.4.33)
Requirement already satisfied: setuptools in c:\users\kyle\anaconda3\lib\site-packages\setuptools-27.2.0-py3.6.egg (from pytest->lama_phenotype_detection) (27.2.0)
Requirement already satisfied: joblib>=0.11 in c:\users\kyle\anaconda3\lib\site-packages (from scikit-learn>=0.19.2->lama_phenotype_detection) (0.15.1)
Requirement already satisfied: threadpoolctl>=2.0.0 in c:\users\kyle\anaconda3\lib\site-packages (from scikit-learn>=0.19.2->lama_phenotype_detection) (2.0.0)
Requirement already satisfied: imageio>=2.3.0 in c:\users\kyle\anaconda3\lib\site-packages (from scikit-image>=0.15.0->lama_phenotype_detection) (2.8.0)
Requirement already satisfied: networkx>=2.0 in c:\users\kyle\anaconda3\lib\site-packages (from scikit-image>=0.15.0->lama_phenotype_detection) (2.4)
Requirement already satisfied: pillow!=7.1.0,!=7.1.1,>=4.3.0 in c:\users\kyle\anaconda3\lib\site-packages (from scikit-image>=0.15.0->lama_phenotype_detection) (7.1.2)
Requirement already satisfied: tifffile>=2019.7.26 in c:\users\kyle\anaconda3\lib\site-packages (from scikit-image>=0.15.0->lama_phenotype_detection) (2020.5.25)
Requirement already satisfied: PyWavelets>=1.1.1 in c:\users\kyle\anaconda3\lib\site-packages (from scikit-image>=0.15.0->lama_phenotype_detection) (1.1.1)
Requirement already satisfied: patsy>=0.5 in c:\users\kyle\anaconda3\lib\site-packages (from statsmodels>=0.9.0->lama_phenotype_detection) (0.5.1)
Requirement already satisfied: kiwisolver>=1.0.1 in c:\users\kyle\anaconda3\lib\site-packages (from matplotlib>=2.2.0->lama_phenotype_detection) (1.2.0)
Requirement already satisfied: cycler>=0.10 in c:\users\kyle\anaconda3\lib\site-packages (from matplotlib>=2.2.0->lama_phenotype_detection) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in c:\users\kyle\anaconda3\lib\site-packages (from matplotlib>=2.2.0->lama_phenotype_detection) (2.1.4)
Requirement already satisfied: six>=1.5 in c:\users\kyle\anaconda3\lib\site-packages (from python-dateutil>=2.6.1->pandas>=0.23.4->lama_phenotype_detection) (1.10.0)
Requirement already satisfied: decorator>=4.3.0 in c:\users\kyle\anaconda3\lib\site-packages (from networkx>=2.0->scikit-image>=0.15.0->lama_phenotype_detection) (4.4.2)
Installing collected packages: lama-phenotype-detection
Successfully installed lama-phenotype-detection-0.9.51

(C:\Users\Kyle\Anaconda3) C:\Users\Kyle>lama_reg
[W 200624 16:58:28 glcm3d:14] pyradiomics not installed. No glcms will be made
usage: The LAMA registration pipeline [-h] -c CONFIG
The LAMA registration pipeline: error: the following arguments are required: -c

Install after manually installing pyradiomics

(C:\Users\Kyle\Anaconda3) C:\Users\Kyle>pip install pyradiomics
Collecting pyradiomics
Using cached pyradiomics-3.0-cp36-cp36m-win_amd64.whl (121 kB)
Requirement already satisfied: numpy>=1.9.2 in c:\users\kyle\anaconda3\lib\site-packages (from pyradiomics) (1.18.4)
Requirement already satisfied: pykwalify>=1.6.0 in c:\users\kyle\anaconda3\lib\site-packages (from pyradiomics) (1.7.0)
Requirement already satisfied: six>=1.10.0 in c:\users\kyle\anaconda3\lib\site-packages (from pyradiomics) (1.10.0)
Requirement already satisfied: SimpleITK>=0.9.1 in c:\users\kyle\anaconda3\lib\site-packages (from pyradiomics) (1.2.4)
Collecting PyWavelets<=1.0.0,>=0.4.0
Using cached PyWavelets-1.0.0-cp36-none-win_amd64.whl (4.2 MB)
Requirement already satisfied: PyYAML>=3.11 in c:\users\kyle\anaconda3\lib\site-packages (from pykwalify>=1.6.0->pyradiomics) (5.3.1)
Requirement already satisfied: python-dateutil>=2.4.2 in c:\users\kyle\anaconda3\lib\site-packages (from pykwalify>=1.6.0->pyradiomics) (2.8.1)
Requirement already satisfied: docopt>=0.6.2 in c:\users\kyle\anaconda3\lib\site-packages (from pykwalify>=1.6.0->pyradiomics) (0.6.2)
ERROR: scikit-image 0.17.2 has requirement PyWavelets>=1.1.1, but you'll have pywavelets 1.0.0 which is incompatible.
Installing collected packages: PyWavelets, pyradiomics
Attempting uninstall: PyWavelets
Found existing installation: PyWavelets 1.1.1
Uninstalling PyWavelets-1.1.1:
Successfully uninstalled PyWavelets-1.1.1
Successfully installed PyWavelets-1.0.0 pyradiomics-3.0

(C:\Users\Kyle\Anaconda3) C:\Users\Kyle>lama_reg
usage: The LAMA registration pipeline [-h] -c CONFIG
The LAMA registration pipeline: error: the following arguments are required: -c

[nrhorner]

Pyradiomics is not needed at the moment. I am hoping to add texture-based analysis in the near future.

[nrhorner]

I've updated the wiki with your suggestion https://github.com/mpi2/LAMA/wiki/getting-started. Thansk