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@robtoth
robtoth authored Aug 3, 2022
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Expand Up @@ -82,11 +82,11 @@ _[Back to **Table of Contents**](#table-of-contents)_

## Pip Usage
```console
pip3 install collageradiomics
pip3 install --upgrade collageradiomics
```

## Local usage
```console
```shell
# get the code
git clone https://github.com/radxtools/collageradiomics
cd collageradiomics
Expand All @@ -97,7 +97,6 @@ source collageenv/bin/activate

# install requirements
sudo apt -y install build-essential gcc gfortran python-dev libopenblas-dev liblapack-dev cython libjpeg-dev zlib1g-dev

pip3 install -r requirements.txt

# run test script
Expand Down Expand Up @@ -144,7 +143,7 @@ sudo docker run -it -v $PWD:/root radxtools/collageradiomics-pip
If your terminal prompt changes to `root@[random_string]:/#` then you are now working inside the standardized **Docker** sandbox container environment.

1. Test the python module by making sure the following command outputs `True` to the terminal:
```console
```shell
python -c 'import numpy as np; import collageradiomics; print(not not len(collageradiomics.__name__) and not not len(collageradiomics.Collage.from_rectangle(np.random.rand(20,20,3), 2, 2, 10, 10).execute()));'
```
This should display `True`.
Expand All @@ -159,131 +158,3 @@ Type "help", "copyright", "credits" or "license" for more information.
>>> collageradiomics.__name__
'collageradiomics'
```

## Pip
_[Back to **Table of Contents**](#table-of-contents)_

To use this module in your existing **Python** development environment, you can install our **pip** module.

### Linux
1. Install **pip**:
```console
user@machine:~$ sudo apt -y install python3-pip
Reading package lists... Done
Building dependency tree
Reading state information... Done
python3-pip is already the newest version (18.1-5).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
user@machine:~$
```
2. Install our **CoLlAGe** module:
```console
user@machine:~$ pip3 install collageradiomics --upgrade
Collecting collageradiomics
Downloading https://files.pythonhosted.org/packages/58/46/73d6b5a6d0d2b952086a1c9c4ae339087e4678f421044847ab2ea8728adf/collageradiomics-0.0.1a39-py3-none-any.whl
...
(some output omitted for brevity)
...
Successfully installed collageradiomics-...
user@machine:~$
```
*(Note: For some operating systems, the command is simply `pip` instead of `pip3`.)*

### Windows
1. Install **Python** using [this link](https://www.python.org/downloads/windows/).
2. Test that **Python** is properly installed in the Powershell:
```console
Windows PowerShell
Copyright (C) Microsoft Corporation. All rights reserved.

Try the new cross-platform PowerShell https://aka.ms/pscore6

PS C:\Users\user> python --version
Python 3.8.2
PS C:\Users\user> python
Python 3.8.2 (tags/v3.8.2:7b3ab59, Feb 25 2020, 23:03:10) [MSC v.1916 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> quit()
PS C:\Users\user>
```
3. Install pip by downloading this [get-pip.py file](https://bootstrap.pypa.io/get-pip.py) and running the following command:
```console
Windows PowerShell
Copyright (C) Microsoft Corporation. All rights reserved.

Try the new cross-platform PowerShell https://aka.ms/pscore6

PS C:\Users\user> python get-pip.py
Collecting pip
Downloading pip-20.1.1-py2.py3-none-any.whl (1.5 MB)
|████████████████████████████████| 1.5 MB 3.2 MB/s
Collecting wheel
Using cached wheel-0.34.2-py2.py3-none-any.whl (26 kB)
Installing collected packages: pip, wheel
Attempting uninstall: pip
Found existing installation: pip 20.0.2
Uninstalling pip-20.0.2:
Successfully uninstalled pip-20.0.2
Successfully installed pip-20.1.1 wheel-0.34.2
PS C:\Users\user> pip -V
pip 20.1.1 from c:\users\robto\appdata\local\programs\python\python38\lib\site-packages\pip (python 3.8)
PS C:\Users\user>
```
4. Install our module
```console
Windows PowerShell
Copyright (C) Microsoft Corporation. All rights reserved.

Try the new cross-platform PowerShell https://aka.ms/pscore6

PS C:\Users\user> pip install collageradiomics --upgrade
```
5. Verify its installation in **Python**:
```console
Windows PowerShell
Copyright (C) Microsoft Corporation. All rights reserved.

Try the new cross-platform PowerShell https://aka.ms/pscore6

PS C:\Users\user> python
>>> import collageradiomics
>>>
```
6. If you get an error like the one below, which can happen for some versions of python, call `import` again:
```console
Windows PowerShell
Copyright (C) Microsoft Corporation. All rights reserved.

Try the new cross-platform PowerShell https://aka.ms/pscore6

PS C:\Users\user> python
>>> import collageradiomics
Could not import submodules (exact error was: DLL load failed while importing _bbox: The specified module could not be found.).

There are many reasons for this error the most common one is that you have
either not built the packages or have built (using `python setup.py build`) or
installed them (using `python setup.py install`) and then proceeded to test
mahotas **without changing the current directory**.

Try installing and then changing to another directory before importing mahotas.
>>> import collageradiomics
>>>
```

## Python Usage
_[Back to **Table of Contents**](#table-of-contents)_

collageradiomics can be implemented in **Python** through the `collageradiomics` pip module. It has a intuitive interface - simply create a `Collage` object and run the `execute()` function.

# Other Platforms
_[Back to **Table of Contents**](#table-of-contents)_

The RadxTools COLLAGE implementation is now available through the Cancer Phenomics Toolkit (CaPTk), developed by the Center for Biomedical Image Computing and Analytics (CBICA) at the University of Pennsylvania. For more information see https://github.com/CBICA/CaPTk


# Contact
_[Back to **Table of Contents**](#table-of-contents)_

Please report any issues or feature requests via the [Issues](https://github.com/radxtools/collageradiomics/issues) tab

Additional information can be found on the [BrIC Lab](http://bric-lab.com) website.

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