migrate setup from old repo

Author: JoshuaHess12

.gitignore

@@ -1,3 +1,10 @@
+
+.idea/
+.DS_Store
+.Rhistory
+*.tiff
+
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

Dockerfile

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+FROM superelastix/elastix:5.0.1 AS elastix
+
+COPY . /app/
+
+RUN apt update && apt -y upgrade
+RUN apt install python3.8 -y
+RUN apt-get update && apt-get install -y python3-pip
+RUN apt-get -y install git
+RUN ln -sf /usr/bin/pip3 /usr/bin/pip
+RUN ln -sf /usr/bin/python3.8 /usr/bin/python
+
+RUN pip3 install install scikit-image numpy pandas pyimzml nibabel scipy h5py pathlib umap-learn uncertainties seaborn matplotlib scikit-learn PyYAML
+
+RUN pip3 install "dask[complete]"
+
+RUN pip3 install -e git+https://github.com/JoshuaHess12/hdi-utils.git@main#egg=hdi-utils
+RUN pip3 install miaaim-python

MANIFEST.in

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+include Dockerfile
+include LICENSE
+recursive-include miaaim *.dockerignore
+recursive-include miaaim *.jpeg
+recursive-include miaaim *.md
+recursive-include miaaim *.py
+recursive-include miaaim *.yml

README.md

@@ -1,2 +1,58 @@
-# miaaim-python
-MIAAIM: Multi-omics Image Alignment and Analysis by Information Manifolds
+# MIAAIM: multi-modal image alignment and analysis by information manifolds
+MIAAIM is a software to align multiple-omics tissue imaging data. The worflow includes high-dimensional image compression, registration, and transforming images to align in the same spatial domain. MIAAIM was developed at the [Vaccine and Immunotherapy Center at MGH](http://advancingcures.org) in the labs of [Dr. Patrick Reeves](http://advancingcures.org/reeves-lab/) and [Dr. Ruxandra Sîrbulescu](http://advancingcures.org/sirbulescu-lab/).
+
+For further documentation on the MIAAIM Python impementation, please visit [miaaim.org](http://miaaim.org).
+
+## Installation
+You can install MIAAIM in Python using either the MIAAIM-Python Docker container, which would allow for complete workflow
+reproducibility, or you can install the package into your environment with pip.
+
+### Dependencies
+MIAAIM utilizes the [Elastix](https://elastix.lumc.nl) library for image registration computations, which is written in the C++ language. For this reason, we recommend running your workflows with the MIAAIM Python package inside of a Docker container, which we have created to automatically include Elastix. You can still run MIAAIM, however, if you would rather stick with installing packages via pip, you will just need to install Elastix separately. These two options for installing MIAAIM are outlined below:
+
+### Usage without Docker / Install with Pip:
+If you are unable to use Docker on your machine, then you can still use MIAAIM:
+1. [download](https://github.com/SuperElastix/elastix/releases/tag/5.0.1) the latest version of Elastix.
+2. Make Elastix accessible to your `$PATH` environment (Ex. on a Mac, access your `.bash_profile` and add `export PATH=~/elastix-latest/bin:$PATH` and `export DYLD_LIBRARY_PATH=~/elastix-latest/lib:$DYLD_LIBRARY_PATH`)
+3. Run the following command to install MIAAIM on your machine:
+```bash
+ pip install miaaim-python  # install miaaim
+ ```
+
+#### Reproducibility with Pip
+If you are using pip to install MIAAIM, you can reconstruct your working environment easily with the commands:
+1.
+```bash
+ pip freeze > requirements.txt  # create documentation of installed packages
+ ```
+This will create a text file that indicates the specific packages that you are using. You can then
+install the specific packages that were exported into another environment with :
+2.
+```bash
+pip install -r requirements.txt
+```
+We have included a `requirements.txt` file in this repository to use for our convenience.
+
+### Docker
+MIAAIM's Python implementation is containerized using Docker to enable a reproducible environment. Inside of this container,
+the Python distribution of MIAAIM is already installed. It is therefore set up so that users can copy scripts and data into it in order to run analyses that they need.
+
+To get started with MIAAIM using Docker:
+1. [Install Docker](https://docs.docker.com/get-docker/).
+2. Ensure that Docker is available to your system using the command `docker images`
+3. Pull the miaaim-python docker container `docker pull joshuahess/miaaim-python:latest` where `latest` is the version number.
+
+#### Using MIAAIM inside of Docker
+If you are using MIAAIM with Docker, we recommend having a concrete file structure for data and code with relative paths so that your script doesn't rely on absolute file paths outside of the Docker container.
+
+You can mount your custom scripts and data into the virtual environment as follows:
+4. Mount your data and scripts into Docker from your local path (`src-path`)
+```bash
+docker run -it -v /path/to/data:/data joshuahess/miaaim-python:latest bash    # mount data in the "dest-path" folder
+```
+Here, we assumed that the folder `data` contains your new script and your input data that goes with it.
+5. Run your script (named here `script.py`) from the data folder:
+```bash
+python ./data/scipt.py
+```
+Note here that any additional packages that you use to process your data that are not included in the docker image will not be found!

docs/CNAME

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+miaaim.org

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= python -msphinx
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_static/.gitkeep

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/make.bat

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+div.leftside {
+    width: 414px;
+    padding: 0px 3px 0px 0px;
+    float: left;
+}
+
+div.rightside {
+    margin-left: 425;
+}
+
+

docs/source/_static/custom.css

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+Acknowledgements
+================
+
+The development of this software using the Nextflow language was
+influenced by the `MCMICRO <https://github.com/labsyspharm/mcmicro>`_ software
+developed by `Denis Schapiro <https://github.com/DenisSch>`_ and
+`Artem Sokolov <https://github.com/ArtemSokolov>`_ at the `Laboratory of Systems
+Pharmacology at HMS <https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/about/>`_.