Add container support

ClearMap/Settings.py

@@ -58,7 +58,15 @@ def setup():
     #elif hostname == 'your-host-name':
     #    IlastikPath = 'path-to-ilastik';
     #    ElastixPath = 'path-to-elastix';   
+    elif hostname == 'MH02086639MACLT':
+       IlastikPath = '/usr/local/bin/ilastik-v0.5.12';
+       ElastixPath = '/usr/local/bin/elastix_macosx64_v4.8/bin/elastix';   
     ##
+    elif os.environ.get('CLEARMAP_CONTAINER'):
+       IlastikPath = '/opt/conda/src/ilastik/ilastik-1.3.0-Linux/';
+       ElastixPath = '/usr';
+
+
 
     # check existence:
     if not ElastixPath is None:

ClearMap/__init__.py

@@ -22,7 +22,13 @@
 
 __copyright__ = '2016 Christoph Kirst'
 
-__all__ = ["Settings", "Parameter", "IO", "ImageProcessing", "Analysis"]
-
-import ClearMap.Settings
-import ClearMap.Parameter
+__all__ = [
+"Alignment",
+"Analysis",
+"ImageProcessing",
+"IO",
+"Parameter",
+"Settings",
+]
+
+from ClearMap import *

Dockerfile

@@ -0,0 +1,97 @@
+FROM ubuntu:16.04
+
+ENV LANG="en_US.UTF-8" \
+    LC_ALL="C.UTF-8" \
+    ENTRYPOINT_SCRIPT="/entrypoint/startup.sh"
+
+# Prepare environment
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends --allow-unauthenticated \
+                    curl \
+                    bzip2 \
+                    ca-certificates \
+                    cython3 \
+                    build-essential \
+                    autoconf \
+                    libtool \
+                    pkg-config \
+                    libsm6 \
+                    elastix \
+                    libxext6 \
+                    libxrender1 \
+                    vim
+
+RUN chmod 777 /opt && chmod a+s /opt \
+    && mkdir -p /entrypoint \
+    && if [ ! -f "$ENTRYPOINT_SCRIPT" ]; then \
+         echo '#!/usr/bin/env bash' >> $ENTRYPOINT_SCRIPT \
+         && echo 'set +x' >> $ENTRYPOINT_SCRIPT \
+         && echo 'if [ -z "$*" ]; then /usr/bin/env bash; else $*; fi' >> $ENTRYPOINT_SCRIPT; \
+       fi \
+    && chmod -R 777 /entrypoint && chmod a+s /entrypoint
+
+
+ENTRYPOINT ["/entrypoint/startup.sh"]
+
+# Create new user: neuro
+RUN useradd --no-user-group --create-home --shell /bin/bash neuro
+USER neuro
+RUN mkdir -p /opt/conda/src/clearmap
+RUN mkdir /opt/conda/src/ilastik
+RUN cd /opt/conda/src/ilastik  \
+    && curl http://files.ilastik.org/ilastik-1.3.0-Linux.tar.bz2 >ilastik.tar.bz2 \
+    && tar xjf ilastik.tar.bz2 \
+    && sync \
+    && rm ilastik.tar.bz2
+
+#------------------
+# Install Miniconda
+#------------------
+
+ENV CONDA_DIR=/opt/conda \
+    PATH=/opt/conda/bin:$PATH
+RUN echo "Downloading Miniconda installer ..." \
+    && miniconda_installer=/tmp/miniconda.sh \
+    && curl -sSL --retry 5 -o $miniconda_installer https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh \
+    && /bin/bash $miniconda_installer -u -b -p $CONDA_DIR \
+    && rm -f $miniconda_installer \
+    && conda config --system --prepend channels conda-forge \
+    && conda config --system --set auto_update_conda false \
+    && conda config --system --set show_channel_urls true \
+    && conda update -n base conda \
+    && conda clean -tipsy && sync
+
+# Installing precomputed python packages
+RUN conda install -c conda-forge -y openblas=0.2.14; \
+    sync && \
+    conda install -c conda-forge -y \
+    cython=0.23.1 \
+    h5py=2.6.0 \
+    mahotas \
+    matplotlib \
+    numpy \
+    opencv=2.4.10 \
+    scikit-image=0.12.3 \
+    scipy=0.16.0 \
+    natsort \
+    tifffile \
+    ipython \
+    libgfortran==1 \
+    ; \
+    sync \
+    && conda clean -tipsy && sync
+
+RUN python -c "from matplotlib import font_manager"
+
+# Installing clearmap
+ENV CLEARMAP_CONTAINER="yes"
+USER root
+WORKDIR /opt/conda/src/clearmap
+COPY . /opt/conda/src/clearmap
+RUN  pip install -e . && \
+    rm -rf ~/.cache/pip
+RUN chmod -R a+rX /opt/conda/src/clearmap && \
+    chmod +x /opt/conda/bin/*
+
+
+

README.md

@@ -0,0 +1,99 @@
+# ClearMap
+
+
+ClearMap is a toolbox for the analysis and registration of volumetric data
+from cleared tissues.
+
+ClearMap is targeted towards large lightsheet volumetric imaging data
+of iDISCO+ cleared mouse brains samples, their registration to the Allen brain atlas,
+volumetric image processing and statistical analysis.
+
+The method is fully described in this [Cell paper](http://www.cell.com/cell/abstract/S0092-8674%2816%2930555-4).
+For further details visit the [iDISCO website](https://idisco.info) and 
+the [ClearMap documentation](https://rawgit.com/ChristophKirst/ClearMap/master/docs/_build/html/index.html).
+
+
+## Installation
+
+### Using Docker
+
+The easiest way to use clearmap is to run it in a docker container. For example, with docker installed on a Unix-like system, to get shell access to an environment with clearmap installed:
+
+
+
+    $ docker pull timdanaos/clearmap
+    $ docker run -v $PWD:/mnt --rm -ti timdanaos/clearmap
+
+To change to the directory that was being used outside the container and start an ipython session:
+
+
+    $ cd /mnt
+    $ ipython
+
+To import ClearMap:
+
+
+    In [1]: import ClearMap
+
+
+
+### Using Singularity
+
+Singularity is a solution to using ClearMap on HPC systems where Docker cannot be used. To use ClearMap using Singularity:
+
+
+    $ mkdir ~/temporary_directory_for_singularity
+    $ umask 002
+    $ singularity pull docker://timdanaos/clearmap
+    $ singularity shell -B $PWD:/mnt -H ~/temporary_directory_for_singularity clearmap*img
+
+
+### ClearMap software development with containers
+
+For the development of ClearMap, this repository can be mounted in the container so that changes made to the code can be run in the context of the working container.
+For example in docker:
+
+
+    $ docker run  -v [absolute_path_to_repo]:/opt/conda/src/clearmap/ timdanaos/clearmap
+
+
+In singularity:
+
+    $ singularity shell -B $PWD:/mnt -B [absolute_path_to_repo]:/opt/conda/src/clearmap/ -H ~/temporary_directory_for_singularity [path_to_clearmap_image]
+
+
+
+
+### Manual installation
+
+Install ClearMap by first cloning this repository.
+
+See [GIT.md](https://github.com/ChristophKirst/ClearMap/blob/master/GIT.md) for basic help with git.
+
+If you want to register data to reference images via elastix or
+classify pixels via ilastik configure the /ClearMap/Settings.py file.
+
+You will most likely also need to install several python packages e.g. via 
+pip or apt-get.
+
+See the [documentation](https://rawgit.com/ChristophKirst/ClearMap/master/docs/_build/html/index.html) for more details.
+
+Additional files for mouse brain registration can be found on the `[iDISCO website](https://idisco.info/).
+
+
+## Quickstart
+
+* see the template scripts in the [./ClearMap/Scripts](https://github.com/ChristophKirst/ClearMap/tree/master/ClearMap/Scripts) folder 
+* see the [ClearMap documentation](https://rawgit.com/ChristophKirst/ClearMap/master/docs/_build/html/index.html)
+
+
+## Copyright
+    (c) 2016 Christoph Kirst
+    The Rockefeller University, 
+    ckirst@rockefeller.edu
+
+## License
+    GPLv3, see LICENSE.txt for details.
+
+
+