Merge branch 'fiji-abtem-webtop-draft' into 'develop'

Fiji abtem webtop draft

See merge request !77

docker/abtem/02-exec-cmd

+#!/usr/bin/with-contenv bash
+
+echo "/usr/local/miniconda3/bin/conda run -n base jupyter-lab $CWD" > /config/.config/openbox/autostart
+

docker/abtem/Cheatsheet.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "88054eb2",
+   "metadata": {},
+   "source": [
+    "![FAIRmat](FAIRmat_S.png)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9ecf3020",
+   "metadata": {},
+   "source": [
+    "# abtem-webtop container cheatsheet"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4091c1e2",
+   "metadata": {
+    "tags": []
+   },
+   "source": [
+    "The abtem-webtop container provides preinstalled and configured software for<br>\n",
+    "ab-initio-guided image simulation in the field of electron microscopy.<br>\n",
+    "The container contains the following tools:<br>\n",
+    "* VESTA by K. Momma and F. Izumi (https://doi.org/10.1107/S0021889811038970) is a GUI tool for creating crystal structures.<br>\n",
+    "* GPAW by J. J. Mortensen, E. J. Enkovaara et al. (https://iopscience.iop.org/article/10.1088/0953-8984/22/25/253202)<br>\n",
+    "  an projector augmented-wave electronic structure code.<br>\n",
+    "* abTEM by J. Madsen et al. (https://open-research-europe.ec.europa.eu/articles/1-24) a tool for<br>\n",
+    "  simulating transmission electron microscopy images.<br>\n",
+    "***"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "69238a64",
+   "metadata": {
+    "tags": []
+   },
+   "source": [
+    "# Getting started with VESTA"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6e324fa1",
+   "metadata": {},
+   "source": [
+    "VESTA is available under /home/vesta/VESTA/VESTA. The GUI can be started by opening a terminal by clicking a terminal<br>\n",
+    "panel on the right part of the jupyter-lab screen. The following command line call will start VESTA:<br>"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5fd98af7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "! /home/vesta/VESTA/VESTA"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1aa22278",
+   "metadata": {},
+   "source": [
+    "## Getting started with gpaw and abTEM"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "49e09d74-b0d6-4512-8929-38fd715d3948",
+   "metadata": {},
+   "source": [
+    "This is a draft version of the container, created for testing and debugging purposes.<br>\n",
+    "Further descriptions should be placed here once the container has been finalized.<br>"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docker/abtem/Dockerfile

+# recipe to create the nomad-remote-tools-hub ewr_abinit_em_webtop container via a dockerfile
+FROM gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/webtop
+
+# for testing the container locally without running in oauth errors
+# FROM ghcr.io/linuxserver/webtop:amd64-ubuntu-openbox-version-e1079163
+# FROM ghcr.io/linuxserver/webtop:amd64-ubuntu-xfce-version-c603dc47
+# start of borrowed from gitlabmpcdf customized webtop
+# ENV CUSTOM_PORT=8888
+# ENV PUID=1000
+# ENV PGID=1000
+# ports and volumes
+# EXPOSE 8888
+# VOLUME /config
+# end of borrowed from north webtop
+
+USER root
+
+# ### set the environment already, knowing where miniconda will be installed
+ENV PATH=/usr/local/miniconda3/bin:$PATH
+
+RUN mkdir -p /home \
+  && mkdir -p /home/vesta \
+  && mkdir -p /home/gpaw \
+  && mkdir -p /home/abtem
+
+COPY Cheatsheet.ipynb FAIRmat_S.png /home/
+COPY 02-exec-cmd /config/custom-cont-init.d/02-exec-cmd
+
+# install operating system dependencies
+RUN apt update \
+  && apt-get install -y git=1:2.25.1-1ubuntu3.5 \
+  && apt-get install -y unzip=6.0-25ubuntu1 \
+  && apt-get install -y wget=1.20.3-1ubuntu2 \
+  && apt-get install -y libgtk-3-dev=3.24.20-0ubuntu1.1 \
+  && apt-get install -y build-essential=12.8ubuntu1.1 \
+  && apt-get install -y cmake=3.16.3-1ubuntu1 \
+  && apt-get install -y libglu1-mesa-dev=9.0.1-1build1 \
+  && apt-get install -y libblas-dev=3.9.0-1build1 \
+  && apt-get install -y liblapack-dev=3.9.0-1build1 \
+  && apt-get install -y libxc-dev=4.3.4-1build1 \
+  && wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+  && chmod +x Miniconda3-latest-Linux-x86_64.sh \
+  && bash ./Miniconda3-latest-Linux-x86_64.sh -b -p /usr/local/miniconda3 \
+  && rm -f Miniconda3-latest-Linux-x86_64.sh \
+  && cd /home \
+  && conda config --add channels conda-forge \
+  && conda config --set channel_priority strict \
+  && conda install python=3.10.6 ipykernel=6.16.0 jupyterlab=3.4.7 nodejs=18.9.0 \
+  && pip install jupyterlab_h5web[full]==6.0.1 \
+  && pip install gpaw \
+  && pip install abtem \
+  && conda clean -afy \
+  && chown -R ${PUID}:${PGID} /usr/local/miniconda3 \
+  && cd /home/vesta \
+  && wget https://jp-minerals.org/vesta/archives/3.5.7/VESTA-gtk3.tar.bz2 \
+  && tar -xvf VESTA-gtk3.tar.bz2 \
+  && rm -f VESTA-gtk3.tar.bz2 \
+  && chown -R ${PUID}:${PGID} /home
+
+WORKDIR /home
+
+# how to call this container for development purposes for example
+# docker run -p 3000:8888 ewr-abinit-em-webtop

docker/fiji/02-exec-cmd

+#!/usr/bin/with-contenv bash
+
+echo "/usr/local/miniconda3/bin/conda run -n base jupyter-lab $CWD" > /config/.config/openbox/autostart
+

docker/fiji/Cheatsheet.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "88054eb2",
+   "metadata": {},
+   "source": [
+    "![FAIRmat](FAIRmat_S.png)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9ecf3020",
+   "metadata": {},
+   "source": [
+    "# fiji-webtop container cheatsheet"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4091c1e2",
+   "metadata": {},
+   "source": [
+    "The fiji-webtop container provides preinstalled and configured imagej and fiji imagej versions<br>\n",
+    "for preparing data from electron microscopy experiment for e.g. focal series reconstruction.<br>\n",
+    "ImageJ is configured with several plug-ins from the SALVE microscopy group in Ulm (tools<br>\n",
+    "which where developed by Michael Mohn et al. in Prof. Ute Kaiser's group). Specifically,<br>\n",
+    "https://github.com/mmohn/SER_Reader<br>\n",
+    "https://github.com/mmohn/Stack_Alignment<br>\n",
+    "***"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "69238a64",
+   "metadata": {
+    "tags": []
+   },
+   "source": [
+    "# Getting started with imagej"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6e324fa1",
+   "metadata": {},
+   "source": [
+    "imagej (https://imagej.net/) is available under /home/imagej/ImageJ. The GUI can be started by opening a terminal by clicking a terminal<br>\n",
+    "panel on the right part of the jupyter-lab screen. The following command line call will start imagej:<br>"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5fd98af7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "! /home/imagej/ImageJ/ImageJ\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1aa22278",
+   "metadata": {},
+   "source": [
+    "## Getting started with fiji"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "49e09d74-b0d6-4512-8929-38fd715d3948",
+   "metadata": {},
+   "source": [
+    "Fiji (https://imagej.net/software/fiji/downloads) is an extension of the imagej image processing suite with many additional plug-ins.<br>\n",
+    "The tool is available under /home/fiji/Fiji.app. The GUI can be started by opening a terminal by clicking a terminal panel<br>\n",
+    "on the right part of the jupyter-lab screen. The following command line call will start fiji:<br>"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3e9edd09-e4ee-4163-8138-b33311fe8f8c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "! /home/fiji/Fiji.app/ImageJ-linux64\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "503e63a2-4586-4365-84bd-08692c3b2324",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docker/fiji/Dockerfile

+# # recipe to create the nomad-remote-tools-hub apmtools container via a dockerfile
+FROM gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/webtop
+
+# for testing the container locally without running in oauth errors
+# FROM ghcr.io/linuxserver/webtop:amd64-ubuntu-openbox-version-e1079163
+# FROM ghcr.io/linuxserver/webtop:amd64-ubuntu-xfce-version-c603dc47
+# # found that newest system python is 3.8.something
+# # rest should come only from and be managed through (mini)conda not pip!
+# # start of borrowed from gitlabmpcdf customized webtop
+# ENV CUSTOM_PORT=8888
+# ENV PUID=1000
+# ENV PGID=1000
+# ports and volumes
+# EXPOSE 8888
+# VOLUME /config
+# # end of borrowed from north webtop
+
+USER root
+
+# not update but upgrade, otherwise depending on when the container is build a particular version may no longer
+# be available as a consequence of which the following specifically-versioned packages will not be installable
+
+# set the environment already, knowing where miniconda will be installed
+ENV PATH=/usr/local/miniconda3/bin:$PATH
+
+RUN mkdir -p /home \
+  && mkdir -p /home/imagej/ImageJ/plugins/FAIRmat \
+  && mkdir -p /home/fiji/Fiji.app
+
+# get Michael Mohn et al. plugins for ImageJ (these have been developed for imagej)
+# https://github.com/mmohn/SER_Reader.git (using e7828be)
+# https://github.com/mmohn/Stack_Alignment.git (1563c59)
+# we are using here the files from the respective repository commits as indicated in the brackets
+# the individual plug-in *.java source code files in this repository were then compiled using Compile and run
+# on a Linux instance of the same imagej version as is unzip in this container
+# the compiled plug-ins have been made available in /home/imagej/ImageJ/plugins/FAIRmat
+# in ImageJ, we have done the compilation on the same ImageJ version which is used in this
+# container, using the Compile and Run, the resulting java and class files are copied into the image
+COPY Cheatsheet.ipynb FAIRmat_S.png /home/
+COPY Alignment_Roi.class Prealign_Stack.class SER_Reader.class /home/imagej/ImageJ/plugins/FAIRmat/
+COPY 02-exec-cmd /config/custom-cont-init.d/02-exec-cmd
+
+# install operating system dependencies
+# get and install miniconda and customize it into a specific base environment
+RUN apt update \
+  && apt-get install -y git=1:2.25.1-1ubuntu3.5 \
+  && apt-get install -y unzip=6.0-25ubuntu1 \
+  && apt-get install -y wget=1.20.3-1ubuntu2 \
+  && apt-get install -y libglu1-mesa-dev=9.0.1-1build1 \
+  && apt-get install -y build-essential=12.8ubuntu1.1 \
+  && apt-get install -y cmake=3.16.3-1ubuntu1 \
+  && wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+  && chmod +x Miniconda3-latest-Linux-x86_64.sh \
+  && bash ./Miniconda3-latest-Linux-x86_64.sh -b -p /usr/local/miniconda3 \
+  && rm -f Miniconda3-latest-Linux-x86_64.sh \
+  && cd /home \
+  && conda config --add channels conda-forge \
+  && conda config --set channel_priority strict \
+  && conda install python=3.10.6 ipykernel=6.16.0 jupyterlab=3.4.7 nodejs=18.9.0 \
+  && pip install jupyterlab_h5web[full]==6.0.1 \
+  && conda clean -afy \ 
+  && chown -R ${PUID}:${PGID} /usr/local/miniconda3 \
+  && cd /home/fiji \
+  && wget https://downloads.imagej.net/fiji/archive/20220922-1417/fiji-linux64.zip \
+  && unzip fiji-linux64.zip \
+  && rm -f fiji-linux64.zip \
+  && cd /home/imagej \
+  && wget https://wsr.imagej.net/distros/linux/ij153-linux64-java8.zip \
+  && unzip ij153-linux64-java8.zip \
+  && rm -f ij153-linux64-java8.zip \
+  && chown -R ${PUID}:${PGID} /home
+
+# customize the webtop autostart to spin up jupyter-lab
+WORKDIR /home

tools.json

@@ -117,6 +117,19 @@
             }
         ]
     },
+    "fiji-container": {
+        "short_description": "ImageJ and Fiji for image processing",
+        "description": "ImageJ and Fiji with amongst others several electron-microscopy specific plug-ins",
+        "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/fiji-webtop",
+        "icon": "jupyter_logo.svg",
+        "mount_path": "/config",
+        "maintainer": [
+            {
+                "name": "Markus Kühbach",
+                "email": "markus.kuehbach@physik.hu-berlin.de"
+            }
+        ]
+    },
     "frwr": {
         "short_description": "Inline electron holography by C. Koch",
         "description": "FRWR3 in-line holography/focus series reconstruction code",
@@ -129,5 +142,18 @@
                 "email": "markus.kuehbach@physik.hu-berlin.de"
             }
         ]
+    },
+    "abtem": {
+        "short_description": "Electronic structure supported image simulation for transmission electron microscopy.",
+        "description": "VESTA, GPAW, and abTEM configured in one container for simulating images and diffraction patterns in transmission electron microscopy",
+        "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/abtem-webtop",
+        "icon": "jupyter_logo.svg",
+        "mount_path": "/config",
+        "maintainer": [
+            {
+                "name": "Markus Kühbach",
+                "email": "markus.kuehbach@physik.hu-berlin.de"
+            }
+        ]
     }
 }
\ No newline at end of file