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miykaelmiykael
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Merge pull request #85 from miykael/initiate_cast_examples
Adds datalad's terminal cast routine - allows interactive nipype intro
2 parents 80b9358 + 7674c5b commit 42a6e9f

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‎casts/cast_ipython.rc

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# This file contains ipython configuration variables to be used for generating
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# asciinema demos to guarantee consistent appearance.
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# make a fake temporary home dir and go into it
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SCREENCAST_HOME=~/demo
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if [ ! -e "$SCREENCAST_HOME" ]; then
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mkdir -p ${SCREENCAST_HOME} || {
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echo "FAILED to create $SCREENCAST_HOME" >&2
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exit 1; # we need demo directory!
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}
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fi
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cd $SCREENCAST_HOME
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ipython
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# cleanup at the end
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trap "cd ; rm -rf ~/demo > /dev/null 2>&1" EXIT

‎casts/cast_live_python

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#!/bin/bash
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#
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set -u -e
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test ! -e $1 && echo "input file does not exist" && exit 1
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title="$(echo $(basename $1) | sed -e 's/.sh$//')"
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bashrc_file="$(dirname $0)/cast_ipython.rc"
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# shortcut for making xdotool use the right window
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function xdt() {
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winid=$1
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shift
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xdotool windowactivate --sync $winid
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if [ "$#" -gt 0 ]; then
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xdotool "$@"
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fi
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}
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# make sure the target xterm is up and running
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width=106
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height=29
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fs=15
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text_width=$(($width - 8))
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geometry=${width}x${height}
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this_window=$(xdotool getwindowfocus)
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# For consistent appearance
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xterm +sb -fa Hermit -fs $fs -bg black -fg white -geometry $geometry -title Screencast-xterm -e "bash --rcfile cast_ipython.rc" &
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xterm_pid=$!
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sleep 2
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xterm_window=$(xdotool search --pid $xterm_pid)
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# By default should stay in the xterm window, so when we need to deal with
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# current one (waiting etc), then switch
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function wait () {
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xdt $this_window
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read -p "$@" in
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echo "$in"
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xdt $xterm_window
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}
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function instruct () {
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xdt $this_window
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wait "$@"
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}
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function type () {
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xdt $xterm_window type --clearmodifiers --delay 40 "$1"
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}
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function key () {
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xdt $xterm_window key --clearmodifiers $*
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}
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function sleep () {
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xdotool sleep $1
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}
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function execute () {
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xdt $xterm_window sleep 0.5 key Return
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sleep 0.2
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}
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function say()
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{
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ac=$(instruct "SAY: $1")
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if [ "$ac" != "s" ] ; then
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echo "skipping"
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return
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fi
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type "$(printf "#\n# $1" | fmt -w ${text_width} --prefix '# ')"
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key Return
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}
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function show () {
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xdt $xterm_window type --clearmodifiers --delay 10 "$(printf "\n$1" | sed -e 's/^/# /g')"
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sleep 0.1
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key Return
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}
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function run () {
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help="Press Enter to type, s to skip this action"
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ac=$(instruct "EXEC: $1. $help")
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if [ "$ac" = "s" ]; then
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echo "skipping"
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return
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fi
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type "$1"
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ac=$(instruct "EXEC: $1. $help")
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if [ "$ac" = "s" ]; then
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echo "skipping"
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return
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fi
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execute
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}
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function run_expfail () {
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# TODO we could announce or visualize the expected failure
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run "$1"
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}
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xdt $xterm_window sleep 0.1
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echo "xterm PID $xterm_pid (window $xterm_window) this window $this_window"
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# now get the process tree attached to the terminal so we can
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# figure out when it is idle, and when it is not
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# XXX must happen after asciinema is running
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xterm_pstree="$(pstree -p -A $xterm_pid)"
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. $1
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sleep 1
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show "$(cowsay "Demo was using $(datalad --version 2>&1 | head -n1). Discover more at http://datalad.org")"
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# key Control_L+d
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echo "INSTRUCTION: Press Ctrl-D or run exit to close the terminal"

‎casts/nipype_tutorial_showcase.sh

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say "Import nipype building blocks"
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show "Import nipype building blocks"
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run "from nipype import Node, Workflow"
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say "Import relevant interfaces"
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show "Import relevant interfaces"
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run "from nipype.interfaces.fsl import SliceTimer, MCFLIRT, Smooth"
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say "Create SliceTime correction node"
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show "Create SliceTime correction node"
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run "slicetimer = Node(SliceTimer(index_dir=False,
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interleaved=True,
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time_repetition=2.5),
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name='slicetimer')
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"
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say "Create Motion correction node"
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show "Create Motion correction node"
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run "mcflirt = Node(MCFLIRT(mean_vol=True,
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save_plots=True),
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name='mcflirt')
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"
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say "Create Smoothing node"
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show "Create Smoothing node"
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run "smooth = Node(Smooth(fwhm=4), name='smooth')"
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say "Create Workflow"
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show "Create Workflow"
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run "preproc01 = Workflow(name='preproc01', base_dir='.')"
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say "Connect nodes within the workflow"
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show "Connect nodes within the workflow"
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run "preproc01.connect([(slicetimer, mcflirt, [('slice_time_corrected_file', 'in_file')]),
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(mcflirt, smooth, [('out_file', 'in_file')])])
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"
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say "Create a visualization of the workflow"
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show "Create a visualization of the workflow"
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run "preproc01.write_graph(graph2use='orig')"
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say "Visualize the figure"
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show "Visualize the figure"
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run "!eog preproc01/graph_detailed.png
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"
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say "Feed some input to the workflow"
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show "Feed some input to the workflow"
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run "slicetimer.inputs.in_file = 'path/to/your/func.nii.gz'"
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say "Run the Workflow and stop the time"
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show "Run the Workflow and stop the time"
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run "%time preproc01.run('MultiProc', plugin_args={'n_procs': 5})"
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say "Investigate the output"
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show "Investigate the output"
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run "!tree preproc01 -I '*js|*json|*pklz|_report|*.dot|*html'"
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say "Change the size of the smoothing kernel"
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show "Change the size of the smoothing kernel"
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run "smooth.inputs.fwhm = 2"
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say "Rerun the workflow"
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show "Rerun the workflow"
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run "%time preproc01.run('MultiProc', plugin_args={'n_procs': 5})"
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say "Create 4 additional copies of the workflow"
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show "Create 4 additional copies of the workflow"
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run "preproc02 = preproc01.clone('preproc02')
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preproc03 = preproc01.clone('preproc03')
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preproc04 = preproc01.clone('preproc04')
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preproc05 = preproc01.clone('preproc05')
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"
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say "Create a new workflow - metaflow"
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show "Create a new workflow - metaflow"
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run "metaflow = Workflow(name='metaflow', base_dir='.')"
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say "Add the 5 workflows to this metaflow"
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show "Add the 5 workflows to this metaflow"
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run "metaflow.add_nodes([preproc01, preproc02, preproc03,
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preproc04, preproc05])
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"
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say "Visualize the workflow"
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show "Visualize the workflow"
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run "metaflow.write_graph(graph2use='flat')
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!eog metaflow/graph_detailed.png
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"
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say "Run this metaflow in parallel"
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show "Run this metaflow in parallel"
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run "%time metaflow.run('MultiProc', plugin_args={'n_procs': 5})"
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say "Investigate the output"
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show "Investigate the output"
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run "!tree metaflow -I '*js|*json|*pklz|_report|*.dot|*html'"
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say "The End."
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show "The End."

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