git clone https://github.com/carlohamalainen/volgenmodel-nipype
cd volgenmodel-nipype/vagrant-puppet
vagrant box add debian80 http://carlo-hamalainen.net/vagrant/debian-jessie-minimal-2014-06-04.box
vagrant up # This takes about 20 minutes to run.
Use vagrant to ssh and then run the tests:
vagrant ssh
cd /opt/code/volgenmodel-nipype
python -m doctest -v nipypeminc.py
Copy the files to a scratch directory on the VM. Hint: in the VM,
/vagrant is an automatic mount of the directory where the the
vagrant was provisioned, in this case volgenmodel-nipype/vagrant
on the host.
Files that you'll need:
vagrant@vagrant:/scratch/fast-example$ ls -lh
total 5.7M
-rw-r--r-- 1 vagrant vagrant 440 Jun 5 08:12 fit.10-genmodel.conf
-rw-r--r-- 1 vagrant vagrant 439K Jun 5 08:12 sml01.mnc
-rw-r--r-- 1 vagrant vagrant 439K Jun 5 08:12 sml02.mnc
-rw-r--r-- 1 vagrant vagrant 439K Jun 5 08:12 sml03.mnc
-rw-r--r-- 1 vagrant vagrant 439K Jun 5 08:12 sml04.mnc
-rw-r--r-- 1 vagrant vagrant 439K Jun 5 08:12 sml05.mnc
-rw-r--r-- 1 vagrant vagrant 439K Jun 5 08:12 sml06.mnc
-rw-r--r-- 1 vagrant vagrant 439K Jun 5 08:12 sml07.mnc
-rw-r--r-- 1 vagrant vagrant 439K Jun 5 08:12 sml08.mnc
-rw-r--r-- 1 vagrant vagrant 439K Jun 5 08:12 sml09.mnc
-rw-r--r-- 1 vagrant vagrant 439K Jun 5 08:12 sml10.mnc
-rw-r--r-- 1 vagrant vagrant 439K Jun 5 08:12 sml11.mnc
-rw-r--r-- 1 vagrant vagrant 439K Jun 5 08:12 sml12.mnc
-rw-r--r-- 1 vagrant vagrant 439K Jun 5 08:12 sml13.mnc
Note that /opt/code/volgenmodel-nipype/volgenmodel.py has the directory /scratch/fast-example hardcoded.
Pop into the right directory and load ipython:
cd /scratch/fast-example
ipython
In ipython, load the volgenmodel code (which creates the workflow) and then run the workflow:
%run /opt/code/volgenmodel-nipype/volgenmodel.py
workflow.run()
Main output files:
$ find /scratch/fast-example/volgenmodel_final_output/
/scratch/fast-example/volgenmodel_final_output/
/scratch/fast-example/volgenmodel_final_output/model
/scratch/fast-example/volgenmodel_final_output/model/sml_mincbigaverage_output_reshape_output_volsymm_output.mnc
/scratch/fast-example/volgenmodel_final_output/stdev
/scratch/fast-example/volgenmodel_final_output/stdev/sml_mincbigaverage_sd_file_output_volsymm_output.mnc
Workflow directory:
$ ls -l /scratch/fast-example/workflow/
total 512
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:32 bigaverage_00_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:34 bigaverage_01_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:40 bigaverage_02_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:25 blur_00_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:32 blur_01_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:37 blur_02_
-rw-r--r-- 1 vagrant vagrant 145927 Jun 5 10:37 d3.v3.min.js
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:41 datasink
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:37 datasource_sml
-rw-r--r-- 1 vagrant vagrant 29970 Jun 5 10:37 graph1.json
-rw-r--r-- 1 vagrant vagrant 13388 Jun 5 10:37 graph.json
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:25 identity_transformation
-rw-r--r-- 1 vagrant vagrant 6691 Jun 5 10:37 index.html
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:25 initial_model
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:25 initial_model_fwhm3d
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:27 merge_lastlin_initxfm_01_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:27 merge_lastlin_initxfm_02_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:32 merge_xfm_00_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:33 merge_xfm_01_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:39 merge_xfm_02_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:32 merge_xfmavg_and_step100_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:33 merge_xfmavg_and_step101_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:39 merge_xfmavg_and_step102_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:27 merge_xfm_mapnode_result_00_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:33 merge_xfm_mapnode_result_01_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:39 merge_xfm_mapnode_result_02_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:25 mincmath_00_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:32 mincmath_01_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:37 mincmath_02_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:33 nlpfit_01_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:39 nlpfit_02_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:25 norm_00_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:32 norm_01_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:37 norm_02_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:34 pik_check_iavg_00_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:34 pik_check_iavg_01_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:40 pik_check_iavg_02_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:32 pik_check_resample_00_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:34 pik_check_resample_01_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:41 pik_check_resample_02_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:25 pik_check_voliso00_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:32 pik_check_voliso01_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:41 pik_check_voliso02_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:32 pik_on_stage_model_00_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:37 pik_on_stage_model_01_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:41 pik_on_stage_model_02_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:25 preprocess_normalise
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:25 preprocess_pik
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:25 preprocess_threshold_blur
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:25 preprocess_volcentre
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:25 preprocess_voliso
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:25 preprocess_volpad
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:27 register_00_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:32 resample_00_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:34 resample_01_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:40 resample_02_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:32 resample_to_short_00_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:34 resample_to_short_01_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:40 resample_to_short_02_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:25 select_first_datasource
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:25 select_first_volpad
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:25 voliso_00_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:32 voliso_01_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:37 voliso_02_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:41 volsymm_final_model_02_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:32 volsymm_on_short_00_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:37 volsymm_on_short_01_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:41 volsymm_on_short_02_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:25 write_conf_01_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:25 write_conf_02_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:32 xfmavg_00_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:33 xfmavg_01_
drwxr-xr-x 3 vagrant vagrant 4096 Jun 5 10:39 xfmavg_02_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:32 xfmconcat_00_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:33 xfmconcat_01_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:39 xfmconcat_02_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:27 xfmconcat_for_nlpfit_01_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:27 xfmconcat_for_nlpfit_02_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:27 xfminvert_00_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:33 xfminvert_01_
drwxr-xr-x 4 vagrant vagrant 4096 Jun 5 10:39 xfminvert_02_
This Vagrant/Puppet recipe is experimental, and not intended for production systems that will run nipype or volgenmodel-nipype. In particular the Vagrantfile calls the script build_minc_tools.sh which builds the latest minc-toolkit from source, which takes some time.