added demo3d59

demos/3D/demo3D59/demo3D59.sh

@@ -0,0 +1,83 @@
+#!/bin/bash
+
+# demo3D59
+#
+#Synthesize one 3D image with nuclear, cell shape and a vesicular channel.
+#This demo exports portions of the synthetic image as an SBML Spatial instance.
+
+# Input 
+# ------
+# * a valid CellOrganizer model file
+#
+# Output
+# ------
+# * SBML Instance
+# * single channel tif files
+# * ometiff file
+#
+# Created: Robert F. Murphy
+#
+# Copyright (C) 2013-2019 Murphy Lab
+# Lane Center for Computational Biology
+# School of Computer Science
+# Carnegie Mellon University
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published
+# by the Free Software Foundation; either version 2 of the License,
+# or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
+# 02110-1301, USA.
+#
+# For additional information visit http://murphylab.web.cmu.edu or
+# send email to [email protected]
+
+wget -nc http://www.cellorganizer.org/model_repository/models/3D/tfr.mat
+wget -nc http://www.cellorganizer.org/model_repository/models/3D/spharm/lamp2.mat
+
+echo -e "options.output_filename = 'combined_model.mat';
+options.selection = [1,1,0;0,0,1];
+files = {'lamp2.mat','tfr.mat'};
+" > input_combine.txt
+slml2slml input_combine.txt
+
+echo -e "options.seed = 639848;
+try; state = rng( options.seed ); catch err; rand( 'seed', options.seed ); end;
+options.targetDirectory = pwd;
+options.prefix = 'img';
+options.compression = 'lzw';
+options.sampling.method = 'disc';
+options.debug = false;
+options.verbose = true;
+options.synthesis = 'all';
+options.model.spharm_rpdm.synthesis_method = 'random_sampling';
+options.model.spharm_rpdm.imageSize = [205, 205, 18];
+options.numberOfSynthesizedImages = 1;
+options.numberOfGaussianObjects = 100;
+options.rendAtStd = 1;
+options.overlapthresh = 1;
+options.output.tifimages = true;
+options.output.OMETIFF = true;
+options.output.indexedimage = true;
+options.output.SBMLSpatial = true;
+options.SBML.spatial_use_compression = true;
+options.SBML.spatial_use_analytic_meshes = true;
+options.SBML.spatial_image = false;
+options.SBML.spatial_vcell_compatible = false;
+options.oobbuffer = 0.1;
+
+filenames = {'combined_model.mat'};
+" > input.txt
+
+slml2img input.txt
+
+rm input_combine.txt
+rm input.txt