upgrade all built-in binary files to JData formatted JSON files #94

example/colin27/README.txt

@@ -18,6 +18,18 @@ the original MCX paper [Fang2009].
 This example is a built-in dataset in MCX. Run "mcx --bench" to show
 the full list of built-in examples.
 
+The JSON files (.json, .jnii) utlizes the JData specifiation (https://github.com/fangq/jdata) 
+to include binary data with compression support. Please download JSONLab from
+
+https://github.com/fangq/jsonlab
+
+to open these files in MATLAB and GNU Octave, or PyJData from 
+
+https://github.com/fangq/pyjdata
+
+to open such in Python.
+
+
  [Fang2009] Qianqian Fang and David A. Boas, "Monte Carlo simulation
   of photon migration in 3D turbid media accelerated by graphics processing
   units," Opt. Express 17, 20178-20190 (2009)

example/colin27/dump_volume.sh

@@ -0,0 +1,2 @@
+#!/bin/sh
+../../bin/mcx --bench colin27 --dumpmask -F jnii

example/digimouse/README.txt

@@ -4,12 +4,7 @@ In this example, we demonstrate light transport simulation in a mouse
 atlas template (Digimouse). There are 21 tissue types in the atlas. The volume
 is made of 190 x 496 x 104 0.8 mm^3 isotropic voxels. See [Fang2012].
 
-To run the simulation, you must first unzip the domain binary file using 
-unlzma on Linux or 7-zip on Windows. For example, on Linux:
-
- unlzma digimouse_0.8mm.bin.lzma
-
-and then run it using
+To run this example, please call
 
  ./run_atlas.sh
 
@@ -20,6 +15,18 @@ or
 to specify a different photon number
 
 
+The JSON files (.json, .jnii) utlizes the JData specifiation (https://github.com/fangq/jdata) 
+to include binary data with compression support. Please download JSONLab from
+
+https://github.com/fangq/jsonlab
+
+to open these files in MATLAB and GNU Octave, or PyJData from 
+
+https://github.com/fangq/pyjdata
+
+to open such in Python.
+
+
 === Reference ===
 
 [Fang2012] Fang Q and Kaeli D, "Accelerating mesh-based Monte Carlo method