Merge pull request #550 from MRtrix3/doctest

updates to user docs
MRtrix3 · Apr 15, 2016 · e7783ef · e7783ef
2 parents e18d748 + ea11f19
commit e7783ef
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Showing 88 changed files with 323 additions and 69 deletions.
diff --git a/docs/generate_user_docs.sh b/docs/generate_user_docs.sh
@@ -21,7 +21,7 @@ List of MRtrix3 commands
     filepath='getting_started/commands'
     filename=`basename $n`
     $n __print_usage_rst__ > $filepath/$filename.rst
-    sed -ie "1i$filename\n===========\n" $filepath/$filename.rst
+    sed -ie "1i.. _$filename:\n\n$filename\n===========\n" $filepath/$filename.rst
     echo "
 .. include:: commands/$filename.rst
 .......
@@ -36,7 +36,7 @@ Scripts for external libraries
 ################" > getting_started/scripts_list.rst
 
   mkdir -p getting_started/scripts
-  for n in `find ../scripts/ -type f -print0 | xargs -0 grep -l "lib.app.initParser"`; do
+  for n in `find ../scripts/ -type f -print0 | xargs -0 grep -l "lib.app.initParser" | sort`; do
     filepath='getting_started/scripts'
     filename=`basename $n`
     $n __print_usage_rst__ > $filepath/$filename.rst

diff --git a/docs/getting_started/commands/5tt2gmwmi.rst b/docs/getting_started/commands/5tt2gmwmi.rst
@@ -1,3 +1,5 @@
+.. _5tt2gmwmi:
+
 5tt2gmwmi
 ===========
 

diff --git a/docs/getting_started/commands/5tt2vis.rst b/docs/getting_started/commands/5tt2vis.rst
@@ -1,3 +1,5 @@
+.. _5tt2vis:
+
 5tt2vis
 ===========
 

diff --git a/docs/getting_started/commands/5ttedit.rst b/docs/getting_started/commands/5ttedit.rst
@@ -1,3 +1,5 @@
+.. _5ttedit:
+
 5ttedit
 ===========
 

diff --git a/docs/getting_started/commands/afdconnectivity.rst b/docs/getting_started/commands/afdconnectivity.rst
@@ -1,3 +1,5 @@
+.. _afdconnectivity:
+
 afdconnectivity
 ===========
 

diff --git a/docs/getting_started/commands/amp2sh.rst b/docs/getting_started/commands/amp2sh.rst
@@ -1,3 +1,5 @@
+.. _amp2sh:
+
 amp2sh
 ===========
 

diff --git a/docs/getting_started/commands/connectome2tck.rst b/docs/getting_started/commands/connectome2tck.rst
@@ -1,3 +1,5 @@
+.. _connectome2tck:
+
 connectome2tck
 ===========
 

diff --git a/docs/getting_started/commands/dcmedit.rst b/docs/getting_started/commands/dcmedit.rst
@@ -1,3 +1,5 @@
+.. _dcmedit:
+
 dcmedit
 ===========
 

diff --git a/docs/getting_started/commands/dcminfo.rst b/docs/getting_started/commands/dcminfo.rst
@@ -1,3 +1,5 @@
+.. _dcminfo:
+
 dcminfo
 ===========
 

diff --git a/docs/getting_started/commands/dirflip.rst b/docs/getting_started/commands/dirflip.rst
@@ -1,3 +1,5 @@
+.. _dirflip:
+
 dirflip
 ===========
 

diff --git a/docs/getting_started/commands/dirgen.rst b/docs/getting_started/commands/dirgen.rst
@@ -1,3 +1,5 @@
+.. _dirgen:
+
 dirgen
 ===========
 

diff --git a/docs/getting_started/commands/dirmerge.rst b/docs/getting_started/commands/dirmerge.rst
@@ -1,3 +1,5 @@
+.. _dirmerge:
+
 dirmerge
 ===========
 

diff --git a/docs/getting_started/commands/dirorder.rst b/docs/getting_started/commands/dirorder.rst
@@ -1,3 +1,5 @@
+.. _dirorder:
+
 dirorder
 ===========
 

diff --git a/docs/getting_started/commands/dirsplit.rst b/docs/getting_started/commands/dirsplit.rst
@@ -1,3 +1,5 @@
+.. _dirsplit:
+
 dirsplit
 ===========
 

diff --git a/docs/getting_started/commands/dirstat.rst b/docs/getting_started/commands/dirstat.rst
@@ -1,3 +1,5 @@
+.. _dirstat:
+
 dirstat
 ===========
 

diff --git a/docs/getting_started/commands/dwi2adc.rst b/docs/getting_started/commands/dwi2adc.rst
@@ -1,3 +1,5 @@
+.. _dwi2adc:
+
 dwi2adc
 ===========
 

diff --git a/docs/getting_started/commands/dwi2fod.rst b/docs/getting_started/commands/dwi2fod.rst
@@ -1,3 +1,5 @@
+.. _dwi2fod:
+
 dwi2fod
 ===========
 
@@ -57,7 +59,7 @@ Spherical deconvolution options
 
 -  **-threshold value** the threshold below which the amplitude of the FOD is assumed to be zero, expressed as an absolute amplitude (default = 0).
 
--  **-niter number** the maximum number of iterations to perform for each voxel (default = 0). Use '-niter 0' for a linear unconstrained spherical deconvolution.
+-  **-niter number** the maximum number of iterations to perform for each voxel (default = 50). Use '-niter 0' for a linear unconstrained spherical deconvolution.
 
 Stride options
 ^^^^^^^^^^^^^^

diff --git a/docs/getting_started/commands/dwi2mask.rst b/docs/getting_started/commands/dwi2mask.rst
@@ -1,3 +1,5 @@
+.. _dwi2mask:
+
 dwi2mask
 ===========
 

diff --git a/docs/getting_started/commands/dwi2noise.rst b/docs/getting_started/commands/dwi2noise.rst
@@ -1,3 +1,5 @@
+.. _dwi2noise:
+
 dwi2noise
 ===========
 

diff --git a/docs/getting_started/commands/dwi2tensor.rst b/docs/getting_started/commands/dwi2tensor.rst
@@ -1,3 +1,5 @@
+.. _dwi2tensor:
+
 dwi2tensor
 ===========
 

diff --git a/docs/getting_started/commands/dwiextract.rst b/docs/getting_started/commands/dwiextract.rst
@@ -1,3 +1,5 @@
+.. _dwiextract:
+
 dwiextract
 ===========
 

diff --git a/docs/getting_started/commands/dwinormalise.rst b/docs/getting_started/commands/dwinormalise.rst
@@ -1,3 +1,5 @@
+.. _dwinormalise:
+
 dwinormalise
 ===========
 

diff --git a/docs/getting_started/commands/fixel2sh.rst b/docs/getting_started/commands/fixel2sh.rst
@@ -1,3 +1,5 @@
+.. _fixel2sh:
+
 fixel2sh
 ===========
 

diff --git a/docs/getting_started/commands/fixel2tsf.rst b/docs/getting_started/commands/fixel2tsf.rst
@@ -1,3 +1,5 @@
+.. _fixel2tsf:
+
 fixel2tsf
 ===========
 

diff --git a/docs/getting_started/commands/fixel2voxel.rst b/docs/getting_started/commands/fixel2voxel.rst
@@ -1,3 +1,5 @@
+.. _fixel2voxel:
+
 fixel2voxel
 ===========
 

diff --git a/docs/getting_started/commands/fixelcfestats.rst b/docs/getting_started/commands/fixelcfestats.rst
@@ -1,3 +1,5 @@
+.. _fixelcfestats:
+
 fixelcfestats
 ===========
 

diff --git a/docs/getting_started/commands/fixelcorrespondence.rst b/docs/getting_started/commands/fixelcorrespondence.rst
@@ -1,3 +1,5 @@
+.. _fixelcorrespondence:
+
 fixelcorrespondence
 ===========
 

diff --git a/docs/getting_started/commands/fixeldivide.rst b/docs/getting_started/commands/fixeldivide.rst
@@ -1,3 +1,5 @@
+.. _fixeldivide:
+
 fixeldivide
 ===========
 

diff --git a/docs/getting_started/commands/fixelmult.rst b/docs/getting_started/commands/fixelmult.rst
@@ -1,3 +1,5 @@
+.. _fixelmult:
+
 fixelmult
 ===========
 

diff --git a/docs/getting_started/commands/fixelstats.rst b/docs/getting_started/commands/fixelstats.rst
@@ -1,3 +1,5 @@
+.. _fixelstats:
+
 fixelstats
 ===========
 

diff --git a/docs/getting_started/commands/fixelthreshold.rst b/docs/getting_started/commands/fixelthreshold.rst
@@ -1,3 +1,5 @@
+.. _fixelthreshold:
+
 fixelthreshold
 ===========
 

diff --git a/docs/getting_started/commands/fod2dec.rst b/docs/getting_started/commands/fod2dec.rst
@@ -1,3 +1,5 @@
+.. _fod2dec:
+
 fod2dec
 ===========
 

diff --git a/docs/getting_started/commands/fod2fixel.rst b/docs/getting_started/commands/fod2fixel.rst
@@ -1,3 +1,5 @@
+.. _fod2fixel:
+
 fod2fixel
 ===========
 

diff --git a/docs/getting_started/commands/label2colour.rst b/docs/getting_started/commands/label2colour.rst
@@ -1,3 +1,5 @@
+.. _label2colour:
+
 label2colour
 ===========
 

diff --git a/docs/getting_started/commands/label2mesh.rst b/docs/getting_started/commands/label2mesh.rst
@@ -1,3 +1,5 @@
+.. _label2mesh:
+
 label2mesh
 ===========
 

diff --git a/docs/getting_started/commands/labelconfig.rst b/docs/getting_started/commands/labelconfig.rst
@@ -1,3 +1,5 @@
+.. _labelconfig:
+
 labelconfig
 ===========
 

diff --git a/docs/getting_started/commands/maskfilter.rst b/docs/getting_started/commands/maskfilter.rst
@@ -1,3 +1,5 @@
+.. _maskfilter:
+
 maskfilter
 ===========
 

diff --git a/docs/getting_started/commands/mesh2pve.rst b/docs/getting_started/commands/mesh2pve.rst
@@ -1,3 +1,5 @@
+.. _mesh2pve:
+
 mesh2pve
 ===========
 

diff --git a/docs/getting_started/commands/meshconvert.rst b/docs/getting_started/commands/meshconvert.rst
@@ -1,3 +1,5 @@
+.. _meshconvert:
+
 meshconvert
 ===========
 

diff --git a/docs/getting_started/commands/meshfilter.rst b/docs/getting_started/commands/meshfilter.rst
@@ -1,3 +1,5 @@
+.. _meshfilter:
+
 meshfilter
 ===========
 

diff --git a/docs/getting_started/commands/mrcalc.rst b/docs/getting_started/commands/mrcalc.rst
@@ -1,3 +1,5 @@
+.. _mrcalc:
+
 mrcalc
 ===========
 

diff --git a/docs/getting_started/commands/mrcat.rst b/docs/getting_started/commands/mrcat.rst
@@ -1,3 +1,5 @@
+.. _mrcat:
+
 mrcat
 ===========
 

diff --git a/docs/getting_started/commands/mrclusterstats.rst b/docs/getting_started/commands/mrclusterstats.rst
@@ -1,3 +1,5 @@
+.. _mrclusterstats:
+
 mrclusterstats
 ===========
 

diff --git a/docs/getting_started/commands/mrconvert.rst b/docs/getting_started/commands/mrconvert.rst
@@ -1,3 +1,5 @@
+.. _mrconvert:
+
 mrconvert
 ===========
 

diff --git a/docs/getting_started/commands/mrcrop.rst b/docs/getting_started/commands/mrcrop.rst
@@ -1,3 +1,5 @@
+.. _mrcrop:
+
 mrcrop
 ===========
 

diff --git a/docs/getting_started/commands/mrfilter.rst b/docs/getting_started/commands/mrfilter.rst
@@ -1,3 +1,5 @@
+.. _mrfilter:
+
 mrfilter
 ===========
 

diff --git a/docs/getting_started/commands/mrinfo.rst b/docs/getting_started/commands/mrinfo.rst
@@ -1,3 +1,5 @@
+.. _mrinfo:
+
 mrinfo
 ===========
 

diff --git a/docs/getting_started/commands/mrmath.rst b/docs/getting_started/commands/mrmath.rst
@@ -1,3 +1,5 @@
+.. _mrmath:
+
 mrmath
 ===========
 

diff --git a/docs/getting_started/commands/mrmesh.rst b/docs/getting_started/commands/mrmesh.rst
@@ -1,3 +1,5 @@
+.. _mrmesh:
+
 mrmesh
 ===========
 

diff --git a/docs/getting_started/commands/mrpad.rst b/docs/getting_started/commands/mrpad.rst
@@ -1,3 +1,5 @@
+.. _mrpad:
+
 mrpad
 ===========
 

diff --git a/docs/getting_started/commands/mrresize.rst b/docs/getting_started/commands/mrresize.rst
@@ -1,3 +1,5 @@
+.. _mrresize:
+
 mrresize
 ===========
 

diff --git a/docs/getting_started/commands/mrstats.rst b/docs/getting_started/commands/mrstats.rst
@@ -1,3 +1,5 @@
+.. _mrstats:
+
 mrstats
 ===========
 

diff --git a/docs/getting_started/commands/mrthreshold.rst b/docs/getting_started/commands/mrthreshold.rst
@@ -1,3 +1,5 @@
+.. _mrthreshold:
+
 mrthreshold
 ===========
 

diff --git a/docs/getting_started/commands/mrtransform.rst b/docs/getting_started/commands/mrtransform.rst
@@ -1,3 +1,5 @@
+.. _mrtransform:
+
 mrtransform
 ===========
 

diff --git a/docs/getting_started/commands/mrview.rst b/docs/getting_started/commands/mrview.rst
@@ -1,3 +1,5 @@
+.. _mrview:
+
 mrview
 ===========
 

diff --git a/docs/getting_started/commands/msdwi2fod.rst b/docs/getting_started/commands/msdwi2fod.rst
@@ -1,3 +1,5 @@
+.. _msdwi2fod:
+
 msdwi2fod
 ===========
 

diff --git a/docs/getting_started/commands/peaks2amp.rst b/docs/getting_started/commands/peaks2amp.rst
@@ -1,3 +1,5 @@
+.. _peaks2amp:
+
 peaks2amp
 ===========
 

diff --git a/docs/getting_started/commands/sh2amp.rst b/docs/getting_started/commands/sh2amp.rst
@@ -1,3 +1,5 @@
+.. _sh2amp:
+
 sh2amp
 ===========
 

diff --git a/docs/getting_started/commands/sh2peaks.rst b/docs/getting_started/commands/sh2peaks.rst
@@ -1,3 +1,5 @@
+.. _sh2peaks:
+
 sh2peaks
 ===========
 

diff --git a/docs/getting_started/commands/sh2power.rst b/docs/getting_started/commands/sh2power.rst
@@ -1,3 +1,5 @@
+.. _sh2power:
+
 sh2power
 ===========
 
@@ -14,11 +16,15 @@ Synopsis
 Description
 -----------
 
-compute the power contained within each harmonic degree.
+compute the total power of a spherical harmonics image.
+
+This command computes the sum of squared SH coefficients, which equals the mean-squared amplitude of the spherical function it represents.
 
 Options
 -------
 
+-  **-spectrum** output the power spectrum, i.e., the power contained within each harmonic degree (l=0, 2, 4, ...) as a 4-D image.
+
 Standard options
 ^^^^^^^^^^^^^^^^