From 566099ad810ec6d3821d25dcb93fcb36dde661d5 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Fri, 15 Feb 2019 18:52:47 +0100
Subject: [PATCH] automatic documentation for some post processing scripts

---
 .gitlab-ci.yml                             | 21 +++++++++++++++++++++
 PRIVATE                                    |  2 +-
 processing/post/addAPS34IDEstrainCoords.py | 13 ++++---------
 processing/post/addCurl.py                 |  2 +-
 processing/post/addDivergence.py           |  2 +-
 processing/post/addGradient.py             |  2 +-
 6 files changed, 29 insertions(+), 13 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f1af6259f..6ee973092 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -496,6 +496,27 @@ Spectral:
   only:
     - development
 
+Processing:
+  stage: createDocumentation
+  script:
+    - cd $DAMASKROOT/processing/post
+    - $DAMASKROOT/PRIVATE/documenting/scriptHelpToWiki.py
+      addAPS34IDEstrainCoords.py
+      addCauchy.py addCumulative.py addCurl.py
+      addDerivative.py addDeterminant.py addDeviator.py addDivergence.py
+      addEhkl.py
+      addGradient.py
+      addIndexed.py
+      addInfo.py
+      addLinked.py
+      addMises.py
+      addNorm.py
+      addPK2.py
+      addSpectralDecomposition.py addStrainTensors.py > post.html
+  except:
+    - master
+    - release
+
 ##################################################################################################
 backupData:
   stage: saveDocumentation
diff --git a/PRIVATE b/PRIVATE
index beb9682ff..30434a528 160000
--- a/PRIVATE
+++ b/PRIVATE
@@ -1 +1 @@
-Subproject commit beb9682fff7d4d6c65aba12ffd04c7441dc6ba6b
+Subproject commit 30434a528f69d77eef1be91e8a2f2fc5e0f85054
diff --git a/processing/post/addAPS34IDEstrainCoords.py b/processing/post/addAPS34IDEstrainCoords.py
index 1071baa91..78202d9a9 100755
--- a/processing/post/addAPS34IDEstrainCoords.py
+++ b/processing/post/addAPS34IDEstrainCoords.py
@@ -19,15 +19,10 @@ Transform X,Y,Z,F APS BeamLine 34 coordinates to x,y,z APS strain coordinates.
 
 """, version = scriptID)
 
-parser.add_option('-f',
-                  '--frame',
-                  dest='frame',
-                  metavar='string',
-                  help='APS X,Y,Z coords')
-parser.add_option('--depth',
-                  dest='depth',
-                  metavar='string',
-                  help='depth')
+parser.add_option('-f','--frame',dest='frame', nargs=3, metavar='string string string',
+                                 help='APS X,Y,Z coords')
+parser.add_option('--depth',     dest='depth',          metavar='string',
+                                 help='depth')
 
 (options,filenames) = parser.parse_args()
 
diff --git a/processing/post/addCurl.py b/processing/post/addCurl.py
index 2716849b4..cae1ef8b0 100755
--- a/processing/post/addCurl.py
+++ b/processing/post/addCurl.py
@@ -49,7 +49,7 @@ def curlFFT(geomdim,field):
 
   curl_fourier = np.einsum(einsums[n],e,k_s,field_fourier)*TWOPIIMG
 
-  return np.fft.irfftn(curl_fourier,s=shapeFFT,axes=(0,1,2)).reshape([N,n])
+  return np.fft.irfftn(curl_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,n])
 
 
 # --------------------------------------------------------------------
diff --git a/processing/post/addDivergence.py b/processing/post/addDivergence.py
index 0aa4b05ae..73eb4ed9e 100755
--- a/processing/post/addDivergence.py
+++ b/processing/post/addDivergence.py
@@ -45,7 +45,7 @@ def divFFT(geomdim,field):
 
   div_fourier = np.einsum(einsums[n],k_s,field_fourier)*TWOPIIMG
 
-  return np.fft.irfftn(div_fourier,s=shapeFFT,axes=(0,1,2)).reshape([N,n//3])
+  return np.fft.irfftn(div_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,n/3])
 
 
 # --------------------------------------------------------------------
diff --git a/processing/post/addGradient.py b/processing/post/addGradient.py
index 83cb54064..676efb27e 100755
--- a/processing/post/addGradient.py
+++ b/processing/post/addGradient.py
@@ -45,7 +45,7 @@ def gradFFT(geomdim,field):
   k_s = np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3).astype('c16')                           
   grad_fourier = np.einsum(einsums[n],field_fourier,k_s)*TWOPIIMG
 
-  return np.fft.irfftn(grad_fourier,s=shapeFFT,axes=(0,1,2)).reshape([N,3*n])
+  return np.fft.irfftn(grad_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,3*n])
 
 
 # --------------------------------------------------------------------